Molecular Ecology
Fall 2006

Molecular Ecology Supplemental References

Avise, John C. Molecular markers, natural history, and evolution. Sunderland, Mass.: Sinauer Associates. 2004. (on reserve in library).

Beebee, Trevor J. C. and Rowe, Graham. An introduction to molecular ecology. Oxford New York: Oxford University Press, 2004. (on reserve in library).

Conner, J.K., and D.L. Hartl. 2004. A primer of ecological genetcs. Sinauer, Associates, Sunderland, MA.

Freeland, J.R. 2005. Molecular Ecology. John Wiley & Sons, West Sussex, England. (on reserve in library).

Lodish, Harvey, Arnold Berk, Paul Matsudaira, Chris A. Kaiser, Monty Krieger, Matthew P. Scott, Lawrence Zipursky, and James Darnell. 2004. Molecular Cell Biology, 5th edition. W.H. Freeman, New York.
Fourth edition of this book available free online here. See other books at NCBI as well.

Parker,P.G., Snow,A.A., Schug,M.D., Booton,G.C., and Fuerst,P.A. 1998. What molecules can tell us about populations: Choosing and using a molecular marker. Ecology 79: 361-382.

Molecular Methods

Hillis, D.M., C. Moritz, and B.K. Mable. 1996. Molecular Systematics. Sinauer, Associates, Sunderland, MA.

Sambrook, J., Fritsch, E.F., and Maniatis, T. 2001. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, NY, Vol. 1, 2, 3. See companion website.

An extensive list of molecular protocols from Gerard Lazo, USDA

Analytical Approaches

Falconer, D.S. 1996. Introduction to Quantitative Genetics. 4th ed. Longman, Essex.

Ford,M.J. 2002. Applications of selective neutrality tests to molecular ecology. Molecular Ecology 11: 1245-1262.

Hartl, D.L., and A.G. Clark. 1997. Principles of Population Genetics. Sinauer, Associates, Sunderland, MA.

Schlotterer,C. 2002. Towards a molecular characterization of adaptation in local populations. Current Opinion in Genetics & Development 12: 683-687.

Yang,Z.H. and Bielawski,J.P. 2000. Statistical methods for detecting molecular adaptation. Trends in Ecology & Evolution 15: 496-503.

Diversity

View a worked example of Simpon's Diversity Index

F-Statistics

View a worked example on Dr. David McDonald's class page

Allozymes

Hamrick, J.L., and M.J.W. Godt. 1989. Allozyme diversity in plant species. In A.D.H. Brown, M.T. Clegg, A.L. Kahler, and B.S. Weir (eds.), Plant Population Genetics, Breeding, and Genetic Resources. Sinauer, Sunderland, Massachusetts.

Lynch,M. 1983. Ecological Genetics of Daphnia pulex. Evolution 37: 358-374.

Mitton,J.B. and Grant,M.C. 1984. Associations Among Protein Heterozygosity, Growth Rate, and Developmental Homeostasis. Annual Review of Ecology and Systematics 15: 479-499.

Murphy, R.W., J.W. Sites, Jr., D.G. Buth, and C.H. Haufler.  1996.  Proteins:  Isozyme electrophoresis.  Chapter 4, pp. 51-120, in: D.M. Hillis C. Moritz and B. K. Mable (eds.).  Molecular Systematics, 2nd ed.  Sinauer Assoc. Inc., Sunderland, Mass pdf from R. Murphy's site.

Richardson,B.J., Baverstock,P.R., and Adams,M. 1986. Allozyme Electrophoresis: A Handbook for An imal Systematics and Population Structure. Academic Press, Sydney.

PCR

PCR Overview/Animation-Cold Spring Harbor

Excellent Guide to PCR Optimization-Yale Medical School

Primer3 Primer Design Site-See extensive user manual also

AFLP

ALFIE: for simulating AFLP profiles from sequences

RAPD/ISSR

ISSR Resource Page

Microsatellites

Dettman,J.R. and Taylor,J.W. 2004. Mutation and Evolution of Microsatellite Loci in Neurospora. Genetics 168: 1231-1248.

Sainudiin,R., Durrett,R.T., Aquadro,C.F., and Nielsen,R. 2004. Microsatellite Mutation Models: Insights From a Comparison of Humans and Chimpanzees. Genetics 168: 383-395.

Microsatellites for Ecologists Guide

Travis Glenn's Microsat Guide, including excellent bead-based protocol for isolation, and links to isolation services

Restriction Enzymes/RFLP

REBASE: A database of Restriction Enzymes

Fermentas database of restriction enzymes

WebCutter, a nice application that predicts cut sites in a DNA sequence

Microarrays

Gibson,G. 2002. Microarrays in ecology and evolution: a preview. Molecular Ecology 11: 17-24.

Morphology

Turelli,M., Schemske,D.W., and Bierzychudek,P. 2001. Stable two-allele polymorphisms maintained by fluctuating fitnesses and seed banks: Protecting the blues in Linanthus parryae. Evolution 55: 1283-1298.

Metagenomics

Xu,J.P. 2006. Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Molecular Ecology 15: 1713-1731.

Organelles

Adams,K.L., Daley,D.O., Qiu,Y.L., Whelan,J., and Palmer,J.D. 2000. Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants. Nature 408: 354-357.

Birky,C.W. 2001. THE INHERITANCE OF GENES IN MITOCHONDRIA AND CHLOROPLASTS: Laws, Mechanisms, and Models. Annu. Rev. Genet. 35: 125-148.

Ribosomal RNA

Grossnickle,S.C., Sutton,B.C.S., Folk,R.S., and Gawley,R.J. 1996. Relationship between nuclear DNA markers and physiological parameters in Sitka x interior spruce populations. Tree Physiology 16: 547-555.

Weider,L.J., Elser,J.J., Crease,T.J., Mateos,M., Cotner,J.B., and Markow,T.A. 2005. The functional significance of ribosomal (r)DNA variation: Impacts on the evolutionary ecology of organisms. Annual Review of Ecology Evolution and Systematics 36: 219-242.