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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.
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:
| 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% |
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!
| 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 |
| 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