MSc Taxonomy and Biodiversity
&
MRes Biosystematics
taught by
Imperial College London
and
The Natural History Museum
Course Handbook for 2012-2013
Name: …………………………………
Email: …………………………………
Phone: …………………………………
CONTENTS
MSc Taxonomy and Biodiversity
Aims of the course
Course organisers
Course structure
Time Table Summary
List of modules, codes, organisers and contact details
Projects
Trips and field course
Additional participants
Student feedback
Tutorials
Assessments
Personal tutors
Student representatives
Useful contacts
Health/personal issues
Graduate School – Imperial College London
Student complaints and appeals
2
2
2
3
4
4
4
4
4
5
5
5
5
6
6
6
6
MRes Biosystematics
Aims of the course
Course structure
Course organisers
Programme Structure
Student teaching record
7
7
7
8
9
The Museum
The Upper Bridge Room
The Lower Bridge Room
Computers
Security Passes and Keys
Emergency Evacuations
Out of Hours Working
Museum Libraries
Photocopying
Museum Seminars
Postgraduate activities at the NHM
Map of the Natural History Museum
10
10
10
10
10
11
11
11
11
11
12
MSc Course Modules
One
Two
Three
Four
Five
Six
Seven
Eight
Nine
Ten
Induction Week
Tree of Life
Phylogenetic Reconstruction: Theory and Practice
Biodiversity 1: Concepts
Molecular Systematics
Ordination (Biometric) Techniques in Taxonomy
Introduction to Taxonomic and Systematic Principles
Biodiversity 2: Applied
Palaeontology and Stratigraphy
Statistics – R
Field Course
13
16
19
25
31
37
48
51
58
62
64
Projects
Contacts for discussing projects
The Project write-up
Some project proposals
Project proposal form (MSc)
Project proposal form (MRes)
Marking criteria and markers feedback forms
65
66
69
92
93
94
Examining of the MSc and MRes
Degree Regulations
Past examination papers
104
105
1
MSc Taxonomy and Biodiversity
The MSc in Taxonomy and Biodiversity (previously called Advanced Methods in Taxonomy and Biodiversity) is
th
a one year full-time course which was introduced in 1996 and is now in its 17 year. The course is taught
jointly by staff and lecturers of the Natural History Museum and Imperial College London, with close research
links between the two establishments. Although the majority of lectures are held at the Museum, students are
offered the opportunity to undertake research projects at either establishment. The taught part of the course
provides as wide as possible an overview of the theory and practice of modern taxonomy and systematics,
with associated biodiversity studies, allowing students to specialise on particular groups of organisms during
their research project.
Aims of the course
Students are trained in practical and conceptual issues in taxonomy and biodiversity, starting from
phylogenetic principles. The course provides methodological background, quantitative skills, practical skills in
morphological and molecular techniques of taxonomy and systematics, and experience with computer
applications. The most up-to-date ideas and research in taxonomy and biodiversity are taught, to a large
extent from primary literature. Hands-on training in conducting research in this area is provided by project
supervisors, with specialisation in the students’ field of choice.
After completing the course, students will be able to:
Apply a wide range of techniques to the study of systematics, including taxonomic revision, phylogeny
reconstruction, key construction, identification, collections management, and comparative methodologies
Understand the diversity of living organisms in space and time and be familiar with methods for measuring
this diversity and monitoring changes due to both anthropogenic and natural factors
Select appropriate methods to solve taxonomic and biodiversity problems, and be able to acquire and
analyse taxonomic data, including both traditional and molecular data
Understand fully the conceptual basis of taxonomy and phylogenetics and in particular, cladistics, and to
understand “biodiversity” within this framework
Apply these concepts to issues of biodiversity and conservation management and research, to set
priorities for sustainable development, environmental assessment and inventories; apply these concepts
to other areas of biology such as parasitology and epidemiology
Course organisers
The course is directed by Professor Donald Quicke who is based at Imperial College, Silwood Park (Tel. 020
7594 2238; [email protected]), and Professor Alfried Vogler who is based in the Department of Life
Sciences at the NHM (Ext. 5613; [email protected]). They can both be contacted with regards to the
content of the course, projects etc. The course organiser is Amoret Whitaker who is based in the Department
of Life Sciences at the NHM (Ext. 5998; [email protected]) and who should be contacted with regards to
administrative issues.
Course structure
The MSc course is comprised of ten compulsory modules, including a one week field course at Silwood Park,
and a 4 month research project. Each module includes lectures, practicals, seminars, tutorials, and
computing and library research projects, as appropriate. For the research projects, students are given the
opportunity to specialise in their chosen field, and the research project can cover any subject relating to
systematics, including library based research, molecular methods, or morphological techniques.
2
MSc Timetable Summary 2012-2013
Term 1 : 1st October – 14th December 2012
WEEK
MODULE
MONDAY
TUESDAY
WEDNESDAY
THURSDAY
FRIDAY
1st October
2nd October
4th October
5th October
8h October
9th October
11th October
12th October
15th October
16th October
17th October
18th October
19th October
4
22nd October
23rd October
24h October
25th October
26th October
5
29th October
30th October
Induction Week
1
3rd October
Tree of Life
2
ONE
10th October
Phylogenetic Reconstruction: Theory and Practice
3
TWO
THREE
th
Biodiversity 1: Concepts
31st October
1st November
th
6
5 November
7
12th November
13th November
19th November
20th November
th
6 November
2nd November
8 November
9th November
14th November
15th November
16th November
21st November
22nd November
23rd November
7 November
th
Molecular Systematics
8



FOUR
th
th
th
th
9
26 November
27 November
28 November
29 November
30th November
10
3rd December
4th December
5th December
6th December
7th December
11
10th December
11th December
Reading Week
12th December
13th December
14th December
10th Annual LERN Conference 2nd October 2012
14th Young Systematists Forum 29th November 2012
Christmas Break 15th December 2012 – 6th January 2013
Term 2 : 7th January – 22nd March 2013
WEEK
12
MODULE
FIVE
13
MONDAY
TUESDAY
WEDNESDAY
THURSDAY
Ordination (Biometric) Techniques in Taxonomy
FRIDAY
7th January
8th January
9th January
10th January
11th January
14th January
15th January
16th January
17th January
18th January
Introduction to Taxonomic and Systematic Principles
14
SIX
st
21 January
22nd January
23rd January
24th January
25th January
Reading Week & 1st Oral Presentation
15
th
th
31st January
1st February
6th February
7th February
8th February
12th February
13th February
14th February
15th February
18th February
19th February
20th February
21st February
22nd February
19
25th February
26th February
27th February
28th February
1st March
20
4th March
5th March
6th March
7th March
8th March
11th March
12th March
13th March
14th March
15th March
21st March
22nd March
28 January
29 January
4th February
5th February
11th February
18
Biodiversity 2: Applied
16
17
30th January
SEVEN
Exam Revision
Palaeontology and Stratigraphy
EIGHT
21
Statistics – R
22








NINE
th
18 March
th
20th March
19 March
1st Assessed Oral Presentation: during week 28th January – 1st February 2013
EASTER BREAK: 23rd March – 28th April 2013
Examinations: 15th – 19th April 2013
Module Ten: Field Course at Silwood Park: 22nd – 26th April 2013
Projects: 29th April – 22rd August 2013
Completion and handing-in of projects: by 5:00pm Thursday 22nd August 2013
2nd Assessed Oral Presentation: during week 26th – 30th August 2013
Vivas and Examiner’s meeting: during weeks 16th – 20th September 2013
3
List of modules, codes, organisers and contact details
No
Code
Topic
Organiser(s)
Telephone
E-mail
1
2
TOL
PR
Donald Quicke
Ian Kitching
020 7594 2238
NHM Ext. 5608
[email protected]
[email protected]
3
4
5
BC
MS
OTT
Alfried Vogler
Alfried Vogler
Norman MacLeod
NHM Ext. 5613
NHM Ext. 5613
NHM Ext. 5295
[email protected]
[email protected]
[email protected]
6
TSP
Donald Quicke
020 7594 2238
[email protected]
7
8
9
BA
S-R
PS
Alfried Vogler
Donald Quicke
Norman MacLeod
NHM Ext. 5613
020 7594 2238
NHM Ext. 5295
[email protected]
[email protected]
[email protected]
10
FC
Tree of Life
Phylogenetic Reconstruction:
Theory and Practice
Biodiversity 1: Concepts
Molecular Systematics
Ordination (Biometric)
Techniques in Taxonomy
Introduction to Taxonomic
and Systematic Principles
Biodiversity 2: Applied
Statistics – R
Palaeontology and
Stratigraphy
Field Course
Donald Quicke
01344 294238
[email protected]
All lectures, practicals, demonstrations, etc. have been given unique codes. Each of these comprises the
module code followed by /L, /P, /S, /D, /T, and /E denoting lectures, practicals, seminars, demonstrations,
tutorials and 'in house' experience respectively; some sessions are part practical and part lecture.
Projects
A large part of the MSc comprises an individual project. Some students may have particular projects in mind
by the time they arrive, whilst others will develop ideas during the course of the taught part of the course. As a
guide to the wide range of possibilities, a list of some suggested projects along with brief descriptions are
provided towards the end of this handbook. This list is by no means exhaustive but if any student wants to
find out more about any of these projects, they are encouraged to discuss the projects with the supervisors
named.
Trips and field course
During the course of the MSc a few trips have been organised. In most cases the places to be visited are
readily accessible by public transport, and students are expected to cover the cost of getting to these places
themselves. During the field course at Silwood Park, students will be self-catering and will be expected to pay
for their accommodation in the student halls there, where the rates are very reasonable. For those with private
transport (or friends with) it is possible to travel there on a daily basis. At the end of the field course, it is the
student’s responsibility to pay their accommodation bill to the Accommodation Office at Silwood Park.
Additional participants
Some modules are offered as short courses in addition to being part of the MSc, and they are also
recommended as part of the training of MRes and PhD students within the NHM. Therefore there may
sometimes be a few extra people joining you, and we hope that you will make them feel welcome and show
them the ropes if they have any problems.
Student Feedback
At the end of each module, students will be asked to complete a feedback form, giving their views on all
aspects of the module, including its organisation, content and lecturers. The opinions of the students are
valued, and the feedback given by former students has resulted in changes being made to the course. You
are therefore asked to make the effort to complete these forms and return them to the administrator.
4
Tutorials
The purpose of the tutorials is to give students an opportunity to discuss and explore any areas of a module
within a small group. The students are therefore encouraged to communicate with the tutorial organiser prior
to each tutorial, in order to decide what format the tutorial should take, and what subjects should be
discussed. Some tutorials may be structured whereas others will be open discussions.
Code
BC/T1
MS/T2
MS/T3
BA/T4
Module
Biodiversity 1: Concepts
Molecular Systematics
Molecular Systematics
Biodiversity 2: Applied
Date
th
Tuesday 6 November
th
Friday 30 November
th
Tuesday 4 December
st
Thursday 21 February
Time
15:00-16:30
15:30-17:00
15:45-17:15
14:45-16:15
MSc Assessments
During the course, you will be required to compled the following assessed work:
Code
TB1
TB2
TB3
TB4
TB5
Oral 1
Oral 2
Related Module
PR: Theory and Practice
Biodiversity I: Concepts
Molecular Systematics
Ordination (Biometric) Techniques
Field Course
Oral Presentation One
Oral Presentation Two
Format
Lepidoptera write-up
TREE article
Molecular systematics write-up
Multivariate Analysis
Poster presentation
Journal article of your choice
Your research project
Personal Tutors
All students will be assigned a personal tutor from whom they can seek advice with regards to academic work,
projects, personal problems etc. Each student will be allocated a personal tutor at the start of the course, and
an initial meeting will be arranged. Thereafter, students should approach their tutor as and when they feel it is
necessary.
Tutor
Steve Brooks
Mark Carine
Paul Eggleton
Adrian Glover
Ian Kitching
David Williams
Division
Aquatic Invertebrates
Plants
Terrestrial Invertebrates
Aquatic Invertebrates
Terrestrial Invertebrates
Genomics & Microbial Diversity
Email
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
Tel
Ext. 5198
Ext. 5541
Ext. 5723
Ext. 5056
Ext. 5608
Ext. 5114
Student representatives
The students will nominate 2 MSc and 1 MRes student to act as Student Reps, who will be expected to attend
a minimum of two meetings during the year, with the course organisers. The Student Reps should collate
feedback from the rest of the students to report to the course organisers.
Also required are:
Computer Rep:
Printer Rep:
Library Rep:
Domestic Rep:
to help out the other students, and to liaise with the IT Department
to monitor and fix the printer/photocopier
to organise and take responsibility for the MSc/MRes library books
to ensure the kitchen is kept tidy and that rubbish is appropriately disposed of
5
Useful contacts
Most information can be found on the NHM Intranet, but the following gives a few useful pointers.
Computer problems:
Estates department:
Security:
In an emergency:
Removal of waste:
Photocopying:
Paper/print cartridges:
To receive faxes:
Ring the IT helpdesk on Ext. 6000, then press 2
Ring the Estates department on Ext. 6000, then press 4
Ring the Control Room on Ext. 5888
Ring Security on Ext. 6666
Contact the Porters via the intranet (Forms – General)
Contact Lorraine Portch, photocopy unit on Ext. 5647 or [email protected]
rd
Contact Amoret Whitaker in DC2 3 floor South
nd
020 7942 5229: located in Admin Office in DC2 2 floor South
Health/personal issues
Students who are experiencing difficulties during the course, whether they relate to financial, personal, health
or other issues, should inform the course organisers at the earliest opportunity, as in some cases these can
be taken into consideration when reviewing the student’s performance.
In cases of learning difficulties (eg. dyslexia) the student will be referred to the Disabilities Officer at Imperial
College London, who will instruct them as to the correct course of action.
Where a student suffers from ill health, this can only be taken into account when backed up by official original
documentation (e.g. doctor's note or consultant's statement) from the institution where the student is being
treated. College regulations state that medical certificates for absence due to illness must be submitted within
seven days of the absence. Photocopies or faxed copies of medical certificates cannot be accepted. It is
important to submit the relevant documentation at the earliest opportunity, as it will not be accepted
retrospectively.
Graduate School – Imperial College London
All postgraduate students at Imperial, whether following taught or research programmes, belong to the
Graduate School. The Graduate School was established to be the focus of postgraduate education and
research in the College - to ensure quality and to develop and enhance postgraduate training and excellence.
Follow us on Twitter – follow @ImperialGradSch for news, events and highlights
Find us on Facebook at Imperial College Graduate School
By email at [email protected]
Visit the Graduate School website: www.imperial.ac.uk/graduateschool
Student complaints and appeals
Imperial College aims to give the highest specialised instruction and service to all its students; however, in
some cases it recognises that students may not always be satisfied with the service they have received.
If you wish to raise a concern, there are a number of possible options open to you:
Firstly, you could raise the matter with the individual concerned. If you feel unable to do this, you could seek
advice from your student representatives, who may be able to assist and advise you, and they may decide to
raise the issue at the next staff/student committee meeting.
If you feel your complaint warrants more
immediate action or a more formal approach, you should discuss it with the course administrator or one of the
course directors.
If you are not satisfied with the outcome, you should consult the College’s Registry website which provides
clear and consistent procedures that indicate how you can take your comments further:
http://www3.imperial.ac.uk/registry/proceduresandregulations/policiesandprocedures/complaintsappeals
6
MRes Biosystematics
th
The MRes in Biosystematics is a full-time postgraduate course, introduced in October 2002 and now in its 11
year. The course is run jointly by the Natural History Museum and Imperial College London, and students will
be closely integrated into a large community of researchers in the area biosystematics, both at Imperial
College, Silwood Park, and at The Natural History Museum, one of the major institutions worldwide with a long
tradition of research in systematics and taxonomy. The Department of Biological Sciences at Imperial has
close links with the Museum, not least through the joint appointment of the two course organisers.
Aims of the course
Students are provided with training in research techniques in systematics, taxonomy, evolutionary biology and
bioinformatics, as a stepping-stone to a PhD or other research-related career. The MRes will provide the
student with a solid grounding in a range of professional and transferable skills and a variety of specific
research techniques. For those students going on to do a PhD (which we expect to be the majority) it provides
the opportunity to make a more informed decision on the area of research and specific projects they wish to
pursue.
On completion of the course, the students will have:
a good understanding of the state of knowledge of the field, together with relevant practical experience, in
three areas of biosystematic science in which he or she has expressed an interest;
where applicable, the ability to contribute to the formulation and development of ideas underpinning
potential PhD projects in areas of interest, and to make an informed decision on the choice of potential
PhD projects;
a broad appreciation of the scientific opportunities within the NHM and Imperial College;
knowledge of a range of specific research techniques and professional and transferable skills.
Course structure
Each student will complete three 15 week research projects during the year, at least one within an NHM
Research Group laboratory and one at Imperial College, Silwood Park. The projects should each cover one of
the following topics: Bioinformatics, Molecular Systematics and Morphological Phylogeny. Each project will
culminate in a short report and a presentation to the course organisers, project supervisors and NHM
students.
The MRes students will participate in selected lectures and seminars, drawing on the weekly IC and NHM
seminar series and other specialist subject seminars, many given by acknowledged international experts,
together with a broad range of established courses within the College across all basic science disciplines,
including particularly the MSc course in Advanced Methods in Taxonomy and Biodiversity. As Research
Group members, students will participate in all group discussions, seminars, work-in-progress lab meetings,
and journal clubs.
Course organisers
The course is directed by Professor Alfried Vogler who is based in the Department of Life Sciences at the
NHM (Ext. 5613; [email protected]) and Professor Donald Quicke who is based at Imperial College,
Silwood Park (Tel. 020 7594 2238; [email protected]). They can both be contacted with regards to the
content of the course, projects etc. The course organiser is Amoret Whitaker who is based in the Department
of Life Sciences at the NHM (Ext. 5998; [email protected]) and who should be contacted with regards to
administrative issues.
7
MRes Programme Structure 2012-2013
Week
Date
Activity
Week
Date
Activity
1
01.10.12
Registration & Induction
27
01.04.13
2 project / Easter Break
2
08.10.12
1 project preparation
st
28
08.04.13
2 project / Easter Break
3
15.10.12
1 project / Phylogenetics
st
29
15.04.13
2 project / Easter Break
4
22.10.12
1 project / Phylogenetics
st
30
22.04.13
2 project / Term Start
5
29.10.12
1 project / Biodiversity 1
st
31
29.04.13
2 project
6
05.11.12
1 project / Biodiversity 1
st
32
06.05.13
2 project
7
12.11.12
1 project / Molecular Systematics
st
33
13.05.13
2 project hand-in
8
19.11.12
1 project / Molecular Systematics
st
34
20.05.13
3 project prep. / 2 oral
9
26.11.12
1 project / Molecular Systematics
st
35
27.05.13
3 project
10
03.12.12
1 project / Molecular Systematics
st
36
03.06.13
3 project
11
10.12.12
1 project / Molecular Systematics
st
37
10.06.13
3 project
12
17.12.12
1 project / Xmas Break
st
38
17.06.13
3 project
13
24.12.12
1 project / Xmas Break
st
39
24.06.13
3 project
14
31.12.12
1 project / Xmas Break
st
40
01.07.13
3 project
15
07.01.13
1 project / Term Start/ Ordination
st
41
08.07.13
3 project
16
14.01.13
1 project / Ordination
st
42
15.07.13
3 project
17
21.01.13
1 project hand-in
st
43
22.07.13
3 project
18
28.01.13
2 project prep. / 1 oral
44
29.07.13
3 project
19
04.02.13
2 project / Biodiversity 2
nd
45
05.08.13
3 project
20
11.02.13
2 project / Biodiversity 2
nd
46
12.08.13
3 project
21
18.02.13
2 project / Biodiversity 2
nd
47
19.08.13
3 project
22
25.02.13
2 project
nd
48
26.08.13
3 project
23
04.03.13
2 project / Palaeo & Stratigraphy
nd
49
02.09.13
3 project hand-in
24
11.03.13
2 project / Palaeo & Stratigraphy
nd
50
09.09.13
Revision for viva / 3 oral
25
18.03.13
2 project / Statistics – R
nd
51
16.09.13
Viva voce & Exam Board
nd
52
23.09.13
MRes completion
26
25.03.13
nd
st
2 project / Easter Break
8
nd
nd
nd
nd
nd
nd
nd
rd
nd
rd
rd
rd
rd
rd
rd
rd
rd
rd
rd
rd
rd
rd
rd
rd
rd
MRes student teaching record
MRes students are required to undertake a certain amount of formal learning, and to complete a
report form at the end of the academic year. The following table gives a list of recommended
lectures, practicals, seminars and transferable skills courses.
MSc LECTURES / PRACTICALS
Phylogenetic Reconstruction module:
Characters, character states and homology (PR/L3)
Characters and coding (PR/L4)
Tree support & goodness-of-fit statistics (PR/L11)
Consensus v. total evidence, including ILD test (PR/L12)
Biodiversity 1: Concepts module:
Speciation and cladogenesis: pattern and process (BC/L3)
Phylogeography and population genetics (BC/L4)
DNA taxonomy and barcoding (BC/L5)
Speciation: patterns and processes (BC/L6)
Speciation in asexuals (BC/L7)
Molecular Systematics module:
Patterns of variation in sequence data (MS/L5)
Sequence alignment – theory (MS/L7)
Overview of tree building methods (MS/L10)
Models of evolution and maximum likelihood (MS/L11 & L12)
Bayesian analysis (MS/L13)
Molecular clocks (MS/L15)
Ordination (Morphometrics) module:
Biometric analysis in systematics I & II (OTT/L2 & L3)
Survey of biometric methods I & II (OTT/L5 & L6)
15 Oct 12 13:00-14:00
15 Oct 12 14:15-15:15
19 Oct 12 13:30-14:30
25 Oct 12 10:00-11:00
30 Oct 12 10:00-10:50
30 Oct 12 11:00-11:50
30 Oct 12 13:00-13:50
01 Nov 12 10:00-10:45
01 Nov 12 11:00-12:00
19 Nov 12 13:00-14:00
20 Nov 12 11:00-12:00
21 Nov 12 10:00-11:30
22 Nov 12 10:00-13:00
23 Nov 12 10:00-12:00
26 Nov 12 10:00-12:00
07 Jan 13 10:30-12:30
08 Jan 13 10:00-12:30
IMPERIAL COLLEGE LONDON – TRANSFERABLE SKILLS
Applied Writing Skills
Courses run by the Graduate School of Life
Sciences & Medicine (GSLSM) in the Autumn and
Creativity and Ideas Generation
Spring terms only at Imperial College South
Writing for Publication
Kensington.
Introduction to Regression Modelling
For course dates see http://learn.imperial.ac.uk
Introduction to Statistical Thinking
OTHER SEMINARS / TUTORIALS
To be held monthly, arranged by Alfried Vogler
Regularly held in each of the four Science
Departments and announced by email
NHM / Imperial College Silwood Park
Lab meetings, seminars, journal club meetings
14th Young Systematists’ Forum
29th November 2012, 09:00, Flett Theatre, NHM
See http://www.systass.org/ysf/ for details
Register free to David Bass ([email protected])
CEE Seminar Series
Wednesdays 5pm at UCL
(Centre for Ecology and Evolution)
See http://www.ucl.ac.uk/~ucbtcee/ for details
LERN Meetings
(London Evolutionary Research Network)
See http://londonevolution.net/ for details
MRes Tutorials
NHM Departmental Seminars
9
The Museum
It should be recognised that the Natural History Museum is a unique environment in which to undertake
postgraduate study. The majority of the teaching part of the course takes place at the Museum where,
although not strictly a teaching institution, excellent facilities are provided in order to enable you to undertake
and complete your studies. Due to the presence of the general public and the value of the collections, security
measures are tight, and therefore Museum regulations must be strictly adhered to by everyone working within
the building, whether staff or students.
The Upper Bridge Room
Most of the MSc lectures will be held in the Upper Bridge Room (EG482), located within the Earth Galleries.
The room has an internal telephone, extension 7076. Lockers are provided for use by the students, and a £5
returnable deposit is given for keys. Valuables should not be left in the room unattended at any time, as
neither the Museum nor the College will be liable for any loss or damage incurred, and you are therefore
asked to keep it locked when unattended, both at night and during the day.
The Lower Bridge Room
Most of the MSc practicals will be held in the Lower Bridge Room (EG 280), located within the Earth Galleries.
The room has an internal telephone, extension 6880. The room holds a large number of computers, and you
are therefore asked to keep it locked when unattended, both at night and during the day. Valuables should not
be left in the room unattended at any time, as neither the Museum nor the College will be liable for any loss or
damage incurred.
Computers
The Lower Bridge Room has a number of networked PC and Mac computers for the exclusive use of the MSc
and MRes students. The various software that you will need for the MSc course is already installed. It is
expected that the students will make full use of these computers in order to complete their practicals, etc.
Students are strongly recommended to keep back-up copies of their personal data and text files on their own
memory sticks or external hard drives.
E-mail addresses will be provided for all students, and you will also have access to the Museum Intranet.
There is folder on the Museum server \\Amber\entom\MSc specifically for use by the MSc/MRes students,
where information such as lecture notes, reading lists, practical datasets etc. can be accessed.
In the event of any computer hardware/software problems, please contact the Museum's IT Helpdesk on
extension 6000 or e-mail [email protected], giving them the location and number of the computer. There
is a printer/scanner/photocopier in the Lower Bridge Room which is networked to the computers there. This is
managed and serviced by an external company, so please contact Amoret if there are any problems with it.
rd
Paper can be collected from Amoret’s office in DC2, 3 Floor South.
N.B. You should not install your own software without permission; all software installed must be covered by the
appropriate licences. Any unauthorised software will be removed. Specifically, do not download software from
the internet without permission.
Security Passes and Keys
All MSc and MRes students will be issued with a Museum security pass, valid for one year. The pass allows
students to be in the Museum between 07:00 and 19:30 each weekday. Please note that this pass must be
worn and be visible at all times whilst in the Museum. Students will be issued with a DVS11 key which allows
entrance to the Upper and Lower Bridge Rooms, Libraries and other non-public areas.
Emergency Evacuations
Any announcements made concerning emergency evacuations must be obeyed. If instructed, please leave
the Museum immediately, without stopping to collect personal belongings. The muster point for occupants of
the Upper and Lower Bridge Rooms is the back car park, directly outside the Control Room.
10
Out of Hours Working
Students must leave the Museum premises by 19.30 in the evening, and will not be admitted before 07:00 in
the morning on weekdays. Students wishing to stay later than 19:30 must phone the Control Room to inform
security and sign out when they leave (Ext.5888). Students who wish to gain access to non-public areas of
the Museum at weekends and on Bank Holidays can do so only from 09:30 until 19:00 – they must sign in and
out, inform security of where they will be working in the Museum, and cannot be accompanied by anyone who
does not hold a Museum pass.
Museum Libraries
A talk and tour of the Museum libraries will be given at the start of the course. MSc students are allowed to
take library books and journals out of the libraries, once they have filled in a black bookboard. Any books,
journals etc. borrowed from the Libraries must be kept in the Upper Bridge Room cupboard on the shelf
marked “Library Materials”, or in their project supervisor’s office, with the location clearly marked on the
bookboard. Under no circumstances are books, journals, etc. to be removed from the Museum premises,
without completing the overnight loan book located in the Library. Inter-library loans can only be organised
through your project supervisor. The Library Services Team will be able to answer any queries about the
Library and its facilities - contact the Library on 020 7942 5460 or via email at: [email protected].
A set of reference books has been purchased for use by the students, and a single copy (to comply with
copyright legislation) of most cited references are also provided for the class. These will be kept in the
cupboard in the Upper Bridge Room. Please do not abscond with these; they are the property of the class as
a whole and not of any single individual.
Photocopying
A4 copies are charged at the staff rate of 5p per sheet, and colour photocopying facilities are also available.
Each student will be issued with a PIN to use on the Museum photocopiers. At the beginning of the year each
student will be allocated £10 worth of photocopying units. Any photocopying done above that will be invoiced
at the end of each quarter to the individual with that PIN number. In order to avoid possible misuse, students
should not disclose their PIN to anyone else, as individuals will be held responsible for all copying carried out
with their PIN. Photocopiers can be found in all the Museum libraries and in various locations within each
department.
Museum Seminars
Several series of seminars are organised within the Natural History Museum. These include Departmental
ones (e.g. Life Sciences and Earth Sciences) and topic based (e.g. Systematics). MSc and MRes students
are welcome to attend any of these and are strongly encouraged to do so. Details about forthcoming
seminars are generally advertised on global emails.
Postgraduate activities at the NHM
There are currently more than 150 M.Phil and PhD students who are affiliated with the Natural History
Museum. The museum has student representatives and also staff members who act as student co-ordinators
in each department – Eileen Cox ([email protected]) is the Head of Postgraduate Studies in the Museum. An
effort is made to unify all postgraduate students who are based here at the NHM for much of their studies, and
to try to build up a student community. The MSc and MRes students are an important part of the student buzz
and as such we really want you to feel part of the museum as a whole, and most importantly, feel part of the
student community at NHM.
To these ends a student website has been established, which you are actively encouraged to use as a
noticeboard for anything - pub meetings, finding a squash partner... it’s your page and up to you what you want
to put on it. The page lists info on training courses, job opportunities and also the "cheapo" deals you can get
using your museum pass - free entry to galleries and museums, half price theatre tickets etc.
Check out the web page: http://intranet.nhm.ac.uk/infostore/intrarco/postgrads/index.htm
11
The Natural History Museum Staff Map
HR Training Room
Darwin Centre Phase One
North East
Building
North West
Building
(3rd Floor)
Boilerhouse
(sub-basement)
Conference & Events
Temporary Contractors
Buildings
Rear car park
De la Beche IT Training Suite
(6th Floor)
Room
(Ground Floor)
Union Room
Museum Lane
(2nd Floor)
Staff Entrance &
Visitor Reception
Colonnade
Colonnade
Colonnade
Darwin
Centre
Phase
Two
(opens
2009)
Board
Room
Security/Control Room
Staff Notice Board
Goods In/Out
Post Room
(1st Floor)
QUEEN'S GATE
(Basement)
Earth Galleries
Building
(1st Floor)
Dorothea Bate Room
Earth Galleries
Entrance
Flett Theatre
(1st Floor)
Bronze Gate Entrance
(Ground Floor)
Staff Restaurant & Notice Board
(1st Floor)
Information
Desk
(Ground Floor)
Palaeontology
Staff Gym & Notice Board
(Basement)
EXHIBITION ROAD
Gavin de
Beer Room
(1st Floor)
Waterhouse Building East
Waterhouse Building West
Life Galleries Entrance
West Gardens
East Gardens
KEY
CROMWELL ROAD
Darwin Centre Phase One
(Zoology)
Wolfson Wellcome Biomedical
Laboratories – Ground floor
Darwin Centre Phase Two
(opens 2009)
North West Building (NW):
Zoology – Ground to 9th floor
Waterhouse building (West):
Zoology – Basement
Temporary Entomology offices and
collections - 1st floor and mezzanine
Botany and Botany Library – 2nd floor
Central Towers:
Botany – 1st, 2nd and 3rd floor
Meeting rooms/staff facilities
North East Building (NE):
Photo Unit (PEG) – Basement
Staff notice board – Ground floor at the lifts
General/Zoology Library Enquiry Desk – Ground floor
Archives, management and administration – 1st floor
Library and Information Services – Ground, 1st and 2nd floor
Human Resources and Health and Safety – 3rd floor
Finance – 4th floor
Directorate and Science Directorate – 5th floor
Estates – 6th floor
DC Project Office and RCO – 7th floor
Earth Galleries Tower (EG):
Earth Science Library – 1st and 2nd floor
Public Engagement Group (PEG) – 1st to 6th floor
UK Biodiversity Team, Microscopy Unit – 5th floor
Audit and Assurance – 5th floor
IT Support and Membership – 6th floor
Electron Microscopy and
Mineral Analysis (EMMA) – Basement
Palaeontology
Mineralogy and Earth Science Library – 4th floor
Waterhouse building (East):
Design and Installation Team (PEG) – Basement
Mineralogy – Basement and 1st floor (East End)
Botany labs – North East Tower
Botany Library, Botany Special
collections – 2nd floor
Third Floor
Second Floor
First Floor
Ground Floor
Mineralogy – Earth Galleries 3rd floor
Fire Assembly Zone Points
Basement
DS2351
1st – 5th October 2012
INDUCTION WEEK
Organisers:
Dr Donald Quicke, Division of Biology, IC, Silwood Park ([email protected])
Ms Amoret Whitaker, Dept of Entomology, NHM ([email protected])
Students will be introduced to the facilities at the Natural History Museum and Imperial College London,
including tours of the libraries and a glimpse behind the scenes at the NHM. Students will also be issued
with email addresses and ID passes and be introduced to the computing facilities. In addition, some
introductory lectures will be given outlining the basic principles of phylogenetics.
Initials
APV
DQ
APW
DP
NA-A
LDT
NM
KON
Lecturer
Alfried Vogler
Donald Quicke
Amoret Whitaker
David Peek
Nadia Aref-Adib
Lisa di Tommaso
Nic Marrafino
Sir Keith O’Nions
Location
Genomics & Microbial Biodiversity, Life Sciences, NHM
Division of Biology, Imperial College Silwood Park
Department of Life Sciences, Natural History Museum
ICT Department, Natural History Museum
Central Library, Imperial College London
Library and Archives, Natural History Museum
Security Team, Natural History Museum
Imperial College London, South Kensington
Email address
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
Schedule
WEEK 1
st
Monday 1 October
10:00-12:00
DQ/APW
13:00-15:00
NM/APW
15:00-16:00
KON
Introduction to the MSc/MRes courses
Issuing of Museum Passes in the Control Room
Welcome from the Rector, Great Hall, Sherfield Building, Imperial College
ND
Tuesday 2 October
10:00-12:00
LDT
11:00-16:00
12:00-15:00
APV
15:00-17:00
DP
17:30-19:30
APW
NHM Library tours (meet in Upper Bridge Room)
Freshers’ Fare: South Kensington Campus
Discussion of MRes research projects
Introduction to computing and network system at the NHM (LBR)
th
Welcome Party (DC2 8 Floor Common Room)
rd
Wednesday 3 October
Reading day
th
Thursday 4 October
10:00-11:00
DQ
11:15-12:15
DQ
13:15-15:45
APW
16:00-17:00
NA-A
What is Systematics? History of Systematics
Importance of Systematics and Taxonomy
Tour of the Museum (meet in the Upper Bridge Room)
Imperial College London library tour
th
Friday 5 October
10:00-11:00
APV
11:15-12:45
APV
12:45-13:15
APV
Introduction to phylogenetics
Taxonomy and biodiversity: a debate
Prepare TREE article (assessed coursework for Biodiversity I Module)
13
Lecture and practical synopses
WEEK 1
Monday 1st October
Donald Quicke and Amoret Whitaker will spend the first part of the morning going through the Course
Handbook, sorting out the necessary paperwork and answering any questions.
In the afternoon you will be able to get your NHM passes from the Control Room, organised by Nic
Marrafino.
There will be a welcome address for all GSLSM postgraduate taught course students from 15:00 – 16:00 in
the Great Hall, Sherfield Building, Imperial College. The welcome talk will be led by the Rector, and will
include talks from the Graduate School and the Graduate Student Association, and an introduction to
the Graduate School Professional Skills Development Programme.
Most students will have already completed registration online. Only a few students who need to show
original certificates will need to register in person at Registry, Sherfield Building. ID cards can be collected
from the office on the ground floor of the Sherfield Building.
Tuesday 2nd October
Outline of NHM Libraries
Lisa di Tommaso
A talk explaining how to use the Natural History Museum libraries, and the facilities they offer, including
using bookboards and accessing electronic resources. Followed by tours of the Zoology, Botany or Earth
Sciences Library.
Introduction to the computing and network system at the NHM
David Peek
You will be issued with NHM email addresses, shown how to use the Museum Intranet, how to access the
Internet, and you will be taught about the UBR computers and other equipment.
During the lunch break you will be free to attend the Freshers’ Fare at Imperial, South Kensington.
Welcome Party
At 17:30 there will be a welcoming party where students, module lecturers and other key people associated
with the MSc and MRes will have the opportunity to meet and talk informally with each other over a drink.
Afterwards some may wish to visit a local pub to carry on discussions.
Thursday 4th October
What is Systematics? History of Systematics
Donald Quicke
This lecture will cover the many types of classification that have been applied in the past and present, and
will cover the history of herbals and bestiaries from ancient times, through the age when increasing numbers
of organisms were being discovered through exploration, culminating in the development of the binary
system of nomenclature of Linnaeus that we all use today.
Importance of Systematics and Taxonomy
Donald Quicke
The nature and interrelation of taxonomy, systematics and classification will be outlined. The need for
nomenclature and the basic principles of stability and uniqueness will be introduced. Some of the many
purposes of classifications and their uses will be discussed. Distinctions will be made between ad hoc
classifications and those based on estimates of phylogeny.
Tour of the Museum
Amoret Whitaker
You’ll be taken on a whistle-stop tour of the Museum, so you can start to get your bearings, including a
“behind-the-scenes” look and an introduction to the science departments and their collections.
Imperial College London library tour
Meet at main entrance of Imperial College Library.
Nadia Aref-Adib
14
Friday 5th October
Introduction to phylogenetics
Alfried Vogler
This lecture will be a very basic introduction to phylogenetics, demonstrating the principle procedure of tree
reconstruction and introducing the relevant terminology. This topic will be treated in a lot more detail later in
the course but the basic idea is important to many lectures in the first term.
Taxonomy and biodiversity: a debate
Alfried Vogler
Working in small groups, we will explore various definitions of “taxonomy” and “biodiversity”, and debate the
relevance of taxonomic research to our understanding of the living world.
Prepare TREE article (assessed coursework for Biodiversity I Module)
Alfried Vogler/students
Prepare article for Trends in Ecology and Evolution on the biodiversity of the large-scale evolutionary history
of a clade of your choice. The article is intended to summarise the current information on historical-ecological
patterns of diversity and highlight the most interesting observations to an audience with general science
background. In a later session we will compare the articles prepared by each student to discover
commonalities in the patterns of diversity.
Reference: Schuh, R. T. 2000. Biological Systematics: Principles and Applications. Cornell University
Press, Ithaca, NY.
15
Module One
8th – 12th October 2012
INTRODUCTION TO THE TREE OF LIFE
Organiser: Prof Donald Quicke, Imperial College Silwood Park ([email protected])
Aims:
To provide everyone with a broad outline of the Tree of Life.
Objective: Describe some of the major adaptations of life from domain level to selected major groups and
explain how they diversified.
Initials
MB
JB
TF
AG
RJ
KJ
PK
IO
DQ
DR
JR
CS
Lecturer
Martin
Bidartondo
Juliet Brodie
Tim Ferrero
Adrian Glover
Ronald Jenner
Kate Jones
Paul Kenrick
Ian Owens
Donald Quicke
Dave Roberts
James Rosindell
Chris Stringer
Location
Division of Biology, Imperial College Silwood Park and
Royal Botanic Gardens, Kew
Genomics &Microbial Biodiversity, Life Sciences, NHM
Aquatic Invertebrates, Life Sciences, NHM
Aquatic Invertebrates, Life Sciences, NHM
Aquatic Invertebrates, Life Sciences, NHM
University College London and Institute of Zoology
Invertebrates & Plants, Earth Sciences, NHM
Science Directorate, NHM
Life Sciences, Imperial College Silwood Park
Genomics & Microbial Biodiversity, Life Sciences, NHM
Life Sciences, Imperial College Silwood Park
Vertebrates, Anthropology & Micropalaeontology, Earth
Sciences, NHM
Email address
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
Schedule
WEEK 2 – Tree of Life
th
Monday 8 October
10:00-10:50
TOL/L1
DR
The Three Domains of life
11:00-11:50
TOL/L2
DR
Protists: the vast microbial dimensions of eukaryote diversity
12:10-13:00
TOL/L3
JR
Presenting the Tree of Life *
* This special lecture will be held in the Flett Lecture Theatre. There is a press embargo on its content.
th
Tuesday 9 October
10:00-10:50
TOL/L4
PK
11:00-11.50
12:00-12:50
14:00-14:50
RJ
CS
TF
The Devonian Explosion: the origin and early evolution of land
plants
Evolution of the Crustaceae
Human Evolution
Nematodes and the Tree of Strife
DQ
DQ
The Insects I
The Insects II
JB
MB
MB
AG
Algae and the Tree-of-Life
Fungal biodiversity I
Fungal biodiversity II
Introduction to annelid diversity
KJ
KJ
Mammals
Mammals 2
IO
Birds
TOL/L5
TOL/L6
TOL/L7
th
Wednesday 10 October
10:00-10:50
TOL/L8
11:00-11:50
TOL/L9
th
Thursday 11 October
10:00-10:50
TOL/L10
11:00-11:50
TOL/L11
12:00-12:50
TOL/L12
15:00-15:50
TOL/L13
th
Friday 12 October
10:00-10:50
TOL/L14
11:00-11:50
TOL/L15
th
Monday 15 October
10:00-10:50
TOL/16
16
Lecture and practical synopses
WEEK 2 – Tree of Life
Monday 8th October
TOL/L1
The three domains of life
Dave Roberts
Microbial diversity has always been elusive and, until the development of electron microscopes, was poorly
understood. Since then, and in particular with the recent advances in molecular systematics the vast
diversity of the microbial world is slowly becoming apparent. The development of molecular ecology has
further demonstrated the enormous rôle played by the microbes in our planet's economy.
TOL/L2
Protists: the vast microbial dimensions of eukaryote diversity
Dave Roberts
A large fraction, if not the largest, of eukaryote diversity is microbial. Microbial eukaryotes occupy a
staggering range of sizes, shapes, cellular organisations, ecology and taxonomic groups collectively known
as protists. A brief review of the 6 major protists groups that are currently recognised and the impact of both
ultrastructural and molecular investigations on studying their systematics will be presented.
TOL/L3
A new way of looking at the Tree of Life
James Rosindell
Scientific knowledge of the tree of life is expanding rapidly, but the methods used for visualising it are
restrictive. In this lecture, we will look at existing and future methods of tree of life visualisation. In
particular we will cover a new method that makes use of fractal geometry and a zooming interface. This
method should help scientists explore large datasets and also help communicate ecological and
evolutionary concepts to the public.
Tuesday 9th October
TOL/L4
The Devonian Explosion: the origin and early evolution of land plants Paul Kenrick
Evidence from fossils shows that the first land plants were diminutive, ankle-high, stick-like organisms
lacking true roots and leaves. From this unpromising start, plants evolved most of their major organs such
as roots, stems, leaves, and seeds. These developments are recorded in rocks of Devonian age (354-417
million years ago), and they afford unprecedented insights into early cladogenesis in land plants and the
assembly of plant body plans
TOL/L5
An introduction to the diversity of Crustacea
Ronald Jenner
This will introduce Crustaceans as the most diverse group of arthropods in terms of basic body plans. They
occur everywhere – from ocean trenches to deserts, and from polar latitudes to hot springs, and from caves
to hydrothermal vents. I will survey the diversity of the main crustacean taxa and highlight important aspects
of morphology for each Recent group. A brief comparison will be made of recent estimates of phylogenetic
relationships within the Crustacea. The objective is to provide an overview of the diversity of a pivotal group
in aquatic and some terrestrial ecosystems and to provide a phylogenetic context for understanding
relationships within the group
TOL/L6
Human Evolution
Chris Stringer
TOL/L7
Nematodes and the Tree of Strife
Tim Ferrero
It is ten years since the entire genome of the nematode worm Caenorhabditis elegans was published and
five years since the sequencing of the genome of the related species C. briggsae was also completed. The
importance of these model organisms for biomedical research is considerable, but belies a startling wider
ignorance of the phylum Nematoda. The most abundant and possibly most diverse metazoans on the
planet remain fundamentally understudied. This talk will introduce the taxonomy, ecology and biodiversity of
the nematodes and illustrate some of the current thinking on nematode phylogeny
Wednesday 10th October
TOL/L8
The Insects I
Donald Quicke
The overall pattern of the evolution of the Insecta will be discussed in the light of living and fossil taxa.
Emphasis will be given to past patterns in diversity and the problem of interpretting the insect fossil record.
TOL/L9
The Insects II
Donald Quicke
The key biological features of the megadiverse insect orders will be assessed in order to try to interpret the
reasons for their success.
17
Thursday 11th October
TOL/L10
Algae and the Tree-of-Life
Juliet Brodie
The major revisions to the lower eukaryote groups effected by the molecular systematics revolution has
confirmed the existence of several complex basal clades composed of both photosynthetic and non
photosynthetic organisms. A number of the photosynthetic eukaryotes were once grouped together with a
few green 'plants' and called the 'algae'. This lecture will cover the diversity of the algae and current ideas
on their relationships in the Tree-of-Life. I will also discuss ideas of endosymbiosis on the evolution of the
algae and the impact of photosynthesis on the world’s atmosphere.
TOL/L11
Fungal Biodiversity I
Martin Bidartondo
Fungi are dominant recyclers, pathogens and symbionts in terrestrial ecosystems. Fungi and their
metabolic products are everywhere: from soft drinks, beer, wine, bread and cheese to unfortunate immunosuppressed patients. We will survey fungal diversity in the broadest sense focusing on some of the major
fungal evolutionary lineages and their exceptionally divergent life cycles. We begin with slime moulds,
oomycetes, and arbuscular mycorrhizal fungi.
TOL/L12
Fungal Biodiversity II
Martin Bidartondo
We continue with the two most diverse fungal phyla of the ten that are studied by mycologists:
ascomycetes and basidiomycetes.
TOL/L13
Introduction to annelid biodiversity
Adrian Glover
Annelids are a major clade of the metazoa that include some rather familiar animals (earthworms) and
some rather more exotic forms, such as 'zombie worms' and the giant tube worms that live at deep-sea
vents. In this talk I will discuss what annelids actually are, where did they come from (evolution) and what
are they doing (ecology). I will also include some of the latest research in deep-sea biology.
th
Friday 12 October
TOL/L14
Mammals
Kate Jones
As in other taxonomic groups, molecular phylogenetics has revolutionised our understanding of how we and
our closest relatives, the other mammals have evolved. In this lecture, I will explore how our understanding
of the current evolutionary relationships of mammals has changed how we think they have evolved.
Reference:
Bininda-Emonds et al. 2007. The delayed rise of present-day mammals. Nature 446:507-512
TOL/L15
Mammals 2
Kate Jones
Phylogenetic trees not only tell us about how species are related to each other but can also be used as time
machines to see into the biodiversity of the past and sometimes into the future. In this lecture, I discuss
what the mammal evolutionary tree can tell us about their past biogeography, speciation and extinction
rates, diversification, current patterns of species richness and what their future biodiversity might look like.
Reference:
Davies, T.J. et al. 2008. Phylogenetic trees and the future of mammalian biodiversity. Proceedings National
Academy of Sciences 105: 11556–11563
th
Monday 15 October
TOL/L16
The Birds
Ian Owens
Reference
Perry, J. J., Staley, J. T. and Lory, S. 2002. Microbial Life. Sinauer.
18
Module Two
15th – 26th October 2012
PHYLOGENETIC RECONSTRUCTION: THEORY AND PRACTICE
Module Organiser: Dr Ian J. Kitching, Entomology Department, NHM ([email protected])
AIMS: This module considers the theory and practice of phylogenetic reconstruction under the principle of
parsimony, and with particular reference to the analysis of morphological data. The principles of cladistics are
introduced and the methods used to construct and assess cladograms explained.
OBJECTIVES: Upon completion of this module, students should be able to:
Understand the theory of cladistic analysis for phylogenetic reconstruction;
Collect data suitable for a cladistic analysis;
Code data appropriately;
Analyse data fully using a range of methods;
Assess the support accorded to a cladogram and its included groups;
Convert the resulting preferred hypothesis of relationships into a formal classification.
Initials
IJK
MC
ABS
Lecturer
Ian Kitching
Mark Carine
Andrew Smith
Location
Life Sciences, Natural History Museum
Life Sciences, Natural History Museum
Earth Sciences, Natural History Museum
Email address
[email protected]
[email protected]
[email protected]
Schedule
WEEK 3
th
Monday 15 October
[10:00-10:50
TOL/16
IO
Birds]
10:00-10:30
10.45-11:45
13:00-14:00
14:15-15:15
PR/L1
PR/L2
PR/L3
PR/L4
IJK
MC
MC
MC
General introduction to module
Introduction to cladistic terms & concepts
Characters, character states and homology
Characters and coding
Tuesday 16 October
10:00-11:00
PR/P1
11:00-13:00
PR/P2
14:00-15:00
PR/L5
15:15-16:15
PR/L6
MC
MC
IJK
IJK
Practical - general concepts
Practical - from observation to analysis
Polarity determination
Cladogram construction & rooting
IJK
ABS
ABS/IJK
Missing values & optimization
PAUP4* & MacClade
Practical – PAUP4* & MacClade
IJK
IJK
IJK
Lepidoptera morphology & classification
CI, RI & character weighting
Tree support & goodness-of-fit statistics
th
th
Wednesday 17 October
Reading day
th
Thursday 18 October
10:00-11:00
PR/L7
11:15-12:15
PR/L8
13:15-16:00
PR/P3
th
Friday 19 October
10:00-11.00
PR/L9
11:15-12:15
PR/L10
13:15-14:15
PR/L11
WEEK 4
nd
Monday 22 October
10:00-16:00
PR/P4
IJK
Practical - Lepidoptera phylogeny (data acquisition)
IJK
Practical - Lepidoptera phylogeny (data acquisition)
ABS
ABS
IJK
Consensus v. total evidence, including ILD test
Practical - consensus v. total evidence
Practical - Lepidoptera phylogeny (data analysis/write-up)
IJK
Practical - Lepidoptera phylogeny (data analysis/write-up)
rd
Tuesday 23 October
10:00-16:00
PR/P4
th
Wednesday 24 October
Reading day
th
Thursday 25 October
10:00-11:00
PR/L12
11:00-12:30
PR/P5
13:00-16:00
PR/P4
th
Friday 26 October
10:00-16:00
PR/P4
st
Wednesday 21 November
11:30-13:00
PR/P4
IJK
Lepidoptera phylogeny workshop and feedback
Lecture and practical synopses
WEEK 3
Monday 15th October
PR/L1
General introduction to module
Ian Kitching
Overview of the module. Introduction to each of the topics to be covered and associated practical classes.
PR/L2
Introduction to cladistic terms & concepts
Mark Carine
Cladistic concept of relationship: apomorphy and plesiomorphy; autapomorphy, synapomorphy and
symplesiomorphy. Tree length and introduction to consensus trees. Dynamics of the interrelationships among
characters. Monophyletic, polyphyletic, paraphyletic groups. Homology equals synapomorphy. Cladograms and
trees.
PR/L3&L4
Characters, character states, continuous variables and coding
Mark Carine
Data for phylogeny reconstruction are in the form of a data matrix and the construction of the matrix is the prime
determinant in the outcome of an analysis. The stage between observation and coding into data matrices is
dependent upon a number of different criteria. Are our characters dependent or independent? Should they be
coded as binary or multistate? Should they be treated as ordered of unordered? How do we code apparently
continuous variables in a form suitable for cladistic analysis? These questions are addressed in the session and
the associated practical provides theoretical and practical solutions to the problems of real data.
References:
Garcia-Cruz, J. and Sosa, V. (2006). Coding quantitative character data for phylogenetic analysis: a comparison
of five methods. Systematic Botany 31: 302—309.
Gift, N & Stevens, P.F. 1997. Vagaries in the delimitation of character states in quantitative variation – an
experimental study. Systematic Biology 46: 112 – 125.
Reid, G. and Sidwell, K. (2002). Overlapping variables in botanical systematics. In . Macleod, N. and Forey, P.
(eds) Morphology, Shape and Phylogenetics. Taylor and Francis, London.
Scotland, R.W. & Pennington, R.T. 2000. Homology and systematics. Coding characters for phylogenetic
analysis. Systematics Association Special Volume 58. Taylor & Francis, London. [Chapters 1-4
particularly]
Sereno, P.C. (2007) Logical basis for morphological characters in phylogenetics. Cladistics 23: 565—587.
Stevens, P.F. 1991. Character states, morphological variation, and phylogenetic analysis: a review. Systematic
Botany 16, 553-583.
Thiele, K. 1993. The Holy Grail of the perfect character: the cladistic treatment of morphometric data. Cladistics
9, 275-304.
Tuesday 16th October
PR/P1
General concepts
Mark Carine
Using simple data sets, the students will practice constructing optimal cladograms, making consensus trees and
mapping characters by hand.
PR/P2
From observation to analysis
Mark Carine
Real examples are used as class exercises to determine the outcomes of different coding methods.
PR/L5
Polarity determination
Ian Kitching
Theory and application of outgroup comparison and the ontogenetic criterion for determining character polarity a
priori. The FIG/FOG and algorithmic methods of outgroup comparison. Advantages and disadvantages of
ontogeny versus outgroup comparison.
References:
Maddison, W.P., Donaghue, M.J. and Maddison, D.R. 1984. Outgroup analysis and parsimony. Systematic
Zoology 33, 83-103.
Watrous, L.E. and Wheeler, Q.D. 1981. The outgroup comparison method of character analysis. Systematic
Zoology 30, 1-11
PR/L6
Cladogram construction & rooting
Ian Kitching
Exact methods of cladogram construction and their practical limitations. Principles of heuristic methods of
cladogram construction. Algorithms that attempt to optimise heuristic solutions: stepwise addition sequence and
branch swapping. The deficiencies of Hennigian sequential constrained cladistic analysis and the advantages of
simultaneous, unconstrained analysis. The irrelevance of a priori polarity determination to modern cladistic
analysis. Methods for rooting cladograms and polarity determination as an a posteriori consequence of cladistic
analysis.
References:
Clark, C and Curran, D.J. 1986. Outgroup analysis, homoplasy, and global parsimony: a response to Maddison,
Donaghue and Maddison. Systematic Zoology 35, 422-426.
Nixon, K.C. and Carpenter, J. M. 1993. On outgroups. Cladistics 9, 413-426.
Thursday 18th October
PRL7
Missing values & optimisation
Ian Kitching
Missing data as the result of incomplete sampling; genuine missing data for fossils; polymorphic taxa (including
teratology); 'missing' due to evolutionary divergence. Problems of multiple equally parsimonious trees. Problems
of spurious theories of character evolution. Incorrect selection of trees due to coding with question marks.
References:
Maddison, W. 1993. Missing data versus missing characters in phylogenetic analysis. Systematic Biology 42,
576-581.
Platnick, N.I., Griswold, C.E. & Coddington, J.A. 1991. On missing entries in cladistic analysis. Cladistics 7,
337-343.
PR/L8 PAUP 4*
Mark Carine
Introduction to the cladistic analysis computer program, PAUP4*, via worked examples of simple data sets. Data
matrix input and manipulation; character types; outgroups, ancestors and roots; cladogram construction and
output; character optimization; consensus trees.
Reference:
Swofford, D.L. 1999. PAUP4*. Phylogenetic analysis using parsimony. Illinois Natural History Survey,
Champaign.
PR/P3 PAUP 4* practical
Mark Carine/Ian Kitching
Students will manipulate a variety of data sets, as well as creating their own, using PAUP 4.
Friday 19th October
PR/L9
Introduction to Lepidoptera morphology & classification
Ian Kitching
An introduction is given into basic lepidopteran morphology, terminology and its use in phylogenetic
reconstruction in preparation for the Lepidoptera Phylogeny practical.
PR/L10
CI, RI & character weighting
Ian Kitching
Given a set of equally parsimonious cladograms, is there a rational way to choose one from among the many?
Weighting of characters can be divided into a priori and a posteriori methods. The former can be subdivided into
character analysis and character compatibility, while the latter includes two similar approaches based on cladistic
consistency, which is measured using the consistency index and retention index. Successive approximations
character weighting uses the rescaled consistency index, while implied weighting uses the number of extra steps
per character.
References:
Carpenter, J.M. 1988. Choosing among equally parsimonious cladograms. Cladistics 4, 291-296.
Farris, J.S. 1969. A successive approximations approach to character weighting. Systematic Zoology 18, 374385.
Goloboff, P.A. 1993. Estimating character weights during tree search. Cladistics 9, 83-91.
PR/L11
Tree support & goodness-of-fit statistics
Ian Kitching
Introduction to the theory and application of the most commonly used tree support and goodness of fit statistics,
including data decisiveness, Bremer support, bootstrapping and jackknifing.
References:
Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
Siddall, M.E. 1996. Another monophyly index: revisiting the jackknife. Cladistics 11, 33-56.
WEEK 4
Monday 22nd October
PR/P4
Lepidoptera phylogeny
Ian Kitching
Students will divide into groups to derive data sets for families of Lepidoptera. Photocopies of wing venations
and prepared microscope slides of legs and antennae are provided, together with the specimens from which
they were obtained. The data sets will be analysed subsequently and students will write up their results as a
report. These reports will be assessed but will also provide an opportunity for feedback on the content of the
module.
Tuesday 23rd October
PR/P4
Lepidoptera phylogeny
Continuation of practical: data acquisition.
Ian Kitching
Thursday 25th October
PR/L12
Consensus v. total evidence, incl. ILD test
Andrew Smith
Introduction to why conflict arises within single data sets and between multiple data sets and techniques used to
resolve conflict. Consensus techniques; types of consensus methods and their advantages and disadvantages.
Total evidence as an alternative; basic rationale behind approach; advantages and disadvantages compared to
consensus. Tests for congruence among cladograms derived from different data sets, including Templeton’s
Test and the ILD Test. Worked example using morphological and molecular data from echinoids.
References:
Cunningham, C.W. 1997. Can three incongruence tests predict when data should be combined? Molecular
Biology and Evolution 14, 733-740
Farris, J.S., Källersjö, M., Kluge, A.G. & Bult, C. 1994. Testing significance of incongruence. Cladistics 10,
315-320.
Larson, A. 1994. The comparison of morphological and molecular data in phylogenetic systematics. In
Schierwater, B., Streit, B., Wagner, D.C. & DeSalle, R. (Eds). Molecular approaches to ecology and
evolution. Basel, Birkhauser Verlag, pp. 371-390.
Nixon, K. C. & Carpenter, J. M. 1996. On simultaneous analysis. Cladistics 12: 221-241.
PR/P5
Consensus v. total evidence
Andrew Smith
Analysis of morphological and molecular data independently using Amauris butterfly data set. Construction of
consensus trees. Application of Templeton's test for congruence between morphological and molecular data.
Comparison with total evidence approach.
References:
Farris, J. S., Källersjö, M., Kluge, A. G. & Bult, C. 1994. Testing significance of incongruence. Cladistics 10: 315319.
Nixon, K. C. & Carpenter, J. M. 1996. On simultaneous analysis. Cladistics 12: 221-241.
PR/P4
Lepidoptera phylogeny
Continuation of practical: data analysis/write-up.
Ian Kitching
Friday 26th October
PR/P4
Lepidoptera phylogeny
Continuation of practical: data analysis/write-up.
Ian Kitching
General reading list
Course text
Kitching, I.J., Forey, P.L., Humphries, C.J. and Williams, D.M. (Eds), 1998. Cladistics (Second edition). The
theory and practice of parsimony analysis. Systematics Association Publication 11. Oxford University
Press, Oxford.
Schuh, R.T. & Brower, A.V.Z. 2009. Biological systematics: principles and applications (second edition).
Comstock Publishing Associates, Cornell University Press.
General background reading
Ax, P. 1987. The phylogenetic system. John Wiley & Sons, Colchester.
Eldredge, N. & Cracraft, J. 1980. Phylogenetic patterns and the evolutionary process. Columbia University
Press, New York.
Gould, S.J. 1977. Ontogeny and phylogeny. Belknap Press of Harvard University Press, Cambridge,
Massachusetts.
Hennig, W. 1966. Phylogenetic systematics. University of Illinois Press, Urbana.
Humphries, C.J. (Ed.) 1988. Ontogeny and Systematics. British Museum (Natural History), London.
Nelson, G.J. & Platnick, N.I. 1981. Systematics and biogeography: cladistics and vicariance. Columbia University
Press, New York.
Rieppel, O. 1988. Fundamentals of comparative biology. Birkhauser Verlag.
Platnick, N.I. & Funk, V.A. 1983. Advances in cladistics, volume 2. Proceedings of the Second Meeting of the
Willi Hennig Society. Columbia University Press, New York.
Schuh, R.T. 2000. Biological systematics: principles and applications. Princeton University Press.
Scotland, R.W. & Pennington, R.T. 2000. Homology and systematics. Coding characters for phylogenetic
analysis. Systematics Association Special Volume 58. Taylor & Francis, London.
Scotland, R.W., Siebert, D.J. & Williams, D.M. (Eds) 1994. Models in phylogeny reconstruction. Systematics
Association Special Publication No. 52. Oxford University Press, Oxford.
Wiley, E.O. 1981. Phylogenetics: the theory and practice of phylogenetic systematics. Wiley Interscience, New
York.
Wiley, E.O., Siegel-Causey, D., Brooks, D.R. & Funk, V.A. 1991. The compleat cladist. A primer of
phylogenetic systematics. University of Kansas Special Publication No. 19.
Module Three
29th October – 9th November 2012
BIODIVERSITY 1: CONCEPTS
Organiser: Prof Alfried Vogler, Life Sciences, NHM ([email protected])
This module will provide a deeper understanding of “biodiversity” and the processes that generated the
diversity of living things on Earth. There are many aspects to this. Here we can only touch on selected
topics. We will discuss the geographic distribution of species richness, (ii) differences in diversity in
evolutionary lineages, (iii) the generation and maintenance of diversity in ecosystems and communities, and
(iv) the genetic diversity within species and populations. The role that taxonomy plays in biodiversity
assessment will be an important point. The second week of the module will be devoted to the difficult
problem of "species" and the process of speciation.
Coursework:
th
Students will be required to hand in a written assignment (TREE article) by Monday 19
November 2012 at 10:00.
Initials Lecturer
Location
Email address
AML
Division of Biology, Imperial College Silwood Park
a.moreno-letelier
@imperial.ac.uk
[email protected]
[email protected]
CT
PE
SB
APV
DMW
AH
JT
MC
Alejandra MorenoLetelier
Cuong Tang
Paul Eggleton
Steve Brooks
Alfried Vogler
David Williams
Aelys Humphreys
Jon Todd
Mark Carine
Division of Biology, Imperial College Silwood Park
Terrestrial Invertebrates, Life Sciences, NHM
Aquatic Invertebrates, Life Sciences, NHM
Genomics & Microbial Biodiversity, Life Sciences, NHM
Genomics & Microbial Biodiversity, Life Sciences, NHM
Division of Biology, Imperial College Silwood Park
Invertebrates & Plants, Earth Sciences, NHM
Plants, Life Sciences, NHM
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
Schedule
WEEK 5 – Species and speciation
th
Monday 29 October
10:00-11:00
BC/L1
11:15-12:15
BC/L2
JT
JT
What are species?
Species concepts: pros and cons
APV
APV
APV
Speciation and cladogenesis: pattern and process
Phylogeography and population genetics
DNA taxonomy and barcoding
AML
CT
CT/AML
Speciation: patterns and processes
Speciation in asexuals
Delimiting species
APV
MC
tbc
APV
Genetic variation in populations, gene trees
Speciation in plants
Genomics of speciation
Common patterns in radiations: TREE article, discussion
th
Tuesday 30 October
10:00-10:50
BC/L3
11:00-11:50
BC/L4
13:00-13:50
BC/L5
st
Wednesday 31 October
Reading day
st
Thursday 1 November
10:00-10:45
BC/L6
11:00-12:00
BC/L7
13:00-15:00
BC/P1
nd
Friday 2 November
10:00-11:00
BC/L8
11:15-12:00
BC/L9
13:00-14:00
BC/L10
14:15-15:30
BC/S1
25
WEEK 6 – Biodiversity: the distribution and evolution of life on Earth
th
Monday 5 November
10:00-11:00
BC/L11
11:15-12:15
BC/L12
13:15-14:15
BC/L13
PE
PE
PE
Biodiversity: the basics
Biodiversity processes at different scales
The use of taxonomy in biodiversity studies
th
Tuesday 6 November
10:00-12:00
BC/L14&L15 SB
13:00-15:00
15:00-16:30
BC/L16&L17 DMW
BC/T1
What we can learn from palaeontology: Changes
in species diversity during the Quarternary
Biogeographic and temporal patterns in microfossils
Tutorial
th
Wednesday 7 November
Reading day
th
Thursday 8 November
10:00-10:50
BC/L18
APV
11:00-11:50
13:00-14:00
APV
APV
BC/L19
BC/L20
Testing macroevolutionary hypotheses using
interspecies phylogenies
Phylogenies and extinction
Macroecological patterns of species diversity; neutral
theory of biodiversity
th
Friday 9 November
10:00-11:00
BC/L21
11:15-12:00
BC/L22
13:00-14:00
BC/L23
AH
AH
AH
Adaptive radiation
Competition and diversification
Geographic patterns of diversity
Lecture and practical synopses
WEEK 5 – Species and speciation
Monday 29th October
BC/L1
What are species?
Jon Todd
Species is a term widely used through much of biology. But what do we mean by species? Is the term
universally understood to refer to the same sorts of entities? Perhaps the greatest fundamental difference
amongst contemporary systematists in this regard is between those who consider species as a real and
„special‟ unit of taxonomy or evolution and those who regard species as a taxon like any other, a clade at
the tip of a tree with only the importance we choose to give it.
Reference:
Wheeler, Q.D. & Meier, R. (2000). Species concepts and phylogenetic theory: a debate. Columbia
University Press, New York. [Excellent debate between systematists with different philosophies].
BC/L2
Species concepts: pros and cons
Jon Todd
Given the variety of ways in which life is structured into species, the differences in how these may be
delimited and identified, and systematists‟ different requirements, it is unsurprising that a range of different
species concepts have been developed. It is important to understand the different meanings of species as
described by different authors in different groups of organisms. What are the differences underlying the
most widely used species concepts? How practical are they? Is a universal concept possible or desirable?
References: Wilson, R. A. (ed) (1999) Species. New Interdisciplinary Essays. MIT Press. [detailed
treatments of the Species problem]
Otte, D. & Endler, J.A. (Eds) (1989) Speciation and its consequences. Sinauer Associates, Inc.,
Sunderland, Massachusetts. [Good reference source]
Coyne, J.A. & Orr, H.A. (2004) Speciation. Sinauer. [Discussion of concepts by strong proponent
of Biological species concept]
26
Tuesday 30th October
BC/L3
Speciation and cladogenesis: pattern and process
Alfried Vogler
Various species concepts emphasise different aspects of what species are and how they arise; we will
dinstinguish pattern-based and process-based species concepts and their applicability to particular
biological questions. This also has implications for how we determine species limits using quantitative
methods and how many species we recognise for conservation.
Reference: Agapow, P. M., O. R. P. Bininda-Emonds, K. A. Crandall, J. L. Gittleman, G. M. Mace, J. C.
Marshall, and A. Purvis. 2004. The impact of species concept on biodiversity studies. Quart. Rev.
Biol. 79:161-179. Sites, J. W., and J. C. Marshall. 2004. Operational criteria for delimiting species.
Annu. Rev. Ecol. Evol. Syst. 35:199-227.
BC/L4
Phylogeography and population genetics
Alfried Vogler
Fuelled by studies of mitochondrial DNA since the late 1980‟s, phylogeography has revealed historical
biogeographic patterns and processes at the level of closely related populations. We will discuss the major
findings of phylogeographic research and its numerous applications in conservation genetics. We will then
have a quick introduction to population genetics (allele frequency, Hardy-Weinberg equilibrium and Fstatistics, etc.) and discuss how phylogeography attempts to link these ideas with the notion of speciation.
Reference: Avise, J. C. 2000. Phylogeography: the history and formation of species. Harvard University
Press, Cambridge, MA. Knowles, L.L. and W.P. Maddison. 2002. Statistical phylogeography. Mol.
Ecol. 11:2623-2635.
BC/L5
DNA taxonomy and barcoding
Alfried Vogler
The idea that DNA sequencing may play a central role in taxonomy has met with much scepticism but now
seems unstoppable. Different approaches focus on DNA-based identification, clustering of sequences or
propose a purely DNA-based taxonomic system. A universal finding is that mtDNA in animals is strongly
clustered (but not in plants), giving rise to the notion of a „barcoding gap‟ that separates different species.
We will discuss whether it is okay to use short DNA fragments as opposed to complex morphological traits
in species recognition and how molecular processes near the species boundary (including hybridisation)
may confound species recognition.
Reference: Vogler, A. P., and M. T. Monaghan. 2007. Recent advances in DNA taxonomy. J. Zool. Syst.
Evol. Res. 45:1-10. Hickerson, M. J., C. P. Meyer, and C. Moritz. 2006. DNA barcoding will often
fail to discover new animal species over broad parameter space. Syst. Biol. 55:729-739.
Thursday 1st November
BC/L6
Speciation: patterns and processes
Alejandra Moreno-Letelier
Geographic isolation is traditionally viewed as the main cause of speciation. The theory of
different geographic modes of speciation will be introduced, before turning to tests of these
ideas, particularly using systematics. Even with state-of-the-art DNA trees it can be hard to distinguish the
importance of alternative modes of speciation. Possible solutions to these limitations will be discussed
with reference to study groups of birds, mammals and insects. Ecological speciation is caused by divergent
selection, for example adaptation to different habitats. It can occur in allopatry or sympatry. The theory
of ecological speciation will be presented, highlighting i) why sympatric speciation is thought to be difficult in
sexual organisms, ii) how ecological divergence speeds up speciation rates compared to
geographical isolation alone, and iii) how these theories can be tested using data from so-called 'natural
experiments' on islands.
Reference: Coyne and Orr. 2004. Speciation. Sinauer Associates. Chpt 3 (and 4).
BC/L7
Speciation in asexuals
Cuong Tang
Species are often thought of as a property of sexual organisms, but in this lecture we will explore how
similar mechanisms can operate to generate discrete and independently evolving units in asexual
organisms. These theories will be tested in the ancient asexual clade of bdelloid rotifers.
BC/P1
Delimiting species
Cuong Tang & Alejandra Moreno-Letelier
We will use R to delimit species of electric fish based on molecular data and morphological trait data. The
practical gives a feel for what can be done with this powerful software.
27
References:
Feulner, P.G.D, Kirschbaum, F., Mamonekene, V. Ketmaier, R. Tiedemann. 2007. Adaptive radiation
in weakly electric fish (Teleostei: Mormyridae: Campylomormyrus): a combined molecular and
morphological approach. J. Evol. Biol. 20: 403-414.
D. Fontaneto, E. Herniou, C. Boschetti, M. Caprioli, G. Melone, C. Ricci and T.G. Barraclough. 2007.
Independently evolving species in asexual bdelloid rotifers. PLoS Biology. 5:e87
Friday 2nd November
BC/L8
Genetic variation in populations, gene trees
Alfried Vogler
The effect of stochastic (neutral) processes in population divergence. Chance processes also affect the
outcome of gene phylogenies due to stochastic lineage sorting, resulting in the gene tree-species tree
problem. Migration between populations is a critical factor, but in real populations may be constrained by
barriers of various kinds. Therefore, a metapopulation model may be more appropriate to describe gene
flow.
Reference: Slatkin, M. 1985. Gene flow in natural populations. Annu. Rev. Ecol. Syst. 16:393-430.
Knowles, L.L. and B.C. Carstens. 2007. Delimiting species without monophyletic gene trees. Syst.
Biol. 56:887-895.
BC/L9
Speciation in plants
Mark Carine
This lecture will introduce recent developments in the study of speciation in plants, especially the role of
hybridisation and polyploidisation. The "multiple origins" of plant species and the practical difficulties posed
to the taxonomist by these modes of speciation. Genomics approaches are now providing a much clearer
idea of how species originate despite gene flow at numerous loci and hybrid origin of many plant species.
References:
Givnish, T. J. 2010. Ecology of plant speciation. Taxon 59: 1326-1366.
Hegarty, M. J., G. L. Barker, A. C. Brennan, K. J. Edwards, R. J. Abbott, and S. J. Hiscock. 2008. Changes
to gene expression associated with hybrid speciation in plants: further insights from transcriptomic
studies in Senecio. Phil. Trans. Roy. Soc. B 363:3055-3069.
Lexer, C., and A. Widmer. 2008. The genic view of plant speciation: recent progress and emerging
questions. Phil. Trans. Roy. Soc. B 363:3023-3036.
Paun, O. et al. 2007 Genetic and epigenetic alterations after hybridization and genome doubling. Taxon
56:649-656
Popadopulis, A.S.T., Baker, W. J., Crayn, D., Butlin, R. K., Kynast, R.G., Hutton, I. & Savolainen, V. 2011.
Speciation with gene flow on Lord Howe Island. PNAS 108: 13188-13193.
Soltis, P. E. & Soltis, D. E.. 2009. The role of hybridization in plant speciation. Annual Review of Plant
Biology 60: 561-588.
BC/L10
Genomics of speciation
tbc
The extent and nature of asexuality in plants and how these lineages are treated taxonomically.
Mechanisms of asexuality and its distinction from non- sexuality. Current taxonomic treatment of asexual
taxa. The role of sexual reproduction versus other mechanisms as a necessary cohesive force in the
maintenance of species.
References:
Bicknell, R.A. & Koltunow, A.M. 2004. Understanding apomixis: Recent advances and remaining
conundrums. The Plant Cell 16, S228-S245.
nd
Richards, A.J. 1997. Plant Breeding Systems, 2 Ed. London: Chapman & Hall.
BC/S1
Common patterns in radiations: TREE article discussion
28
Alfried Vogler
WEEK 6 – Biodiversity: the distribution of life on Earth
Monday 5th November
BC/L11
Biodiversity: the basics
Paul Eggleton
What is biodiversity? Definitions of diversity. Units of biodiversity. Hierarchies of diversities. Why biodiversity
usually means „species diversity‟. Species richness v species density. The overlapping elements of
biodiversity. The scales of biodiversity: temporal and spatial.
Reference: Gaston, K.G. & Spicer, J. (2003) Biodiversity – an Introduction. Blackwell Publishing.
BC/L12
Biodiversity processes at different scales
Paul Eggleton
Global, regional and local processes. Deep time events. Climatic events: latitudinal effects. Global climate:
heating and warming. Effect of humans. Regional effects: history and ecology. Local effects: productivity,
niche density. Relationship between area, richness and individuals. Synthesising examples.
Reference: Gaston, K.G. & Spicer, J. (2003) Biodiversity – an Introduction. Blackwell Publishing.
BC/L13
The use of taxonomy in biodiversity studies
Paul Eggleton
The role and position of taxonomy: perception and reality. Alpha-taxonomy and its contribution. Assessment
of biodiversity is dependent on taxonomic skills (e.g. biological and morphospecies, expert identification,
higher taxonomic entities). Alpha- and beta-diversity. The problems of species limits and concepts.
Parataxonomists v. taxonomists. The contribution of phylogenetic systematics.
Reference: Krell, F-T. (2004) Parataxonomy vs. taxonomy in biodiversity studies – pitfalls and applicability
of „morphospecies‟ sorting . Biodiversity and Conservation, 13: 795-812
Tuesday 6th November
BC/L14&L15
What we can learn from palaeontology: Changes in
species diversity during the Quaternary
Steve Brooks
The distributions of animals and plants have been strongly influenced during the last two million years by
cycles of glacials and interglacials. In these two lectures we will examine the past response of faunas and
floras throughout the world to climate change. We will examine how insects, plants and mammals have
responded by either shifting the distributional range, by going extinct or by evolution. We will consider how
these past responses influence biogeography, competition and predator-prey relationships, population
genetics, and why some groups of organisms are more likely to go extinct than others. We will also consider
the implications of present and future global warming.
References:
Birks, H.J.B. and Birks, H.H. 2008. Biological responses to rapid climate change at the Younger DryasHolocene transition at Kråkenes, western Norway. The Holocene 18: 19-30.
Smol, J.P., Wolfe, A.P., Birks,H.J.B., Douglas, M.S.V. and 22 others. 2005. Climate-driven regime shifts in
the biological communities of arctic lakes. PNAS 102: 4397-4402.
Willis, K.J. Bennett, K.D. & Walker, D. [eds] 2004. The evolutionary legacy of the Ice Ages. Phil. Trans Roy.
Soc. (Biol. Sci.) 359: 155-303.
BC/L16&L17
Biogeographic and temporal patterns in microfossils
David Williams
Microscopical organisms, such as diatoms, preserve well after death leaving a 'good' fossil record hence
they are ideal organisms for studying aspects of evolutionary distributions in space and time. As they are
microscopic, certain assumptions concerning their present day global ubiquity have recently been made,
particularly the view that they are widely distributed and it is their ecological requirements, rather than their
history, that dictates present day floral composition. Given their good fossil record such ideas can be
examined from a historical point of view, tracking changes in floral composition over time. The sensitivity of
diatoms to environmental changes will be discussed relative to some causes of the changing floral
composition.
References:
Finlay, B.J., Monaghan, E.B., & Maberly, S.C. 2002. Hypothesis: The rate and scale of dispersal of
freshwater diatom species is a function of their global abundance. Protist, 153, 261-273.
Williams, DM. & Reid, G. Diatom Biogeography and Water Babies: The Search for Meaning among the
Protists. Diatom Research 21: 457-462.
29
Williams, DM & Reid, G. Dealing with large taxonomic groups: Diatoms species and geography. In
Hodkinson TR. & Parnell JAN. (eds), Towards the Tree of Life: The Taxonomy and Systematics of
Large and Species Rich Taxa. CRC Press, pp. 305-322.
Smol, J.P. and Stoermer, E.F [Editors]. (In Press). The Diatoms: Applications for the Environmental and
Earth Sciences. 2nd edition. Cambridge University Press, Cambridge.
Thursday 8th November
BC/L18
Testing macroevolutionary hypotheses using interspecies phylogenies
Alfried Vogler
In nearly all major groups of organisms, species are shared very unevenly among taxa. Does this mean that
chances of diversification have differed among groups? If so, are there traits that confer high rates of
diversification? And have rates of diversification changed through time? This lecture introduces a big and
very active research field, covering some general principles and a few detailed examples.
Reference: Mayhew, P. Why are there so many insect species? Perspectives from fossils and phylogenies.
Biological Reviews (2007) vol. 82 (3) pp. 425-454
BC/L19
Phylogenies and extinction
Alfried Vogler
The rate of species extinction is much higher now than it has been for thousands, perhaps millions, of
years. Does it strike species at random, or are there patterns among the causalties? And what traits
predispose species to decline in the face of human impacts? This lecture introduces the phylogenetic
approach needed to tackle these questions.
References:
Purvis, A. Phylogenetic approaches to the study of extinction. Annual Review in Ecology, Evolution and
Systematics (2008) vol. 39 pp. 301-319
Fisher, D C, and Owen,s I P F. The comparative method in conservation biology. Trends in Ecology &
Evolution (2004) vol. 19 pp. 391-398
BC/L20
Macroecological patterns of species diversity; neutral theory of biodiversity
Alfried Vogler
Macroecological patterns of species diversity. Area species curve, island biogeography, abundance and
range size, regional and local diversity, and turnover of diversity. Neutral processes of drift and dispersal to
explain patterns of species diversity and community composition.
Reference: Bell, G. 2001. Ecology - Neutral macroecology. Science 293:2413-2418. Hu, X. S., F. L. He,
and S. P. Hubbell. 2006. Neutral theory in macroecology and population genetics. Oikos 113:548-556.
Friday 9th November
BC/L21
Adaptive radiation
Aelys Humphreys
Two components of species diversity can be identified: i) number of species (species richness) and ii)
amount of morphological, ecological etc. variation (disparity). The question underlying the concept of
adaptive radiation is whether disparity among species & clades is an important part of evolution of species
richness, or whether differences among species are merely incidental consequence of their independent
evolution. This lecture looks at evidence for this idea, covering the issues of key innovations, island
radiations and community convergence, with examples from a wide range of plant and animal groups.
Reference: Schluter, D. 2000. The Ecology of Adaptive Radiation. Oxford University Press.
BC/L22
Competition and diversification
Aelys Humphreys
Size patterns among competitors: Ecological character displacement and character release. The guild
concept and the structure of ecological communities. Phylogenetic over- and under-dispersion.
Reference: Kraft, NJB et al. 2007. Trait evolution, community assembly and the phylogenetic structure of
ecological communities. American Naturalist. 170: 271-283
BC/L23
Geographic patterns of diversity
Aelys Humphreys
We will discuss two recent papers on this topic; papers to be announced at the beginning of the week.
30
Module Four
12th November – 7th December 2012
MOLECULAR SYSTEMATICS
Module Organiser: Prof Alfried Vogler, Life Sciences, NHM ([email protected])
Aims:
This module will lead through the recent methods of generating and analysing DNA data for
phylogenetic reconstruction. This includes hands-on experience of DNA extraction and
sequencing; editing and compilation of sequence data; procedures for DNA sequence
alignment; and the range of current methods for tree building. Particular attention will be paid
to model-based tree building, in the context of cladistic principles treated in the Phylogenetics
Module. Associated lectures will provide a solid background about the patterns of variation in
molecular data and how these affect the phylogenetic conclusions. The module will also
cover bioinformatics and basic computing. This is particularly important for exploiting the
great opportunities for molecular systematics arising from the quickly growing public DNA
databases and their increasing taxonomic coverage.
Objectives:
A detailed knowledge of the procedures of current methods in molecular systematics and
bioinformatics should be gained. This includes an in-depth understanding of the different
conceptual approaches to reconstruct phylogenetic trees from DNA sequences, in particular
through the use of model-based approaches; the different types of morphological and
molecular data and the appropriateness of different techniques for their analysis; the
problems associated with sequence alignment and homology assessment in phylogenetics
broadly; and the great possibilities for DNA-based approaches to establish the deep and tip
level branches of the Tree-of-Life.
Coursework:
Students will be required to hand in a written assignment on the data analysis by 17
December 2012 at 10:00.
Initials
th
DB
CB
MC
PGF
AA
APV
AP
Lecturer
David Bass
Chris Barton
Mark Carine
Peter Foster
Alex Aitken
Alfried Vogler
Alex Papadopulos
Location
Life Sciences, Natural History Museum
Division of Biology, Imperial College
Life Sciences, Natural History Museum
Life Sciences, Natural History Museum
Life Sciences, Natural History Museum
Life Sciences, Natural History Museum
Division of Biology, Imperial College
SR
Stephen Russell
Life Sciences, Natural History Museum
Email address
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
alexander.papadopulos
[email protected]
[email protected]
Schedule
WEEK 7
th
Monday 12 November
10:00-10:30
MS/L1
10:30-11:30
MS/L2
13:00-17:00
MS/P1
APV
Introduction to practical and assessed coursework
AA
Optional: DNA for beginners
AA/SR/APV Introduction to laboratory procedures
th
Tuesday 13 November
10:00-17:00
MS/P2
AA/SR/APV Specimen to Tree: Intro, PCR setup, genomic DNA extraction
set-up
th
Wednesday 14 November
Reading day
th
Thursday 15 November
10:00-17:00
MS/P3
AA/SR/APV Specimen to Tree: agarose gel, PCR purification, genomic
DNA purification continued
31
th
Friday 16 November
10:00-15:30
MS/P4
15:30-17:30
MS/S1
AA/SR/APV Specimen to Tree: Intro to DNA sequencing, sequencing
reaction set-up
tba
Visit to sequencing facility
WEEK 8
th
Monday 19 November
10:00-11:00
MS/L3
MC
11:15-12:00
13:00-14:00
14:15-17:00
MC
MC
PGF
Homology and character concepts in morphological and
molecular data
Combining DNA and morphology
Patterns of variation in sequence data
Computing
APV
APV
DB
The problem of paralogy: gene families, repetitive DNA etc.
Sequence alignment - theory
Genomics/Metagenomic/Next-gen Sequencing
APV
IJK
Overview of tree building methods
Lepidoptera phylogeny workshop and feedback]
PGF
PGF
Models of evolution and maximum likelihood
Tutorial Maximum Likelihood
PGF
PGF
PGF
Bayesian analysis
Advanced topics in models
Tutorial Bayesian analysis
AP
AP
Phylogenetic Reconstruction feedback session
Molecular clocks
Dating plant molecular phylogenies
CB
CB
Data bases for molecular biology and phylogenetics data mining
Bioinformatics for evolutionary biology
MS/L4
MS/L5
MS/P5
th
Tuesday 20 November
10:00-10:45
MS/L6
11:00-12:00
MS/L7
13:00-15:00
MS/L8-L9
st
Wednesday 21 November
10:00-11:30
MS/L10
[11:30-13:00 PR/P4
nd
Thursday 22
10:00-13:00
14:00-15:30
November
MS/L11-L12
MS/S2
rd
Friday 23 November
10:00-12:00
MS/L13
12:00-13:00
MS/L14
14:00-15:30
MS/S3
WEEK 9
th
Monday 26 November
10:00-11:30
12:30-14:30
MS/L15
14:30-15:30
MS/P6
th
Tuesday 27 November
10:00-11:00
MS/L16
11:00-15:00
MS/P7
th
Wednesday 28 November
Reading day
th
Thursday 29 November
Young Systematists’ Forum
Flett Theatre, NHM
th
Friday 30 November
11:00-15:00
MS/P8
15:30-17:00
MS/T2
APV/CB
Compilation of own DNA sequence data: Sequencher
Tutorial: Molecular Systematics Practical
32
WEEK 10
rd
Monday 3 December
10:00-16:30
MS/P9
APV/CB
Compilation of own DNA sequence data
APV/CB
Practical: Choosing a model; ML analysis of own data
Tutorial
APV/CB
Practical: Bayesian analysis of own data
th
Tuesday 4 December
10:00-15:30
MS/P10
15:45-17:15
MS/T3
th
Wednesday 5 December
Reading day
th
Thursday 6 December
11:15-15:00
MS/P11
th
Friday 7 December
Write-up molecular systematics practical
th
Hand in write-up by 17 December 2012 at 10:00.
Lecture and practical synopses
WEEK 7
Monday 12th November
MS/L1
Introduction to practical and assessed coursework
Alfried Vogler
MS/L2
DNA for beginners
Alex Aitken
The basic types of molecular data. Methodological aspects of sequencing techniques, PCR, the choice of
molecular markers, the pitfalls of primer design. Deposit and retrieval of DNA sequences. Overview on data
analysis.
MS/P1
Introduction to laboratory procedures
Alex Aitken/Stephen Russell/Alfried Vogler
Tuesday 13th November
MS/P2
Specimen to Tree: Intro, PCR setup, genomic DNA extraction set-up
Alfried Vogler / Alex Aitken / Stephen Russell
Thursday 15th November
MS/P3
Specimen to Tree: agarose gel, PCR purificaition, genomic DNA purification
Alfried Vogler / Alex Aitken / Stephen Russell
Friday 16th November
MS/P4
Specimen to Tree: Intro to DNA sequencing, sequencing reaction set-up
Alfried Vogler / Alex Aitken / Stephen Russell
MS/S1
Visit to sequencing facility
tba
33
WEEK 8
Monday 19th November
MS/L3 Homology and character concepts in morphological and molecular data
Mark Carine
Homology is the relation that systematists use in generating hypotheses of relationship. Many authors have
highlighted the challenges and pitfalls associated with establishing homologies using morphological data. In
this lecture, morphological and molecular data are compared to address the question: are molecular data any
easier?
MS/L4
Combining DNA and morphology
Mark Carine
Molecular data have greatly increased the numbers of characters available for phylogenetic studies (except
those involving extinct organisms). This has led to arguments that DNA may overwhelm morphology or that it
is so noisy that it's of little value. In this lecture, the issues will be discussed and various strategies described
and compared for dealing with both molecular and morphological data, combined or separately.
MS/L5
Patterns of variation in sequence data
Mark Carine
Different genes and non-coding regions of DNA, both nuclear and mitochondrial and plastid, show different
rates of evolution. We will consider different rates of evolution in different genomes, differences between
codon positions, loops and stems in ribosomal DNA and variation in spacer regions and concerted evolution.
Differences in rates of variation between DNA regions make them more or less appropriate for answering
questions at different hierarchical levels.
MS/P5
Computing
Peter Foster
Tuesday 20th November
MS/L6
The problem of paralogy: gene families, repetitive DNA etc.
Alfried Vogler
The types of repetitive DNAs and the consequences of gene duplication for phylogenetic reconstruction.
Tandemly repeated genes, gene families, gene duplications, and pseudogenes (including nuclear
mitochondrial DNA; “numts”). Orthology vs paralogy. Concerted evolution. Simple sequences (microsatellites
etc.).
Reference: Graur, D and Li, W.-H. 2000. Fundamentals of Molecular Evolution. Sinauer, Sunderland MA.
MS/L7
Sequence alignment - theory
Alfried Vogler
The importance of sequence alignment in molecular systematics. By eye vs. computer. Algorithms for
alignment, and their limitations. Distance vs. parsimony approaches to sequence alignment. The homology
concept in sequence alignment. Variation of alignment parameters and their effect on inferred phylogenies.
References:
Gardner, P.P., A. Wilm, and S. Washietl. 2005. A benchmark of multiple sequence alignment programs upon
structural RNAs. Nucl. Acids Res. 33:2433-2439.
Simmons, M.P. and H. Ochoterena. 2000. Gaps as characters in sequence-based phylogenetic analyses.
Syst. Biol. 49:369-381.
Wheeler, W.C. 1996. Optimization alignment: the end of multiple sequence alignment in phylogenetics?
Cladistics 12:1-9.
Wong, K.M., M.A. Suchard, and J.P. Huelsenbeck. 2008. Alignment uncertainty and genomic analysis.
Science 319:473-476.
MS/L8-L9
Genomics/Metagenomics/Next-gen Sequencing
34
David Bass
Wednesday 21st November
MS/L10
Overview of tree building methods
Alfried Vogler
Maximum parsimony. Distance methods. Model-based methods. Maximum likelihood. Bayesian methods.
References:
Baldauf, S.L. 2003. Phylogeny for the faint of heart: a tutorial. Trends Genet. 19:345-351.
Foster, P. G. 2007. Inferring phylogenetic relationships from sequence data. Chapter 12. Pp 265-282 in
Bioinformatics: Methods Express (P. Dear, ed.) Scion, Bloxham, Oxfordshire.
Huelsenbeck, J.P., F. Ronquist, R. Nielsen, and J.P. Bollback. 2001. Evolution - Bayesian inference of
phylogeny and its impact on evolutionary biology. Science 294:2310-2314.
Thursday 22nd November
MS/L11-L12
Models of evolution and maximum likelihood
Peter Foster
Neutral evolution. Hidden mutations and long branch attraction in parsimony. Simple likelihood calculations.
Simple models of evolution. Gamma-distributed among site rate variation. Choosing a model. Simulating
evolution.
References:
Bergsten, J. 2005. A review of long-branch attraction. Cladistics 21:163-193.
Lewis, P.O. 2001. Phylogenetic systematics turns over a new leaf. Trends In Ecology & Evolution 16:30-37.
Steel, M. 2005. Should phylogenetic models be trying to 'fit an elephant? Trends Genet. 21:307-309.
Friday 23rd November
MS/L13
Bayesian analysis
Peter Foster
Prior distributions and nuisance parameters. Markov chain Monte Carlo methods. Practical Bayesian
analysis. Summarizing the results of a Bayesian analysis. Making consensus trees. Assessment of
convergence of MCMC.
Reference: Holder, M., and P. O. Lewis. 2003. Phylogeny estimation: Traditional and Bayesian approaches.
Nature Reviews Genetics 4:275-284.
MS/L14
Advanced topics in models
Peter Foster
Model-based comparison of the goodness of trees. Comparing tree topologies using the approximately
unbiased (AU) test. More models. Bayes factors. Model fit and model adequacy.
Reference: Brandley, M. C., A. Schmitz, and T. W. Reeder. 2005. Partitioned Bayesian analyses, partition
choice, and the phylogenetic relationships of scincid lizards. Syst. Biol. 54:373-390.
WEEK 9
Monday 26th November
MS/L15
Molecular clocks
Alex Papadopulos
The molecular clock as a model in molecular phylogenetics. Relaxed clocks, rate smooting and penalized
likelihood. Searching trees and calculating the clock together. Dating phylogenetic trees.
References:
Drummond, A.J., S.Y.W. Ho, M.J. Phillips, and A. Rambaut. 2006. Relaxed phylogenetics and dating with
confidence. PLoS Biol. 4:699-710.
Sanderson, M.J., J.L. Thorne, N. Wikstrom, and K. Bremer. 2004. Molecular evidence on plant divergence
times. Am. J. Bot. 91:1656-1665.
MS/P6
Dating plant molecular phylogenies
35
Alex Papadopulos
Tuesday 27th November
MS/L16
Data bases for molecular biology and phylogenetics and DNA data mining
Chris Barton
An overview of the various DNA and protein databases publicly available, and their relevance to
phylogenetics. Extracting phylogenetically relevant data from public databases: an introduction to the most
commonly used approaches for obtaining and manipulating DNA data using Perl scripting. This will be
illustrated using a concrete example from a large scale phylogenetic analysis of insects.
Reference: Jones, M. and M. Blaxter. 2006. TaxMan: a taxonomic database manager. BMC Bioinformatics
7:e536.
MS/P7
Bioinformatics for evolutionary biology
Chris Barton
Elementary scripting and automation. Sequence formats and interconversion. Specialized blast (local blast
and blastcl3). Translation of DNA sequences.
Thursday 29th November
Young Systematists Forum – Flett Theatre, NHM
Friday 30th November
MS/P8
Compilation of own DNA sequence data: Sequencher
Alfried Vogler / Chris Barton
WEEK 10
Monday 3rd December
MS/P9
Compilation of own DNA sequence data
Alfried Vogler / Chris Barton
Tuesday 4th December
MS/P10
Practical: Choosing a model; ML analysis of own data
Alfried Vogler/Chris Barton
Choosing a model with Modeltest. The site-specific models. Apply ML analysis to own data from alignment
exercise. Careful and justified choice of a model (likelihood ratio test, AIC).
Reference: Posada, D., and K. A. Crandall. 1998. MODELTEST: testing the model of DNA substitution.
Bioinformatics 14:817-818.
Thursday 6th December
MS/P11
Practical: Bayesian analysis of own data
Alfried Vogler / Chris Barton
Friday 7th December
Write-up molecular systematics practical
MS/P2-P11
st
Hand in write-up by 21 December 2012 at 10:00.
General reading list
Hillis, D. M, Moritz, C. and Mable, B. K. (Eds). 1996. Molecular Systematics. 2nd edition. Sinauer
Graur, D and Li, W.-H. 2000. Fundamentals of Molecular Evolution. Sinauer, Sunderland MA
Page, RDM, and EC Holmes. 1998. Molecular Evolution. A phylogenetic approach. Blackwell
Hall, B.G., 2007. Phylogenetic trees made easy: a how-to manual. Third Edition. Sinauer, Sunderland MA.
Felsenstein, J., 2004. Inferring phylogenies. Sinauer, Sunderland MA.
Nei and Kumar 2000. Molecular Evolution and Phylogenetics Oxford University Press.
36
7th – 18th January 2013
Module Five
Organisms are characterized by many patterns of similarity and difference. Most of systematics
involves the study of these patterns and use of the results of such studies to test hypotheses in
taxonomy, phylogeny, evolution, biogeography, ecology, etc. The quantitative study of biological data
is variously termed biometrics or, in a strictly systematic context, phenetics. Biometric approaches to
systematics are becoming increasingly popular, especially in terms of the geometric assessment of
morphological variation.
Aims
This module will deal with the theory and practice of a wide range of biometric techniques including
the use of descriptive statistics, regression models, multivariate methods (e.g., principal components
analysis, linear discriminant methods), geometric morphometrics, and neural nets. Emphasis will be
placed on methods that can be used to characterize morphological variation (e.g. allometry, various
types of
analysis, eigenshape analysis, neural nets). Students will be expected to become
familiar with the concepts involved in the use of such methods, interpretation of results, and the
operation of simple software packages designed to implement basic data-analysis techniques.
• Recognize situations in which ordination techniques can be used to answer systematic
•
•
•
questions in species identification, functional morphology, ecology, and biogeography.
Acquire a knowledge of image analysis-image processing techniques sufficient to extract
landmark and boundary-coordinate data from images of biological objects.
Acquire a qualitative-procedural knowledge of the following ordination techniques as they are
applied to biological data: regression analysis, principal component analysis (PCA), linear
discriminant analysis (LDA/CVA), relative warps analysis (RWA.
Understand the relation between morphometric and phylogenetic approaches to biological data
analysis.
NM: Norman MacLeod, Earth Sciences, NHM
Prof. Norman MacLeod
Office: Palaeontology Building PA306
Phone: 0207 942-5204
Email: [email protected]
Schedule appointments through Palaeo. Dept. Secretary:
Nichola Morris, [email protected]
37
Monday, 7 January
10:00-10:30 OTT/L1
NM
Introduction to the module
10:30-11:00 OTT/L2
NM
Biometric analysis in systematics I
11:15-12:30 OTT/L3
NM
Biometric analysis in systematics II
14:00-14:30 OTT/L4
NM
Morphometric data collection theory & software
14:30-17:00 OTT/P1
NM
Practical: Morphometric data collection exercise
10:00-11:00 OTT/L5
NM
Survey of biometric methods I
11:15-12:30 OTT/L6
NM
Survey of biometric methods II
14:00-17:00 OTT/P2
NM
Practical: Morphometric data collection exercise
10:00-11:00 OTT/L7
NM
Allometry
11:15-12:30 OTT/L8
NM
Allometry analysis using bivariate linear regression
10:00-10:30 OTT/L9
NM
Discussion of morphometric data collection exercise
10:30-11:30 OTT/L10
NM
Principal components analysis (PCA)
11:45-12:30 OTT/L11
NM
Principal coordinates analysis (PCoord) & singular value
decomposition (SVD)
14:00-14:30 OTT/L12
NM
Linear regression software
14:30-17:00 OTT/P3
NM
Practical: Bivariate allometry exercise
10:00-10:30 OTT/L13
NM
Discussion of bivariate allometry exercise
10:30-11:45 OTT/L14
NM
Landmarks, shape coordinates &
12:00-12:30 OTT/L15
NM
Shape theory
14:00-15:00 OTT/L16
NM
PCA Software
15:00-17:00 OTT/P4
NM
Practical: PCA allometry exercise
10:00-10:30 OTT/L17
NM
Discussion of PCA allometry exercise
10:30-11:15 OTT/L18
NM
11:30-12:30 OTT/L19
NM
14:00-14:30 OTT/L20
NM
14:30-17:00 OTT/P5
NM
Tuesday, 8 January
Wednesday, 9 January
Thursday, 10 January
Friday, 11 January
superposition
Monday, 14 January
PCA & shape modeling
Thin plate splines, principal/partial warps analysis, and relative
warps analysis
PCA/tpsRelW software
Practical:
PCA exercise
38
Tuesday, 15 January
10:00-10:30 OTT/L21
NM
Discussion of
PCA exercise
10:30-11:15 OTT/L22
NM
Semilandmarks & outline morphometrics
11:30-12:30 OTT/L23
NM
Multidimensional scaling (MDS) and partial least-squares (PLS)
14:00-17:00 OTT/P6
NM
Practical: write-up time
10:00-10:30 OTT/L24
NM
Discussion of practical write-up issues
10:30-11:15 OTT/L25
NM
Hybrid morphometrics (extended & coordinate-point
eigenshape analyses)
11:30-12:30 OTT/L26
NM
Eigensurface analysis
10:00-10:30 OTT/L27
NM
Discussion of practical write-up issues
10:30-11:15 OTT/L28
NM
Linear discriminant analysis
11:30-12:30 OTT/L29
NM
Multiple-group linear discriminant analysis
14:00-15:00 OTT/L30
NM
Non-linear discriminant analysis & neural nets
15:00-17:00 OTT/P7
NM
Practical: write-up time
10:00-11:00 OTT/L31
NM
Lecture/Demonstration: PSOM Neural Nets & DAISY
11:15-12:30 OTT/L32
NM
Future use of morphometrics in systematics
14:00-17:00 OTT/P8
NM
Practical: write-up time
Wednesday, 16 January
Thursday, 17 January
Friday, 18 January
Monday 7th January
This lecture is intended as an orientation for the students to the general topics, rationale, schedule,
structure, assignments, and expectations of the module. In particular, module resources available on
the NHM intranet will be discussed as well as the computer skills required for accessing those
resources, data, and information. The goal of this lecture is to provide (1) a context for understanding
how ordination methods relate to other branches of systematics and (2) provide a clear statement as
to what the student is expected to do in order to master the material presented.
A series of two lectures intended as a historical overview of the use quantitative, biometric,
morphometric, and statistical approaches to hypothesis testing in biology. Throughout particular
attention will be paid to the manner in which to properly construct an analysis of biological data and
the role of ordination in conducting biological hypothesis tests. Goals of these lectures will be to have
the students (1) develop an appreciation of the fact that the application of quantitative methods has
been part of the corpus of biology and systematics from the very beginnings of these subjects and (2)
understand how biometric methods and ordination have historically, can now, and will in the future
contribute to the biological research problems.
39
This will constitute a lecture-demonstration of a series of alternative morphological data acquisition
software systems. Each student will be encouraged to explore the capabilities of each system on a
selection of example systematic images. In particular, the lecture will explain how to use supplied
software to record scaled
coordinate locations of landmarks and linear distances. The goals of this
lecture are to (1) familiarize the student with an advanced image analysis/morphological data
collection systems, and (2) enable the student to gain confidence in accessing and measuring images
of biological specimens.
This exercise will require that the student use software provided to collect scaled landmark and/or
distance data for images of small collection of specimens, migrate those data into MS-Excel, and
obtain
plots of the data using the MS-Excel graphing capabilities. These data will form a series of
morphologically-based ordination analyses throughout the module.
Tuesday 8th January
This lecture is intended as a general introduction to ordination methods in systematics. The account
will be organized along historical and methodological lines and will contain examples of the use of
quantitative ordinations in morphological, geographical, ecological, and phylogenetic contexts. In
addition, many references to past and ongoing controversies in which biometric analysis played a
significant role (e.g., punctuated equilibria, disparity analysis) will be touched upon. These lectures will
also stress the interrelations among biometric methods and serve as a brief introduction to methods
that are not going to be discussed in detail later in the module. The goals of this lecture are to (1)
introduce the students to the wide range of ordination applications in systematics, (2) allow them to
appreciate which data analysis tools are suitable for which types of problems, and (3) serve as a brief
introduction to methods that are not going to be discussed in detail later in the course.
Reference
James, F. C., and C. E. McCulloch. 1990. Multivariate analysis in ecology and systematics: panacea
or Pandora's box. Annual Review of Ecology and Systematics 21:129–166.
This exercise will require that the student transform his/her landmark data into a series of Euclidean
distances that will be used in subsequent analyses. It will also serve as additional time for students to
collect their landmark data in case they didn’t complete this task on Monday.
Wednesday 9th January
This lecture will introduce the students to the concept of allometry, the analysis of the effects of size
variation on other parameters of biological interest. A detailed discussion of covariance between size
ad shape will serve to make the general allometric concept plain as well as presenting conceptual
differences between the concepts of size and shape. The lecture will also show how such concepts
can be investigated using quantitative methods and how the use of ordination techniques can help
both in the formulation of specific biological hypotheses to test as well as in testing them. In this
regard, use of theoretical models (e.g., isometry, similitude, elastic similarity) will be stressed, along
with recent examples of the application of scaling relations in systematic investigations. Goals for this
lecture include (1) understanding of the difference between size and shape (relative size), (2)
understanding of the different types of allometry, (3) understanding the analytic implications and
advantages of parsing biometric data across groups (= horizontal) and within groups (= vertical)
structures, and (4) explain how quantitative methods can be used to test the predictions of
qualitatively-formulated biological hypotheses.
References
LaBarbera, M. 1989. Analyzing body size as a factor in ecology and evolution. Annual Review of
Ecology and Systematics 20:97–117.
MacLeod, N. 2008. Distances Landmarks & Allometry. Palaeontological Association Newsletter
68:30–39.
40
Allometric analysis will also serve to introduce the student to the method of bivariate regression; a
fundamental concept that will be built upon in the explanation of multivariate methods. The lecture will
discuss various regression models (e.g., least squares, reduced major axis, major axis) and
techniques for estimating statistical significance as these apply to allometric studies. Goals include (1)
understanding of the importance of choosing a correct numerical model in biometric ordination studies,
(2) interpretation of regression results, (3) understanding various strategies for assessing the
goodness-of-fit between the regression model and the data.
References
MacLeod, N. 2004. Prospectus & Regressions 1. Palaeontological Association Newsletter 55:28–36.
MacLeod, N. 2004. Regression 2. The Palaeontological Association Newsletter 56:60–71.
The primary lecturer will report on progress made with his lab exercise emphasizing decisions made in
terms of landmark definition, landmark coverage and geometry of the distance net used to represent
the shapes present in the dataset. This will be followed by a brief discussion of basic principles of
designing morphometric measurement schemes.
This lecture will introduce the student to the most widely used family of ordination methods; principal
component analysis (PCA). While not intended as a mathematical treatment of these topics, the
concepts inherent in PCA will be presented with reference to models of multivariate allometry (in order
to establish continuity with previous discussions) before engaging issues unique to the PCA approach.
In addition, care will be taken to describe practical situations best treated via bivariate and multivariate
approaches.
References
MacLeod, N. 2005. Principal components analysis (eigenanalysis & regression 5). Palaeontological
Association Newsletter 59:42–54.
Somers, KM. 1986. Multivariate allometry and the removal of size with principal components analysis.
Systematic Zoology 35: 359–396.
value decomposition (SVD)
This lecture will introduce the student to principal coordinates analysis (PCoord) — the dual of PCA —
and facilitate a discussion of the differences and relations between -mode and -mode data
analyses. In particular, the need to use indices of similarity suitable to the data and sort of problem at
hand with be emphasized (e.g., variables-based indices for -mode analysis, distance-based indices
for -mode analyses. The lecture will end with a discussion of singular value decomposition as this
technique unites wit two modes in a single analysis and is used as the basis for several methods that
will be discussed subsequently (e.g., warps analysis, eigenshape analysis).
Reference
MacLeod, N. 2006. Minding your Rs and Qs. Palaeontological Association Newsletter 61:42–60.
This lecture will introduce the student to the software that will be provided to undertake an analysis of
allometry in their data using bivariate linear regression, its operation, its options, the results produced
and their interpretation. Throughout care will be taken to connect the input, options, and output of the
software to the concepts discussed in the lectures (see above). The goals of this lecture are to (1)
enable the student to undertake a regression-based analysis of their distance data, (1) to select
appropriate data-analysis options, and (3) understand the geometric and biological meaning(s) of the
results.
41
This exercise will require that the student use their linear distance data as input into a regressionbased allometric analysis. Results will then be used to (1) identify the presence of allometry in their
measurements, (2) map regions of the morphology over which allometric relations are similar and
different, (3) summarize broad patterns of allometric variation in the sample, and (4) interpret these
patterns within both geometric and systematic contexts.
This lecture will report on progress made with the lab exercise emphasizing the decisions made in
terms of regression model, results obtained, interpretation of results, and any problems encountered in
the analysis. This will be followed by a brief discussion of basic principles involved in conducting
bivariate regression analyses.
This lecture will introduce the student to the underlying rationale of landmark-based morphometrics.
After a brief, historical introduction to the topic the concept of a ‘landmark’ will be introduced. A
classification of landmarks will then be developed along with a discussion of the manner in which
landmarks relate to the concepts of biological and geometric similarity. The sorts of information that
can be provided by landmarks will then be emphasized and contrasted with the sorts of information
provided by linear (inter-landmark) distances. Finally, the concept of shape coordinates will be
introduced and used to develop a model of allometric shape change using landmark data.
References
MacLeod, N. 2008. Size and shape coordinates. Palaeontological Association Newsletter 69:26–36.
MacLeod, N. 2009. Who is
and what has he done with my data? Palaeontological
Association Newsletter 70:21–36.
This lecture will introduce the student to the manner in which landmark-defined shapes are distributed
in geometric space and the implications this has for the use of landmark methods to analyze biological
shapes. Topics covered in this lecture include shape manifolds, the
shape space, the
Kendall shape space, the effect of shape variance on the interpretability of shape distributions in a
linear space, the concept of the reference shape, and various methods of projecting shape data into
linear spaces.
Reference
MacLeod, N. 2009. Shape theory. Palaeontological Association Newsletter 71:34–47.
This lecture will introduce the student to the software that will be provided to undertake an analysis of
allometry in their distance data using PCA, its operation, its options, the results produced and their
interpretation. Throughout care will be taken to connect the input, options, and output of the software
to the concepts discussed in the lectures (see above). The goals of this lecture are to enable the
student to undertake a PCA-based analysis of their distance data, select appropriate options, and
understand the biological meaning of the results.
This exercise will give the student the opportunity to use their linear distance data as input into a PCA
analysis. Results will then be used to (1) identify the presence of multivariate allometry in their
measurements, (2) map regions of the morphology over which allometric relations are similar and
different, (3) summarize broad patterns of allometric variation in the sample, (4) interpret these
patterns within both geometric and systematic contexts, and (5) compare and contrasts results
obtained from univariate and multivariate allometric analyses.
42
This lecture will report on progress made with his lab exercise emphasizing the decisions necessary to
implement a PCA analysis option, results obtained, interpretation of results, comparison of results with
bivariate regression results, and any problems encountered in the analysis. This will be followed by a
brief discussion of basic principles used in conducting linear distance-based PCA analyses.
This lecture will build on the material presented in previous lectures to extend the concept of the PCA
analysis of
superposed data as a generalized morphometric ordination method. In addition,
the method of creating shape models that enable direct visualization of the patterns of shape variation
represented by the
PCA axes will be explained, demonstrated, and compared to the
methods used to interpret standard PCA axes. The goals of this lecture are to provide the student with
a qualitative understanding of most routinely applied method of geometric morphometrics.
References
MacLeod, N. 2009. Who is
and what has he done with my data? Palaeontological
Association Newsletter 70:21–36.
MacLeod, N. 2009. Form & shape models. Palaeontological Association Newsletter 72:14–27.
This lecture will introduce the student to other landmark-based ordination methods, (e.g., thin-plate
spline analysis TPS, principal warps analysis, partial warps analysis, relative warps analysis). While
not intended as a mathematical treatment of these topics, the concepts involved in each technique will
be presented with reference to models of multivariate allometry (to establish continuity with previous
technical discussions) before engaging issues unique to these approaches to ordination analyses. In
addition, care will be taken to describe practical situations best treated by these analytic approaches.
The goals of this lecture are to (1) introduce the student with methods used in landmark-based
analyses using the thin-plate spline and (2) establish points of similarity and difference between these
methods and the regression/PCA approaches discussed to this point.
References
MacLeod, N. 2010. Shape models II: the thin plate spline. Palaeontological Association Newsletter
73:24–39.
MacLeod, N. 2010. Principal & partial warps. Palaeontological Association Newsletter 74:35–45.
MacLeod, N. 2010. Principal warps, relative warps and
PCA. Palaeontological Association
Newsletter 75:22–33.
This lecture will introduce the student to the software that will be provided to undertake an analysis of
allometry in landmark data using a
PCA approach, its operation, its options, the results
produced and their interpretation. Throughout care will be taken to connect the input, options, and
output of the software to the concepts discussed in the lectures (see above). The goals of this lecture
are to (1) enable the student to undertake a
PCA-based analysis of their landmark data, (2)
select appropriate data-analysis options, and (3) understand the geometric biological meanings of the
results.
This exercise will require that the student use their landmark data as input into a
PCA or
tps/RelW analysis (results will be equivalent). Results will then be used to (1) identify the presence of
multivariate allometry in their landmark data, (2) map regions of the morphology over which allometric
relations are similar and different, (3) summarize broad patterns of allometric variation in the sample,
(4) interpret these patterns within both geometric and systematic contexts, and (5) compare and
contrasts results obtained from univariate and multivariate allometric analyses.
43
This lecture will report on progress made with the lab exercise emphasizing decision made in
implementing a
PCA analysis, results obtained, interpretation of results, comparison of
results with linear-distance PCA and bivariate regression results, and any problems encountered in
the analysis. This will be followed by a brief discussion of basic principles involved in conducting
PCA analyses.
This lecture will introduce the student to the underlying rationale of outline-based morphometrics. After
a brief, historical introduction the concept of an ‘outline’ will be introduced, along with a discussion of
the manner in which outlines relate to the concepts of biological and geometric similarity. The sorts of
information that can be provided by landmarks will then be emphasized and contrasted with the sorts
of information provided by linear (inter-landmark) distances and landmarks. Finally, the concept of
semilandmarks will be related to outlines and used to develop a model of outline-based shape change.
This lecture will also introduce the student to the classical, radial Fourier approach to the analysis of
biological outlines. After developing basic concepts of the Fourier series, the discussion will move on
to cover sampling of the outline via radius vectors, instabilities introduced as a result of the need to
locate the object’s centroid, non-centroid-based shape functions, and elliptical Fourier analysis. While
not intended primarily as a mathematical treatment of these topics, the concepts involved in each
technique will be present with reference to models of multivariate allometry (in order to establish
continuity with previous technical discussions) before engaging issues unique to these approaches to
ordination analyses. In addition, care will be taken to describe practical situations best treated by
these analytic approaches. This lecture will close with an introduction to eigenshape analysis in its
original form.
While not intended as a mathematical treatment of these topics, the concepts involved in each
technique will be presented with reference to models of multivariate allometry (in order to establish
continuity with previous technical discussions) before engaging issues unique to these approaches to
ordination analyses. As above, care will be taken to describe practical situations best treated by these
analytic approaches.
References
MacLeod, N. 2011. Semilandmarks and radial Fourier analysis. Palaeontological Association
Newsletter 76:25-42.
MacLeod, N. 2011. Centroids, complex outlines and shape functions. Palaeontological Association
Newsletter 77:36–45.
Lohmann, G. P. 1983. Eigenshape analysis of microfossils: A general morphometric method for
describing changes in shape. Mathematical Geology 15:659-672.
(PLS)
This lecture will describe the methods of multidimensional scaling (MDS) and two-block partial least
squares (PLS) analysis ways of better representing the fine-scale ordination of biological data (MDS)
and modeling relations between independent datasets (PLS). The lecture will compare and contrast
MDS and PLS with PCA, providing the student with a clear understanding of which method to use for
which data in order to answer which type of question. A variety of examples will also be presented and
discussed including those drawn from the research projects of previous NHM-IC MSc students.
References
MacLeod, N. 2008. Multidimensional scaling and ordination. Palaeontological Association Newsletter
67:26–44.
MacLeod, N. 2006. Data blocks and partial least squares analysis. Palaeontological Association
Newsletter 63:36–48.
This time is provided to work on completing the lab practical reports as well as discussing data
analysis and interpretational issues with the module instructors.
44
This lecture will present practical aspects of writing a formal scientific report and answer questions
regarding the interpretation/presentation of results, organizing discussions sections, illustrating the
text, drafting graphics, etc.
eigenshape analyses
This lecture will introduce the student to two advanced forms of eigenshape analysis While not
intended as a mathematical treatment of these topics, the concepts involved in each technique will be
presented with reference to models of multivariate allometry (in order to establish continuity with
previous technical discussions) before engaging issues unique to these approaches to ordination
analyses. As above, care will be taken to describe practical situations best treated by these analytic
approaches.
References
MacLeod, N. 1999. Generalizing and extending the eigenshape method of shape visualization and
analysis. Paleobiology 25(1): 107–138.
Figueirido, B., N. MacLeod, J. Krieger, M. De Renzi, J. A. Pérez-Claros, and P. Palmqvist. 2011.
Constraint and adaptation in the evolution of carnivoran skull shape. Paleobiology 37(3):490–
518.
This lecture will introduce the student to a 3D form of eigenshape analysis, eigensurface analysis
While not intended as a mathematical treatment of these topics, the concepts involved in this
technique will be presented with reference to models of multivariate allometry (in order to establish
continuity with previous technical discussions) before engaging issues unique to these approaches to
ordination analyses. As above, care will be taken to describe practical situations best treated by the
eigensurface approach.
Reference
MacLeod, N. 2008. Understanding morphology in systematic contexts: 3D specimen ordination and
3D specimen recognition. Pages 143–210 The New Taxonomy (Q. Wheeler, ed.) CRC Press,
Taylor & Francis Group, London.
This lecture will discuss practical aspects of writing a formal scientific report and answer questions
regarding the interpretation/presentation of results, organizing discussions sections, illustrating the
text, drafting graphics, etc.
This lecture will consider techniques for the analysis of systematic datasets that are
structured
into group-level subdivisions. The first part of the lecture will cover generalized methods of statistically
testing for differences between two groups. The second part will focus on ordination-based methods
that can be used to assess the general quality of the group-discrimination result (e.g., Mahalanobis
distance table, confusion matrix). The third part will focus on formally statistical methods available for
test hypotheses of group separation. Comparisons and contrasts to PCA will be made throughout the
discussion. The goal of the presentation is to familiarize the student with the general concepts inherent
in group-discrimination analysis and the manner in which this cab be allied in both qualitative and
statistical senses to biological data.
References
MacLeod, N. 2007. Groups I. Palaeontological Association Newsletter 64:35–45.
MacLeod, N. 2007. Groups II. Palaeontological Association Newsletter 65:36–49.
45
This lecture builds on the previous lecture to consider the multiple-group situation, which is the domain
of canonical variates analysis (CVA) and soft modeling (e.g., SIMCA-PCA). The lecture will focus
primarily on CVA as that is the more commonly encountered method, but will use the SIMCA-PCA
approach in order to discuss similarities and differences between CVA and PCA. Particular attention
will be paid to interpreting the geometric meaning of CVA and SIMCA-PCA ordinations/axes including
presentation of a new strategy to make this easier for CVA analyses. Finally a discussion of the ‘curse
of dimensionality’ will be provided as well as a Monte Carlo simulation approach to testing CVA and
SIMCA-PCA results for statistical significance.
References
Wold, S. 1976. Pattern recognition by means of disjoint principal component models. Pattern
Recognition 8:127–139.
MacLeod, N. 2007. Groups II. Palaeontological Association Newsletter 65:36–49.
This lecture will introduce the student to scene-based artificial intelligence/computer vision approaches
to the classical multivariate discriminant analysis problem. Both supervised neural net and
unsupervised neural net (DAISY) approaches will be compared and contrasted with measurementbased canonical variates analysis and the strengths and weaknesses of all three approaches
discussed. Goals of this lecture will be (1) to familiarize students with scene-based approaches to
automated object identification and (2) to introduce them to practical situations in which measurementbased and scene-based applications should be preferred.
References
Lang, R. 2007. Neural networks in brief. Pages 47–68 Automated taxon recognition in systematics:
theory, approaches and applications (N. MacLeod, ed.) CRC Press, Taylor and Francis Group,
Boca Raton, Florida.
MacLeod, N., M. O'Neill, and A. S. Walsh. 2007. Automated tools for the identification of taxa from
morphological data: face recognition in wasps. Pages 153–188 Automated taxon recognition
in systematics: theory, approaches and applications (N. MacLeod, ed.) CRC Press, Taylor &
Francis Group, Boca Raton, Florida.
This time is provided to work on completing the lab practical reports as well as discussing data
analysis and interpretational issues with the module instructors.
This optional lecture will constitute a discussion/demonstration of the DAISY data analysis software.
The goals of this lecture are to familiarize the student with the potential of an artificial intelligence
approach to automated object identification.
Although many of the goals and concepts of qualitative morphological analysis and morphometrics are
similar, systematists have been slow to appreciate the power morphometric methods in phylogenetic
analysis. This lecture challenges the oft-stated assumptions that continuous variables (e.g., shape
factor scores) cannot be used in the context of a phylogenetic analysis by demonstrating through an
exploration of the concepts of a cladistic character and a morphometric variable, the role of
morphometric methods in discovering and documenting new morphological character and character
states, and the nature of continuous variables. Using example analyses the potential contribution of
morphometrics to phylogenetic analysis is reassessed. Goals of this lecture will be (1) to encourage
students to use the information they have been presented with to think critically about how
morphometrics can be used in a phylogenetic context and (2) to reflect on how ordination methods in
general, and morphometric methods in particular, may contribute to their research projects.
References
MacLeod, N. 2002. Phylogenetic signals in morphometric data, MacLeod, N., and Forey, P., eds.,
Morphometrics, shape, and phylogenetic: Taylor and Francis, London, 100-138.
46
Catalano, S. A., P. A. Goloboff, and N. P. Giannini. 2010. Phylogenetic morphometrics (I): the use of
landmark data in a phylogenetic framework. Cladistics 26:539–549.
This time is provided to complete work on the lab practical reports.
For small collections of objects, you will
1. Design measurement systems that:
1.1. capture the geometry of the objects
1.2. quantify major patterns of within-sample morphological variation
2. Measure the objects using appropriate tools and software
2.1. Analyze the bivariate allometry, including
2.2. estimation of allometric equations
2.3. identification of types of expressed allometries
2.4. interpretation of allometry of clade
3. Analyze the multivariate evolutionary allometry using a PCA approach
3.1. interpret first few PC axes in terms of their expression of size and/or shape variation
3.2. recalculate PC-1 (if appropriate) to facilitate comparison w/ bivariate results
3.3. interpret first few PC axes in terms of original variables
3.4. plot ordinations of objects in space of first few PC axes and interpret
3.5. compare and contrast w/ cladogram
4. Analyze the multivariate evolutionary allometry using a
PCA/relative warps approach
4.1.
i
nterpret first few -PCA/RW axes in terms of their expression of shape variation and the
relationship of that variation to size variation.
4.2.
i
nterpret first few -PCA/RW axes in terms of original variables
4.3.
p
lot ordinations of objects in space of first few -PCA/RW axes and interpret
4.4.
c
ompare and contrast w/ cladogram
47
Module Six
21st – 25th January 2013
TAXONOMIC AND SYSTEMATIC PRINCIPLES
Module organiser: Dr Donald Quicke, Division of Biology, IC, Silwood Park ([email protected])
This module offers lectures on the history of taxonomy and the need for and uses of classifications and
phylogenies; nomenclature; revisionary taxonomy and the general practice of taxonomy including scientific
description. The module also includes an introduction to the various Codes of Nomenclature and their
underlying principles.
Aims:
This module aims:
To describe the history of taxonomy and classification from Aristotle to the present day, with special
reference to animals, and to explain the utilities of classificatory systems.
To outline how taxonomic work is actually carried out and the differences between systematics,
taxonomy, classification and nomenclature.
To explain the essential principles of taxonomy and nomenclature as encompassed by the various
Codes; to explain their extents; to explain the Type concept; to distinguish between diagnoses and
descriptions; to explain good working taxonomic practice.
To provide definitions, and worked examples, of the concept of priority and the various types of
synonymy and homonymy.
To discuss future developments of the Codes in the light of new technologies.
Objectives:
Students should be able to:
Outline the stages in the development of classification and taxonomy in the Western World from Aristotle
to Linnaeus and the present time.
Enumerate and explain the reasons for the essential principles of taxonomy as they apply to the various
Codes.
Point out major differences between the Codes and have an understanding of the reasons why they
exist.
Provide definitions of, recognise cases of, and apply appropriate nomenclatural solutions to, problems
involving type identities, priority, homonymy, synonymy, valid publication and authorship.
Produce a good working description and diagnosis of an organism in a group they are familiar with.
Argue in a reasoned way, based on the above, what future developments of the Code(s) they think
would be most beneficial to taxonomic practice.
Initials
DQ
EM
MS
Lecturer
Donald Quicke
Ellinor Michel
Mark Spencer
Location
Division of Biology, Imperial College Silwood Park
International Commission of Zoological Nomenclature, NHM
Life Sciences, Natural History Museum
Email address
[email protected]
[email protected]
[email protected]
Schedule
WEEK 14
st
Monday 21 January
10:00-10:50
TSP/L1
11:00-11:50
TSP/L2
DQ
DQ
12:00-12:50
14:00-15:00
TSP/L3
TSP/L4
DQ
EM
January
TSP/L5
TSP/L6
TSP/L7
MS
MS
MS
nd
Tuesday 22
10:00-10:50
11:00-11:50
12:00-12:50
History and principles of nomenclature and the codes
The International Code of Zoological Nomenclature Basic principles governing the scientific names of animals
Zoological Nomenclature (continued)
Animal name databases and registers - ZooBank
- the future of zoological nomenclature
Botanical nomenclature and typification
Changes at the 2011 ICB
Fungi
48
rd
Wednesday 23 January
Reading day
th
Thursday 24 January
10:00-10:50
TSP/L8
DQ
11:00-11:50
14:00-14:50
DQ
DQ
TSP/L9
TSP/S1
Rates of species descriptions and the current state of
alpha-taxonomic work - the future of taxonomy
The Codes of Nomenclature: Bacteria and Viruses
Examining a taxonomic publication - priority, etc.
th
Friday 25 January
Reading day
Lecture and practical synopses
WEEK 14
Monday 21st January
TSP/L1
History and principles of nomenclature and the codes
Donald Quicke
The origins of the International Commissions will be described and the reasons why changes have had to be
introduced over the years will be discussed. The basic principles of uniqueness and priority will be
emphasised. The basic features specific to the International Code of Zoological Nomenclature will be
introduced. Types, priority, valid publication, homonymy, and synonymy will be covered in some detail.
Independence of codes.
The International Code of Zoological Nomenclature – Basic principles governing the
scientific names of animals
Donald Quicke
A summary of the key points of the current Botanical and Zoological codes of Nomenclature (the ICBN and
the ICZN) will be presented. Emphasis will be placed on the shared underlying principles while pointing out
many of the differences . Until quite recently, bacteria were included under the ICBN. All this changed in
1980, and bacteria now have their own Code which differs substantially from the ICBN which will be the
subject of a later lecture.
TSP/L2-L3
TSP/L4
Priority vs Usage; purists and pragmatists in zoological nomenclature, and Animal
name databases and registers - ZooBank - the future of zoological nomenclature
Ellinor Michel
Types provide a way of fixing the meaning of taxonomic groups. They can be specimens upon which
species concepts are based, or subordinate taxa upon which higher taxa are based.
What constitutes a taxonomic revision and what does one entail? What are the processes involved? What
purpose do descriptions serve? How complete or incomplete should they be? Can they ever be adequate?
Diagnoses. Illustration. Common practice. A flow chart will be presented that covers the majority of things
that taxonomists do and the sequence they do them in (or maybe should).
Tuesday 22nd January
TSP/L5
Botanical nomenclature - are plants different to animals?
Mark Spencer
Plants are named using the International Code for Botanical Nomenclature (ICBN), rather than the
International Code of Zoological Nomenclature. I will trace the history of the development of the two Codes,
and their main differences. I will also introduce you to the other important Codes of Nomenclature - for
bacteria and for cultivated plants. All of the Codes differ in subtle and sometimes seemingly illogical ways.
These differences may have profound effects on how taxonomy can be presented on-line; we will discuss
some of these issues during the course of this and the next session. Type specimens are not typical. We
will discuss the philosophical basis for species delimitation and the mechanism for how species are given
names using the type method. The type method is a recent development in both botany and zoology.
Names coined by earlier scientists often do not have designated types, and must be retrospectively
"typified". Using examples from my own and other's work, I will go through how botanists do this task,
highlighting the fundamental differences between typification in plants and animals.
49
TSP/L6
Major changes in the Botanical Code 2012 onwards - implications
Mark Spencer
Changes to the ICBN take place at 6-yearly intervals at Nomenclature Sections of the International Botanical
Congresses – the latest of which (the XVIII IBC) was held in July 2011 in Melbourne, Australia. Several
major changes were made to the Code – among them changing the name of the Code to better reflect our
knowledge of the Tree of Life, doing away with the requirement for a Latin diagnosis or description for new
plant names, and allowing electronic-only publication of new taxa covered by the Code. We will discuss how
these changes to the ICBN happen and what implications they might have in the future.
TSP/L7
Nomenclature of Fungi
Mark Spencer
Fungi, despite being the sister group of the animals, are treated nomenclaturally under the ICVN. At the IBC
in Melbourne, several important changes were made that affect the naming of fungi – I will review these,
along with a discussion of why fungal and plant nomenclature have been on strongly diverging paths in the
past, and what might be done to unify nomenclature of all groups (including animals!) better in the future.
Thursday 24th January
TSP/L8
Rates of species descriptions & current state of -taxonomy
Donald Quicke
This lecture will illustrate the major trends in the rates at which organisms have been described to date and
provide evidence relating to the magnitude of undescribed species. It will discuss ways that this large
amount of undescribed biodiversity can be handled.
TSP/L9
The Codes of Nomenclature: Bacteria and Viruses
Donald Quicke
The International Code for the Nomenclature of Bacteria involved a major restructuring of bacterial
nomenclature and is very different from the other major Codes in its requirements for valid description.
Recent introduction of ‘candidatus’ status will be discussed, and also the implications of the molecular
revolution as regards the discovery of a vast wealth of non-culturable organisms. The viruses present a very
different nomenclatural situation from other organisms. They are not monophyletic in themselves; although
not lacking morphology, it is seldom of use at species level; they have a long history of being referred to by
non-binomial names. This lecture will explain how the viral Code has tried to accommodate these features.
TSP/S1
Examining a taxonomic publication - priority, etc
Donald Quicke
The class will go through an example of a taxonomic paper (Shaw, 1997) that illustrates many points about
the practical difficulties entailed in identification and finding the correct name for an organism, and will
provide revision of concepts of priority, synonymy and homonymy.
Reading list
Blackwelder, R. E. 1967. Taxonomy a Text and Reference Book. John Wiley, New York.
Claridge, M.F. Dawah, H. A. & Wilson, M. R. (Eds) (1997) Species: the units of diversity. Systematics
Association publication. 54.
Mayr, E. & Ashlock, P. D. 1991. Principles of Systematic Zoology, 2nd Edition. McGraw Hill.
Quicke, D. L. J. 1993. Principles and techniques of contemporary taxonomy. Chapman & Hall, London.
Shaw, M.R. 1997. The genus Heterospilus Haliday in Britain, with description of a new species and rremarks
on related taxa (Hymenoptera: Braconidae: Doryctinae). Zool. Mededelingen, Leiden, 71(5): 33-41.
Wiley, E.O. 1981. Phylogenetics: The theory and practice of phylogenetic systematics. Wiley Interscience,
New York.
Winston, J. E. 1999. Describing Species. Columbia University Press, 518pp.
References
Barlow, N.D. 1994 Size distributions of butterfly species and the effect of latitude on species sizes. Oikos,
71: 326-332.
Belk, M.C. & Houston, D.D. (2002) Bergmann's Rule in ectotherms: a test using freshwater fishes. The
American Naturalist, 160: 803-808.
Hawkins, B.A. & Lawton, J.H. (1995) Latitudinal gradients in butterfly body sizes: is there a general pattern?
Oecologia, 102: 31-36.
Traynor RE & Mayhew PJ. 2005. A comparative study of body size and clutch size across the parasitoid
Hymenoptera. Oikos 109: 305-316
rd
Webster J & Weber RWS. 2007. Introduction to Fungi, 3 ed. Cambridge UP.
50
Module Seven
4th – 22nd February 2013
BIODIVERSITY 2: APPLIED
Organiser: Prof Alfried Vogler, Life Sciences, NHM ([email protected])
Overview: This module takes students through the stages of applied biodiversity work, as it relates to
taxonomy and collection based research. First, we address aspects of long-term
preservation of specimens and the management of large collections. The many issues
relating to setting up collections and the major risks to their long term preservation (from
specimen handling, preservation techniques to logistic aspects of managing large
collections) are covered. Further, the role of collections in biodiversity monitoring,
taxonomic research and as an important part of our biological heritage are introduced.
Following this, we address issues related to the problems of identification, that is,
assigning an unknown specimen to a particular taxon. Identification tools are important
products of taxonomy and are constantly being refined and re-designed both to reflect
changes in classification and to accommodate new data-types that were not previously
available. Increasingly, resources for taxonomy are web-based and identification keys is
increasingly computerised. The final part of the module considers the practical aspects of
specimen based research in biodiversity, and the conclusions about large scale patterns
of biodiversity that can be drawn from biodiversity surveys. This includes tasks from
sorting samples from canopy fogging, their identification, and counting, and an extensive
statistical analysis. We also consider the political issues of biodiversity preservation, and
the implementation of findings from biodiversity and taxonomy research into global
conservation strategies.
Initials
JB
CC
PE
RE
RH
CHCL
MM
DN
VS
DQ
DMR
SR
Lecturer
Jon Bielby
Chris Collins
Paul Eggleton
Rob Ewers
Rob Huxley
Chris Lyal
Martin Munt
David Notton
Vince Smith
Donald Quicke
Dave Roberts
Sue Ryder
Location
Division of Biology, Imperial College Silwood Park
Conservation Centre, Earth Sciences, NHM
Terrestrial Invertebrates, Life Sciences, NHM
Division of Biology, Imperial College Silwood Park
Genomics & Microbial Biodiversity, Life Sciences, NHM
Terrestrial Invertebrates, Life Sciences, NHM
Invertebrates & plants, Earth Sciences, NHM
Terrestrial Invertebrates, Life Sciences, NHM
Terrestrial Invertebrates, Life Sciences, NHM
Life Sciences, Imperial College Silwood Park
Genomics & Microbial Biodiversity, Life Sciences, NHM
Terrestrial Invertebrates, Life Sciences, NHM
Email address
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
Schedule
WEEK 16
Museums and Collections Management
th
Monday 4 February
10:00-10:15
BA/L1
10:15-11:00
BA/L2
11:15-12:00
BA/L3
14:15-15:00
BA/L4
RH
RH
RH
RH
Introduction
The history of Natural History Collections
The value of collections today
How collections work
CC/RH/SR
CC
DMR
CHCL
Prevention and cure: managing risks to collections
The chemistry of collections deterioration
Culture collections
Web access to biodiversity information
th
Tuesday 5 February
10:00-11.15
BA/L5
11:30-12:15
BA/L6
13:30-14.30
BA/L7
14:45-15:45
BA/L8
51
th
Wednesday 6 February
Reading day
Biodiversity - The political dimension
th
Thursday 7 February
10:00-11:00
BA/L9
11:15-12:30
BA/P1
13:30-14:30
BA/L10
14:45-15:45
BA/L11
JB
JB
CHCL
CHCL
Red lists – practical issues
incl. Conservation priority-setting; EDGE
Convention on Biological Diversity
Challenges for taxonomy
MM
MM
Curation experience
Curation experience
th
Friday 8 February
10:00-12:30
BA/P2
13:30-16:30
BA/P2
Week 17
Museums and Collections Management – cont’d
th
Monday 11 February
10:00-11:00
BA/L12
11:00-17:00
BA/P3
VS
VS
Scratchpads
Scratchpads practical
VS
VS
Computerised identification
Demonstration of software methods
Prepare questions for interviews with NHM curators
Interviews with staff for Friday's presentations
MM
MM
Curation experience
Curation experience
RH
Seminar: Setting priorities and maintaining
RH/DN/MM
with dwindling resources
Prepare for presentations
Workshop and student presentations: Summing up
th
Tuesday 12 February
11:15-12:15
BA/L13
13:00-14:00
BA/P4
14.00-15.00
15.00-17.00
th
Wednesday 13 February
10:00-12:30
BA/P2
13:30-16:30
BA/P2
th
Thursday 14 February
10:00-11:30
BA/S1
collections
11:30-12:30
13:30-16:00
BA/P5
Measuring and measures of biodiversity
th
Friday 15 February
10:00-10:45
BA/L14
11:00-17:00
BA/P6
DQ
PE
The maths behind keys
Sampling soil biodiversity, The Wildlife Garden, NHM
PE
Practical: invertebrate sorting, data preparation,
data analyses
PE
Statistical analysis of biodiversity samples – an
PE
Statistical analysis of biodiversity samples – an
PE
Statistical analysis of biodiversity samples –
ordination basics
Week 18
th
Monday 18 February
10:00-17:00
BA/P7
th
Tuesday 19 February
10:00-11:00
BA/L15
overview
11:30-12:30
BA/L16
overview
13:30-16:30
BA/L17
52
th
Wednesday 20 February
Reading day
st
Thursday 21 February
10:00-11:00
BA/L18
11:00-12:00
BA/L19
13:00-14:00
BA/L20
14:45-16:15
BA/T4
PE
PE
PE
Statistical analysis of biodiversity data
Measuring biodiversity value
Area-selection methods for conserving biodiversity
Tutorial
RE
RE
RE
Geographic Information Systems
GIS applications: modelling species ranges
Mapping and modelling species ranges
nd
Friday 22 February
10:00-11:00
BA/L21
11:00-12:00
BA/L22
13:00-14:30
BA/P8
Lecture and practical synopses
WEEK 16
Museums and Collections Management
Monday 4th February
BA/L1
Introduction
Rob Huxley
The aims of the module, a synopsis of lectures, what is expected, explanation of exercises, details of
visits, reading lists etc.
BA/L2
The history of Natural History Collections
Rob Huxley
The earliest natural history collections, what they were created for, herbals and curios. The first
scientific collections, the development of research collections, the development of the NHM.
BA/L3
The value of collections today
Rob Huxley
What do systematics collections cost to maintain, who foots the bill, is the cost justified, what are the
arguments against retention of collections. The value to science and society of natural history
collections, ethics of collections management.
How are resources allocated, prioritization.
Relationship with funding bodies, trustees and researchers.
BA/L4
How collections work
Rob Huxley
The collections management issues associated with access to collections. Balancing access and use
against long term preservation. The various forms of access and how they are managed.
Tuesday 5th February
BA/L5
Prevention and cure: managing risks to collections
Chris Collins / Rob Huxley / Sue Ryder
Introduction to risks. Collections can be put at risk by factors at many levels from overall management
practice to direct risks such as insect pests. Reducing risk through staff training, good documentation,
policies and procedures. The chemical and physical agents of deterioration. Risks to Natural History
Collections from pests, primarily insect pests. Integrated Pest Management (IPM) programmes. The
importance of monitoring, housekeeping, working practices, adequate collection furniture and
environmental control. An introduction to treatment and prevention How to select the correct
materials, methods, furniture and buildings to minimise these risks. What can be done to reduce
major threats to collections such as fire. Disaster planning for when the worst happens
53
BA/L6
The chemistry of collections deterioration
Chris Collins
Chemical aspects of deterioration in natural history collections. the deterioration path from the
chemical composition of the freshly collected specimen or other artefact to the altered states which
threaten the value of collections. Materials covered include skin and bones, rocks and fossils, DNA,
spirit collections, and printed materials. Destructive interactions between the collections object and the
environment in which it is stored and studied.
BA/L7
Culture Collections
Dave Roberts
The role of culture collections. Practical considerations of keeping live cultures e.g. high cost., the unit
of conservation (species, strain etc.), taxonomic coverage and the challenges to be met in the next
century.
BA/L8
Web access to biodiversity information
Chris Lyal
Importance of databases as a tool for collection management of biological collections. Considerations
and constraints in developing such databases. Rapid development of wider needs for biodiversity
information. Role of museum databases in this process. Initiatives for web access to databases and
other biodiversity data. Problems, opportunities and imperatives.
Biodiversity – The political dimension
Thursday 7th February
BA/L9&P1
Red lists – practical issues
Jon Bielby
How the Red list information can be used to inform conservation initiatives, focusing on the 'EDGE of
existence' programme [www.edgeofexistence.org]. Conserving evolutionary history: from theory to
practice.
References:
Baillie, J. E. M., Hilton-Taylor, C. and S.N. Stuart. 2004. 2004 IUCN Red List of Threatened Species.
A Global Species Assessment. Gland, Switzerland: IUCN.
Baillie, J. E.M., Collen, B., Amin, R., Akcakaya, H. R., Butchart, S., Brummitt, N., Meagher, T., Ram,
M., Hilton-Taylor., C., and G. M. Mace. 2008. Toward Monitoring Global Biodiversity.
Conservation Letters 1: 18-26
Butchart, S. N. M., Akçakaya, H. R., Chanson, J., Baillie, J. E. M., Collen, B., Quader, S., Turner, W.
R., Amin, R.,Stuart, S. N., and C. Hilton-Taylor. 2006. PLoS ONE 2: e140
Isaac, N., Turvey, S., Collen, B., Waterman, C., and J. E. M. Baillie. 2007. Highlighting the most
Evolutionarily Distinct and Globally Endangered mammals PLoS ONE. 3: e296.
BA/L10
Convention on Biological Diversity
Chris Lyal
Convention on Biological Diversity: its relevance to taxonomy and its main implications; focus on
Global Taxonomy Initiative.
BA/L11
Challenges for taxonomy
How the NHM is responding, challenges of developing new taxonomic products etc.
Chris Lyal
Friday 8th February
BA/P2
Curation experience
Martin Munt
Practical experience working with collections in one of the Museum's Science Departments. Students
th
should decide which Department they would prefer to visit by Wednesday 17 January.
54
Week 17
Museums and Collections Management – cont’d
Monday 11th February
BA/L12 & P3 Scratchpads
Vince Smith
Scratchpads are social networking tool to build, share and publish information on the diversity of life
<http://scratchpads.eu>. The project offers a free web site to any community that wants one. You will
be introduced to the features available in Scratchpads and shown how to create a basic site."
Tuesday 12th February
BA/L13
Computerised Identification
Vince Smith
The recent exponential growth in biological data is changing the way we share, manage and publish
information on biodiversity. In this lecture we will look at biocuration (the activity of organizing,
representing and publishing biological data) and how this is impacting biodiversity science. We will
then focus on computerized identification and the role of taxonomic keys in identifying biological
diversity.
BA/P4
Demonstration of software methods
Vince Smith
Biocuration and computerized identification tools will be demonstrated followed by a short practical
comparing identification methods covered during the previous lecture.
References: D. Howe et al (2008). Big data: The future of biocuration. Nature 455, 47-50. doi:10.1038/455047a.
D.E. Walter and S. Winterton (2007). Keys and the Crisis in Taxonomy: Extinction or Reinvention? Ann. Rev. Ent.
2007. 52:193–208, doi:10.1146/annurev.ento.51.110104.151054.
Wednesday 13th February
BA/P2
Curation experience
Martin Munt
Practical experience working with collections in one of the Museum's Science Departments. Students
th
should decide which Department they would prefer to visit by Wednesday 18 January.
Thursday 14th February
BA/S1
Seminar: Setting priorities and maintaining collections
Rob Huxley
Hard decisions – tough choices - setting priorities and maintaining collections with dwindling
resources. Fictional example of a collection under threat.
BA/P5
Workshop: Summing up
Rob Huxley / David Notton / Martin Munt
Group exercise and presentations to bring together information gathered during discussion with
nd
curators on Tuesday 22 February, other tours and practical curation sessions. Groups of students
will be allocated collections management topics such as "major disasters" to report on to the group as
a whole with particular reference to how the Natural History Museum performs on these issues.
Measuring and measures of biodiversity
Friday 15th February
BA/L14
The maths behind the keys
Donald Quicke
No matter how well written a key is, people will occasionally make mistakes. This can be the result of
many things - using the wrong key, not understanding the question, not seeing what is being
described, having a poor or intermediate specimen, getting the question right but going to the wrong
place in the key. Because of these, the 'shape' of a key has an effect on the mean probability of
making a correct identification, and understanding these will help in designing your keys. This lecture
will explain the mathematics of the extremes of comb-like and fan-like keys.
55
BA/P6
Sampling soil biodiversity, The Wildlife Garden, NHM
Paul Eggleton
An all-day visit to sample insects and other soil organisms, to be analysed in the following practicals.
Week 18
Monday 18th February
BA/P7
Sorting and identifying soil macrofauna
Paul Eggleton
Sorting and identification of material sampled in the Wildlife garden. Use of keys to the main groups of
soil and litter invertebrates, including a new field guide to British earthworms. A database of
taxomnomic and environmental variables will be setup. Discussions of how diversity patterns might be
analysed.
Tuesday 19th February
BA/L15&L16 Statistical analysis of biodiversity samples: an overview
Paul Eggleton
How are diversity patterns uncovered: indices, clustering and ordination. A brief introduction to basic
analytical techniques and their strengths and weaknesses. Introduction to ordination. This will be
taught in the context of understanding the data collected in the wildlife garden.
Reference: Krebs,CJ. 1999. Ecological Methodology (2
nd
edition), Addison, Wesley, Longman
BA/ L17
Statistical analysis of biodiversity samples: ordination basics
Paul Eggleton
Biodiversity sampling produces large amounts of data in complex hyperdimensional forms (usually
many sites, many species and numerous associated environmental variables). The task of biologists
is to simplify these data into forms that summarise meaningful variation in time and space. Multivariate
techniques to achieve this are numerous, but this lecture will concentrate on simple techniques and
illustrate them using the real data that collected over previous days..
Reference: Jongman, RHG., ter Braak, CJF & van Tongeren, OFR. 1995.
community and landscape ecology. CUP.
Data analysis in
Thursday 21st February
BA/L18
Statistical analysis of biodiversity sampling
Paul Eggleton
More advanced ordination methods: constrained and unconstrained analyses, TWINSPAN, NMDS,
RLQ analyses. Summing up.
Reference: Jongman, RHG., ter Braak, CJF & van Tongeren, OFR. 1995.
community and landscape ecology. CUP.
Data analysis in
BA/L19
Measuring biodiversity value
Paul Eggleton
How do we measure the value of biodiversity? A hierachical value-based approach is outlined using
different model habitats. Overall, the formulation of a measure of biodiversity for conservation
purposes requires identification of an appropriate underlying value. These values must either be
distinguished and separated if they are viewed as essentially different (e.g. diversity and rarity), or
else must be reduced to a common currency. For example, among several approaches to valuing the
diversity of organisms, possibilities include attaching value to the genetic or phenotypic diversity of
organisms, which can be estimated using phylogenetic information.
Reference: Snaddon, JL, Turner, EC & Foster, WA, 2008. Children's Perceptions of Rainforest
Biodiversity: Which Animals Have the Lion's Share of Environmental Awareness? PLoS ONE.
3(7): e2579.
56
BA/L20
Area-selection methods for conserving biodiversity
Paul Eggleton
One goal of area-selection methods for biodiversity conservation is to maximise the representation of
this diversity for the future. Aside from issues of politics and economics, biological aspects concern
the where and how of conservation management. In considering the where, two common questions
are (1) which areas are needed to represent everything (the minimum set problem); and (2) which
areas can represent the most for a particular budget or total area commitment (the maximum
coverage problem).
Reference: Paul H. Williams. PH, Burgess, ND & Rahbek, C. 2000. Flagship species, ecological
complementarity and conserving the diversity of mammals and birds in sub-Saharan Africa.
Animal Conservation, 3: 249-260.
Friday 22nd February
BA/L21
Geographic Information Systems
Rob Ewers
Introduction to the use of Geographic Information Systems, including how to generate and import data
for use in a GIS, how to check the reliability of that data, and how to present geographic data in an
informative manner.
BA/L22
GIS applications: modelling species ranges
Rob Ewers
We will investigate how geographic data on species presence can be combined with data on the
physical world to predict and map the geographic distributions of species. We will also look at the use
of geographic data and models for issues such as reserve design and deciding where to direct future
sampling effort.
Reference: Raxworthy, C. J., E. Martinez-Meyer, N. Horning, R. A. Nussbaum, G. E. Schneider, M.
A. Ortega-Huerta, and A. T. Peterson. 2003. Predicting distributions of known and unknown reptile
species in Madagascar. Nature 426:837-841.
BA/P8
Mapping and modelling species ranges
Rob Ewers
This lab will provide hands-on use of geographic information systems. During the practical, you will
learn how to: (1) import and map a geographic dataset into ArcGIS, an industry standard GIS software
package; and (2) use the freeware program Maxent to construct a basic niche model to predict the
geographic range of a species.
Reference: Phillips, S. J., R. P. Anderson, and R. E. Schapire. 2006. Maximum entropy modeling of
species geographic distributions. Ecological Modelling 190:231-259.
References
Gaston, K. J. & Spicer, J. I. (2004) Biodiversity: An introduction. 2nd edition. Blackwell.
Magurran, A. E. (2004) Measuring Biological Diversity. Blackwell.
57
th
th
4 – 12 March 2013
Module Eight
PALAEONTOLOGY AND STRATIGRAPHY
Module organiser: Prof. Norman MacLeod, The Natural History Museum ([email protected])
Outline:
A 1.5-week module composed of eleven lectures, four practicals and a field trip.
Aims:
This module aims to explore the special role palaeontological data has to play in taxonomic
studies.
Objectives:
From this course the student will gain an appreciation of the nature of the fossil record and
the types of question that are currently being addressed using palaeontological data. He/she
will also learn about some of the problems that may be encountered when using fossil data
in phylogeny reconstruction or the mapping of speciation and biodiversity patterns over
geological time.
Initials
GE
PK
AL
NM
PDT
KJ
Lecturer
Greg Edgecombe
Paul Kenrick
Adrian Lister
Norman MacLeod
Paul Taylor
Ken Johnson
Location
Earth Science Department, Natural History Museum
Earth Science Department, Natural History Museum
Earth Science Department, Natural History Museum
Earth Science Department, Natural History Museum
Earth Science Department, Natural History Museum
Earth Science Department, Natural History Museum
Email address
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
[email protected]
Schedule
Week 20
th
Monday 4 March
10.00-11.00
PS/L1
11.15-12.15
PS/L2
14:00-15:00
PS/L3
PDT
PDT
AL
Introduction to fossils
Introduction to stratigraphy and dating
Evolution and speciation in the fossil record: examples from
Quaternary Mammals
PDT/PK
Field trip to the Cretaceous of Folkestone and Dover
8.00 am departure! Return ca. 6 pm.
KJ
KJ
NM
Estimating diversity & extinction in the past
Biodiversity
Comparing the fit between cladograms and stratigraphic
trees
GE
GE
GE
Fossils in phylogenetic analysis
Fossils and missing data
Fossils in phylogenetic analysis
Monday 11 March
10.00-11.00
PS/L8
11.00-12.00
PS/L9
GE
AL
13:30-16:00
NM
Fossils and biogeography
Molecular palaeontology: what can (and can't) be done with
ancient DNA
Biodiversity estimates with and without phylogenetic data
th
Tuesday 5 March
th
Wednesday 6 March
Reading day
th
Thursday 7 March
10:00-11:00
PS/L4
11.15-12.15
PS/L5
13:30-16:00
PS/P1
th
Friday 8 March
10.00-11.00
PS/L6
11.00-12.00
PS/L7
13:30-16:00
PS/P2
Week 21
th
PS/P3
58
th
Tuesday 12 March
10:00-11:00
PS/L10
11.15-12.15
PS/L11
PK
AL
Fossils and climate change
Responses of mammals to climate change: clues from the
Late Quaternary extinction event
Lecture and practical synopsis
Week 20
Monday 4th March
PS/L1
Introduction to fossils
Paul Taylor
Aims: to provide a broad introduction to fossils and fossilization
Objectives: you will gain an appreciation of how fossils are formed and preserved, and what kinds of
organisms are most commonly fossilized • different kinds of fossils, including body fossils and trace fossils •
varying information content of fossils • taphonomy.
PS/L2
Introduction to stratigraphy and dating
Paul Taylor
Aims: to provide a broad introduction to the ways in which relative and absolute time are estimated.
Objectives: you will gain an appreciation of stratigraphical data, how it is gathered and what it tells us •
lithostratigraphy and biostratigraphy • stratigraphical correlation • absolute time and radiometric dating • the
geological timescale.
PS/L3
Evolution and speciation in the fossil record: examples from
Adrian Lister
Quaternary mammals
Aims: To examine how the fossil record can help test between models of species evolution.
Objectives: to appreciate the potentials and limitations of using fossil data to infer evolutionary modes. To
learn about some classic cases of evolution in the Quaternary mammals, such as the origin of the woolly
mammoth and the dwarfing of mammals on islands.
Thursday 7th March
PS/L4
Estimating diversity in the past
Ken Johnson
Aims: to examine biodiversity patterns from the fossil record, and why a direct reading of the fossil record
might be misleading and to explore the special problems associated with estimating extinction and
origination patterns over time.
Objectives: you will gain an appreciation of • the taxic approach to biodiversity • major sampling biases that
can affect the fossil record • taxonomic biases • how biodiversity estimates can be improved using
cladograms • analyses that can be applied to estimate the quality of the fossil record • how extinction rates
are estimated • paraphyly and pseudo-extinction/pseudo-origination and why this is a special problem for
palaeontology • how good our current fossil data base is • periodicity of extinction, a case study
PS/L5
Biodiversity Patterns in Deep Time
Ken Johnson
Aims: to explore the application of paleobiodiversity data from various sources to understanding the longterm history of life on Earth, including intervals of mass extinction and biotic response to accelerated
environmental change
Objectives: To learn how to access and analyze data available from various online sources, including
understanding how do account with variations in data quality resulting from how data has been compiled and
maintained, including methods to cope with variable accuracy of taxonomic, location, and stratigraphic
information provided, and we will discuss new initiatives aiming to increase the quality of the data. We will
discuss case studies concerning global Phanerozoic biodiversity patterns, diversity change across critical
intervals in the past, and analysis of regional and local biotas during the past few million years.
PS/P1
Comparing the fit between cladograms and stratigraphic trees
Norm MacLeod
In this practical you will apply two commonly applied techniques to test the match between stratigraphic
order of appearance of fossils and their inferred branching order.
59
Friday 8th March
PS/L6 Fossils in phylogenetic analysis
Greg Edgecombe
Aims: to explore the advantages and disadvantages of incorporating fossil taxa into a phylogenetic analysis.
Objectives: you will gain an appreciation of • the distinction between cladograms and trees • how including
fossils in phylogenetic analysis helps to (1) break up long branches, (2) stabilize theories of character
evolution, (3) arbitrate amongst competing hypotheses, (4) provide roots for cladograms, (5) calibrate rates
of evolution • matching patterns of cladogenesis against Earth history.
PS/L7
Fossils and missing data
Greg Edgecombe
Aims: to review the alleged problems created for phylogenetic analysis by including fossil taxa with missing
data.
Objectives: you will gain an appreciation of • why introducing fossil taxa, despite missing data, does not
necessarily inflate the number of equally parsimonious cladograms • whether there is a relationship between
the amount of missing data and the influence fossil taxa may have in the phylogenetic analysis • techniques
available for safely pruning taxa prior to analysis • whether fossils are important, i.e. whether the addition of
fossils can overturn a theory of relationship or a theory of character evolution based on data from modern
organisms alone.
PS/P2
Fossils in phylogenetic analysis
Greg Edgecombe
In this practical you will explore the pros and cons of adding fossil taxa to a phylogenetic analysis.
Week 21
Monday 11th March
PS/L8
Fossils and biogeography
Greg Edgecombe
Aims: to explore the role of palaeontological data in establishing biogeographic histories and outline current
methods that are being applied.
Objectives: you will gain an appreciation of the importance of considering spatial as well as stratigraphic
data in understanding evolutionary patterns and processes
current analytical methods in
palaeobiogeography
the benefits and difficulties of incorporating biogeographic data into evolutionary
analyses.
PS/L9
Molecular palaeontology: what can (and can't) be done
Adrian Lister
with ancient DNA
Aims: To highlight the advantages and difficulties of using ancient biomolecules, especially DNA, preserved
in the fossil record, with emphasis on the Quaternary mammalian record.
Objectives: you will learn about the factors favouring the preservation of ancient biomolecules in the
geological record and about the ways in which these can be put to use to give us a deep-time perspective on
population genetics and phylogeography as well as the reconstruction of extinct phenotypes.
PS/P3
Biodiversity estimates with and without phylogenetic data
Ken Johnson
In this practical you will construct diversity and extinction plots from raw taxonomic data and phylogenetic
data for two clades and compare the results.
Tuesday 12th March
PS/L10
Fossils and climate change
Paul Kenrick
Aims: to show the ways in which fossil data can be used to reconstruct how climate has changed over time.
Objectives: using examples drawn from the plant fossil record you will gain an understanding of taxon based
(e.g., nearest living relative) and taxon free (e.g., physiognomy based) methods of inferring various key
climate indicators through geological time.
PS/L11
Responses of Mammals to Climate Change: Clues from the
Adrian Lister
late Quaternary Extinction Event
Aims: To examine what the Quaternary mammalian record has to tell us about the effects of climate change.
Objectives: to gain an understanding of the dynamic nature of species’ ranges in the face of climate change.
To gain insight into the late Quaternary extinction event, including the methods used and the patterns
revealed, and their relevance to present-day extinction threats.
60
Reading list
Cobbett, A., Wilkinson, M. & Wills, M.A. 2007. Fossils impact as hard as living taxa in parsimony analysis of
morphology. Systematic Biology 56 253-266.
Cowen, R. 2005. History of Life. Fourth Edition. Blackwell, Oxford, 324 pp.
Foote, M. & Miller, A. I. 2007. Principles of Paleontology (third edition). W. H. Freeman & Co., New York.
Hermsen, E. J. & Hendricks, J. R. 2008. W(h)ither fossils? Studying morphological character evolution in the
age of molecular sequences. Ann. Missouri Bot. Gard. 95: 72-100.
Hofreiter, M. & Stewart, J. 2009. Ecological Change, Range Fluctuations and Population Dynamics during
the Pleistocene. Current Biology 19, R584-R594; DOI 10.1016/j.cub.2009.06.030
Kearney, M. & Clark, J.M. 2003. Problems due to missing data in phylogenetic analyses including fossils: a
critical review. Journal of Vertebrate Paleontology 23: 263-274.
Lister, A.M. & Stuart, A.J. 2008. The impact of climate change on large mammal distribution and extinction:
evidence from the last glacial/interglacial transition. Comptes Rendus Géosciences 340: 615-620.
McGowan, A. J. & Smith, A. B. (eds) Comparing the rock and fossil records: Implications for biodiversity
studies. Geological Society Special Publication 358
Mosbrugger, V., Utescher, T. & Dilcher, D. L. 2005 Cenozoic continental climatic evolution of Central Europe.
Proc. Natl. Acad. Sci. USA 102(42), 14964–14969 (doi: 10.1073/pnas.0505267102).
Parenti, L.R. and Ebach, M.C. 2009. Comparative Biogeography. University of California Press, 295 pp.
Smith, A. B. 2007 Marine diversity through the Phanerozoic: problems and prospects. Journal of the
Geological Society 164: 731-746.
Smith, A.B. 2007. Marine diversity through the Phanerozoic: problems and prospects. Journal of the
Geological Society 164, 731-745.
Spicer, R. A., Valdes, P. J., Spicer, T. E. V., Craggs, H. J., Srivastava, G., Mehrotra, R. C. & Yang, J. 2009
New developments in CLAMP: Calibration using global gridded meteorological data.
Palaeogeography, Palaeoclimatology, Palaeoecology 283, 91–98 (doi:
10.1016/j.palaeo.2009.09.009).
61
18th – 22nd March 2013
Module Nine
STATISTICS – R
Module organiser: Dr Donald Quicke, Division of Biology, IC, Silwood Park ([email protected])
This week will combine an introduction to using and carrying out statistical analyses in the very versatile
computing language R, and an analysis of latitudinal trends based on an existing set of data sets.
Aims



To present basic features of the programming language R
To provide basic understanding of statistical analysis in biology
To show how collections are non-random samples
Objectives
 Students will be able to use R for data input and manipulation and graphical output and statistics
 To be able to select appropriate statistical tests and understand their output
Initials
DQ
Lecturer
Donald Quicke
Location
Division of Biology, Imperial College Silwood Park
Email address
[email protected]
Schedule
WEEK 22
th
Monday 18 March
10:00-10:50
S-R/L1
11:00-15:00
S-R/P1
DQ
DQ
Introduction to R: input, output, dataframes
Computer practical: I
DQ
DQ
Introduction to statistics in R
Computer practical: II
DQ
DQ
Exploring the NHM dataset I - latitudinal trends
Computer practical: III
DQ
DQ
Exploring the NHM dataset II- latitudinal trends
Discussion
th
Tuesday 19 March
10:00-10:50
S-R/L2
11:00-13:00
S-R/P2
th
Wednesday 20 March
Reading day
st
Thursday 21 March
10:00-10:50
S-R/L3
11:00-13:00
S-R/P3
nd
Friday 22 March
10:00-10:50
S-R/L4
11:00-11:50
S-R/S1
62
Lecture and practical synopses
WEEK 22
Monday 18th March
S-R/L1&P1
Introduction to R: input, output, dataframes
Data input and output. The R console. Simple graphics
Donald Quicke
Tuesday 19th March
S-R/L2&P2
Introduction to statistics in R
Donald Quicke
Means, variances, testing differences between means, ANOVA, linear models, regression.
Thursday 21st March
S-R/L3&P3
Exploring the NHM dataset - latitudinal trends - I
Applying previously learnt skills to explore and compare real data sets.
Donald Quicke
Friday 22nd March
S-R/L4
Exploring the NHM dataset - latitudinal trends - II
Donald Quicke
We will examine what you have found out regarding latitudinal gradients from your analyses of body size
and discuss how this compares with previously published findings. Various statistical issues such as sample
size and multiple statistical tests will be considered.
S-R/S1
Discussion
Donald Quicke/students
Reference
Beckerman, A. P. & Petchey, O. L. Getting Started with R: An introduction for biologists. ISBN-13: 9780199601622
Crawley, M. J. 2007. The R Book. John Wiley & Sons. ISBN-13: 978-0-470-51024-7
Quicke, D.L.J. 2012. We know too little about parasitoid wasp distributions to draw any conclusions about
latitudinal trends in species richness, body size and biology. PLoS ONE 7: e32101.
doi:10.1371/journal.pone.0032101
63
22nd – 26th April 2013
Module Ten
FIELD COURSE
Module organiser: Prof Donald Quicke, Imperial College Silwood Park ([email protected])
Course Outline
This will involve sampling and identification exercises based at Silwood Park, paying particular attention
to interpreting the quality of data obtained using different sampling strategies. The analysis and
interpretation of data obtained will give insights into the power and limitations of sampling programmes
and will help students to design efficient systems of their own. The field course will also provide an
opportunity for students to assume the role as parataxonomist and to gain an insight into the types of
data that parataxonomist based programmes obtain.
The aim is to show the effects of sampling on estimates of biodiversity, cost-effectiveness of sampling
techniques, use of cumulative species acquisition data to estimate total numbers of species, and we will
examine the inter-relationship of size and species richness.
In the event of the weather being atrociously wet which, touch wood it won’t be, some field exercises
can be replaced by library ones. Unfortunately, Silwood bar does not have a tremendously high beer
diversity!
Students should work in pairs or threesomes.
What will you do?
It is up to you what group of organisms you choose to work with. I would encourage you to look at
insects or small plants. Irrespective of what group you choose, you should design a sampling
programme so that you can, by the end of the week, produce most or all of the following:
1) Species abundance curve (graph of number of species in various abundance categories) across
many taxa; such curves approximate a log-normal distribution.
2) Species versus size plot.
3) Species accumulation curve and jackknife estimate of total number of species.
4) Chao 1 and Chao 2 estimates of numbers of species in sampled sites (at this time of year).
5) Diversity as opposed to species richness estimates.
Having done these you should think carefully about their interpretation and possible problems with your
sampling techniques.
Suggested subjects could be:
beetles, bugs, parasitic hymenoptera in various samples, e.g. sweeping, beeting, hand-searching,
of grassland, trees, tree-trunks etc
plants in turf
lichens/mosses on trees
moths in light traps
Additional things one could attempt to do:
Ratios of insects of different biology in samples, e.g. carnivore/detritivore/herbivore,
ectoparasitoid/endoparasitoid, generalist/specialist
Tree/plant specificity
Focal taxon estimates,
Effects of quadrat shape on diversity/richness estimates – why?
Practice using keys – testing your untrained parataxonomy sorting with the real McCoy!
64
Projects
Too many potential research project topics exist to list them all here. The following are a selection of
possible projects. Each project is indicated as being suitable for the MSc or/and MRes. Students may like
to talk to these supervisors or to develop others in conjunction with appropriate Museum or College staff.
Anything practicable and which is related to the general subject area of systematics and/or biodiversity and
which gives scope for original observation or experimental design may be considered. Students should bear
in mind that if they wish to undertake field work as part of their project, many organisations which offer
st
funding to cover this may have early deadlines, eg. the British Ecological Society (31 December) and the
st
Systematic Assocation (1 January), and therefore any field-work associated projects should be planned
early on in the course. Please discuss any ideas with Donald Quicke or Alfried Vogler before making any
firm committments. If the project is going to be undertaken at another institution, the course organisers
must be informed in good time and an internal supervisor must also be nominated.
Contacts for discussing projects
Name
Email
Entomology, NHM
Alfried Vogler
[email protected]
Ian Kitching
[email protected]
Steve Brooks
[email protected]
Paul Eggleton
[email protected]
Chris Lyal
[email protected]
Zoology, NHM
David Rollinson
[email protected]
Tim Littlewood
[email protected]
Peter Foster
[email protected]
Adrian Glover
[email protected]
Pete Olson
[email protected]
Ellinor Michel
[email protected]
David Gower
[email protected]
Beth Okamura
[email protected]
Ronald Jenner
[email protected]
David Bass
[email protected]
Botany, NHM
Fred Rumsey
[email protected]
Mark Carine
[email protected]
Sandy Knapp
[email protected]
Alex Munro
[email protected]
Juliet Brodie
[email protected]
Dave Williams
[email protected]
Anne Jungblut
[email protected]
Palaeontology, NHM
Norman MacLeod
[email protected]
Andrew Smith
[email protected]
Jon Todd
[email protected]
Adrian Lister
[email protected]
Imperial College Silwood Park
Donald Quicke
[email protected]
Andy Purvis
a.purvis@ imperial.ac.uk
Tim Barraclough
[email protected]
Mike Tristem
[email protected]
Austin Burt
[email protected]
Vincent Savolainen
[email protected]
Martin Bidartondo
[email protected]
Speciality
Molecular systematics of insects
Phylogenetics of butterflies; cladistic theory
Freshwater insects as indicators of environmental change
Biodiversity; phylogenetics and ecology of termites
Insect functional morphology and classification
Schistosome biology and evolution
Evolution of parasitism among flatworms
Models of molecular evolution; bioinformatics
Ecology, biodiversity and evolutionary origin of polychaetes
Molecular of the parasitic flatworms (Platyhelminthes)
Speciation of molluscs in ancient lakes
Systematic evolution of reptiles and amphibians
Evolutionary systematics of Bryozoa and Myxozoa
Macroevolution of the Metazoa
Biodiversity, phylogeny and ecology of protists
Molecular systematics of ferns
Molecular systematics of bindweeds
Systematis of the Solanaceae
Systematics of the flowering plant family Urticaceae
Evolution of marine algae
Systematics of diatoms
Cyanobacterial diversity and ecology in polar aquatic systems
Methodology of morphometrics
Palaeontology of echinoderms; cladistic theory
Species radiation in molluscs
Quaternary mammal fossils: evolution and extinction
Biology and systematics of parasitic wasps
Comparative biology, biodiversity and conservation
Evolutionary models of biological radiations
Molecular systematics of retroviruses
Population genomics and phylogenetics of Yeasts
Evolution and conservation of small plant species
Ecology and evolution of mycorrhizas
65
The Project write-up
General Comments
The size of the thesis will vary according to the student and project, but aim to make it as short as necessary
to describe the work done and to discuss it in a general context. However, do NOT omit relevant data and
information such as experimental procedures. A thesis normally contains more detail than would the
published paper on the same work, but much of this should be put in an Appendix. Always aim to be clear
and concise. The MSc thesis should not normally exceed 10,000 words in length (excluding references and
appendices). Each MRes thesis should not normally exceed 3,000 words in length (excluding references
and appendices).
An acceptable approach is to set out the work in the form of a scientific paper set exactly in the style of a
journal that it might be appropriate for submission to. If the results of your project are publishable, this
approach will save much time and will provide valuable experience in paper writing. Papers for submission
to journals should always pay particular attention to house style. If it is your intention to follow this approach,
you should still provide appendices if appropriate that would not normally be included in published work, and
you should provide a slightly general introduction suitable to an MSc thesis. You should also state clearly on
the cover page the fact that the work has been written up in the style of a manuscript appropriate for
submission to a specified journal.
The latter format is probably a much bigger challenge. e.g. the Introduction needs to be shorter but the
references have to be chosen prudently and quotes need to be precisely to the point of what is said in the
referenced papers. This certainly requires very good knowledge of the pertinent literature.
In either case (thesis or paper format) you want to include all data matrices, procedures, analytical tools and
other relevant information in the Appendix if they are not included in the Material and Method or Results
sections. As one example, a molecular study may state in the Methods section of the main text only that
you extracted DNA according to a phenol/chloroform extraction protocol according to a particular reference.
In the Appendix, you present the individual steps of your lab protocol, described in sufficient detail that other
people could reproduce this procedure with your description in hand.
The marking will not be biased if you go for one or the other format. We realise that different students have
very different career goals, etc., and some of you will end up at a job writing reports that are more "thesis"
style, whereas those of you who will proceed with a Ph.D. will get better training if they go for journal
submission format. But please keep in mind that it is generally better to be concise. Limit yourself to the
important findings rather than recording every detail of what you've done. Boring stuff won't give you good
marks no matter the format.
A Typical Format
Title Page
Abstract
Table of Contents
Introduction
Materials and Methods
Results
Discussion
Summary
Acknowledgements
References
Appendices
The Title Page
The Title page must bear, in addition to the title and the student’s name, the following wording:
“A thesis submitted in partial fulfilment of the requirements for the
degree of Master of *Science/Research of Imperial College London and
the Diploma of Imperial College”
*Delete as applicable: Master of Science (MSc) or Master of Research (MRes)
66
The Introduction
A good Introduction should leave the reader with a clear idea of the problem to be tackled and looking
forward to the more detailed chapters to follow. An essential part of the Introduction is to clearly define the
aims of the research project. This need be no longer than a paragraph or two. It should be accompanied by
a section on the general way the problem has been approached.
Materials and Methods
Details of general materials and methods may be put in a separate chapter. This should contain details of
any methods used extensively during the project, layout of field experiments, general methods of statistical
analyses etc. If field work is done, a general description of the study area may be included here.
Results of Experiments
Depending on the project this section may be divided into separate sections e.g. laboratory data, field
experiments. Describe them in logical order, which is not necessarily the order in which you did the
experiments. It is a common failing to assume that the reader knows the project as well as you do.
Therefore refer appropriately to figures or tables and remember to emphasise and perhaps quote significant
results. Briefly summarise the main results at the end of each main experiment or sequence of associated
experiments. Avoid duplication of results - put a table or a graph but not both unless the two methods of
presentation demonstrate different points of importance.
Discussion
This should attempt to tie together the results, what they indicate in a broader context, the extent to which
the original aims have been satisfied and what future work is suggested. Great care is needed here.
References
Collect all references together at the end of the thesis and list in standard form. Follow the style of the
appropriate journal.
Appendices
Large sets of data (e.g. census results, ‘raw' experimental results) should go in an Appendix if these are of
value, e.g. indicating an interesting range of variation. All summary tables or graphs and outline results of
analysis should be put in the text. Any useful parts of the study not directly relevant to the main theme may
also be put in an Appendix (e.g. taxonomic descriptions and drawings in an otherwise ecological study).
Computer Programmes
If the programme has been published, give a reference to it and a brief outline of the methods it uses. If the
programme is original, give a listing, flow chart and a short summary or comments. Define all input
variables.
Illustrations
The standard should approach that required for publication, especially in morphological and taxonomic work
where the quality of the illustration may be an important feature of the thesis. Decide whether photographs
or line drawings give a better representation. Include a caption with each figure and insert figures at the
appropriate points in the text.
Tables
Each table should be numbered and have a full descriptive heading. Column headings should state units of
measurement. Avoid large, complicated tables. If you have a large body of numerical data put it in an
Appendix.
67
Presentation
As word processing systems and laser printers are readily available, these should be used where possible.
A4 is the standard size. The main body of the text should be printed using 1.5 line spacing, and page
numbering should be used.
Binding the Thesis
Use a ring binder to bind the thesis. The front cover should be cellophane, the back plain white card. The
title, etc., must be displayed on the first page.
How many copies
MSc students must produce three bound copies of the thesis, two of these must be handed in on the
specified date (see below), and the third copy you must take with you to your viva examination. Of the two
copies which you hand in, one will eventually go to your supervisor, and the other to Imperial College Library.
MRes students must produce four bound copies of the thesis, three of these must be handed in on the
specified date (see below), and the fourth copy you must take with you to your viva examination. Of the four
copies which you hand in, one will eventually go to your supervisor, and one to Imperial College Library.
Handing in for MSc students
nd
The deadline is 5.00pm on Thursday 22 August 2013. Any theses received after this time will result in a
downgrading of marks. The theses may be handed in to Donald Quicke, Alfried Vogler or Amoret Whitaker,
depending on who is available at the time. Details will be confirmed nearer the time.
Handing in for MRes students
The deadlines for each of the three projects will be January 2013, May 2013 and September 2013; the exact
dates will be given nearer the time. Any theses received after the specified dates will result in a
downgrading of marks. The theses may be handed in to Donald Quicke, Alfried Vogler or Amoret Whitaker,
depending on who is available at the time. Details will be confirmed nearer the time.
68
Some Project Proposals
A bioinformatic approach to the phylogenetic tree of Coleoptera
(beetles)
Supervisors: Alfried Vogler & Chris Barton, NHM ([email protected])
(MSc/MRes)
The taxonomic depth of DNA databases is growing rapidly, permitting the phylogenetic analysis
of an ever more complete portion of the Tree-of-Life. However, the available sequence data are
not uniform in the choice of genes and the density of taxon sampling. For example, population
level studies need to be filtered for a subsample of sequences with relevance for phylogenetic
analysis at the species level. An additional problem is that sequences are frequently deposited
without species names and therefore cannot easily be linked to other data. Consequently,
obtaining phylogenetic trees from publicly available sequence data at the large scale is
complicated. Here we use a bioinformatics approach to build a large data matrix that minimizes
these problems and extracts maximum phylogenetic information content. We will use the
Coleoptera as a model, a group with sequences already available for some 10,000 species. In a
first step, the sequence information for the 10 most widely used loci will be extracted from public
databases, filtered for population variation, and integrated into a single matrix. We will also test,
using resampling procedures, which kind of data provide the most efficient way of filling in the
existing gaps in data availability.
References:
Hunt, T., J. et al. 2007. A comprehensive phylogeny of beetles reveals the evolutionary origins of
a superradiation. Science, 318:1913-1916
Developing next-generation sequencing methods for phylogenetics
and biodiversity studies
Supervisors: Alfried Vogler & Martijn TImmermans, NHM ([email protected]) (MSc/MRes)
Conventional DNA sequencing is gradually superseded by so-called ‘next-generation’
technologies. While very powerful to sequence entire genomes, the application of these
technologies for phylogenetics and biodiversity studies is not straightforward because of the need
to sequence from mixtures of individuals that are difficult to separate. Here we develop a
protocol by which sequences from each individual are tagged with short nucleotide sequences,
which are used to assign these sequences back to a particular specimen. This permits to
analyse hundreds of specimens for multiple genes at a much reduced effort and expense over
conventional methods. The technique will have broad applications for this area of research. The
project provides a good opportunity to learn about these novel sequencing techniques which
currently are changing all areas of biology. In a pilot study the new method will be applied to a
specific phylogenetic question (MRes/MSc) or to a study of communities in insects (MSc), in line
with the interest of the student.
The molecular phylogenetics of Pselaphinae (Coleoptera)
Supervisor: Alfried Vogler & Alex Crampton-Platt, NHM ([email protected])
(MSc/MRes)
This group is very species-rich (~10,000 described species), mostly distributed in the tropics.
They are commonly found in decaying leaf litter on forest floors, and are likely to to be predatory
on springtails (Collembola) and oribatid mites (Oribatidae). They have attracted the interest of
entomologists due to their highly variable morphology, and the spectacular modifications to body
form, including segmental fusions within the abdomen and antennae to form strong rigid plateand club-like structures. Several groups are associated with ants. We have a new collection of
DNA-ready samples to study this group that has been neglected by phylogeneticists. This is a
straightforward molecular systematics project involving marker development, sequencing and
phylogenetic analysis with likelihood and Bayesian methods.
69
Testing plant „barcode‟ markers for identifying the host plants of insect
herbivores
Supervisors: Alfried Vogler & Martijn TImmermans, NHM ([email protected]) (MSc/MRes)
Trophic interactions of plants and herbivores presumably are responsible for the great species
diversity of plant-feeding insect, but critical information for testing the structure of these
interactions is lacking due to the difficulties of determining host specificity and community
structure in natural ecosystems. However, the feeding source can now be assessed by
sequencing chloroplast DNA that is ingested by the beetles in sufficient quantities to permit direct
sequencing from the beetle DNA. The method opens the possibility to study to what degree the
plant distributions determine the distributions of the beetles, i.e. the structure of herbivore-host
plant interactions. The use of chloroplast DNA ‘barcodes’ for identifying a wide spectrum of
plants is not trivial and requires a test of the most appropriate genetic markers. This project will
start with the use of an established marker (the trnL spacer region) and compare its performance
to novel markers. The project requires good skills in the DNA lab.
In a related project we will apply this method for host identification to the study of food plant
distributions on the composition of insect herbivore communities. We have access to samples
from a transect of 20 sites in the Iberian Peninsula that include all local species of leaf beetles
(Chrysomelidae). By sequencing both mitochondrial beetle DNA and chloroplast plant DNA (from
the same DNA extraction), we will be able to analyse the turnover (beta diversity) in beetles and
hostplants, and the turnover of the correlation. This will tell how much the distribution and
turnover of beetle communities is constrained by their food plants.
References:
Jurado-Rivera, J. A., A. P. Vogler, C. A. M. Reid, E. Petitpierre and J. Gómez-Zurita. 2009. DNA
barcoding insect-hostplant associations. Proceedings of the Royal Society Series B,
276:639-648
Biodiversity and phylogenetic relationships of the bladed Bangiales
(Rhodophyta) from Chile
Supervisor: Juliet Brodie, NHM ([email protected])
(MSc/MRes)
Porphyra sensu lato is a cosmopolitan genus of red algae with c. 130 currently accepted species
a similar number of undescribed species and diversity still to be discovered. Species of Porphyra
have been a traditional source of food in many parts of the world (e.g. nori – Japan, laver –
Wales, luche – Chile). As part of a global revision of the Bangiales, we have split Porphyra into 8
genera, a change that has fundamental implications for Porphyra floras around the world.
Over the last few years, these bladed Bangiales have been the subject of a major taxonomic
study in Chile, and the latest results indicate that there is considerably more diversity than
previously recognised. Molecular data (plastid and mitochondrial DNA) revealed over 23
undescribed species in two genera. They also revealed a curious link with species in the North
Atlantic. The scope of this project is to i) obtain nuclear (18S) data for all putative new species ii)
review mitochondrial data and iii) explore relationships with this flora and other regions of the
world. The project will be based on collections and existing DNA from the length of Chile’s
coastline and will use molecular and morphological techniques.
References:
Sutherland, J.E., Lindstrom, S., Nelson, W., Brodie, J., Lynch, M., Hwang, M.S., Choi, H.-G.,
Miyata, M., Kikuchi, N., Oliveira, M., Farr, T., Neefus, C., Mortensen, A., Milstein, D. &
Müller, K. (2011). A new look at an ancient order: generic revision of the Bangiales.
Journal of Phycology 47: 1131-1151.
Brodie, J., Mols Mortensen, A.M., Ramirez, M.E., Russell, S. & Rinkel, B. (2008). Making the
links: towards a global taxonomy for the red algal genus Porphyra (Bangiales,
Rhodophyta). Journal of Applied Phycology 20: 939-949.
70
Biogeography and evolutionary history of Cameroon's crater lakes
based on molecular phylogenetics
Supervisor: Alfried Vogler & Thomas Doherty-Bones, NHM
(MSc/MRes)
The lakes of Cameroon have had a lot of press with regards to the limnic eruption of Lake Nyos,
but patchy collections have revealed them to also hold astonishing biodiversity. This has included
endemic cichlids in lower elevation lakes, and one endemic frog in a high elevation lake. The
biogeography and evolutionary history of the other (mostly fishless) lakes, particularly for smaller
organisms is completely unknown. A recent survey has been made of the crater lakes in north
west Cameroon. This has included collections of diving beetles, caddisflies, snails,
waterboatmen, crabs and other taxa. These lakes have apparently never been sampled before,
thus the presence of endemic taxa unkown. These lakes are potentially threatened ecosystems,
due to pressure to introduce fish, deforestation and developments. Thus, rapid verification of the
evolutionary history of the fauna of these ecosystems is required. This project will use DNAbased methods to: a) ascertain genetic differences of similar taxa (diving beetles, caddisflies,
waterboatmen or crabs) between the differing lakes in the region; and b) use phylogenies to infer
the pattern of colonization of these lakes by various taxa. This project will contribute to a
conservation assessment and planning for Cameroon's crater lake ecosystems.
Testing the species – genetic diversity correlation in community
ecology
Supervisor: Alfried Vogler & Alex Crampton-Platt, NHM ([email protected])
(MSc/MRes)
Biodiversity patterns are usually studied on the species level, but how does species diversity
correlate with other hierarchical levels, such as genetic diversity? The species-genetic diversity
correlation (SGDC) is predicted based on parallel processes of immigration and extinction that
are used to explain diversity patterns at both level under island biogeography and metapopulation
theory, respectively. However, only recently are data becoming available from large-scale DNA
sequencing of entire local communities (including DNA barcoding) that would permit a proper test
of the hypothesis. We will compile appropriate sequence data and assign the variation to genetic
and species levels. We will then test if (a) if the total species richness (alpha diversity) of a
community corresponds to intra-specific genetic diversity of the participating species, as originally
proposed under the SGDC; (b) if turnover of communities among sites (beta diversity) is
correlated on the species and genetic levels, and if so, are there regularities in the decrease of
similarity with distance (‘distance decay’) that assume a uniform process to affect both levels.
Establishing these regularities is of great relevance for theoretical community ecology, in
particular for testing Hubbell’s (2001) Unified Neutral Theory of Biodiversity.
References:
Vellend, M., 2003. Island biogeography of genes and species. Am. Nat. 162, 358-365.
Papadopoulou, A., Anastasiou, I., Spagopoulou, F., Stalimerou, M., Terzopoulou, S., Legakis, A.,
Vogler, A.P., 2011. Testing the species-genetic diversity correlation in the Aegean
archipelago: toward a haplotype-based macroecology? Am. Nat. 178, 241-255.
Overcoming the „taxonomic impediment‟ by next-generation
sequencing to characterize complex tropical arthropod communities
Supervisor: Alfried Vogler & Alex Crampton-Platt, NHM ([email protected])
(MSc/MRes)
It is generally acknowledged that arthropod species diversity is too complex for a comprehensive
taxonomy-based analysis of diversity patterns. Next-generation DNA sequencing methods could
change this situation, if complex communities from the soil or canopy can be analyzed in bulk.
This study will explore a very promising approach to the analysis of bulk samples, and will help to
develop a methodology that will transform the study of biodiversity of small-bodied animals. The
project is suited to students with interest in tropical diversity of insects and willingness to develop
the bioinformatics skills required for handling very large sequence datasets.
71
Variation and Systematics of Quaternary Mammals
Supervisor: Adrian Lister, NHM ([email protected])
MSc
Quaternary Mammals are abundantly represented in the fossil record of the ‘ice ages’
(approximately the last two million years), and the NHM holds major collections, ranging from
large mammals such as mammoths and rhinos, to smaller ones such as rodents, shrews and
bats. Many projects can be devised that make use of these collections, including taxonomic
studies, and metric analysis of size and shape variation of individual species or groups of species
in relation to adaptation, habitat and climate change.
References:
Breda, M., Collinge, S.E., Parfitt, S.A. & Lister, A.M. 2010. Metric analysis of ungulate mammals
in the early Middle Pleistocene of Britain, in relation to taxonomy and biostratigraphy. I.
Rhinocerotidae and Bovidae. Quaternary International 228: 136-156.
Herridge, V.L. & Lister, A.M. 2012. Extreme insular dwarfism evolved in a mammoth. Proc. R.
Soc. B 279: 3193-3200. doi: 10.1098/rspb.2012.0671.
Picocyanobacterial diversity and distribution in Antarctic lakes
Supervisor: Anne D. Jungblut, NHM ([email protected])
(MSc/MRes)
Cyanobacteria are key stone taxa in microbial food webs of Antarctic lakes, and
picocyanobacteria are typically around 1 µm in cross-sectional diameter and belong to several
genera within the Order Chroococcales. Picocyanobacteria have been recorded from many polar
lakes using pigment analysis and fluorescent microscopy, however little is still known of the
genetic diversity of these Antarctic cyanobacteria, nor whether the same taxa will be present in
geographically isolated Antarctica lakes. The project therefore aims 1) to characterise the genetic
diversity of cyanobacteria along chemical and phyisical gradients in permanently ice-covered
lakes located in the McMurdo Dry Valleys Lakes, Antarctica, and 2) to test whether
cyanobacterial commuity composition varies between these geographically isolated lakes using
molecular techniques such as 16S rRNA gene clone library surveys, as well as community
structure and phylogenetic analyses.
'Going for the guts'
Supervisor: Chris Lyal, NHM ([email protected])
(MSc)
The gut of beetles in the superfamily Curculionoidea (‘weevils’) often contains a 'proventriculus', a
complex sclerotised structure associated with breaking down tough foods. This has been
intermittently used in classification at the subfamily and tribe level, but generally in a crude
'present or absent' manner. Publications mentioning it are sparse and disappointing. The project
is to construct a basic nomenclature for proventriculus structures and test whether the
phylogenetic signal from the proventriculus matches that from other structures across the
superfamily.
Sequencing synapomorphies: Exploring molecular homology
Supervisors: David M Williams & Malte C Ebach, NHM ([email protected]) & UNSW,
Australia ([email protected])
(MSc/MRes)
Can different amounts of the same molecular data generate the same phylogenetic trees?
Students are expected to download molecular alignments from GenBank and run them using
parsimony, three-item, maximum likelihood and phenetic programs (i.e., TNT, LisBeth, PAUP).
Synapomorphies from the resulting trees will be compared to determine the informative
characteristics that support molecular homology.
72
Biodiversity of the UK seaweed flora
Supervisor: Juliet Brodie, NHM ([email protected])
(MSc/MRes)
The seaweed flora of Britain and Ireland has c. 650 species of red, brown and green seaweeds,
which represents about 7% of the world’s seaweed biodiversity. Although we now have a good
idea of this flora, we are particularly interested in finding out what is happening to the seaweeds
in this region, including whether and, if so, how species composition has changed with time
based both on herbarium records and surveys that were undertaken in the past. The Isles of
Scilly present a useful model with which to explore these ideas. The shores and subtidal of the
Isles of Scilly are known to support a rich seaweed flora, with at least a third of the red, green and
brown species reported for Britain and Ireland. Until 2010, the last major study of the seaweeds
there was undertaken in 1983 as part of a programme of marine surveys by the Nature
Conservancy Council (now Natural England). In 2010, a survey of the seaweeds of the
archipelago was undertaken which included taking samples for molecular analysis as part of the
Barcode of Life project. Since 1983, knowledge of the seaweed flora of Britain and Ireland has
developed considerably. The application of molecular data has revealed a number of cryptic
species in the flora and the description of a number of new species and this is reflected in the
lists for the 2010 survey.
The scope of this project is to i) analyse molecular data obtained ii) compare species composition
from 2010 with that of previous surveys from the Isles of Scilly. The project will be based on
herbarium specimens, literature and molecular data with scope for additional molecular work
using the collections.
Coralline algae and biofilms
Supervisor: Juliet Brodie, NHM ([email protected])
(MSc/MRes)
The Corallinales are a species-rich group of critically important calcifying macroalgae in marine
ecosystems from the tropics to the poles, and with > 570 species make up c. 10 % of the
described red algae. They are key reef building primary producers, provide niches for many
other species, are known to induce metamorphosis and recruitment of many species of coral
larvae, and provide settlement cues to microphytobenthos. They are major contributors to CO 2
fluxes through high community calcium carbonate production and dissolution in shallow coastal
ecosystems. These slow growing organisms are at risk from e.g. sedimentation, eutrophication,
change in freshwater flows, and will be impacted by global perturbations connected with climate
change and ocean acidification.
As with other macroalgae, these coralline species are host to a wide range of epibiotic and
endobiotic prokaryotic and eukaryotic organisms. We know that the relationship between
macroalgae and these microbiomes is essential: for example, algae need an external source of
Vitamin B12 which they get from microbes, but their ecological roles are poorly understood. The
location of the epibiontic microbial community is directly affected by environmental changes e.g.
water chemistry, while changes in sea surface temperatures (e.g. an increase of 2-4º C) have
been shown to cause stress, bleaching and shifts in microbial community structure1. However,
such community fragility is hard to quantify without accurate and consistent assessment of
microbial diversity. The scope of this project is to undertake an analysis of the biofilm
communities from samples collected over a year.
References:
Nelson, W.A. 2009. Calcified macroalgae – critical to coastal ecosystems and vulnerable to
change: a review. Marine and Freshwater Research 60: 787-801.
Walker R.H., Brodie J, Russell S. & Irvine L.M. 2009. The taxonomy and biodiversity of geniculate
coralline algae in the northeastern Atlantic: Corallina caespitosa sp. nov. (Corallinoideae,
Rhodophyta). Journal of Phycology 45: 287-297.
73
Ecology and evolution of fungi
Supervisor: Martin Bidartondo, Imperial College Silwood Park & Royal Botanic Gardens Kew
([email protected])
(MSc)
1)
Ectomycorrhizas play a crucial ecological role in forests by mediating nutrient acquisition.
Using high-throughput molecular ecology and bioinformatics this project will examine
mycorrhizal diversity across scales, including biomonitoring plots or short- rotation woodfuel
trials with native and exotic trees, and its environmental drivers.
2)
Using a multi-gene genealogical approach to species recognition, this project will identify
patterns of evolutionary, ecological and biogeographic diversification of a group of
macrofungi.
3)
Fungi likely allowed plants to colonise land some 475MYA. This project will use a
molecular approach to test the hypothesis that early fungal lineages form symbioses with
basal plant lineages.
4)
Other projects on the evolution and ecology of plant-fungal interactions.
Does Cope‟s Rule apply to zooid size in bryozoans?
Supervisor: Paul Taylor, NHM ([email protected])
(MSc)
Cope’s Rule states that within an evolutionary lineage, the body size of organismsincreases
through time. With a few notable exceptions, Cope’s Rule has been shown to hold true for many
lineages of unitary organisms, with the evolutionary lineage of horses being the best-known
example. However, little research has been done on Cope’s Rule in colonial animals, including
bryozoans, in which body size can be measured at two hierarchical levels: the zooid and the
colony.
The project will entail a literary review of Cope’s Rule, discussing evidence and possible
explanations for Cope’s Rule. It will also investigate if colonial animals should be expected to
follow Cope’s Rule by comparing and contrasting the different evolutionary pressures on them
and unitary organisms. Cope’s Rule will then be tested by selecting several bryozoan groups
represented in the fossil record and measuring zooid size in each group through time. These
measurements will come both from the literature and directly by measuring specimens in some
cases. Wherever possible taxa (e.g. Metrarabdotos) with a published cladistic phylogeny will be
used. Where this is not possible zooid size will be measured in species belonging to the same
clade from different slices of geological time. In addition, size change in defensive polymorphs
(avicularia and eleozooids) will be tracked. All measurements will be subjected to statistical
analysis to test the null hypothesis implied by Cope’s Rule that zooid size within bryozoan
lineages has increased through time. The analysis will be interpreted for specific bryozoan
lineages and within the wider context of the applicability of Cope’s Rule to colonial animals.
References:
Alroy, J. 1998. Cope’s Rule and the dynamics of body mass evolution in North American fossil
mammals. Science 280: 731–734.
Benton, M.J. 2002. Cope’s Rule. In: Encyclopedia of Evolution (M. Pagel, ed.), pp. 185–186.
Oxford University Press, Oxford, UK.
Jablonski, D. 1997. Body-size evolution in Cretaceous molluscs and the status of Cope’s Rule.
Nature 385: 250–252.
74
Violating Models (the phylogenetic kind) – a survey of recent highprofile studies.
Supervisor: Peter Foster, NHM ([email protected])
(MSc/MRes)
Phylogenetic analyses often fail to find the correct tree, and can provide contradictory support in
favour of an incorrect tree. This probably happens often, but is difficult to detect because we can
only identify these errors where we know the correct tree. Finding the wrong tree can occur when
the model of substitution is inappropriate for the data being analysed. One problem that is
mentioned repeatedly is that DNA sequences often differ from each other in their proportions of
nucleotide bases (i.e. their base composition) and that our commonly used phylogenetic models
do not accommodate this base composition heterogeneity. We have recently completed a survey
of genes that span the three domains of life (Eubacteria, Archaea, and Eukaryotes) and found
that most show a marked compositional heterogeneity over the tree.
Since these sequences are highly diverged, this is a somewhat expected, although disturbing,
result. However we have seen such problems within a single genus of insects, enough to make
the resulting analysis wrong.
We would like to expand these examples to see how general and widespread is the
compositional heterogeneity problem. We propose that the student survey a number (<30) of
recently published data sets, derived from high profile scientific articles, for their degree of model
violation with regard to phenomena such as composition heterogeneity. The student will benefit
from working with novel and cutting-edge phylogenetic software and modes of analysis, and we
would anticipate that if on successful completion of the study that the work would merit
publication.
Speciation and adaptive evolution in sexual and asexual rotifers
Supervisor: Tim Barraclough, Imperial College Silwood Park ([email protected])(MSc/MRes)
Sex is thought to be a major driving force for speciation and adaptive evolution. Bdelloid rotifers
have been asexual for well over 35 million years, unlike their sexual cousins, the monogononts how do they get away with it? Possible topics include: field sampling of bdelloid and monogonont
rotifers, DNA sequencing and morphometrics to compare speciation rates; field samples, lab
experiments and/or PCR to investigate the interaction and coevolution between bdelloids and
their parasites, Rotiferophthora fungi; molecular lab work to explore mechanisms of adaptive
evolution in bdelloids, including the role of selfish DNA and 'recombination genes'. The results will
provide new insights into the evolution of a fascinating group, fuelling debates on the evolution of
sex and speciation.
Evolution in multi-species systems
Supervisor: Tim Barraclough, Imperial College Silwood Park ([email protected])(MSc/MRes)
Adaptation to the environment can be fast in simple systems, particularly in microorganisms with
rapid generation times. But most organisms exist in diverse assemblages and changes in species
composition are also rapid, perhaps reducing the opportunity for evolution to occur. The project
would study experimental evolution in beech tree-hole bacterial communities manipulated to
include different numbers of species. It would also incorporate molecular work to identify the
sampled bacteria.
General patterns of speciation
Supervisor: Tim Barraclough, Imperial College Silwood Park ([email protected])(MSc/MRes)
If you have ideas about general patterns of speciation you’d like to test using data gathered from
the literature, I’m happy to discuss feasibility of such projects.
75
Investigation of the possible ecological radiation of the neo-tropical
tree genus Brosimum (Moraceaea) during presumed expansion out of
the Amazon basin
Supervisors: Alex Monro & Tonya Lander, NHM ([email protected])
(MSc)
In the Quaternary era a variety of species appear to have expanded out from the ‘refuge’ of the
Amazon basin into Central America and across South America (Freita et al. 2001, Mayle et al.
2007). The process of expanding from the Amazonian tropical lowlands into the Andes
mountains, the Cerrado savanna of central Brazil, through the bottleneck of the Isthmus of
Panama and into the dry and wet forests of Central America has been associated with ecological
radiations and speciation (Pennington et al. 2004, Rull 2008, Dexter et al. 2012, Alfaro et al.
2012), although the subject is complex and much debated (Willis and Whittaker 2000). In this
project we will (1) generate the first phylogenetic tree for the 13 species in the neotropical tree
genus Brosimum (Moraceae), which has its centre of diversity in Brazil, (2) investigate whether
there is significant ecological ‘niche separation’ within the genus, and whether that separation
accompanied or followed speciation using the newly published SEEVA program (Struwe et al.
2011).
The project will involve:
Phylogenetic analysis of existing sequence data for 3 specimens from each of the
13 species in the genus Brosimum (Moraceae) using PAUP and MrBayes programs.
This sequence data is being generated as part of the current NHM Darwin project
focused on B. alicastrum.
Download and edit specimen point location data for the 13 Brosimum species from
the TROPICOS and GBIF databases.
Georeference the specimens that lack coordinates based on location descriptions.
Collect and download ecological, geological, and topographical GIS layers (e.g.
WorldClim, US Geological Survey maps online).
Overlay the specimen point location data with ecological, geological, and
topographical data in ArcGIS.
References:
Alfaro, J. W. L., J. P. Boubli, L. E. Olson, A. D. Fiore, B. Wilson, G. A. Gutiérrez-Espeleta, K. L.
Chiou, M. Schulte, S. Neitzel, V. Ross, D. Schwochow, M. T. T. Nguyen, I. Farias, C. H.
Janson, and M. E. Alfaro. 2012. Explosive Pleistocene range expansion leads to
widespread Amazonian sympatry between robust and gracile capuchin monkeys. Journal
of Biogeography 39:272-288.
Dexter, K. G., J. W. Terborgh, and C. W. Cunningham. 2012. Historical effects on beta diversity
and community assembly in Amazonian trees. Proceedings of the National Academy of
Sciences of the United States of America 109:7787-7792.
Freita, H. A. d., L. C. R. Pessenda, R. Aravena, S. E. M. Gouveia, A. d. S. Ribeiro, and R. Boulet.
2001. Late Quaternary Vegetation Dynamics in the Southern Amazon Basin Inferred from
Carbon Isotopes in Soil Organic Matter. Quaternary Research 55:39-46.
Mayle, F. E., R. P. Langstroth, R. A. Fisher, and P. Meir. 2007. Long-term forest-savannah
dynamics in the Bolivian Amazon: implications for conservation. Philosophical
Transactions of the Royal Society B 362:291-307.
Pennington, R. T., M. Lavin, D. E. Prado, C. A. Pendry, S. K. Pell, and C. A. Butterworth. 2004.
Historical climate change and speciation: neotropical seasonally dry forest plants show
patterns of both Tertiary and Quaternary diversification. Philosophical Transactions of the
Royal Society B 359:515-538.
Rull, V. 2008. Speciation timing and neotropical biodiversity: the Tertiary-Quaternary debate in
the light of molecular phylogenetic evidence. Molecular Ecology 17:2722-2729.
Struwe, L., P. E. Smouse, E. Heiberg, S. Haag, and R. G. Lathrop2011. Spatial evolutionary and
ecological vicariance analysis (SEEVA), a novel approach to biogeography and speciation
research, with an example from Brazilian Gentianaceae. Journal of Biogeography
38:1841-1854.
Willis, K. J. and R. J. Whittaker. 2000. The Refugial Debate. Science 287:1406-1407.
76
Species delimitation in the murky world of nettles
Supervisors: Alex Monro & Mark Spencer, NHM ([email protected])
(MSc)
The Urticaceae represent ca 2,600 taxa in 45 genera. The family is remarkable for the great
variation in female flower and inflorescence morphology and for being species-rich despite
lacking many of the recognised drivers of diversification in Flowering plants. The Urticaceae are
most diverse in the humid tropics where they include important components of secondary
vegetation. A number of species are of economic importance in Africa and Asia (Girardinia,
Boehmeria), principally as a source of fibres but also for their anti-inflammatory and anti-microbial
properties. A phylogeny of the family has recently been completed.
This project will use existing molecular data to assess and test for congruence between
monophyletic clades, species concepts and geography within the genus Parietaria. Parietaria is
unique within the Urticaceae in the possession of bisexual flowers. Species delimitation within the
genus is very problematic with little agreement between specialists on the interpretation or
delimitation of morphological characters. This makes assessment of its diversity and contribution
to floristic analyses difficult. The genus consists of ca 20 herbaceous species, usually associated
with disturbed sites. It is pan-temperate with lowland tropical taxa occurring in Africa. Within the
UK there are two recorded species, P. officinalis L. and P. judaica L. and there is no effective key
or clear delimitation between the taxa.
This project will consist of an analysis of molecular data from representative accessions of each
of the species recognized in the RBG Kew and Natural History Museum herbaria. Molecular data
will comprise sequence data for two chloroplast and one nuclear ribosomal region. The sequence
data will already have been generated for this project. Analyses will aim to use well supported
monophyletic clades to test for congruence with current species delimitation. There will be an
emphasis on the UK and European taxa so as to support the curation of the British and Irish
herbarium at the NHM. Existing literature on the genus will then be used to identify potentially
informative morphological characters for species delimitation and the collections at RBG Kew and
NHM surveyed for these characters. Collections will also be surveyed for any additional
characters that are congruent with the molecular analyse. The results of these two activities will
provide the basis for the revision of type material for the UK and European species and a robust
delimitation and classification of the UK and European taxa.
Evolutionary and conservation biology
Supervisor: Andy Purvis, Imperial College Silwood Park ([email protected]) (MSc/MRes)
I offer projects on a wide range of topics in evolutionary biology and conservation biology, using
statistical approaches, simulations and phylogenetic analysis. My main current research focus is
modelling and projecting biodiversity responses to human impacts in terrestrial systems; I have a
collaboration with UNEP-WCMC and the University of Sussex to produce the models to be used
in UN projections of biodiversity – there are many options for research projects associated with
this. Other current projects in my group include: phylogenetic approaches to the study of
community assembly processes; understanding when species distribution modelling succeeds or
fails (both of these are in collaboration with the Biological Records Centre at CEH Wallingford);
responses of pollinators to changing patterns of land cover and land use; and using the
microfossil record of planktonic foraminifera to study biotic responses to major climatic changes
in the past.
References:
Ezard TH, Aze T, Pearson PN, Purvis A, Interplay between changing climate and species'
ecology drives macroevolutionary dynamics., Science, 2011, Vol:332, Pages:349-351
Rapacciuolo G, Roy DB, Gillings S, Fox R, Walker K, Purvis A , Climatic associations of British
species distributions show good transferability in time but low predictive accuracy for
range change., PLoS One, 2012, Vol:7
Fritz SA, Bininda-Emonds ORP, Purvis A, Geographical variation in predictors of mammalian
extinction risk: big is bad, but only in the tropics, Ecology Letters, 2009, Vol:12,
Pages:538-549.
77
Metapopulation Dynamics and Dispersal Ability of the small blue
Cupido minimus
Supervisors: Alfried Vogler, NHM, ([email protected]) & Dave Warburton, Sutton Ecology
Centre ([email protected])
(MSc)
Britain’s smallest butterfly has undergone a severe population decline (25-50%) in the UK in the
last 25 years and is restricted in its distribution to areas containing the early successor kidney
vetch Anthyllis vulneraria, the sole Larval Host Plant. A highly sedentary species, there is little
quantitative evidence for dispersal to new sites. This project will require the student to undertake
basic fieldwork in the north Surrey Downs for collecting the raw material for DNA sequencing to
determine definitely whether outlier sites are related to a specific donor site and form a landscape
scale metapopulation, actual dispersal ability, and potentially answering questions on inbreeding
coefficients within small populations. Further questions on the ecological conditions of sites,
habitat fragmentation and site management could also be sought.
Reference:
Swaay, C. van and Warren, M.S. (1999). Red Data Book of European Butterflies (Rhopalocera),
Nature and Environment, No. 99. Council of Europe, Strasbourg.
Termite functional diversity across a South-east Asian forest
disturbance gradient
Supervisor: Paul Eggleton, NHM ([email protected])
(MSc)
The rain forests of south-east Asia are under constant threat from logging, population pressure
and clearance for agriculture. This last problem is particularly concentrated in the demand for
land for oil palm plantations. The SAFE (Stability of Altered Forest Ecosystems) project (Ewers et
al. 2011) in Sabah, East Malaysia, has set up a series of plots to allow the study of the
disturbance of forest ecosystems. The plots are set up as a gradient of increasing forest
disturbance from old-growth forest, through logged forest and through to oil palm. Recent studies
have examined the diversity of ants and termites across that gradient, and revealed much greater
resilience of ant diversity to disturbance than that of termites.
Further work has recently looked in more detail at changes in the functional diversity of ants, and
their community assembly processes, across the gradient, using modern statistical methods
including ordination and null model analysis. Functional diversity studies of this kind, by focusing
on the ecological traits of species, often yield much greater insight into biodiversity decline than
studies of species numbers alone. Given the ecological dominance of both ants and termites in
south-east Asian tropical forests, and the likely significance of trophic and other interactions
between the two taxa, it is of great interest to similarly explore the community functional diversity
of termites, and their covariation with ants.
This MSc project will use modern statistical techniques to examine how functional diversity and
community assembly processes change across the disturbance gradient. The work will involve (1)
species level identifications of already sampled termite specimens, which are already broadly
identified to genus level; (2) measurements of ca. 12 functionally significant traits across the
identified species; (3) analysis of the resulting functional diversity data; and (4) comparisons with
ant results and synthesis. The results are expected to show much larger declines in functional
diversity when compared with the ant data, as south-east Asian termites are predominantly
forest-dwelling and most cannot cope with the greater climatic variation found in disturbed areas
(Davies et al. 2003)
References:
Davies R. G., Eggleton P., Jones D. T., Gathorne-Hardy F. J. & Hernandez L. M. (2003)
Evolution of termite functional diversity: analysis and synthesis of local ecological and
regional influences on local species richness. Journal of Biogeography 30, 847-77.
Ewers R. M., Didham R. K., Fahrig L., Ferraz G., Hector A., Holt R. D., Kapos V., Reynolds G.,
Sinun W., Snaddon J. L. & Turner E. C. (2011) A large-scale forest fragmentation
experiment: the Stability of Altered Forest Ecosystems Project. Philosophical Transactions
of the Royal Society B-Biological Sciences 366, 3292-302.
78
Populations and Species – Molecular ecology and conservation issues
in the Malagarasi River, western Tanzania
Supervisor: Ellinor Michel, NHM ([email protected])
(MSc/MRes)
The Malagarasi River, the second largest in Tanzania, is the focus of an international programme
to build a dam across its spectacular waterfall system. This currently relatively pristine cascade
system appears to be a centre of evolutionary origin for several newly discovered endemic fish, a
snail and a plant species. Preliminary genetic studies indicate that the cascade creates a
vicariance barrier in different ways for different species. This project would allow you to expand
on previous work, comparing phylogeographic response for several snail species in the river. The
data collection would be relatively straightforward, involving sequencing nuclear genes to
compare with patterns revealed in mitochondrial DNA. However the results would be of high
topical relevance and might require some struggles with ethical questions at the intersection of
taxonomy, conservation and development.
Website: http://www.sorayavillalba.com/ellinor/malagarasi.php
Temperate-tropical diversity patterns: exploring the structure of
macrofauna assemblages of closed-canopy forests in the New Forest,
UK and East Sabah, Malaysian Borneo.
Supervisor: Paul Eggleton, NHM ([email protected])
(MSc)
It has long been recognised that closed-canopy humid forest systems are among the most
diverse (Morley 2000), particularly for invertebrates. It is also well documented that tropical
forests are far more diverse than temperate ones, despite the elements that they have in
common: tree canopies, understory vegetation, leaf litter and soil. However, these differences
have never been fully explored at the whole landscape level. The Soil Biodiversity Group at the
NHM have been undertaking a series of ‘quantitative inventories’(QIs) intended to document
biodiversity patterns within and between forest landscapes. The first of these QIs was undertaken
between 2010 and 2012 in the New Forest, England [ref]; the second was undertaken in 2012 in
Sabah, East Malaysia. Both studies involve multiple plots (15 in the New Forest, 22 in Sabah)
across a broadly comparable mosaic of old growth and regenerating plots. Both areas also have
standardised samples taken in the soil, litter, ground surface, understory, and lower canopy. The
New Forest QI is essentially complete but the Sabah QI has only just been undertaken.
This project examines the broad patterns of similarities and differences between the New Forest
and Sabah plots. This might involve the characterisation of a few of the Sabah plots at the
species level or a less focused full-analysis identified to the sub-family or genus level. The
emphasis will be on the large scale structural differences between the latitudinally-separated
areas and the generation of hypotheses to explain mechanisms that mighty explain the
differences. The student will be expected to undertake sorting and identification work, analysis of
resulting data matrices using multivariate techniques, literature review and synthesis, as well as
hypothesis generation.
References:
Carpenter, D, Hammond, PM, Sherlock, E, Lidgett, A, Leigh, K & Eggleton, P. (2012). Biodiversity
of soil macrofauna in the New Forest: a benchmark study across a national park
landscape. Biodiversity & Conservation, online first.
Morley R. J. (2000) Origin and evolution of tropical rain forests. John Wiley & Sons, Chichester.
79
The nature of diversification in bacteria
Supervisor: Tim Barraclough, Imperial College Silwood Park ([email protected])(MSc/MRes)
Bacteria do not engage in sexual reproduction typical of most eukaryotes, but do engage in a
range of activities that can move genes around between individuals. Because many theories of
speciation have been based on sexual reproduction, this has led to uncertainty over the nature of
speciation in bacteria. You would assemble multi-locus sequence data for a clade of bacteria,
seeking to include genes involved in important ecological traits as well as so-called housekeeping genes. You would then use phylogenetic analyses to test alternative hypotheses for the
mode of diversification and look for signatures of adaptive divergence in the ecological genes.
Ideal for someone wanting to learn lab skills, phylogenetics and bioinformatics analyses.
Beta diversity in tropical rain forests: a spatially explicit analysis of
Bornean ants
Supervisor: Paul Eggleton, NHM ([email protected])
(MSc)
Both alpha diversity and beta diversity are thought to be high in tropical rain forests: any given
patch of forest has many species and it and a neighbouring patch may well not share the same
species (Whitmore 1998). However, this assertion has had very little empirical testing, particularly
given that answers to these sorts of questions are often spatial-scale specific. Recent sampling in
Sabah, Malaysian Borneo, has attempted to address this problem by sampling soil/litter
macrofauna across an entire 100 km wide landscape and at a series of nested spatial scales
(from 100m to 100 km). This will allow the documentation of the most important spatial scales for
beta diversity differences (once environmental factors are controlled for).
The project will examine this new data source for beta diversity patterns in ants, probably the
most important group of invertebrates in tropical rain forests. The student will identify (to genus
and morphospecies) ants from leaf litter extractions from ca. 20 plots sampled across the Sabah
landscape at a variety of spatial scales. The resulting data matrix will be analysed for pure spatial
effects (with environmental/habitat differences factored out) to examine the resulting turnover
levels (Baselga 2010). The main question that will be asked is whether there is significant
turnover across a 100 km stretch of forest, or whether the ant fauna is essentially the same
across the landscape, suggesting that stochastic sampling from a single species pool accounts
for most of the variation in species diversity across the landscape.
References:
Baselga A. (2010) Partitioning the turnover and nestedness components of beta diversity. Global
Ecology and Biogeography 19, 134-43.
Whitmore T. C. (1998) An introduction to tropical rain forests, 2nd Edition. Oxford University
Press, Oxford.
Morphometrics of a hyperdiverse endemic radiation
Supervisors: Ellinor Michel ([email protected]) & Jonathan Todd ([email protected]), NHM
(MSc/MRes)
The endemic gastropods of Lake Tanganyika have been commonly claimed to be ‘the most
morphologically diverse’ radiation of freshwater molluscs on the planet. But quantitative metrics
of this diversity have been elusive. This project would allow you to apply a range of cutting-edge
morphometric techniques (landmark geometric morphometrics, extended eigenshape analysis,
and/or 3-D morphometric scanning) to the Tanganyika radiation, compare it with other gastropod
radiations and provide a quantification of both the disparity (degree of difference) and diversity
(number of different units) of this radiation. If you are interested in phylogenetic character
determination, there is also scope for incorporation of character analysis in this project. (This
builds on very successful previous MRes projects by Olivia Cheronet and Martine Claremont.)
80
Molecular genetic surprises and population genetic answers to
conservation issues for Neothauma, the molluscan mammoth of the
Tanganyikan deep
Supervisor: Ellinor Michel, NHM ([email protected])
(MSc/MRes)
Neothauma tanganyicensis is a large, viviparous gastropod that is famous for creating a critical
biogenic habitat in the depths of Lake Tanganyika. The acres of unique substrate formed by
Neothauma shells are home to a number of apparently specialized, sometimes miniaturised taxa
of fish, crabs, sponges, etc. On our recent SCUBA surveys, however, we became concerned
that living populations seemed surprisingly rare, small, and potentially at threat from
sedimentation (the major conservation issue in the African Rift lakes). In testing for degree of
population isolation of Neothauma using mtDNA, a past project uncovered unusual results that
indicate potential heteroplasmy (paternal mitochondrial leakage) and/or pseudogenes. This
project would involve further exploration of the mt genetics of Neothauma and would generate
population genetics using nuclear DNA to answer conservation questions. (This builds on a
successful MSc project by Joanna Griffin).
Ins and outs of Tanganyikan snails? Morphological phylogenetics and
calibration of a radiating clade
Supervisors: Ellinor Michel ([email protected]) & Jonathan Todd ([email protected]), NHM
(MSc/MRes)
Among the species-rich endemic radiations within Lake Tanganyika the cerithioid snails are
famous for their morphological disparity. The ‘Lavigeria clade’ (Nassopsinae) contains more than
50 species and occurs both within the lake and in neighbouring rivers of the Congo drainage. The
relationship of the handful of riverine species to the speciose lacustrine taxa is controversial –
either the Congo River seeded Lake Tanganyika and an enormous radiation followed (as in many
cichlid clades) or one or more lake taxa crawled out and conquered the rivers. This project allows
you to test these alternative hypotheses by undertaking detailed morphological analysis of fossil
and living ‘Lavigeria’ from the region. Newly obtained material offers you the possibility of deriving
the first independent fossil calibration for any living East African Rift lake radiation. This project
offers detailed shell character analysis using SEM, morphological phylogenetics, and, if time
allows, morphometrics to be applied.
Larval trait and species richness in a hyperdiverse snail species
radiation: does repeated evolution of non-planktotrophy underlie
species diversification?
Supervisor: Jon Todd, NHM ([email protected])
(MSc/MRes)
This project will examine whether species richness of molecular and morphologically defined
clades of the tropical marine snail Polystira correlate with modes of larval development. Standard
life history theory would predict that species with non-feeding, dispersing (= non-planktotrophic)
larvae, will have shorter geographic ranges, shorter geologic ranges and be more prone to both
speciation and extinction than species with widely dispersing, feeding (planktotrophic) larvae.
Polystira (Neotropics; Miocene-Recent) is probably the most species-rich regional snail radiation
known with over 100 living species and hundreds of extinct species. This material has been
gathered at the NHM for analysis. A bimodal life history difference is represented with
planktotrophic vs non-planktotrophic larval shells preserved in both recent and fossil material.
The student will document larval traits through SEM analysis, map characters onto molecular
trees and examine the correlation of trait deployment with species richness of clades – to help
answer whether differences in larval development underlie clade-specific morphological,
evolutionary and macroecological patterns.
81
How diverse are the Lauroid Euphorbias of Macaronesia?
Supervisors: Mark Carine ([email protected]) & Fred Rumsey ([email protected]), NHM
(MSc)
Macaronesia comprises the archipelagos of the Azores, Madeira, Selvagems, Canaries and Cape
Verdes located in the North Atlantic Ocean. All of the archipelagos are volcanic and oceanic in
origin and the region is acknowledged as an centre for plant diversity with notable examples of
island radiations and many taxa exhibiting distinctive morphologies. The genus Euphorbia is an
important component of the endemic flora of the region. It has colonised the region several times
independently with some of the colonising lineages subsequently diversifying.
The lauroid Euphorbias are one group that have colonised Macaronesia where they are found
restricted to the temperate rainforest areas (the laurisilva). Euphorbia stygiana is endemic to the
Azores whilst E. mellifera occurs on both Madeira and the Canaries although it is rare and with a
highly fragmented distribution in the latter. Recent molecular work on E. stygiana using the
nuclear ITS region suggested the existence of previously overlooked diversity (Schaefer et al,
2011). The extent to which morphology is congruent with the patterns revealed by molecular data
remains to be determined but the patterns are potentially significant because E. stygiana is
currently treated as a single species widespread across the Azores whereas it might comprise a
series of distinct taxa that are each highly restricted geographically and likely to be under
considerable threat. To date, no work has been done on infraspecfic variation in E. mellifera
within which a similar situation may or may not occur.
The aim of this project is investigate patterns of molecular diversity in E. mellifera, to determine
the extent to which the molecular patterns observed in the Lauroid Euphorbias are congruent with
morphology and to consider the taxonomic and conservation implications of the results.
Morphometric approaches to palaeo-temperature analysis based on
leaf physiognomy
Supervisors: Norman MacLeod ([email protected]) & David Steart, NHM (MSc/MRes)
Recent work on the descriptive morphometrics of leaves (MacLeod 2002a,b, 2005; Krieger et al.
2007) has demonstrated the value of adopting a quantitative and geometric approach to the
analysis of leaf physiognomy data in a variety of systematic contexts; particularly with respect to
the use of morphological patterns as proxy variables for a host of secondary inference-based
descriptors. This study will compare and contrast levels of consistency and correctness in the
inference of palaeotemperatures from leaf-shape data in assemblages of deciduous leaves from
several localities (see Wolfe 1995) using a morphometric and artificial intelligence-based
approach centered on the DAISY species recognition system. This investigation will serve as a
pilot project to decide which of these approaches should will be the preferred method of data
summarization and analysis for a larger, grant-supported project.
References:
Krieger, J.D., Guralnick, R.P., and Smith, D.M. 2007. Generating empirically determined,
continuous measures of leaf shape for paleoclimate reconstruction. PALAIOS 22(2): 212219.
MacLeod, N. 2002a. Phylogenetic signals in morphometric data. 100–138. In N. MacLeod and P.
L. Forey (eds.), Morphology, shape and phylogeny. Taylor & Francis, London.
MacLeod, N. 2002b. Geometric morphometrics and geological form-classification systems. EarthScience Reviews 59(2002): 27–47.
MacLeod, N. 2005. Shape models as a basis for morphological analysis in paleobiological
systematics: dicotyledenous leaf physiography. Bulletins of American Paleontology
369:219–238.
Wolfe, J. A. 1995. Paleoclimatic estimates from Tertiary leaf assemblages. Annual Review of
Earth and Planetary Science 23: 119–142.
82
Supervisors:
Norman
MacLeod,
Margaret
Clegg
&
Heather
Bonney,
NHM
([email protected])
(MSc/MRes)
Estimation of sex, particularly in ancient human populations, is one of the goals of biological
anthropology. The cranium is one region of the skeleton that has traditionally been used to
estimate sex. Traditional methods use either non-metric traits such as size of the mastoid
process (e.g. Walker, 2008) or linear measurements. More recently studies using 3D
morphometrics to analyze dimorphism have been undertaken, with varying degrees of success
(e.g., Kimmerle et al 2008, Bulygina et al. 2006). Degree of dimorphism may vary in different
populations. This study will use adult crania from a known age and sex population to assess if
shape variation in the crania can accurately determine true sex.
References:
Bulygina E., Mitteroecker, P., Aiello, L. 2006 Ontogeny of facial dimorphism & patterns of
individual development within one human population. American Journal of Physical
Anthropology 131:3:432-443.
Kimmerle, E. H., Ross, A., Slice, D. 2008 Sexual dimorphism in America: geometric
morphometric analysis of the craniofacial region Journal of Forensic Science 53:1:54-57.
Walker, P. L. 2008 Sexing skulls using discriminant function analysis of visually assessed traits.
American Journal of Physical Anthropology 136:1:39-50.
Wilson, L. A., MacLeod, N. and Humphrey, L. T. 2008. Morphometric criteria for sexing juvenile
human skeletons using the ilium. Journal of Forensic Sciences 10:269–278.
Supervisors: Norman MacLeod ([email protected]) & Angela Milner, NHM
(MSc)
Diceratosaurus brevirostris is a member of the Diplocaulidae, a family of small late Palaeozoic
nectrideans distinguished by paired tabular horns projecting posteriorly from the hind edge of the
skull roof. Diceratosaurus was a relatively common member of a Pennsylvanian (Upper
Carboniferous) aquatic coal swamp fauna from the Linton Diamond Mine, Jefferson County,
Ohio, USA, discovered originally in the 1850’s. More than 50 specimens of varying completeness
are known with mid-line skull lengths ranging from 14-28mm.
Access to a previously unstudied collection from a neo-contemporary locality, Five Points,
Mahoning County, Ohio, housed in the Carnegie Museum, was recently given to the Palaeo.
Department.It includes > 57 specimens of a horned diplocaulid similar to Diceratosaurus except
that two distinct snout shapes, broad and narrowly pointed, are present within the same range of
skull lengths.
This project will investigate the morphometrics of the skull and palate of D. brevirostris and the
Five Points specimens with the aim of addressing the following questions:
1. Do all the specimens from both localities belong to the same species or are there
consistent diagnostic differences?
2. Do the broad and narrow snouted skulls from Five Points occupy distinct morphospace
and hence likely represent two different taxa, separate from D. brevirostris?
All specimens for the project are high fidelity peels (latex or synthetic silicone) of acid etched
skulls in counterpart made by A.C. Milner from material in American and European museums.
They reveal detailed anatomy of the dorsal aspect of the skull roof and ventral aspect of palate
and offer an opportunity to work on original undescribed material. Study and measurements may
be made from either digital images or directly from the peels using a binocular microscope. Peels
of 14 complete D. brevirostris skulls and 26 Five Points skulls, eight broad-snouted and 14
narrow snouted individuals are available, making a total of 54 skull roofs and palates to be
sampled.
83
Redefining modern and fossil oospecies: the quantification of the
polymorphism of oological characters
Supervisors: Xavier Panades, University of Leeds, & Norman Macleod, NHM
([email protected])
(MSc)
Oospecies are defined by the exact ranges of egg’s morphologies and eggshells’ macro-and
microstructures. However, oologists have yet to develop a universal methodology to quantify the
polymorphism of oospecies. Oological analyses do not consider the biomineral structures of
eggs, inherent morphometric variation in different regions of the eggs, and collect insufficient
measurements and execute limited statistical analyses. This project aims to produce the basis for
the quantification of the polymorphism of modern and fossil avian and reptile oospecies following
three steps.
1. Revise the concept of oopecies, and the methodologies to quantify the variation of
morphologies and macro- and microstructures of modern and fossil oopecies.
2. Create a dataset from measurements of two eggshell macrostructures, eggshell thickness
(or height of unit) and eggshell width (width of unit), and structural layers and layers’ ratios.
3. Establish a concise methodology of quantifying based on the comparative biostatistical
analyses between modern and fossil oospecies.
References:
Barta, Z. and Szekely T. (1997). The optimal size of eggs. Funct. Ecol. 11:656-662
Gill BJ (2000) Morphometrics of moa eggshell fragments (Aves: Dinornithiformes) from Late
Holocene dune-sands of the Karikari Peninsula, New Zealand. Jour. of The RoyL Soc. of
New Zeal. 30(2):131 145
Gill BJ (2006) A catalogue of moa eggs (Aves: Dinornithiformes). Rec. Auckland Mus. 43:55–80
Gill BJ (2007) Eggshell characteristics of moa eggs (Aves: Dinornithiformes). J R Soc N Z
37:139–150
Gosler AG, Higham, JP, Reynolds SJ (2005) Why are birds’ eggs speckled? Ecol Lett 8:1105–
1113
Grellet-Tinner G (1999) Phylogenetic interpretation of eggs and eggshells of Paleognathae). In:
Bravo A M, Reyes T. (edns.) In: Bravo A M, Reyes T. (edns.) 1er Congrés Internacional
sobre ous i cries de dinosaures, extended abstracts, Museu d’Isona i Conca Della:
Diputació de Lleida, pp. 61-76
Grellet-Tinner G (2006) Phylogenetic interpretation of eggs and eggshells: implications for oology
and Paleognathae phylogeny. Alcher 30:130-180
Grellet-Tinner G, Norell M (2002) An avian egg from the Campanian of Bayn Dzak, Mongolia. J of
Vertebr Paleontol 22 (3):719-721
Mikhailov KE (1997) Avian Eggshells: an Atlas of Scanning Electron Micrographs. Tring: British
Ornithologists' Club
Mikhailov KE, Bray ES, Hirsch KF (1996) Parataxonomy of fossil egg remains (Veterovata): basic
principles and applications. Jour of Vertebr Paleontol 16(4):763-769
Panadès I Blas X, and P. Rajeek (2009) A complete crocodylian egg from the Upper Miocene
(Chinji Beds) of Pakistan and its palaeobiographical implications. PalArch 6(1):1-8
Schleich HH, Gassner P, Maskey TM (1994) Ultrastrukturen und Variabilität der Eischalen von
Gavialis gangeticus (Gmelin, 1789) (Crocodylia, Gavialidae). Cour Forschung Senck
173:299-313.
Varrichio DJ, Jackson FD (2004) A phylogenetic assessment of prismatic dinosaur eggs from the
Cretaceous Two Medicine Formation of Montana. Jour of Vertebr Paleontol 24:931–937
Williams, DLG (1981) Geynormis eggshell (Dromornithidae; Aves) from the Late Pleistocene of
South Australia. Alche., 5: 133-140
Williams, DLG, Vickers-Rich P (1991) Fossil eggs from the Tertiary and Quaternary of Australia.
Pp. 871-891. In: Vickers-Rich, P.; Monaghan, J. M.; Baird, R. F.; Rich, T. H. (ed.)
Vertebrate palaeontology of Australasia. Melbourne, Pioneer Design Studio
Zelenistsky DK, Therrien F (2008a). Phylogenetic analysis of reproductive traits of maniraptoran
theropods and its implications for egg parataxonomy Palaeont 51(4):807-816
Zelenistsky DK, Therrien F (2008b). Unique maniraptoran egg clutch from the Upper Cretaceous
Two Medicine Formation of Montana reveals theropod nesting behaviour Palaeont
51(4):1253-1259
84
Determining human geographic origin using 3D morphometric analysis
of cranial shape
Supervisors: Norman MacLeod, Margaret Clegg & Heather Bonney, NHM
([email protected])
(MSc)
The geographic origins of an individual play an important role in a variety of fields including
forensic, human evolution and provenancing of museum collections. The cranium is the most
commonly used area to estimate geographic origin and has a long history of use. The most
widely used methods today (Fordisc and CRANID) use linear measurements and discriminant
function analysis from a large dataset to estimate origins. More recently studies using 3D
morphometrics to analyse both ontogeny (e.g. Strand Vittasdottir U. et al. 2002, 2003, Gonzales
et al. 2010) and population variation have been undertaken (e.g. Franklin et al. 2007 and
Zollikofer & de Leon, 2002). This study will use adult crania from 4 widely dispersed geographic
locations to assess if shape variation can accurately determine known geographic location.
References:
Strand Vidarsdóttir, U. & O'Higgins, P. 2003. Developmental variation in the facial skeleton of
anatomically modern Homo sapiens. In Patterns of Growth and Development in the
Genus Homo. Thompson J, Krovitz G. & Nelson A Cambridge: Cambridge University
Press. 114-143.
Strand Vidarsdóttir, U, O'Higgins, P. & Stringer, C. B. 2002. A geometric morphometric study of
regional differences in the ontogeny of the modern human facial skeleton. Journal of
Anatomy 201(3): 211-229.
Gonzalez, P.N. Perez, S.I. & Bernal, V (2010) Ontogeny of Robusticity of Craniofacial Traits in
Modern Humans: A Study of South American Populations American Journal of Physical
Anthropology 142 3 367-379
Franklin, D. Freedman, L. Milne, N. & Oxnard, C.E. (2007) Geometric morphometric study of
population variation in indigenous southern African crania. American Journal of Human
Biology 19 1 20-33
Zollikofer, C.P.E. de Leon, M.S.P. (2002) Visualizing patterns of craniofacial shape variation in
Homo sapiens Proceedings of the Royal Society, Series B-Biological Sciences 269 1493
801-807.
Supervisor: Norman MacLeod, NHM ([email protected])
(MSc/MRes)
The interpretation of function in fossil organisms has long been problematic insofar as (1) the
morphologies of fossil animals often present novel combinations of characters when compared to
neontological taxa and (2) the specific morphological correlates of functional groups are often not
known for modern—much less fossil—organisms. This study will seek to forge a new approach to
the inference of function from form. Collecting both 2D images and 3D scans of proximal radial
heads from a selection of modern mammal taxa representing different locomotor guilds a neural
net will be used to devise rules for distinguishing one guild from the other based on a priori group
designation for the modern mammal dataset. These neural net models will then be used to infer
the probable guild assignment for a series of Eocene fossil taxa. Neural net-based guild
assignment will then be compared and contrasted with results obtained from 2D and 3D
morphometric analysis. This study represents a novel extension of the quantitative
ecomorphology research programme and a novel application of neural net technology to
evolutionary systematics and palaeontology.
Reference:
MacLeod, N., and K. D. Rose. 1993. Inferring locomotor behavior in Paleogene mammals via
eigenshape analysis. American Journal of Science 293-A:300-355.
85
Supervisors: Norman MacLeod, Margaret Clegg & Heather Bonney, NHM
([email protected])
(MSc/MRes)
Muscle attachment sites on long bones particularly those of the upper limb are often used for
determining side preference especially handedness. Most studies rely on either scoring
musculoskeletal markers or on linear dimensions (Auerbach et al 2006; Sarringhaus et al. 2005).
This study will examine the use of 3D morphometrics to assess robusticity and determine if
individuals display bilateral asymmetry in the cross sectional geometry of the long bones.
References:
Auerbach, B. M. and Ruff, C. B. 2006 Limb bone bilateral asymmetry: variability & commonality
among modern humans Journal of Human Evolution 50:2:203-218
Sarringhaus, L. A. Stock, J. T. Marchant, and L. F. McGrew, W. C. 2005 Bilateral asymmetry in
the limb bones of the chimpanzee American Journal of Physical Anthropology 128:4:840845
Supervisor: Norman MacLeod, NHM ([email protected])
(MSc/MRes)
One approach to addressing long-standing concerns associated with the taxonomic impediment
and the low reproducibility of taxonomic data is through development of automated species
identification systems. Two generalized approaches are considered relevant in this context,
morphometric systems based on some form of linear discriminant analysis (LDA), and machine
learning systems (ANN). The former is familiar to many systematists, but has rarely been used in
a taxonomic group-identification context. The latter less familiar, but is routinely employed in
various types of mathematical and security-related contexts. Use of such systems is also
necessary in order to (1) raise the quality of taxonomic identifications on which so many scientific
results and interpretation depend, (2) stabilize species concepts, and (3) deliver high-quality
taxonomic identifications to those who need them in academic, educational, industrial,
agricultural, resource management/conservation, government, and cultural (museum) sectors of
the world economy. Comparisons between these two approaches are badly needed in order to
establish appropriate roles for each in taxonomic contexts and to define the limitations of each for
resolving taxonomic problems in all these spheres of human activity. Opportunities exist to
undertake such investigations on a wide range of organismal groups (fossil, modern, fossil +
modern combined) depending on the student’s interests. Previous investigations in which this
approach has been used have focused on butterflies, moths, insect larvae, planktonic
foraminifera, gall wasps, bivalves, and pollen.
References:
MacLeod, N., M. A. O'Neill, and S. A. Walsh. 2004. A comparison between morphometric and
unsupervised, artificial, neural-net approaches to automated species identification in
foraminifera. P. 21. In E. Sheldon, S. Stouge, and A. Henderson, eds. Proceedings, The
Micropalaeontological Society Calcareous Plankton Spring Meeting. Geological Survey of
Denmark and Greenland, Ministry of the Environment, GEUS, Copenhagen, Denmark.
Gaston, K. J., and M. A. O'Neill. 2004. Automated species identification—why not? Philosophical
Transactions of the Royal Society of London, Series B 359:655–667.
MacLeod, N., M. O'Neill, and A. S. Walsh. 2007. Automated tools for the identification of taxa
from morphological data: face recognition in wasps. Pp. 153–188. In N. MacLeod, ed.
Automated taxon recognition in systematics: theory, approaches and applications. CRC
Press, Taylor & Francis Group, Boca Raton, Florida.
MacLeod, N. 2008. Understanding morphology in systematic contexts: 3D specimen ordination
and 3D specimen recognition. Pp. 143–210. In Q. Wheeler, ed. The New Taxonomy. CRC
Press, Taylor & Francis Group, London.
86
Supervisor: Norman MacLeod, NHM ([email protected])
(MSc/MRes)
Studies of morphological adaptation have long aimed to quantify the relation between an
organism’s form and its ecology. In the past such studies have been often hampered by an overreliance on either qualitative observations or the collection of a few, simple linear measurements
as the primary morphological descriptors. Recent advances in morphometric data acquisition and
analysis techniques now provide a means of accurately and comprehensively quantifying the
morphological variation inherent in landmark configurations, 2D boundary outline geometries, and
complex 3D surfaces across any specimen set. The interpretability of the morphological variation
patterns identified by these analyses is enhanced by advanced geometric modelling techniques.
Combined analyses of these data with single or multiple ecological variable sets can be used to
understand how group-specific patterns of morphological variation have responded to ecological
selection pressures. This approach can be used by researchers to understand the significance of
skeletal morphology in ways that cannot be duplicated by visual observation. Opportunities exist
to undertake such investigations on a wide range of organismal groups (fossil, modern, fossil +
modern combined) depending on the student’s interests. Previous investigations in which this
approach has been used have focused on raptors, felids, ursids, carnivores in general, mammals
in general, ungulates, and sauropod dinosaurs.
References:
MacLeod, N., and K. D. Rose. 1993. Inferring locomotor behavior in Paleogene mammals via
eigenshape analysis. American Journal of Science 293-A:300-355.
Figueirido, B., N. Macleod, J. Krieger, M. De Renzi, J. A. Pérez-Claros, and P. Palmqvist. 2011.
Constraint and adaptation in the evolution of carnivoran skull shape. Paleobiology
37(3):490–518.
Sievwright, H., and N. MacLeod. 2012. Eigensurface analysis, ecology, and modeling of
morphological adaptation in the falconiform humerus (Falconiformes: Aves). Zoological
Journal of the Linnean Society 165:390-415.
Supervisor: Norman MacLeod, NHM ([email protected])
(MSc/MRes)
Although many of the goals and concepts of qualitative morphological analysis and
morphometrics are similar, systematists have largely rejected the use of morphometric methods
in phylogenetic analysis on a variety of grounds. The convention notwithstanding, (1) the
concepts of a cladistic character and a morphometric variable are essentially identical, (2)
morphometric methods can be instrumental in discovering and documenting new morphological
character and character states, and (3) prior objections to the use of morphometric variables
because of their continuous nature confuse the issues of variable type with those surrounding the
distributions of sets of observations. MacLeod (2002) suggested that relative warps analysis
could be used to identify patterns of discontinuous variation in morphological characters and
guide the coding of these into states. More recently, Catalano and Globoff (2010) and Globoff
and Catalano (2011) have argued that morphometric data can be used directly in a phylogenetic
analysis as continuous characters. Both alternatives are possible computationally. However, the
ability of continuously coded morphometric characters to find reasonable phylogenies is unknown
at present because the vast majority of phylogenetic analyses that have been conducted to date
have employed discontinuous character data. Opportunities exist to undertake such
investigations on a wide range of organismal groups (fossil, modern, fossil + modern combined)
depending on the student’s interests.
References:
MacLeod, N. 2002. Phylogenetic signals in morphometric data. Pp. 100–138. In N. MacLeod, and
P. L. Forey, eds. Morphology, shape and phylogeny. Taylor & Francis, London.
Catalano, S. A., P. A. Goloboff, and N. P. Giannini. 2010. Phylogenetic morphometrics (I): the
use of landmark data in a phylogenetic framework. Cladistics 26:539–549.
Goloboff, P. A., and S. A. Catalano. 2011. Phylogenetic morphometrics (II): algorithms for
landmark optimization Cladistics 27(1):42–51.
87
Phylogeny and macroevolution of invertebrate body plans
Supervisor: Ronald Jenner, NHM ([email protected])
(MRes/MSc)
These are the best of times if you are interested in studying the mysteries of the deep
evolutionary past of animals. The increasing availability of molecular, developmental and
morphological data on all taxonomic levels, and the development of new methods of analysis
provide an unprecedented opportunity to address fundamental questions about animal phylogeny
and the evolution of animal body plans. My interests range widely, and include higher-level
phylogeny and evolution (of Metazoa and Crustacea, for example), molecular evolution of venom
in invertebrates, important questions in systematic biology (the causes of conflict between
molecular and morphological phylogenies, for example), and more conceptual or theoretical
issues (what is the role of ancestors in modern systematic biology, for example). If you are
interested in any of these topics, please contact me to discuss the possibilities of specific
MSc/MRes projects. Individual projects can be based on the analysis of published literature/data,
but may also include a practical (molecular) lab component.
Evolution of parasitism in flatworms
Supervisor: Tim Littlewood, NHM ([email protected])
(MSc/MRes)
My research interests include the evolution of parasitism in helminths. Using molecular
systematics, and recently comparative mitogenomics, we are interested in resolving phylogenies
of a diversity of animals across a wide range of taxonomic scales, and the developing molecular
tools for (mainly species) diagnostics, especially worms of economic or biomedical importance.
Emphasis is on parasitic helminths and examples include: amplifying, characterizing, annotation
and analysis of complete mitochondrial genomes for primer design and phylogenetics. I prefer
discussing on-going research activities with individual students to see if there are appropriate
(publishable) projects on the near horizon, so that students can be a part of, or indeed lead on
them. To provide adequate supervision, students should seek me out sooner, rather than later.
Examples include:
Finding and assessing suitable barcodes in tapeworms of biomedical and veterinary
importance
Developing PCR primers for high throughput mitogenomics of flatworm parasites
Anomalocaridids are stem-group arthropods, their fossils including the largest animals known
from the Cambrian Period. After a century of their body parts being misidentified as several
different organisms, today’s concept of metre-long pelagic predators emerged in the 1980s. The
Burgess Shale of British Columbia, Canada, includes the articulated bodies of four different
anomalocaridid species, and at least two additional genera/species have recently been
documented from their spinose, segmented frontal appendages. The diversity of Burgess Shale
anomalocaridids known from frontal appendages exceeds that recognised from their mouthparts,
the so-called Peytoia apparatus (popularly likened to a pineapple ring). The mouth opens at the
centre of a 32-plated ring fringed by sharp spines, with four larger plates defining the symmetry of
the ring. A landmark/semilandmark approach to these mouth rings will be aimed at reconciling the
diversity of anomalocaridids known from frontal appendages with the (presently) lesser diversity
of mouthparts.
88
Evidence for latitudinal variation in species interactions: patterns of
defensive zooidal polymorphs in bryozoans
Supervisors: Beth Okamura ([email protected]) & Paul Taylor, NHM
(MSc/MRes)
The latitudinal gradient in species diversity is one of the most striking biogeographic patterns on
Earth. Biotic interactions have played a central role in attempts to understand this latitudinal
diversity gradient (Schemske et al. 2009). Nevertheless, quantitative analyses of how the
importance of biotic interactions may change with latitude are rare. Schemske et al.’s (2009)
recent review of the evidence for latitudinal gradients in biotic interactions outlines several
directions for future research that will enable us to better understand latitudinal diversity
gradients. Amongst these is the suggestion to examine geographical patterns for traits involved in
biotic interactions in taxonomic groups (e.g. genera) that span tropical and extratropical regions
to enable latitudinal comparisons in, for example, structural or chemical defense against
predators.
This project will test the prediction that defenses against enemies will decrease towards higher
latitudes because rates of biotic interactions (e.g. predation, competition) are predicted to
decrease. The project will focus on genera of cheilostome bryozoans, a group of colonial
invertebrates that exhibit polymorphism amongst zooids that constitute colonies. Specifically the
project will test whether the allocation within colonies to non-feeding, defensive polymorphs
(avicularia) increases from polar through temperate to tropical latitudes. Building on the
preliminary work of Kuklinski & Taylor (2008), the proportion and relative surface area of
avicularia to autozooids (feeding zooids) will be compared in a selection of cheilostome genera
and species collected from polar, temperature and tropical sites. Target genera will include the
cosmopolitan genera Microporella, Cellaria, Puellina, Micropora, Parasmittina and Schizoporella,
specimens of which are well represented in the Zoology Collections of the NHM.
The research will entail substantial use of stereomicroscopy and some scanning electron
microscopy for species identification and imaging in order to study the distributions, proportions
and surface areas of defensive polymorphs within colonies.
References:
Kuklinski P, Taylor PD. (2008) Are bryozoans adapted for living in the Arctic? Virginia Museum of
Natural History, Special Publication 15: 101-100.
Schemske DW, Mittelbach GG, Cornell HV, Sobel JM, Roy K. (2009) Is there a latitudinal
gradient in the importance of biotic interactions? Annual Review of Ecology, Evolution,
and Systematics 40: 245-269.
Evolution, development and genomics of parasitic flatworms
Supervisor: Pete Olson, NHM ([email protected])
(MSc/MRes)
We are interested in the evolution of parasitic flatworms (tapeworms, flukes and monogeneans;
phylum Platyhelminthes) and use phylogenetic, developmental and genomic approaches to
address questions relating to both pattern and process. Our research is predominantly empirical
and molecular and provides opportunities for students to become well versed in both basic and
advanced genetic manipulations in the laboratory. However, opportunities also exist for
morphological studies (e.g. using confocal microscopy and electron microscopy) as well as
bioinformatic/genomic studies done entirely in silico. Student projects are always designed for
publication, either in their own right or by contributing to ongoing work. Please visit olsonlab.com
for more information.
.
89
Molecular and morphological investigations of freshwater bryozoan
taxonomy and systematics
Supervisors: Beth Okamura ([email protected]) & Hanna Hartikainen, NHM (MSc/MRes)
The Bryozoa is the only phylum comprised exclusively of colonial animals. Bryozoan colonies are
composed of individual modules, called zooids, which develop through asexual budding.
Bryozoans belonging to the Class Phylactolaemata occur exclusively in fresh waters. Although
not widely recognised phylactolaemates are abundant and ubiquitous residents of freshwater
habitats where colonies grow on surfaces such as roots, submerged branches, macrophytes,
stones, pier pilings and plastics. The Phylactolaemata comprises a relatively small class (70+
described species) but the diversity is certainly underestimated because it is a very poorly studied
group. There are six families (Fredericellidae, Plumatellidae, Cristatellidae, Lophopodidae,
Pectinatellidae, Stephanellidae) whose relationships remain poorly understood with molecular
and morphological characters providing conflicting interpretations.
Species identification based on colony morphology is possible in some cases, especially for
gelatinous forms. However, similar overall patterns of growth, a dearth of macroscopic characters
and microenvironmentally induced plasticity in colony form characterise many species that grow
as tubular, branching colonies. These include species within the Plumatellidae and the
Fredericellidae, the first and third largest families, respectively. Species identification has
therefore emphasised the importance of microscopic or even ultrastructural study of sclerotized
dormant stages called statoblasts. Statoblasts, however, are absent during early periods of
colony growth and may also exhibit substantial variation in overall size and shape and in certain
surface features (e.g. the presence and density of nodules, the presence of reticulations). It is
therefore advisable to examine multiple statoblasts per colony multiple colonies per species.
Molecular barcoding represents a complementary or even an alternative means of taxonomic
assignment due to a) the limitations for species identification imposed by plasticity in colony form,
b) the potential requirement for ultrastructural study of statoblasts, c) the necessary expertise to
interpret highly variable statoblast morphologies and d) the possible absence of statoblasts
during much of the growing season.
Recently, we have utilised a novel molecular marker (rrnS-rrnL) that provides useful
discrimination of phylactolaemates at the species level in order to characterise the diversity of
freshwater bryozoans collected over a wide geographic range. We have also examined the
ultrastructure of statoblasts. This combined approach has enabled us to identify at least two new
species of Plumatella and Fredericella and has demonstrated cases where statoblasts may be
highly problematic for species identification. The aim of this study would be to undertake similar
investigations incorporating material from South Africa, Iceland, California and southeast Asia in
molecular phylogenies and to characterise the associated ultrastructure of statoblasts. Outputs
should include a larger rrnS-rrnL phylogeny with enhanced understanding of species
relationships, further tests of the relative utility of molecules vs. morphology in species
discrimination and potential identification of new species. The student would gain experience in
scanning electron microscopy to characterise statoblast ultrastructure, standard molecular
biological skills (DNA extraction, PCR, sequencing), and phylogenetic analysis.
References
Hirose M, Dick MH, Mawatari SF. 2011. Are plumatellid statoblasts in freshwater bryozoans phylogenetically
informative? Zoological Science. 28: 318-326.
Massard JA, Geimer G. 2008. Global diversity of bryozoans (Bryozoa or Ectoprocta) in freshwater.
Hydrobiologia. 595: 93-99.
Okuyama M, Wada H, Ishii T. 2006. Phylogenetic relationships of freshwater bryozoans (Ectoprocta,
Phylactolaemata) inferred from mitochondrial ribosomal DNA sequences. Zoologica Scripta. 35:
243-249.
Rubini A, Pieroni G, Elia AC, Zippilli L, Paolocci F, Taticchi MI. 2011. Novel morphological and genetic tools
to discriminate species among the family Plumatellidae (Phylactolaemata, Bryozoa). Hydrobiologia.
664: 81-93.
Waeschenbach A, Taylor PD, Littlewood DTJ. 2012. A molecular phylogeny of bryozoans. Molecular
Phylogenetics and Evolution. 62: 718-735.
Wood, T.S. & Okamura, B. (2005) A key to the freshwater bryozoans of Europe and the British Isles with
ecological notes. Freshwater Biological Association Publication Scientific Publication No. 63,
Freshwater Biological Association, The Ferry House, Far Sawrey, Ambleside, Cumbria, UK.
90
Supervisors: Norman MacLeod, Margaret Clegg & Heather Bonney, NHM
([email protected])
(MSc)
All activities that we undertake can leave their mark on our bones. Most studies rely on scoring
musculoskeletal attachment sites or on linear measurements or look at differences in shape
(Rhodes & Churchill 2009). This study will use 3D morphometrics to access shape differences in
the humerus in two human groups of known occupation.
References:
Rhodes, JA Churchill, SE (2009) Throwing in the Middle and Upper Palaeolithic: inferences from
an analysis of humeral retroversion, Journal of Human Evolution 56: 1 1-10.
Gualdi-Russo, E Galletti, L (2004) Human activity patterns and skeletal metric indicators in the
upper limb, Collegium Anthropologicum 28 (1): 131-143.
91
MSc in Taxonomy and Biodiversity
Project Proposal 2012/13
Student‟s Name
Supervisor‟s Name
Location of Work
Project Title
Outline of Work
Special Requirements
eg. equipment, chemicals
Note to supervisor: A maximum of £500 can be given as reimbursement for molecular projects
Collections to be Used
Approved by
Signature of Student
Date
Signature of Supervisor
Date
Approved by
Date
Once completed and signed by both the student and the supervisor, please send this
form to Amoret Whitaker by Friday 5th April 2013.
92
MRes in Biosystematics
Project Proposal 2012/13
Project handing in:
January/May/September
Student‟s Name
Supervisor‟s Name
Location of Work
Project Title
Outline of Work
Special Requirements
eg. equipment, chemicals
Note to supervisor: A maximum of £1000 can be given as reimbursement for molecular projects
Collections to be Used
Approved by
Signature of Student
Date
Signature of Supervisor
Date
Approved by
Date
Once completed and signed by both the student and the supervisor, please send this
form to Amoret Whitaker prior to the start of your project.
93
MARKING CRITERIA for EXAMS and ESSAYS
The following criteria should be used to mark both exam answers and coursework essays.
Literal
Grade
A*
Criteria
(Problem type answers should be marked on a semi-absolute scale)
Exceptional. Answer is an exceptionally well presented exposition of the subject, showing:
(i) command of the relevant concepts and facts, (ii) a high critical or analytical ability**, (iii)
originality, and (iv) evidence of substantial outside reading (where applicable).
A
Excellent. Answer is a very well presented exposition of the subject, showing many of the
above features, but falling short in one or two of them.
B
Good. Answer (i) shows a clear grasp of the relevant concepts and facts, (ii) gives an
accurate account of the relevant taught material (as exemplified in the model answer),and
(iii) shows evidence of some outside reading or of critical or analytical ability**.
C
Adequate. Answer: (i) shows a grasp of the basic concepts and facts, (ii) gives a mainly
accurate account of at least half of the relevant taught material (as exemplified in the model
answer),and (iii) does not go beyond that, or goes beyond that but is marred by significant
errors.
D
Fail. Answer shows only a weak grasp of the basic concepts and facts, and is marred by
major errors or brevity.
Answer shows a confused understanding of the question, contains major errors and
information which is irrelevant to the question and/or is too brief to indicate adequate
knowledge of the subject.
Answer is too inaccurate, too irrelevant, or too brief to indicate more than a vague
understanding of the question.
Answer presents only two or three sentences or facts that are correct and relevant to the
questions.
Answer includes at most one sentence or fact that is correct and relevant to the question.
Answer contains nothing correct that is relevant to the question.
** Analytical = assessing a hypothesis or statement by breaking it down into its elements and examining
their inter-relationships and contribution to the whole; cf. Critical = judging a hypothesis or conclusion by
examining the validity of the evidence adduced for it.
94
SUGGESTED FRAMEWORK FOR COURSEWORK ASSESSMENT
Grade
Criteria
(Problem-type answers should be marked on a semi-absolute scale)
A*
Exceptional. All procedures understood and applied properly, with a clear and logical
write-up. Evidence of background reading, detailed discussion of methodology and
results, full statistical analysis (where relevant), analysis of errors (where relevant),
clear conclusions.
A
Excellent. All procedures understood and applied properly, with a clear and logical
write-up.
B
Good. Most procedures understood and mostly applied properly with a few minor
problems.
C
Adequate. A few procedures misunderstood but important ones grasped.
D
Fail. Shows only a weak grasp of the basic concepts and facts and is marred by
major errors or brevity.
Shows a confused understanding of the work required with less than one third of the
material expected.
Answer is too inaccurate, too irrelevant or too brief to indicate more than a vague
understanding of the question.
Presents only two or three sentences or facts that are correct and relevant.
Includes at most one sentence or fact that is correct and relevant.
Contains nothing correct that is relevant.
Note: These criteria are not necessarily suitable for all coursework.
95
FEEDBACK FORM FOR COURSEWORK
Report Marking Analysis
Student‟s Name …………………………………………….
Course Title ………………………………………………...
Assignment Title …………………………………………....
Objectives
What were the objectives?
Planning, Preparation and Background Reading
Evidence of plenty of research and careful
preparation of material
A* A B C D
Not applicable
Little research, poor presentation
Organisation and Presentation
Logically structured
A* A B C D
Disorganised and confused
A* A B C D
Not applicable
Data missing or in raw state
Data Analysis and Data Presentation
Data carefully analysed. Tables and
graphs used appropriately, labelled and
cross referenced in text, data complete
Overall Understanding and Analysis of the Work
Excellent analysis and synthesis of task.
Work put into context of existing theory/
work done.
A* A B C D
Overall Comments:
Provisional Grade
A*
A
B
C
D (Fail)
Signed …………………………………………………………….
96
Some understanding but some
fundamental errors
FEEDBACK FORM FOR ORAL PRESENTATIONS
Oral Presentation Marking Analysis
Student‟s Name …………………………………………….
Course Title ………………………………………………...
Assignment Title …………………………………………....
Objectives
What were the objectives?
Planning and Preparation
Evidence of plenty of research and
careful preparation of material
A* A B C D
Disorganised and confused
Subject Matter
Content is relevant, accurate, based
on sound evidence
A* A B C D
Anecdotal and fails to
address the title of the talk
A* A B C D
Couldn’t hear voice, tense
posture
A* A B C D
No overheads or other props.
Read from notes.
Voice and Body Language
Good strong voice, relaxed posture
Presentation
Good use of overheads, handouts
prepared. Spoke to audience.
Overall Comments:
Provisional Grade
A*
A
B
C
D (Fail)
Signed: ………………………………………………..
97
FEEDBACK FORM FOR POSTERS
Poster Marking Analysis
Student‟s Name …………………………………………….
Course Title ………………………………………………...
Assignment Title …………………………………………....
Objectives
What were the objectives?
Organisation and Presentation
Logically structured in a form suitable to the task.
Well laid out.
A* A B C D
Disorganised and
confused
Visual Impact
Eye catching and interesting. Considerable
thought has gone into the design.
A* A B C D
Poor visual impact
Overall Understanding and Analysis of the Work
Excellent analysis and synthesis of task.
Work put into context of existing theory/
work done.
A* A B C D
Overall Comments:
Provisional Grade
A*
A
B
C
D (Fail)
Signed: ………………………………………………..
98
Some understanding but
some fundamental errors
MSc/MRes PROJECT ASSESSMENT - Form Ia – Supervisor‟s Assessment
Student's name: . . . . . . . . . . . . . . . . . . . .
Supervisor's name: . . . . . . . . . . . . . . . . . . . . . . .
Tick one box in each section, using the centre box to indicate the normal, adequate standard.
(1) How likely was the project to produce analysable results?
...................................... (almost guaranteed)
(speculative)
(2) How much did the project depend on mastery of difficult techniques?
………………………………….(very easy)
(very difficult)
(3) Were there unanticipated constraints to the project
(bad weather, culture failure etc.)
........................................ (none relevant)
(disastrous)
(4) How much did the student put into the design of the project?
…………………..…. ........ (almost nothing)
(student’s idea)
(5) How diligently did the student work?
............................................... (indolently)
(intensively)
(6) How well did the student perform in the laboratory
or field, or in accessing other data sources?
................................................ (slapdash)
(research level)
(7) How much help did the student get (from anyone)
during the project
........................................... (a great deal)
(hardly any)
(8) How demanding was the analysis of the data,
other material or literature
.................................................... (simple)
(very difficult)
(9) How much help did the student get
in writing up the thesis for
Text (a great deal)
(virtually none)
Analysis (a great deal)
(virtually none)
Figs/Tables (a great deal)
(virtually none)
99
MSc/MRes PROJECT ASSESSMENT - Form Ib - Supervisor‟s Report
Student's name: . . . . . . . . . . . . . . . . . . . . . . . . . Marker’s name: . . . . . . . . . . . . . . . . . . . . . . . . . . .
Continue on a separate sheet if necessary
Proposed Mark (%) ......................................
__________
Initials............................................................
__________
100
MSc/MRes PROJECT ASSESSMENT - Form IIa - Thesis Marker‟s Assessment
Student's name: . . . . . . . . . . . . . . . . . . . . . . . Marker's name: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Tick one box in each section, using the centre box to indicate the normal, adequate standard.
(1) Presentation:
.................................................... (messy)
(publication standard)
(2) Introduction to thesis subject:
...................................................... (trivial)
(publishable)
(3) Methods exposition:
............... (inadequate/incomprehensible)
(perfectly clear)
(4) Quantity of work done
................................................ (very little)
(a great deal)
(5) Quality of data
.............................. (very thin or provided)
(new and publishable)
(6) Analysis of data or other material
.......................................... (very shallow)
(full statistics. etc.)
(7) Discussion
........................................... (very shallow)
(publication standard)
(8) Understanding
................................................ (very little)
(research level)
(9) Scientific rigor
...................................................... (weak)
(strict)
(10) Originality
.......................................... (almost none)
(highly original)
101
Msc/MRes PROJECT ASSESSMENT - Form IIb - Thesis Marker's Report
Student's name: . . . . . . . . . . . . . . . . . . . . . . . . . Marker’s name: . . . . . . . . . . . . . . . . . . . . . . . . . .
Continue on a separate sheet if necessary
Proposed Mark (%) ......................................
__________
Agreed Mark (%) ..........................................
__________
Initials ...........................................................
__________
102
MSc and MRes PROJECT ASSESSMENT – THESIS MARKING CRITERIA
Literal
Grade
Criteria
A*
Exceptional. Thesis is of a publishable standard**. It is an exceptionally well
presented exposition of the project, showing: (i) command of the relevant concepts and
facts, (ii) a high level of analysis, (iii) originality in thought and experimental design, and
(iv) mastery of the relevant literature.
A
Excellent. Thesis is written to a publishable standard** with minor revision. It is a very
well presented exposition of the project, showing most of the above features, but falling
short in one of them.
B
Good. Thesis contains potentially publishable material**, but needs revision of the text
and further research. It is otherwise a well presented exposition of the project,
showing: (i) a clear grasp of the relevant concepts and facts, (ii) appropriate, though
not highly sophisticated analysis, and (iii) a sound knowledge of the relevant literature.
C
Adequate. Thesis is not written to a publishable standard and requires major revision
and substantially more research. It is an adequately presented exposition of the
project, showing: (i) a grasp of the basic concepts and facts, (ii) an adequate use of
statistics in its analyses, and (iii) sufficient knowledge of the relevant literature to set its
results in a scientific context.
D
Fail. Thesis is an incomplete presentation of the project and is marred by major errors
or gaps, missing analysis, lack of references, misconceptions, excessive brevity, etc, at
most showing a weak grasp of the basic concepts and facts.
Thesis as above, but presentation extremely poor and overall impression indicates a
very weak grasp of the basic concepts and facts.
Thesis as above, and in addition no real attempt to analyse data or present results in a
scientific manner.
Thesis as above but incomplete and lacking understanding in all areas.
Thesis not produced.
** This publishability assumes that the data are per se worth publishing.
103
Degree regulations
MSc Taxonomy and Biodiversity
The course comprises two elements, both of which must be passed with a minimum mark of 50%
to obtain the degree of MSc in Taxonomy and Biodiversity. The first element comprises two
components. The first component of the first element is the five items of course work, each of
which is equally weighted in terms of marks and which collectively comprises 20% of the final
degree mark. The second component of the first element is the combined examinations (two
papers, each with two questions to be answered) which collectively constitute 40% of the final
degree mark. The second element comprises the project which accounts for the remaining 40% of
the final degree marks. In addition each student must give two oral presentations, at least one of
which must be passed. Students shall be awarded a Pass degree if they have achieved a
minimum of 50% in each of the two elements, as long as neither component of the first element is
below 40%. Students will be awarded a Pass With Merit if their aggregate mark is greater than or
equal to 60% and neither element mark is below 50%. Students will be awarded a Pass With
Distinction if their aggregate mark is greater than or equal to 70% and neither element mark is
below 60%.
MRes Biosystematics
The course comprises three elements, each of which must be passed with a minimum mark of 50%
to obtain the degree of MRes in Biosystematics. Each element contributes an equal proportion to
the final mark. Each element comprises three components. The components include a written
thesis and oral presentation, whose marks contribute 75% and 25%, respectively, to a preliminary
mark for this element. The third component is a viva voce examination. The preliminary mark from
the first two components will be modulated according to the result of the viva voce which
contributes 25% of the final mark for a given element. Students shall be awarded a Pass degree if
they have achieved a minimum of 50% in all three elements, as long as no component of any of the
three elements is below 40%. Students will be awarded a Pass With Merit if their aggregate mark
is greater than or equal to 60% and no element mark is below 50%. Students will be awarded a
Pass With Distinction if their aggregate mark is greater than or equal to 70% and no element mark
is below 60%.
104
Past Examination Papers
IMPERIAL COLLEGE LONDON
M.Sc. TAXONOMY AND BIODIVERSITY
Exam Paper 1 – Monday 16th April 2012 – 10:00-13:00
Answer one question from Part 1 and one from Part 2. Each part is equally
weighted. Students will be permitted 10 minutes reading time prior to the
commencement of the examination.
Part 1
Answer one question only
1.
The kiwis, Apteryx spp, are a small group of flightless birds (ratites) found nowadays
only in New Zealand and some of its offshore islands. The commonest species, the
brown kiwi (Apteryx australis) is widespread but represented by a number of isolated
populations (shaded areas in Fig. 1). Following their discovery last century, the
North and South Island populations were eventually recognized in 1850 as separate
species (Apteryx mantelli and A. australis, respectively), on the basis of
morphological characters, such as length of facial bristles, size of body parts,
plumage colour, wing quills, and tarsus scutellation. However, subsequent research
with additional specimens suggested that the only valid character separating them
was the stiffer feather tips of the North Island species. Thus, in 1899, Rothschild
relegated the North and South Island brown kiwis to subspecies (Apteryx australis
mantelli and Apteryx australis australis, respectively) and also recognized the
Stewart Island population as Apteryx australis lawryi.
Baker et al. (1995) carried out analyses using allozyme electrophoresis and
sequencing of a 654 base pair region of the mitochondrial cytochrome b gene
(relatively slowly evolving in this group of birds). Samples from the two other extant
kiwis (little spotted (A. oweni) and greated spotted (A. haasti)) were used as
outgroups. Of 29 allozyme loci examined, only 3 showed variation among brown
kiwi samples.
Fig. 1 shows the distribution of brown kiwi populations, and the labelled red dots
show where samples for molecular analysis were collected.
Fig. 2A shows a neighbour-joining tree based on the mitochondrial DNA sequence
data using the Kimura 2-parameter method with bootstrap values greater than 50%
shown; and Fig. 2B shows a UPGMA (distance based method) tree based on Nei’s
unbiased genetic distance for the allozyme variation.
Fig. 3 shows the variable sites for the cytochrome b sequences with dots
representing identity with the A. haasti sequence at the top.
Please turn over
105
Paper 1 Part 1 Question 1 Contd/…
Fig. 1. Distribution of brown kiwi populations. Labelled red dots show where
samples for molecular analysis were collected.
Fig. 2A Neighbour-joining tree based on the mitochondrial DNA sequence data
using the Kimura 2-parameter method with bootstrap values greater than 50%
shown; and Fig. 2B shows a UPGMA (distance based method) tree based on Nei’s
unbiased genetic distance for the allozyme variation.
Please turn over
106
Paper 1 Part 1 Question 1 Contd/…
Fig. 3. Variable sites for the cytochrome b sequences with dots representing identity
with the A. haasti sequence at the top.
a) Based on Figures 2A and B, what do you conclude about the population
structure and systematics of the brown kiwi and the likely background to the
observed pattern? [20%]
b) Based on the molecular data in Fig. 3 in conjunction with the map (Fig. 1), what
can you infer from this about the brown kiwi’s populations? [20%]
c) Considering the DNA tree (Fig. 2A) and Fig. 3, what can you conclude about the
likely biogeographic history of the two major molecular clades within the brown
kiwi? [20%]
d) The two outgroup sequences in Fig. 3 show only 1 base pair difference from one
another, yet they are considered perfectly distinct species and they appear to be
separated by long branches on the NJ tree in Fig. 2A. Provide plausible
explanation(s) for this anomaly. [20%]
e) Given all the above information, explain how you would treat the brown kiwi
taxonomically. [20%]
Please turn over
107
Paper One Part 1 Contd/…
2.
The cnidarian class Anthozoa includes corals and sea anemones. Fig. 1 below from
a recent paper by Kerr et al. (Proc. R. Soc., 2011) shows two major life history
features plotted (based on maximum parsimony) on to one of the 25 randomly
bifurcated supertrees for the corals based on combined molecular and
morphological data. On the left hand side, the sexual system is shown with red
representing gonochorism (i.e. at any one time an individual is either male or
female) and pale green represents hermaphrodite species (in which all individuals
have both male and female gonads). The tree on the right hand side depicts
reproductive mode, where blue corresponds to brood embryos and orange
corresponds to the release eggs and sperm separately into the sea.
The abstract of Kerr et al.’s paper states:
“Reproductive mode in corals has evolved at twice the rate of sexuality, while the evolution
of sexuality has been heavily biased: gonochorism is over 100 times more likely to be lost
than gained, and can only be acquired by brooders.”
a) Define and illustrate the terms ACCTRAN (accelerated transformation) and
DELTRAN (delayed transformation) and explain with the aid of diagrams how
ancestral character state reconstruction operates under maximum parsimony
and maximum likelihood. [20%]
From the information in Fig. 1:
b) Examine whether any other equally parsimonious reconstructions might exist
and, if so, illustrate this in your answer. Determine whether the reconstruction
method used was ACCTRAN or DELTRAN and illustrate your reasoning in your
answer. [20%]
c) Examine the transitions in the reproductive biologies (sexual system and
reproductive mode) of these animals, and determine whether they depart from
null expectations. [20%]
d) Is there any evidence that one of the biological features is influenced by the
other, and if so provide a biological explanation. [20%]
e) Does the abstract of the paper (Kerr et al.) accurately represent the results
presented in their figure (Fig. 1)? [20%]
Please turn over
108
Paper 1 Part 1 Question 2 Contd/…
Fig. 1. MP ancestral reconstructions of sexual system and reproductive mode. On
left, red=gonochorism, green = hermaphroditism; on right, blue = brooding, orange =
broadcast spawning. The pie charts indicate maximum likelihood ancestral state
relative probabilities.
Please turn over
109
Paper 1 Part 1 Question 2 Contd/…
Additional information:
The equation for calculation of the chi-squared statistic is:
The equation for calculation of the chi-squared statistic for a 2x2 contingency table is
where the cells of the 1st row are labelled a and b, the 2nd row c and d, and N=a+b+c+d
Probability of exceeding the probability (p) with 1 degree of freedom is given in the table below:
P
= 0.10
0.05
0.025
0.01
0.001
2
X
= 2.706 3.841 5.024 6.635 10.828
End of Part 1
Please turn over
110
Part 2
Answer one question only
1.
a) Define and illustrate, with an example of your own invention, each of the
following terms: [20%]
i)
ii)
iii)
iv)
v)
vi)
b)
Describe, with examples, the advantages and disadvantages of these six
statistics as measurements of support for individual characters or the most
parsimonious cladogram. [20%]
c)
Support for groups on the most parsimonious cladogram is often assessed by
means of Bremer support and bootstrap support. For each of these two
methods: [40%]
i)
ii)
2.
branch length, l
cladogram length, L
consistency index, ci
retention index, ri
ensemble consistency index, CI
ensemble retention index, RI.
Describe and illustrate, using simple examples, how the two support measures
are calculated and presented;
Discuss at least two advantages and two disadvantages of each method.
d)
Some cladists take the position that phylogenetic analysis is an historical science
and thus not amenable to statistical inference. Present a reasoned argument
either in favour of or against this position. [20%]
a)
What are the main technological differences of conventional Sanger
sequencing and next-generation sequencing (NGS)? What is the critical new
problem that arises from the use of NGS technology for data collection in
molecular systematics, and what solutions might be used to adapt the
technology accordingly? [25%]
b)
What are the main differences in phylogenetics using NGS data compared to
PCR-based sequences, and in particular consider taxon sampling, length of
sequences, homology statements etc. [25%]
c)
As full-genome sequences become increasingly available through the use of
NGS, what problems arise when using genome data for phylogenetic analysis,
and how should genome data be analysed to have the greatest power of
resolving phylogenetic relationships and study evolutionary processes? [25%]
d)
Do you think sequencing a lot of genomes will give us the ‘true’ tree of life?
Please elaborate [25%]
End of Paper
111
IMPERIAL COLLEGE LONDON
M.Sc. TAXONOMY AND BIODIVERSITY
Exam Paper 2 – Tuesday 17th April 2012 – 10:00-13:00
Answer one question from Part 1 and one from Part 2. Each part is equally
weighted. Students will be permitted 10 minutes reading time prior to the
commencement of the examination.
Part 1
Answer one question only
1.
The increasing use of DNA data, and in animals in particular, the use of the
barcoding cytochrome oxidase subunit 1 (CO1) gene fragment, has revealed a large
number of cryptic species among many groups, even for apparently well known
groups such as birds and butterflies. For example, Dinca et al. (2011) wrote:
“Uncovering cryptic biodiversity is essential for understanding evolutionary processes and
patterns of ecosystem functioning, as well as for nature conservation. As European
butterflies are arguably the best-studied group of invertebrates in the world, the discovery of a
cryptic species, twenty years ago, within the common wood white Leptidea sinapis was a
significant event, and these butterflies have become a model to study speciation. Here we
show that the so-called 'sibling' Leptidea actually consist of three species. The new species
can be discriminated on the basis of either DNA or karyological data.”
a) If a newly discovered cryptic species pair is discovered using molecular
techniques, what should the authors do in terms of determining what name or
names apply to these entities? [33%]
b) Given this development in the use of molecular techniques in taxonomy, how
now should natural museum collections be developed in order best to represent
the diversity of the living world? [33%]
c) While large differences between two similar-looking individuals (or groups of
individuals) in their barcoding gene sequence may well indicate that there are
two cryptic species present, there are a number of other possibilities. Explain
what alternative scenarios there are, what other data might resolve these and
how these data would be used. [33%]
Please turn over
112
Paper 2 Part 1 Contd/…
2.
You have discovered an entirely new clade of soil invertebrates in tropical rain forests
in Madagascar. No species has yet been described but there are known to be at
least 50 species waiting for formal description. The invertebrates appear to be
specialists feeding externally on the roots of various tree species and are found in a
number of different soil types. You have been given several million pounds to
undertake research on the biodiversity of the clade, in particular to assess how
environmental change might affect the community composition of the group. Answer
the following questions.
(a) What proportion of the available funds (i.e. high, medium, low) would you
apportion to (i) descriptive taxonomy of the group, (ii) studies of the origin and
phylogenetics of the group, (iii) biodiversity surveys to establish the major
environmental factors influencing the distribution of the group. Justify your
reasons for your chosen proportions given the research questions that are being
asked. [30%]
(b) Concentrating on just the biodiversity survey part of the project, what sort of: (i)
invertebrate sampling would you conduct? and (ii) environmental variables would
you measure? Pay particular attention to problems concerning sample size and
sampling effort. [30%]
c) What sort of data would be generated and how could they be analysed in order to
assess the relationship between the measured environmental variables and the
biodiversity data? You might want to think in terms of general statistical
approaches to the problem rather than specific analytical techniques. [40%]
End of Part 1
Please turn over
113
Part 2
Answer one question only
1.
You have been asked to compare gross morphological patterns of differentiation
among a group of nine trilobite specimens.
a) Using the diagram on the attached sheet, design a system of measurements
that adequately captures the geometrical information presented by these
specimens. [20%]
b) I want to test the validity of a species concept using morphological data. Briefly
describe a quantitative data analysis strategy that will allow me to do this. [20%]
Please turn over
114
Paper 2 Part 2 Question 1 contd/…
c) Explain the difference between a phylogenetic character and a morphometric
variable. [20%]
d) Use a series of standard allometric plots to diagram and explain the differences
between the three primary modes of allometry: ontogenetic, static and
evolutionary. [20%]
e) Write a brief analysis either supporting or refuting the following statement. [20%]
“Continuously varying quantitative data are not suitable for cladistic
analysis because there is no justifiable basis for recognizing discrete states
among them.”
Pimentel and Riggins 1987, p. 201
2.
a) Describe four advantages/disadvantages of including fossil taxa
when constructing a phylogeny. Support your case with examples. [40%]
b) Describe the two primary reasons why the fossil record and molecular clock
estimates can disagree over the dating of divergence times in a phylogeny.
What sensible tests should you take to better understand the discrepancy?
[20%]
c) List four assumptions made when constructing global diversity curves from
taxonomic occurrence databases and explain whether you think these are
realistic or not. [40%]
End of Part 2
End of Paper
115
Use this sheet ONLY to answer Paper 2 Part 2 Question 1
Candidate No. ………………….
116