BIOL 323/324
Plant Systematics
Mike Moore
Associate Professor of Biology
Office: Science Center K111
Phone: 775-6876
Email: [email protected]
Office Hours: posted outside my office; or by appointment
Welcome to Biology 323/324! Even though this course has two numbers, it is really one
integrated whole. I have designed this course with two overall goals in mind. First, I want to
familiarize you with the basic concepts and methods of systematics, which is the study of
organismal diversity. Systematists seek to understand the evolutionary relationships among
organisms and then utilize this information both to classify organisms and to understand
historical processes associated with organismal evolution. As a result, systematics is intertwined
with many other disciplines within biology, including the study of evolution, anatomy, molecular
biology, bioinformatics, ecology, conservation biology, paleontology, and population genetics
(to name a few). Modern systematics has been invigorated by the application of DNA sequence
data to questions of evolutionary relationships. I hope to convey to you not only the nuts and
bolts of systematic theory and practice, but also some of the excitement that currently surrounds
the field as a result of this molecular revolution.
We will be viewing systematics through the prism of plants. Thus, the second overall
goal for this course is to familiarize you with botanical taxonomy and nomenclature, as well as
plant diversity at multiple levels, from globally important large groups of plants to important
species of northern Ohio. We will engage with this material through a mix of lab and
greenhouse exploration, and through five field trips to local natural areas and to the Cleveland
Botanical Garden.
Specific course goals
The specific course goals for Biology 323/324 are as follows:
1. To introduce the principles, concepts, and applications of modern systematics;
2. To enhance the ability of students to think phylogenetically;
3. To improve the ability of students to discover and interpret information related to
systematics, including bioinformatics databases and systematics literature;
4. To familiarize students with the major groups of land plants, particularly angiosperms;
and
5. To introduce important species of the flora of northern Ohio.
Lectures meet Tuesdays and Thursdays from 11:00-12:15 in room W114 of the Science Center.
Lecture time will be devoted mainly to introducing systematics principles, concepts, methods,
problems, and applications. Please see the lecture schedule for specific topics.
Labs meet on Friday from 1:30-4:20 in room A142 of the Science Center. Labs will be largely
devoted to hands-on activities related to systematic methodology or plant diversity. We will also
have short discussions and some short lectures where appropriate. When spring arrives, we will
also go on four field trips to learn important species and families in the flora of northern Ohio.
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Required Texts
The following three books are required for this course (PLEASE DO NOT BUY EARLIER
EDITIONS OF JUDD ET AL.; the fourth edition is much improved):
Judd, W. S. et al. 2016. Plant Systematics: A Phylogenetic Approach. Fourth Edition.
Sinauer Associates, Sunderland, MA.
Newcomb, L. 1989. Newcomb's Wildflower Guide. Little, Brown, & Company, Boston.
Petrides, G. A. 1973. A Field Guide to Trees and Shrubs: Northeastern and North-Central
United States and Southeastern and South-Central Canada. Second Edition. HoughtonMifflin, Boston.
Judd et al. (2016) provides a useful review of historical and modern plant systematics, and also
provides excellent in-depth summaries of major plant groups and families. Newcomb (1989) and
Petrides (1973) are inexpensive and extremely useful field guides to plants in the northeastern
United States. We will use these two guides on our field trips toward the end of the semester,
but hopefully you will find them useful throughout your life.
Grading
You will receive the same grade in both BIOL 323 and 324, which will be based on the
following breakdown:
Exam 1
Exam 2
Final Exam
10%
10%
20%
Lab Practical Exam 1
Lab Practical Exam 2
Plant Diversity Quizzes
10%
10%
10%
Problem Sets
Miscellaneous Assignments
20%
10%
Exams, Practicals, and Quizzes
1. Lecture Exams—There will be two lecture exams and one final exam (see lecture
schedule for specifics). These exams will cover lecture material only. Only the final
exam is comprehensive.
2. Lab Practical Exams—We will have two lab practicals (see lab schedule for specifics).
The first will cover vegetative, floral, and fruit morphology. The second will cover plant
diversity, including Ohio plant identification. These practical exams will cover lab
material only.
3. Plant Diversity Quizzes—We will have four plant diversity quizzes (see lab schedule for
specifics). The material covered will include angiosperm families and Ohio native plant
identification. These quizzes are designed to help prepare you for the second lab
practical exam.
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Policy on missed exams, practicals, and quizzes
If you have a legitimate circumstance (to be judged at my discretion) that causes you to miss a
lecture exam, a makeup exam will be scheduled. Please be prepared to provide documentation
of such legitimate circumstances.
However, makeup lab practicals and plant diversity quizzes will not be given, even if a legitimate
circumstance exists, due to the great effort required to set up such exams and quizzes. Students
with a legitimate reason for missing a lab practical exam will be required to write a 10-page
independent research paper on a plant systematics topic to be chosen in consultation with me. If
a student has a legitimate reason for missing a plant diversity quiz, I will prorate the missing
grade by averaging the remaining plant diversity quiz grades.
Graded Assignments
4. Problem Sets—At regular intervals throughout the semester I will assign problem sets
that are designed to reinforce important concepts and/or principles discussed in lecture.
The format and length of these problem sets will vary somewhat.
5. Miscellaneous Assignments—At least once during the semester we will have an in-class
discussion based on papers that we have read. You will be responsible for turning in
short comments and questions based upon these papers. There will also be other out-ofclass assignments that reinforce key concepts and skills.
Late work will result in a loss of 20% of the total points for a given assignment for every day
late. This policy applies only to problem sets, discussion questions, and other out-of-class
assignments.
Work handed in late due to legitimate circumstances (to be judged at my discretion) will not be
penalized. Please be prepared to provide documentation of such legitimate circumstances.
The Honor Code
The Honor Code will be strictly adhered to in all assignments. Briefly, this means that all work
you produce will be your own (including exams, practicals, problem sets, etc.) and that you will
cite all sources and important ideas that have influenced your thinking. Remember that for all
work you submit, you must write in full and sign the following: “I have adhered to the Honor
Code in this assignment.” In cases where assignments are handed in electronically, you can type
the Honor Code statement and paste in a scanned copy of your signature.
If you have any questions concerning the Honor Code and its application, please refer to the
following link: http://www.oberlin.edu/studentpolicies/honorcode/
Blackboard
The syllabus and other relevant course material will be available as .pdf files on the class
Blackboard page.
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Q&A Sessions
I will host a Q&A session before every lecture exam (date, room, and specific time TBA).
Students with special needs
Any student with a special physical and/or learning need that he/she feels needs accommodation
should inform me as soon as possible and provide appropriate documentation from Student
Academic Services.
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Biology 323 Lecture Schedule—Spring 2017
Science Center W114
Tuesday/Thursday 11:00 AM-12:15 PM
DATE
31 Jan
2 Feb
7 Feb
9 Feb
14 Feb
16 Feb
21 Feb
23 Feb
28 Feb
2 Mar
7 Mar
9 Mar
14 Mar
16 Mar
18-26 Mar
28 Mar
30 Mar
4 Apr
6 Apr
11 Apr
13 Apr
18 Apr
20 Apr
25 Apr
27 Apr
2 May
4 May
10 May
SUBJECT
Why Systematics?
The Philosophy of Taxonomy: Phenetics, Cladistics, and
Evolutionary Taxonomy
Judd (2016) readings
Ch. 1
Pp. 37-41; Ch. 3
Nomenclature and the ICN
Appendix 1
Phylogenetic Nomenclature
Pp. 37-40, 594-595
What is a Species?
Pp. 146-151
Homology, Paralogy, and Homoplasy
Pp. 13-22, 29-30
EXAM 1 (covering lectures 31 Jan – 23 Feb)
The Plant Genomes
Pp. 15-20
DNA Sequences in Phylogenetic Analysis
Pp. 15-20
Treespace, Rooting, and Phylogenetic Optimality Criteria
Pp. 20, 23-33
Mutational Saturation; Parsimony
Pp. 24-32
SPRING BREAK
Parsimony (continued); What is Maximum Likelihood?
Pp. 24-26, 32-33, 41-43
Maximum Likelihood (continued)
Pp. 24-26, 32-33
ML Models and Long Branch Attraction
Pp. 24-26, 32-33
Consensus Trees and Bootstrapping
Pp. 26-27, 34-35
Phylogenetic Incongruence—Gene Trees vs. Species Trees
Pp. 34-37
EXAM 2 (covering lectures 28 Feb – 6 Apr)
Phylogenetic Incongruence—Lineage Sorting
Pp. 34-37
Lineage Sorting (continued); Hybridization
Pp. 126-142
Homoploid Hybridization
Pp. 137-142
Polyploidy
Pp. 141-145
Recognizing Hybridization in a Phylogeny
Pp. 140-142
FINAL LECTURE EXAM, 2:00 PM (cumulative)
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Biology 324 Lab Schedule—Spring 2017
Science Center A142
Friday 1:30-4:20 PM
DATE
3 Feb
10 Feb
17 Feb
24 Feb
3 Mar
9 Mar
10 Mar
17 Mar
18-26 Mar
31 Mar
7 Apr
14 Apr
21 Apr
28 Apr
30 Apr
5 May
10 May
ACTIVITY
Vegetative Morphology I
Vegetative Morphology II
Floral Morphology
PhyloCode Debate; Plant Diversity Overview I
Inflorescence and Fruit Morphology
12:25 PM, Biology Department Seminar—Dr. Ann Sakai, University of California, Irvine
Lab Practical 1; Assembling and Annotating a (Simple) Plant Genome
Genome Mining; Plant Diversity Overview II; Conifer Campus Walk
SPRING BREAK
Angiosperm Diversity I; Phylogenetic Paper Discussion
Angiosperm Diversity II; Phylogenetic Paper Discussion
Field Trip I
Field Trip II; Plant Diversity Quiz 1 (in the field)
Field Trip III; Plant Diversity Quiz 2 (in the field)
Cleveland Botanical Garden field trip (meet at noon, SCTR A142); Plant Diversity Quiz 3
(at the Garden)
Field Trip IV; Plant Diversity Quiz 4 (in the field)
Lab Practical 2, 9:00 AM, SCTR A142
Field Trips and Appropriate Accoutrements
We will meet in A142 and leave promptly at 1:30. The College will provide transportation.
Watch the weather forecasts before field trips—it could be warm or cool, rainy or dry. I would
suggest wearing closed-toed shoes (not sandals) and long pants when we’re out in the field. I
would also strongly suggest bringing water and sunscreen (particularly if you are fair-skinned).
*Please note* that you are REQUIRED to carry the appropriate medication if you are
allergic to insect bites or stings.
Toward the end of the semester there is a required field trip to the Cleveland Botanical
Garden (http://www.cbgarden.org/). This field trip will happen on a Sunday, so please plan
accordingly. We will decide on the exact date and time within the first two weeks of the
semester. The Cleveland Botanical Gardens has 10 acres of outdoor gardens and a great
conservatory that houses recreations of Madagascan spiny desert and Costa Rican cloud forest.
The only legitimate excuses for missing this field trip is for members of Oberlin sports teams or
students in the Conservatory who have a game or performance scheduled for the same time as a
field trip. You must let me know prior to the field trip if these situations apply to you.