CONSERVATION GENETICS
Bio 4311 Fall 2005
Instructor: Christopher T. Cole
Phone: 589-6319
e-mail: colect@morris.umn.edu
The prerequisite for this course is Genetics (Bio 3101). A course in statistics is useful though not required: not because we will use specific methods from a statistics course, but because of the background in thinking about variation in populations from a quantitative perspective. The four-credit course is an elective for Biology majors, and includes a lab.
The main topics in this course are:
Detecting genetic variation in natural populations
Modeling the dynamics of genetic change, emphasizing small and pedigreed populations
Applying theory to real-world populations
This is the general outline for the lectures, text, and lab. I place strong emphasis on developing mathematical models step-by-step, so you see how our assumptions turn into hypotheses and experiments, and on graphical techniques that represent these models, to gain an intuitive understanding beyond the algebra. I also strongly emphasize applying the theory to real-world problems in conservation. Although (from the typical biologist's perspective) there will be several weeks that seem as though we get hijacked by mathematicians, we will look at many, many actual examples in this course, particularly after we develop the mathematical models of our theory.
Text: Introduction to Conservation Genetics (Frankham, Ballou, and Briscoe, 2002), available in the UMM bookstore. Conservation Genetics Lab is the lab manual, and will be provided in class.
Classes: "Lectures" for this course will include a mix of regular lecture and problem-solving sessions. The first labs for this course will be held in my research lab (Science 2060). This series of "wet labs" will introduce you to isozyme electrophoresis and enzyme activity staining. After that, the "labs" for the course will be held in the Science 2530 computer lab, and will include both computer modeling and data analysis, as well as occasional lectures and discussions.
Class meets MWF 9:15-10:20 in Science 3655. Lab meets F 11:45- 1:45.
Grading: grades will be based on the following:
Homework 20% 80 pts
Problem sets: (4@ 5%) (20 pts. ea.)
Midterm exams: 30% 120 pts
(2 @ 15%) (60 pts ea.)
Final Exam: 25% 100 pts
Term Paper: 25% 100 pts total
Prospectus, Outline & Biblio., Paper: (20%) (5, 15, 60 pts, respectively)
Oral summary: (5%) (20 pts)
Total 100% 400 pts
Midterm exams will be scheduled roughly one-third and two-thirds of the way through the course (i.e. roughly weeks 6 and 11); I will look for your input early in the course to pick days for these exams, so check your schedules for other courses and conflicts. The date and time of the final exam is determined by the Registrar, and is available somewhere on the UMM website.
Reasonable accommodations will be provided for students with physical, sensory, learning, and psychiatric disabilities. Contact the instructor for further information.
The following is an outline of the topics planned for the course; this will be subject to change. Specific readings will be assigned in class.
Chapter 1: Introduction
Chapter 2: Background; A Pantheon of Modelers;
Mendel, Darwin, and the Modern Synthesis
Chapter 3: The Search for Genetic Markers
Materials & Methods: technological revolutions
Chapter 4: Introduction to Theoretical Models of Population Genetics
Models, Probability and genetics
Chi-square statistics and other tests
Hardy-Weinberg model
Chapter 5: Modeling Natural Selection
Viability selection model
Equilibria
Stability
Adaptive topographies
Chapter 6: More on Selection; Mutation & Migration; Linkage Disequilibrium
Frequency-dependent selection
Mutation
Mutation/selection balance
Migration
Linkage disequilibrium
Selection with two or more loci
Chapter 7:The Fourth Force: Genetic Drift and Inbreeding
Inbreeding
Identity by descent: estimating F from pedigrees
Gene dropping and peeling
Inbreeding effects in pedigreed populations
Inbreeding depression
Purging
Inbreeding populations and F
Estimating F in real populations
Inbreeding and population size
Random genetic drift: two models
Outbreeding depression
Chapter 8: Bottlenecks and Effective Population Size
Population bottlenecks
Effective population size
Experimental models
Combining effects: the Rodruigues fruit bat
Chapter 9: Bottlenecks in Wild Populations
Wild populations: size and genetic variation
N and Ne
Bottlenecks in the past
Current bottlenecks
Chapter 10: Population Genetic Structure and Gene Flow
Wahlund principle
Wright’s hierarchical F statistics
Examples:
Gene Flow
Neighborhood size
Chapter 11: Strategies for Captive Populations
Numbers needed
Studbooks
Retaining founders' genetic variation
Genetic considerations in mate choices
Experimental models
Conway’s perspective
Species Survival Plans
Reintroduction: Przewalski’s Horse, Condors, Ferrets, Tamarins
Supportive breeding: advantages and hazards
Chapter 12: Special Problems of Plant Conservation Genetics
Thinking like a plant
Plant Genomes
Reproductive hijinks
Patterns in Plant Population Genetics
Consequences for Plant Conservation Genetics
Plants and the Endangered Species Act
Strategies for Conservation
Chapter 13: Genetic Variation, Taxonomy, and Legal Status
Endangered Species Act and Hybrid Policy
Swamping
Triage
One of the most valuable learning exercises you can undertake is to write a review paper. For this course you will write a paper on a topic in conservation genetics. The paper and oral summary will account for 25% of your grade.
Your paper should examine a topic relevant to the conservation of more than a single species. Also, the focus of your paper should not be taxonomic. For example, it should not be on the conservation genetics of gray wolves, or red wolves, or (more generally) of canids, felids, mustelids, accipiters, etc. Instead, I want you to pick a subject that applies to different species and work with that. Certainly you should include examples from different taxa, but the topic should be broader than a single taxon.
That leaves an awful lot of room for you to choose a topic. Here are just a few sample topics, more to serve as examples or to spur your thinking than for you to pick one of them.
What is the effect of inbreeding on genetic variation in wild populations?
What is the relationship between population size and levels of genetic variation in wild populations? (of plants? of animals? of fish? )
How can genetic markers be used to estimate the sizes of populations?
How are (or should) genetic criteria be used in identifying taxa for protection under the Endangered Species Act?
What kinds of genetic markers are most useful for planning captive breeding work? For planning re-introductions?
What have been the genetic consequences of introducing captive-bred organisms (e.g. from hatcheries or game farms) into native populations?
How many organisms are necessary to maintain genetic variation?
Schedule
Those of you who have taken Bio 3701 (Biological Communications) have a general idea of the scope of work that is involved: the term paper will be roughly that amount of work. I cannot over-emphasize the importance of starting NOW!
Rather than just wait until the end of the semester for a final draft, I want you to turn in the following. I would be happy to look at earlier drafts and comment on them.
Prospectus: Title and/or subject, brief description of what the paper will be about, and list of a few sources you will consult. Due: 19 September. Save this for the final draft.
Outline and Bibliography: The outline should be detailed; the bibliography should be close to the final version (though of course there will be some changes) and use proper format (consult Pechenik's Short Guide to Writing in Biology for examples). Attach your Prospectus when you hand this in. Due: 24 October. Save this for the final draft.
Final draft of the paper: Should be 12 pt. font, 1 inch margins. Also include the electronic copy (please send me the file via e-mail), Prospectus, and Outline. Due 5 December.
Here are the characteristics I am looking for in the term paper.
Basics:
- Appropriate topic (see above; this should not be a problem, since you have already submitted the Prospectus and Outline for approval)
- Organized
- Subject introduced clearly
- Mechanics correct (grammar, punctuation, citations: text, figures, tables)
- Draws on primary and secondary literature
- Discusses how results are obtained
- Prospectus & Outline are included (lose points if not)
Most Important:
- General statements supported by specific examples
- Includes comparison, contrast, and synthesis of information from multiple sources, rather than just summaries: i.e. your report is not just summary but an analysis. A good summary gets a B. Adding good analysis is necessary for A.
- Length: Very hard to do well in a half dozen text pages. I have not seen it done yet, though people have tried. People who turn in short reports are invariably disappointed with the grades they earn. I am too.
- Figures & tables used when appropriate to clarify information
Requirements
- Plagiarism of any source may result in a grade of F for the entire course.
- In addition to the printed paper copy, you MUST include an electronic version of your paper, submitted as a disk or as a text file sent to me by e-mail.
If you would like your paper returned to you, include a suitably sized self-addressed envelope when you hand it in.
The grade for the paper will be based not only on the final draft that you hand in but also on the Prosepectus, Outline, and Bibliography, as follows:
Paper: 60 pts
Oral summary: 20 pts
Prospectus: 5 pts
Outline & Bibliography: 15 pts.
This schedule is subject to change for unanticipated problems or opportunities.
Date |
Lab |
Project |
2 Sep |
1 |
Enzyme Electrophoresis Lab 1: Make buffers |
9 Sep |
2 |
Enzyme Eph. Lab 2: Homogenize tissues: run, stain, score gels |
16 Sep |
3 |
Modeling 1 |
23 Sep |
4 |
Modeling 2 |
30 Sep |
5 |
Journal Articles 1 |
7 Oct |
6 |
Modeling 3 |
14 Oct |
7 |
No lab |
21 Oct |
8 |
Modeling 4 |
28 Oct |
9 |
Modeling5 |
30 Oct |
10 |
Analysis 1: Popgene |
4 Nov |
11 |
Analysis 2: Popgene |
11 Nov |
12 |
Journal Articles 2 |
18 Nov |
13 |
Analysis 3: Biosys |
25 Nov |
14 |
No Lab: Thanksgiving Holiday |
2 Dec |
15 |
Analysis 4: Biosys |
9 Dec |
16 |
Project Reports |
SLIDES USED IN CLASS
"Chapter 2 & 3": Introduction, Pantheon, and Variation
LINKS TO OTHER BACKGROUND MATERIAL
Materials and Methods for Molecular Ecology
From Bio 3121: Materials and Methods of Molecular Genetics