CONSERVATION GENETICS


Instructor: Dr. Alan Hale (SC134, 610-606-4666 x3510, abhale@cedarcrest.edu)

Laboratory: Monday 1:00-4:00, Science Center 118
Lecture: Tuesday & Thursday 11:00-12:15, Science Center 138

Course Description: Conservation genetics is the field of study which involves the use of molecular techniques to help populations of threatened and endangered species (e.g., pandas, sea turtles, clouded leopards, black-footed ferrets, tree kangaroos, cheetahs). In lecture we learn about biodiversity, conservation biology, and molecular techniques. The fusion of conservation biology with molecular genetics will be well illustrated with the primary literature. In the laboratory we will be using several techniques (e.g., DNA isolation procedures, PCR, Southerns and RFLP analyses, microsatellite analyses, and DNA cloning and sequencing of specific loci). In addition, we will be learning how to effectively use many bioinformatics and molecular evolution programs that conservation geneticists employ to measure genetic relatedness among individuals within populations (pedigrees), evolutionary relationships among taxonomic groups, and genetic diversity within populations. The course is designed for students with an interest in either molecular biology or ecology/environmental science, or both.

Textbooks:
Drlica, Karl. 1997. Understanding DNA and Gene Cloning: A Guide for the Curious, 3rd ed.

John Wiley and Sons, Inc. New York. 329 pp.
Primack, Richard B. 2000. A Primer of Conservation Biology, 2nd ed.
Sinauer Associates. Sunderland, MA. 319 pp.

Course Web Site: In case you're looking at a hard copy of the syllabus, it can also be found at

http://www.cedarcrest.edu/academic/bio/hale/congen/index.html

Visit the site to check out some interesting web resources that are related to the course material.

Bulletin Board: Half of the bulletin board between my office and the MacLab (SC 132) will be used for this course. I will be posting, among other things, interesting web sites and news articles. Take a break once in a while and check it out. There's a lot going on in the world.

Goals: In this course there are five specific goals. Upon successfully completing Conservation Biology you will:

Supplemental Reading:Keeping current in this rapidly growing field is very important. I will be posting newspaper clippings and web reports on the bulletin board. These should be considered required reading.

Supplies: You will need Macintosh and PC-formatted floppies. For laboratory work please pick up a lab coat and a lab notebook. If you're into designer safety glasses, bring them, otherwise generic glasses will be waiting for you in the lab. All of these supplies are available in the Cedar Crest Bookstore.

Grading: Final course grades will be based on the following:

*Please note: your lab notebook grade, in part, will reflect the quality of the results you obtained. Students with percent averages in the categories shown below will receive the respective letter grades.

Final Grade
Total Percent
A
92.50-100%
A-
89.5-92.49%
B+
86.5-89.49%
B
82.5-86.49%
B-
79.5-82.49%
C+
76.5-79.49%
C
72.5-76.49%
C-
69.5-72.49%
D+
66.5-69.49%
D
59.5-66.49%
F
less than 59.5%

Attendance: Attendance is expected.

Laboratory Notebook:Your lab notebook should become, for you, an irreplacable document. Some of you are planning to go to graduate school, others are planning to work in industry or for a government or private agency. All of you fit somewhere along the molecular-ecological spectrum with respect to your chosen field of study. In all cases, if you want to be a productive practitioner within the sciences, you must keep a thorough record of your laboratory and field work. To do otherwise, wastes time and discoveries. Information within your notebook should reflect your thoughts, your analyses, your work, and your conclusions.

Midterm Examination:This examination will be purely written and will include material covered in lecture AND laboratory, as well as outside readings.

Weekend Trips:Some learning is best accomplished outside the walls of a classroom. Cedar Crest is a beautiful campus, but we normally do not see cheetahs hunting rabbits behind Hartzel or pandas feeding on the ginkgo outside the Administration Building. The proposed times for the weekend road trips will be discussed during the first class. By the end of the first week we should all agree on a time so I can make arrangements for transportation and special tours. If, for a special reason, you cannot make the field trip, please let me know at that time (1st week); we can set up an "equivalent" assignment. Otherwise, short of an emergency, your absence will be graded accordingly.

Presentations:There has been interest in using some of the lecture time for student presentations of articles in the primary literature. The focus of these articles will be, as one would expect, on conservation genetics. I have complete sets of the journals, Molecular Ecology and Conservation Biology. You're welcome to look through these for a paper to present to the class. An on-literature search is also a reasonable approach. If students prefer, I could provide a list of appropriate papers. Presentations should be 25 minutes in length ([+-]2 minutes) with an additional 5 minutes for questions. Deviations from this prescribed length will affect one's grade, therefore a well-prepared presentation is in order. Presentation times are are up to you. Choose a Monday (lab) or Tuesday (lecture) during which you'd like to present your paper, and then place your name (at that session) on the syllabus posted outside the MacLab. Only one person should sign up for any given day. Characteristics of a good presentation are well described in the Bio 121/122 lab manual, feel free to take another look.

Final Examination:The final will be in practicum format. Each student will receive a packet of questions which will require her to pull together her understanding of concepts, laboratory techniques and computer analyses. Time will be spent in the new bioinformatics computer center, in the conservation genetics laboratory, and, if you prefer, in a tree outside the Science Center. It should be fun.

Computer Use Policy and Honor Code: The Biology Department supports the CCC Computer Use Policy and the Honor Code as described in the Customs Book.

Valuable Web Sites: I think you will find these sites useful in this course and in others. Enjoy!

Society for Conservation Biology The Extinction Files National
Zoological Park
Resource List in
Conservation Genetics
World Conservation Monitoring Centre World Wildlife Fund Wildlife Conservation Society United Nations Environment Programme
Natural Resources
Defense Council
Phylogeny Reconstruction Glossary Conservation Biology Conservation of
Exotic Animals
Phylogenetic Analysis Library Molecular Toolkit Phylogenetic Analysis
Computer Programs
PHYLIP
Keck Center for
Computational Biology
VORTEX RSTCALC 2.2 Molecular Biology Protocols
Center for Biodiversity Taxonomy on the Web NCBI Taxonomy Browser National Center for
Biotechnology Information
Endangered Species
Program (USFWS)
Conservation Research Center Bioinformatics
Biology WorkBench
The Hall
of Biodiversity


Laboratory:The laboratory work will consist of three major projects that are closely associated with field of conservation genetics. The first project deals with techniques used to estimate the amount of genetic diversity within a natural population. The second project jumps into DNA sequencing and how sequence data can be used to reconstruct evolutionary relationships among taxonomic groups. The third project focuses on the use of repetitive sequences (microsatellites) in identifying specific genetic groups (populations, subspecies) within a species. This information is very useful when deciding on the fate of isolated pockets of a threatened or endangered species. All in all, during the semester we will cover basic molecular techniques (solutions, restriction digests, gel electrophoresis) plus PCR, cloning, DNA sequencing, Southern blotting and RFLP analyses, microsatellite analyses, and the use of several computer programs that process RFLP, sequence and microsatellite data.


Laboratory Schedule

Date Topic Readings*
Aug 28 Overview of Conservation Genetics
Basic Molecular Techniques
Syllabus
Sept 4 Labor Day - No Lab Take a Walk
Sept 11 "Genetic Diversity Within Natural Populations"
-RFLP Analyses-
handout
Sept 18 "Genetic Diversity Within Natural Populations"
-RFLP Analyses-
handout
Sept 25 "Genetic Diversity Within Natural Populations"
-RFLP Analyses-
handout
Oct 2 "Genetic Diversity Within Natural Populations"
-RFLP Analyses-
handout
Oct 9 Fall Break Take Another Walk
Oct 14-15
Sat/Sun
Pocono Biodiversity Expedition handout
Oct 16 "Reconstruction of Evolutionary Relationships"
-DNA Sequencing-
handout
Oct 23 "Reconstruction of Evolutionary Relationships"
-DNA Sequencing-
handout
Oct 27-29
Fri-Sun
Trip: The National Zoological Park and Cheetah Station
Respective Web Sites
Oct 30 "Reconstruction of Evolutionary Relationships"
-DNA Sequencing-
handout
Nov 6 "Reconstruction of Evolutionary Relationships"
-DNA Sequencing-
handout
Nov 13 "Genetic Markers for Populations and Subspecies"
-Microsatellites-
handout
Nov 20 "Genetic Markers for Populations and Subspecies"
-Microsatellites-
handout
Nov 27 "Genetic Markers for Populations and Subspecies"
-Microsatellites-
handout
Dec 4 "Genetic Markers for Populations and Subspecies"
-Microsatellites-
handout
Dec 11 Synthesis handout
Exam Week Final Examination (Practicum) Lab and Lecture



Lecture:The role of the lecture is to provide an understanding of conservation biology, molecular genetics, and the fusion of these two: conservation genetics. Tuesday lectures will focus on important concepts in conservation biology. Thursday lectures will cover the theory behind many of the molecular techniques we'll be using in the laboratory, and in most cases will prepare us for the following Monday session. Periodically, papers from the primary literature will bring the two fields together.


Lecture Schedule

Date Topic Readings
Aug 29 Introduction; Overview of Conservation Genetics
O'Brien's Cheetahs
Syllabus, paper
Aug 31 Overview of Project #1
Microbial Growth
Drlica 85-97
Sept 5 Biodiversity and Conservation Biology Primack 8-15
Sept 7 Plasmids and Phages Drlica 99-119
Sept 12 Genetic, Community and Ecosystem Diversity Primack 15-26
Sept 14 Restriction Endonucleases and Ligases Drlica 121-141
Sept 19 Biodiversity On Our Planet Primack 26-35
Sept 21 Hybridization and Probes Drlica 143-153
Sept 26 Environmental Ethics Primack 54-61
Drlica 13-16
Sept 28 Analysis of RFLP Data handout
Oct 3 Island Biogeography and Extinction Rates Primack 63-75
Oct 5 Overview of Project #2 -
Oct 10 Fall Break - No Class -
Oct 12 Polymerase Chain REaction and Designing Primers Drlica 153-157; handout
Oct 14-15
Sat/Sun
Pocono Biodiversity Expedition handout
Oct 17 Causes of Extinction Primack 75-86
Oct 19 Cloning a Gene Drlica 161-176
Oct 24 Causes of Extinction Primack 86-97
Oct 26 Cloned Genes and DNA Sequencing Drlica 179-194
Oct 27-29
Fri-Sun
Trip: The National Zoological Park and Cheetah Station
Respective Web Sites
Oct 31 Causes of Extinction Primack 97-106
Nov 2 Analysis of Sequence Data handout
Nov 7
Vote
Causes of Extinction Primack 106-119
Nov 9 Overview of Project #3 -
Nov 14 Small Populations and
Loss of Genetic Variability
Primack 121-128
Nov 16 Microsatellites handout
Nov 21 Effective Population Size
and Stochasticity
Primack 128-135
Nov 23 Thanksgiving Enjoy
Nov 28 Population Viability Analysis
and Metapopulations
Primack 141-147
Nov 30 Analysis of Microsatellite Data handout
Dec 5 An Agenda for the Future Primack 270-279
Dec 7 Synthesis -
Exam Week Final Examination (Practicum) Lab and Lecture



Alan B. Hale (abhale@cedarcrest.edu)
Last updated: 23 August '00
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