MODULE:
Organisms in their environment
MODULE NUMBER:
BIO00036I
JACS CODE: C100
STAGE / YEAR:2
CREDITS:
20
ORGANISER: Dr Andrew Dean
PROGRAMME BIO
COMMITTEE:
VERSION:
4 Jan 2016
TERMS TAUGHT:
Spring & Summer 2017
PREREQUISITES:
BIO00012C Animal & Plant Biology
RECOMMENDATIONS:
BIO00037I Population Biology
MODULE CATALOGUE:
https://www.york.ac.uk/students/studying/manage/programmes/module-catalogue/module/BIO00036I/2016-17
AIMS
This module focuses on the practical aspects of studying organisms in their environment, at two levels of organisation, populations (single species)
and communities (multiple interacting species).
The module has two parts: a set of lectures and practicals run in the spring term, followed by a field course. The students have the choice of either
joining a field course abroad (some costs covered by the student) or in the UK (fully covered by the department). Field courses depend on student
numbers; in 2015-16, students went to Tanzania, Mallorca and the North York Moors.
In the lectures and practicals, the theory and practical considerations of obtaining informative samples in the field will be extensively covered, both
for plants and animals. Then a number of statistical and numerical analyses will be presented to extract fundamental information on populations
(their size and spatial structure) and communities (their diversity, structure and heterogeneity). A strong emphasis will be placed on critically
interpreting the data and information gained by these techniques and understanding their limitations.
In the field course, the students will have the opportunity to discover more directly how plants and animals live in their environment, and to develop
and execute an ecological investigation in groups of 3-4 students for 5 days. After introduction to a range of habitats, the students, under the
supervision of a member of staff, will be responsible for (1) defining the aim of their study, (2) coming up with a sensible scientific design in one of
the available sites, (3) carrying out the survey or experiment, (4) processing the samples and analysing the results, and (5) communicating their
findings by means of a group presentation.
LEARNING OUTCOMES:
On completion of the module, the students will be able to:
- sample plant and animal populations, and analyse the data to identify spatial structure (plants) and abundance (plants and animals);
- sample communities and use ordination methods to unravel the underlying structure of these communities;
- calculate and interpret (with caution) a number of community properties (diversity, similarity, species richness, species accumulation curve,
abundance rank-plot) and use them to compare communities;
- use principles of experimental design to plan their research activities in the field;
- apply the right techniques (both in terms of sampling and analysis) to a variety of ecological questions;
- demonstrate resilience to unexpected events during real and simulated fieldwork and when analysing field data.
At the end of the field course, the students will also be able to:
- describe the constraints and opportunities provided by ecological fieldwork.
- recognize a range of habitats in the vicinity of their field base.
- explain the specific conservation concerns in these areas.
- work in teams to apply specific skills related to data gathering for the particular project that they conducted, including species identification and
field methodology.
SYNOPSIS OF TEACHING:
Event
Duration (Hrs) Topic
Staff
Room type
Colin Beale
Lecture room Post exams Summer
term for 1st years
signed up for the course
in following year
Introductory
lecture
2
Introduction to field courses and sign up
L1
1
Estimating Plant Abundance
Thorunn
Sampling strategies, Spatial distribution, Effect of scale of observation. Helgason
Plant density vs plant cover, Trees vs forbs, and Sampling protocol
(quadrat vs distance sampling).
lecture room
L2
1
Estimating Animal Abundance
Open vs closed populations, Capture-mark-recapture Abundance
estimation techniques. Relative measures of abundance, Indirect
measures of abundance, Calibration.
lecture room
L3
1
The concept of community and patterns of commonness and rarity.
Andrew Dean
Explaining the pattern of commonness and rarity, how many species
coexists. Rank-abundance plots, species abundance distributions and
theoretical models.
lecture room
L4
1
Species richness and its measurement
Andrew Dean
Species accumulation curves, the confounding effect of sampling effort
and ways to account for it: randomisation and rarefaction. Estimating
community species richness using non-parametric estimators and
curve fitting techniques.
lecture room
Thorunn
Helgason
Timing
1 lecture per week in
the Spring term
Practicals in the Spring
term
L5
1
Ecological Diversity
Andrew Dean
The concept of ecological diversity, its measurement through indices of
diversity and evenness. Alpha, beta & gamma diversity, similarity
indices and clustering techniques.
lecture room
L6
1
Community Ordination
Andrew Dean
A short introduction to Ordination techniques, including cluster analysis
and Principal Component Analysis (PCA)
lecture room
L7
1
Experimental Design for Community Research I
Definitions and theory
Andrew Dean
lecture room
L8
1
Experimental Design for Community Research II
Application and discussion
Andrew Dean
lecture room
Workshop 1
3
Coping with disasters
Andrew Dean,
Responding to unexpected events in fieldwork and data analysis. Short Thorunn
talks from invited speakers about their worst disasters and how they
Helgason
coped, followed by discussions and role play in the context of the
upcoming field courses.
Seminar room After lecture 8
Group work 1
1
Introduction to group work
Andrew Dean,
Thorunn
Helgason
Room with
After lecture 1, same
access to
week
PCs (<10
groups, 1 PC
per group
required), with
additional
space if
possible (e.g.
dry workshop
and PC room
in new
teaching
building
Group work 2
1
Group work
*Thorunn
As above
Helgason (drop
in)
After lecture 2, same
week
Group work 3
1
Group work
*Andrew Dean
(drop in)
As above
After lecture 3, same
week
Group work 4
1
Group work
*Andrew Dean
(drop in)
As above
After lecture 4, same
week
Group work 5
1
Group work
*Andrew Dean
(drop in)
As above
After lecture 5, same
week
Group work 6
1
Group work
*Andrew Dean
(drop in)
As above
After lecture 6, same
week
Group work 7
1
Group work
*Andrew Dean
(drop in)
As above
After lecture 7, before
lecture 8
Practical 1
3
Patterns of Spatial Distribution (plants, sessile animals)
Take a simple random sample of the area occupied by a plant
population (on campus).
Thorunn
Helgason
Computer
room (and
fieldwork on
campus)
After lecture 1, during
daylight hours
Practical 2
3
Use the distribution of number of plants per quadrat to determine
Thorunn
whether their spatial distribution conforms to a random pattern and if notHelgason
random, whether it is aggregated or overdispersed. This will illustrate
concepts seen in lecture 1.
Computer
room (and
fieldwork on
campus)
After lecture 2, during
daylight hours
Practical 3
3
Pitfiall trapping of terrestrial arthropods I
Thorunn
Sample a community of terrestrial arthropods by means of pitfall traps Helgason &
(on campus) using a random stratified desgn to test whether the
Andrew Dean
preserving fluid as an effect on trap catches. This will continue to
illustrate concepts seen in lectures 3 and 4, as well as developing the
students understanding of good experimental design. Animal tracking
tunnels will also be put out, to give students experience in this method.
Lab,
Late February, during
Computer
daylight hours
room and field
work on
campus
Practical 4
3
Pitfall trapping of terrestrial arthropods II
Thorunn
Collect pitfall traps from last practical. Learn to identify a number of
Helgason &
common terrestrial arthropods. Learn to Identify animal footprints from Andrew Dean
tracking tunnels Statistical testing of arthropod data using the Friedman
non-parametric test.
Lab,
Approx one week after
computer
practical 3
room and field
work on
campus
Practical 5
3
Community data collection
Plant community data collection using quadrats.
Lab and field After lecture 6, during
work on
daylight hours
campus
Practical 6
3
Ordination techniques
Andrew Dean
Learn how to carry out ordination analyses on some community data
collected previously.
Gain an understanding of the variation in community composition from
these analyses. This will illustrate the concepts covered in Lecture 6.
Computer
room
Seminar 1a
1
Introduction to the field course in Tanzania
Colin Beale
Seminar room Early in Spring term
Seminar 1b
1
Introduction to the field course in Mallorca
Colin Beale
Seminar room Early in Spring term
Seminar 2
1
Introduction to the field course nr York
Peter Mayhew, Seminar room Early in Spring term,
Andrew Dean
not at the same time as
seminars 1a/b
Field trip in
Tanzania
13 days
Field course in Tanzania
Colin Beale
Off campus
Easter holiday
Field trip in
Mallorca
11 days
Field course in Mallorca
Colin Beale
Off campus
Easter holiday
Thorunn
Helgason &
Andrew Dean
After lecture 6 and
practical 5
Presentations 1
2
Presentations for the field trip in TZ assessment
Colin Beale,
Seminar room Summer term week 1
Peter Mayhew,
Andrew Dean
Presentations 2
2
Presentations for the field trip in Mallorca assessment
Colin Beale,
Seminar room Summer term week 1
Peter Mayhew,
Andrew Dean
Lecture
1
Briefing for North York Moors field trip
Sue Firth, Peter Lecture/semin Summer term week 1,
Mayhew,
ar room
day before prep field trip
Andrew Dean
Field trip (York)
4
Preparatory field trip to Ellerburn
Peter Mayhew, Off campus & Summer term Week 1
Andrew Dean
Lab
Seminar 3
2
York field trip experimental design
Peter Mayhew, Seminar room Summer term Week 2
Andrew Dean
Seminar 4
2
York field trip experimental design
Peter Mayhew, Seminar room Summer term Week 3
Andrew Dean
Seminar 5
1
Supported learning seminar (prep for written exam)
Andrew Dean,
Thorunn
Helgasson
Field trip (York)
Peter Mayhew, Off campus & Mon-Fri summer term
Andrew Dean
Day 4-5 Lab Week 8
Presentations for the York field trip assessment
Peter Mayhew, Seminar room Summer term Monday
Andrew Dean,
week 9
Colin Beale,
Field trip (York)
5 days
Presentations 3
2
Seminar room Summer term week 3 or
4
Field Courses Synopsis
Field Courses Abroad
Seminar: Introduction to the field courses abroad.
A 1 hour seminar at the beginning of the Spring term will introduce the potentially interested students to the content of the field courses abroad and
how to prepare and budget for it.
There will be two field courses abroad, currently planned to take place in Tanzania and Mallorca, where Colin Beale, the leader for the field course
has extensive experience. Exact timetables may vary.
In Tanzania, there will be opportunity for the students to observe interesting but potentially dangerous wildlife (lions, elephants, buffalos) whilst also
spending most time in relatively safe places where useful field work can be carried out on foot.
The field course is expected to occur during week 1 and 2 of the Easter break (approx. the last week of March and first week of April), according to
the following likely format:
Day 1: Arrive Kilimanjaro International Airport, drive to Arusha, overnight hotel.
Day 2: Drive to main savannah field site and (if time) briefly explore main habitats as an overview. Camp in purpose built camp in Ndarakwai
Reserve.
Days 3-10: Fieldwork from main campsite designed around the habitats available (savannah, Acacia woodland, riverine forest, etc.). The students
will be given a few general ideas of what projects could be undertaken in the area. The first afternoon will be spent settling into camp and an evening
walk to a hill where an introduction to the processes shaping the savannah is given. Days 3-4 will see full field days, visiting each of the habitats,
and trying to understand the processes that form them. Day 5 sees an introduction to all the field equipment and sampling designs. Days 6-10 are
allocated specifically to conducting the project in the field and processing the samples.
Day 11: Trip to Lake Manyara National Park (overnight Karatu).
Day 12: Trip to Ngorongoro Conservation Area.
Day 13: Return to Arusha, last-minute shopping, etc. Transfer to airport to return.
The main campsite will be built for us: sleeping in 2-person dome tents, with a mess tent for meals and an additional mess tent as classroom. We'll
have a generator to provide some electricity at times. Cooks and basic camp staff (acting as patrol during the days in the field) will be provided.
Food will be fairly basic (rice and beans will feature heavily!).
In Mallorca, there will be opportunity for the students to observe Spring in typical Mediterranean habitats, based in a wetland of international
importance. We will observe plants, birds and reptiles typical of the region.
The field course is expected to occur during week 3 and 4 of the Easter break (30th March - 9th April), according to the following likely format:
Day 1: Arrive Palma international airport, transfer to Parc Natural de S’Albufera, near Alcudia. Settle into dormitories, do shopping.
Day 2: Field trip to NE corner: hills and pine forests. We will do a day trip involving some relatively steep walks in the pine forests and hills, noticing
the influences of rainfall gradients and fire frequencies.
Day 3: Field trip to Tramuntana Mountains. We will visit Oak woodlands and open subalpine meadows, noting the pervasive influence of grazing.
Day 4-5: Staying on the marshes (and collecting bikes for the remainder of the trip), we will divide into groups to explore the marsh land habitats, the
nearby farm landscapes and practice sampling methods.
Day 6-10: Group projects - groups will be able to choose from projects focussed on birds, plants, invertebrates and aquatic systems, or develop
their own idea in discussion with staff.
Day 11: pack up, and return to UK
North York Moors field course
Introductory seminar
A 1 hour seminar at the beginning of the Spring term will introduce the potentially interested students to the content of the field course in the North
York Moors.
Preparatory field trip and workshops
At the beginning of the Summer term, during week 1, a field trip will be organised for half a day at Ellerburn bank to show the students the sort of
habitats available on site and to introduce them to the broad range of projects that they could choose to conduct. Two seminars, during weeks 3 & 4
of the Summer term will then be organised to help the students refine their project ideas and come up with a clear experimental design, ready to be
implemented during the week of field course per se.
The field course in the North York Moors will take place at Ellerburn Bank (near Thornton-le-Dale). There will be opportunity for the students to
observe interesting wildlife (adders, slow worms, butterflies, orchids) and a number of contrasted habitats (calcalreous meadows, coniferous
plantations, deciduous regrowth).
The field course will occur after the exam period during week 8 of the Summer term (approx. mid-June), in a semi-residential format according to
the following format. An additional trip to Bempton Cliffs RSPB reserve to observe bird life and local flora will also be scheduled as part of this field
trip.
Day 1-4 (Monday-Thursday): Fieldwork at Ellerburn bank conducting small group projects (3-4 students supervised by a member of staff) during the
day. In the evenings, the students may (depending on numbers) also get the opportunity to observe badgers and listen to bats. Students will be
resident in 'glamping' pods at Pexton Moor Farm, close to Ellerburn Bank.
Day 4 (Thursday): Return to University in the afternoon. Labs available in the evening for sample processing if required.
Day 5 (Friday): Process samples (if any) in the teaching labs, conduct some preliminary analyses and obtain guidance from the supervisors on how
to prepare for the group presentations.
Day 8 (Monday): Assessed group presentations in the morning (10am-1pm).
KEY TEXTS: These are available in EARL which is accessible through the VLE module site.
ASSESSMENT:
The assessment has two components.
The closed assessment is a closed examination paper (50% of mark) conducted in May-June (weeks 5-7 of Summer term). This will consist of
case study style questions incorporating short, problem and longer answers on experimental design, data analysis and interpretation; students will
have some choice over which questions to answer.
The open assessment is a small group (3-4 students) presentation based on the findings of the short research project conducted during the field
course. These presentations should follow the standard format of scientific presentations (Introduction, Methods, Results and Discussion), should
last no more than 20 minutes and will be organised on a Monday upon return to York by the students (Summer term week 1 for field courses
abroad, Summer term week 9 for North York Moors field course) (35% of marks). Every student of the group must take part in delivering the
presentation and contribute to answering the questions. The attitude and contribution of the students in the field will also factor in the final mark for
the presentation.
Assessment
Type
1 Exam
Title
Duration
(if exam)
Examination
1.5 hours
Weighting
(towards
module)
50
Final Assessment?
N
2 Oral
Group Presentation
50
Y
Formative:
The students will be put into groups and asked to complete weekly tasks based on the previous lecture's material. These will promote independent
and course-long learning and provide some structure for private study. Tasks will be compiled to create an online revision toolkit for students, with
peer and staff feedback online and at the beginning of the next lecture. Sessions will be timetabled in a computer room to facilitate group meetings
(with occasional drop-in from course lecturers to provide guidance in the timetable), but tasks should be finished off in their own time.
Additional tasks will be available through the VLE to give students extra experience of data manipulation and calculation, especially for content in
lectures 1-5. These exercises are self-paced and to be conducted by the students in their own time.
Re-assessment:
A resit exam can be organised.
However, for the group presentation, the mode of re-assessment will depend on the circumstances.
- If a student was unable to attend the field course for good (e.g. medical) reasons, the student is not expected to participate to the group
presentation and will be given an alternative dataset to analyse and write a short report on.
- If a student attended the field course but was unable to attend the group presentation, then the student concerned can deliver a scientific
presentation on his/her small group project, but individually (no longer as a group).
- If a student attended the field course and delivered a group presentation but failed the assessment, then the student can be asked to write a
scientific report on his/her small group project if a resit is required.
DEMONSTRATING REQUIREMENTS:
One or two demonstrators for the practicals, depending on numbers of students.
No demonstrators are required for the field courses.
MAXIMUM NUMBERS:
Students will be partitioned between
the field course in Tanzania (max. 19 students)
the field course in Mallorca (max. 15 students)
and the North York Moors field course (remaining students)
STUDENT WORKLOAD: students’ workload totalling 100 hours per 10 credit module
Lectures: 8 x 1 hours
Workshops:
1 x 3 hours
Supported learning sessions 7 x 1 hours
Practicals: 6 x 3 hours
Tutorials:
Field Course: 40 hours (incl. introductory lecture & workshops)
Assessments (formative and summative): 1.5 hours (exam)
2 hours (presentations)
Total Contact hours:
80.5 hours
Private study: 119.5 hours