BIO 620G - Conservation Genetics Spring 2002

Syllabus

BIO 620 Conservation Genetics

Professor: Brad Swanson

Office: Brooks 184

Lab: Brooks 175

Phone: 3377

e-mail: brad.swanson@cmich.edu

Office hours: T, R 10 am – Noon

                        Feel free to drop by as well, I am usually in my office.

The goal of this course is to

The primary reason that species become endangered is due to the loss or alteration of their habitat.  Management of ecosystems can help preserve species that are threatened.

The science of Conservation Biology investigates individuals and populations that have been affected by habitat loss, exploitation, and/or environmental change.  That information is used to make informed decisions to ensure the survival of that species in the future.

The science of Genetics is the study of inheritance and the investigation of the genes responsible for inherited traits.

Put the two together and you get the Science of Conservation Genetics.  Conservation in the past has been addressed from a mathematical, evolutionary, or taxonomic point of view.  Genetic studies supply conservation scientists and ecological managers with new insights regarding the extent of diversity among the individuals in a population.  Without using genetics, we can be left conserving the wrong population, or wasting valuable resources on a population that isn't endangered!

This course will be run in two parts.  The first 10 weeks of the course will be devoted to lectures relating to the use of population genetics in conservation and the application of various molecular markers.  The last 4 weeks of the course will be laboratory work where you will perform your own study. 

Grading:  Students will be graded on their take home exam (50%), the final paper they produce for the course (40%) and on their presentation of their research findings (10%)

The course powerpoint slides are now also available on the k-drive (data) in Courses->620->Swanson.

This course will be run in two parts.  The first 10 weeks of the course will be devoted to lectures relating to the use of population genetics in conservation and the application of various molecular markers.  The last 4 weeks of the course will be laboratory work where you will perform your own study. 

Grading:  Students will be graded on their take home exam (50%), final paper they produce for the course (40%) and on their presentation of their research findings (10%)

Population / Conservation Genetic Links

Techniques in Molecular Ecology

Molecular Biology Web Sites: Protocols and Indexes

• Octavian Henegariu's Multicolor FISH Page: color changing karyotyping (CCK), custom fluorescent nucleotide synthesis, and Improved cytogenetic slide preparation protocols
• Protocols on the World Wide Web--Hugh Griffin's Jump Station to Protocols, Books, Manuals, etc.
• A Selection of Molecular Biology Protocols -- A list of sites with protocols, by Hugh Griffin and published in Analytical Biochemistry 239, 120-122 (1996)
• Elsevier Trends Technical Tips Online -- Technical tips, reviewed protocols, very useful
• Recombinant DNA Isolation, Cloning, and Sequencing Protocols. Bruce Roe, Department of Chemistry and Biochemistry, University of Oklahoma (fantastic, comprehensive manual of DNA manipulation techniques)
• PCR and multiplex PCR: guide and troubleshooting -- a great site for PCR techniques and troubleshooting from Octavian Henegariu at Indiana University
• Protocols from the Douglas Crawford Laboratory (Molecular Biology and Biochemistry Division of the School of Biological Sciences at The University of Missouri Kansas City)
• Molecular Biology Techniques Manual. Ed Rybicki, Department of Microbiology, University of Cape Town, SA
• The Nest Group Molecular Protocols and Application Guides
• Ambros Lab, Developmental Genetics Protocols (Dartmouth College)
• The E. coli Index. Good comprehensive list of Molecular Biology Web resources.
• BIOSCI/bionet Electronic Newsgroup Network for Biology
  • bionet.molbio.methds-reagnts: Usenet Newsgroup
  • Bionet Methods-Reagents Frequently Asked Questions
  • Bionet Molecular Biology Methods and Reagents FAQ
• Cell and Molecular Biology Online. Well researched and up-to-date listings of links of interest to cell and molecular biologists (methods, journals, professional societies, positions, etc.)

  Journals with a conservation genetics focus

  Biological Conservation
  Conservation Biology
  Environmental Conservation
  Evolution
  Heredity
  Journal of Evolutionary Biology
  Journal of Heredity
  Molecular Ecology
  Restoration Ecology
  Trends in Ecology and Evolution
  Zoo Biology

  People working in conservation genetics by taxa and topic

  Amphibians and reptiles:
  Bowen, B.
  Daugherty, C.H.
  Moritz, C.
  Birds:
  Avise, J.
  Barrowclough, G.
  Haig, S
  Fish:
  Allendorf, F.W.
  Wapels, R.
  Vrijenhoek, R.C
  Invertebrates:
  
  Britten, H.
  DeSalle, R.
  May, B.
  Mammals:
  O'Brien, S.
  Palumbi, S.R.
  Woodruff, D.S.
  Plants:
  Brown, A.H.D.
  Hamrick, J.L.
  Hollingsworth, P.
  Jain, S.K.
  Ritland, K.
  Captive breeding:
  Ballou, J.
  Frankham, R.
  Lacy, R.
  Others not pigeon-holed:
  Hedrick, P.W.
  Lande, R.
  Lynch, M.
  Templeton, A.R.

  Software for conservation genetics

  Arlequin
  CHROMOTEK: Software for chromosome analysis
  BOTTLENECK
  GENEPOP
  Microsat
  PHYLIP
  Relatedness 4.2
  RSTCALC 2.2
  GDA: Software for the Analysis of Discrete Genetic Data
  Software for Genetic Analysis and Simulation
  VORTEX

  Great books in conservation genetics

  In addition, most Conservation Biology textbooks have a section on Conservation Genetics.
  Avise, J.C. and J.L. Hamrick (eds.). 1996. Conservation Genetics: Case Histories from Nature. Chapman and Hall, NY.
  Falk, D.A. and K.E. Holsinger (eds.). 1991. Genetics and Conservation of Rare Plants. Oxford University Press, NY.
  Frankel, O.H. and M.E. Soule. 1981. Conservation and Evolution. Cambridge University Press, NY.
  Loeschcke, V., J. Tomiuk, and S.K. Jain (eds). 1994. Conservation Genetics. Birkhauser Verlag, Berlin.
  Shonewald-Cox, C.M., S.M. Chambers, B. MacBryde and L. Thomas (eds.). 1983. Genetics and Conservation: a Reference for Managing Wild Animal and Plant Populations. Benjamin/Cummings, Menlo Park, CA. (Note: This book is not in the U of M library and can be difficult to obtain).
  Smith, T.B. and R.K. Wayne (eds.). 1996. Moelecular Genetic Approaches in Conservation. Oxford University Press, NY.

  Review papers

  Bruford, M.W. and R.K. Wayne. 1993. Microsatellites and their application to population genetic studies. Current Opinion in Genetics and Development 3:939-943.
  Frankham, R. 1995. Conservation Genetics. Ann. Rev. Genetics 29: 305-327.
  Lacy, R.C. 1993. Vortex: a computer simultation model for population viability analysis. Wildl. Res. 20: 45-65.
  O'Brien, S.J. 1994. Genetic and phylogenetic analyses of endangered species. Ann. Rev. Genetics 28: 467-489.
  Schlotterer, C. and J. Pemberton. 1994. The use of microsatellites for genetic analyses of natural populations. Pp. 203-214 in Schierwater, B.S. , G.P. Wagner and R. DeSalle (eds.), Molecular Ecology and Evolution: Approaches and Applications. Birhauser Verlag, Basel, Switz.
  Soule, M. E. 1986. Section I. The fitness and viability of populations. Pp. 13-116 in Soule, M.E. (ed.), Conservation Biology: the Science of Scarcity and Diversity.

  Other resources

  Bibliography of Genetic Variation in Natural Populations
  The WWW Virtual Library: Biology Departments and Institutes
  NOAA molecular genetic protocols