Genetic/molecular markers required readings + reference texts and articles

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Not yet updated for 2008

Readings related to Exam 1:

Most important readings:
Avise pp. 26-43, 92-126, 204-210, 220-233.

Brookfield. 1996. Curr. Biol. 6: 354;

Gillespie text   Ch. 1; Gillespie text Ch. 2 (for Sections 2.6 and 2.7 you need only know what the point/punchline is, not the mathematical details);  Gillespie text Ch. 4 (you can skim Sections 4.2 and 4.3); Appendices A & B (particularly up to p. 160 and the discussion of the normal distribution on pp. 163-164).

Ch. 11 Mol. Syst. OR Ch. 3 Mol. Zool.

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Other fair game:

Avise Ch. 1, pp. 16-26, 44-91, 210-219

handout (Hoelzel & Dover)

Ch. 7 Mol. Syst. (pp. 205-221 only); Mol. Syst. pp. 249-281, pp. 321-341

You are NOT responsible for the other articles that were in the "calendar/syllabus", but that I didn't put in the cupboard in BioSci 302.

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Codes:

        "Choice" means the reading is one of several possible alternatives

        + means required

Red font denotes readings I recommend or good reference texts

Choice Allendorf, F.W., and R.S. Waples. 1995. Conservation and genetics of salmonid fishes. Ch. 8 (pp. 238-280) In Conservation Genetics: Case Histories from Nature (J.C. Avise, and J.L. Hamrick, eds.). Chapman & Hall, New York.

+ Amos, W., and J. Harwood. 1998. Factors affecting levels of genetic diversity in natural populations. Phil Trans Royal Soc. London B 353: 177-186.

Avise, J. C. 1989. A role for molecular genetics in the recognition and conservation of endangered species. Trends Ecol. Evol. 4: 279-281.

TEXT   Avise, J.C. 1994. Molecular Markers, Natural History and Evolution. Chapman and Hall, New York.

+ Avise, J.C. 1996. Introduction: the scope of conservation genetics. Pp. 1-9 In Conservation Genetics: Case Histories from Nature (J.C. Avise, and J.L. Hamrick, eds.) Chapman & Hall, New York. On Reserve

+ Avise, J.C. 1995. Toward a regional conservation genetics perspective: phylogeography of faunas in the southeastern United States. Ch. 14 (pp. 431-470) In Conservation Genetics: Case Histories from Nature (J.C. Avise, and J.L. Hamrick, eds.). Chapman & Hall, New York.

Avise, J.C. and J.L. Hamrick (eds.). 1995. Conservation Genetics: Case Histories from Nature. Chapman & Hall, New York.

Ayala, F.J. 1982. Population and Evolutionary Genetics: A Primer. Benjamin/Cummings, Menlo Park, CA.* QH 455.A94 1982 •

Ayala, F.J., and W.M. Fitch. 1997. Genetics and the origin of species: An introduction. PNAS 94: 7691-7697. •

Choice Baker, C.S., and S.R. Palumbi. 1995. Population structure, molecular systematics, and forensic identification of whales and dolphins. Ch. 2 (pp. 10-49) In Conservation Genetics: Case Histories from Nature (J.C. Avise, and J.L. Hamrick, eds.). Chapman & Hall, New York.

Barrett, S.C.H., and J.R. Kohn. 1991. Genetic and evolutionary consequences of small population size in plants: implications for conservation. Pp.3-30 In Genetics and Conservation of Rare Plants (D.A. Falk and K.E. Holsinger, eds.) Oxford University Press, New York.

Bohonak, A.J. 1999. Dispersal, gene flow, and population structure. Q. Rev. Biol. 74: 21-

Bossart, J.L., and D.P Prowell. 1998. Genetic estimates of population structure and gene flow: Limitations, lessons and new directions. TREE 13: 202-206.

Choice Bowen, B.S., and J.C. Avise. 1995. Conservation genetics of marine turtles. Ch. 7 (pp. 190-237)In Conservation Genetics: Case Histories from Nature (J.C. Avise, and J.L. Hamrick, eds.). Chapman & Hall, New York.

+ Brookfield, J.F.Y. 1996. Population genetics. Curr. Biol. 6: 354-357.

Brooks, D.R., and D.A. McLennan. 1991. Phylogeny, Ecology, and Behavior. Chicago Univ. Press, Chicago.

Brooks, D.R., D.A. McLennan, J.M. Carpenter, S.G. Weller, and J.A. Coddington. 1995. Systematics, ecology, and behavior - Integrating phylogenetic patterns and evolutionary mechanisms. Bioscience 45: 687-695.

Crow, J.F., and M. Kimura. 1970. An Introduction to Population Genetics Theory. Burgess Publishing, Minneapolis, Minnesota.

Crozier, R.H. 1997. Preserving the information content of species: genetic diversity, phylogeny, and conservation worth. Ann. Rev. Ecol. Syst. 28: 243-268.

+ Davies, N., F.X. Villablanca, and G.K. Roderick. 1999. Determining the source of individuals: multilocus genotyping in nonequilibrium population genetics. TREE 14: 17-21.

de Queiroz, A., M. J. Donoghue, and J. Kim. 1995. Separate versus combined analysis of phylogenetic evidence. Ann. Rev. Ecol. Syst. 26: 657-681.

Dobzhansky, T. 1937. Genetics and the Origin of Species. Columbia University Press, NY.

+ Dowling, T.E., C. Moritz, J.D. Palmer, and L.H. Rieseberg. Nucleic Acids III: analysis of fragments and restriction sites. 1996 Ch. 8 (pp. 249-281 only) In Molecular Systematics (2nd ed., D.M. Hillis, C. Moritz, and B.K. Mable, eds.). Sinauer Assoc. Sunderland, MA.

Ellstrand, N. C. and D. R. Elam. 1993. Population genetic consequences of small population size - implications for plant conservation. Annu Rev Ecol Syst 24: 217-242.

Evett, I.W., and B.S. Weir. 1998. Interpreting DNA Evidence: Statistical Genetics for Forensic Scientists. Sinauer Associates, Sunderland, MA.

Falconer, D.S. 1981. Introduction to Quantitative Genetics. 2nd ed. Longman, Essex

Ferraris, J.D., and S.R. Palumbi (eds.). 1996. Molecular Zoology: Advances, Strategies, and Protocols. Wiley-Liss, NY. 580 pp.

Fisher, R.A. 1958. The Genetical Theory of Natural Selection. 2nd edn. Dover Press, N.Y.

Fleischer, R.C. 1996. Application of molecular methods to the assessment of genetic mating systems in vertebrates. Ch. 7 (pp. 133-162) In Molecular Zoology: Advances, Strategies and Protocols (J. D. Ferraris and S.R. Palumbi, eds.) John Wiley and Sons, New York.

Frankham, R. 1995. Conservation genetics. Annual Review of Genetics 29: 305-327.

Fu, Y.-X., and W.-H. Li. 1999. Coalescing into the 21st century: an overview and prospects of coalescent theory. Theor. Pop. Biol. 56: 1-10.

TEXT  Gillespie, J. H. 1998. Population Genetics: A Concise Guide. The Johns Hopkins University Press, Baltimore, Md.

Goldstein, D.B., and D.D. Pollock. 1997. Launching microsatellites: a review of mutation processes and methods of phylogenetic interference. J Hered. 88:335-342.

Goldstein, D.B., and C. Schlötterer. 1999. Microsatellites: Evolution and Applications. Oxford University Press, New York. * $45.00w paper 0-19-850407-1 •

+ Haig, S.M. 1998. Molecular contributions to conservation. Ecol. 79: 413-425.

Choice   Haig, S.M, and J.C. Avise. 1995. Avian Conservation Genetics. Ch. 6 (pp. 160-189) In Conservation Genetics: Case Histories from Nature (J.C. Avise, and J.L. Hamrick, eds.). Chapman & Hall, New York.

Hall, B.G. 2004. Phylogenetic Trees Made Easy: A How-to Manual (2nd Edn.). Sinauer, Sunderland, MA. ISBN 0-87893-312-3

Choice Hamrick, J.L., and M.W. Godt. 1995. Conservation genetics of endemic plant species. Ch. 9 (pp. 281-304) In Conservation Genetics: Case Histories from Nature (J.C. Avise, and J.L. Hamrick, eds.). Chapman & Hall, New York.

Hartl, D.L. 1999. A Primer of Population Genetics (3rd ed.). Sinauer Associates, Sunderland, MA ISBN 0-87893-304-2 $29.95 paper •

Hartl, D.L., and A.G. Clark. 1989. Principles of Population Genetics. Sinauer Associates, Sunderland, MA. *[3rd edition is now available] •

Hastings, A. 1994. Metapopulation dynamics and genetics. Annual Review of Ecology and Systematics 25: 167-188. •

Hastings, A. 1997. Population Biology: Concepts and Models. Springer-Verlag, New York.

Hedrick, P.W. 1999. Perspective: Highly variable loci and their interpretation in evolution and conservation. Evol. 53: 313-318.

+  Hedrick, P.W., and P.S. Miller. 1992. Conservation genetics: techniques and fundamentals. Ecol. Applic. 2: 30-46.

+  Hillis, D.M., B.K. Mable, A. Larson, S.K. Davis, and E.A. Zimmer. 1996 Ch. 9 (pp. 321-341 only) In Molecular Systematics (2nd ed., D.M. Hillis, C. Moritz, and B.K. Mable, eds.). Sinauer Assoc. Sunderland, MA.

Hillis, D.M., C. Moritz, and B.K. Mable (eds.). 1996. Molecular Systematics (2nd ed.). Sinauer Associates, Sunderland, MA. On Reserve * [Has useful Glossary] •

Hoelzel, A.R., and G.A. Dover. 1991. Molecular Genetic Ecology. IRL Press, Oxford U. Press, Oxford SCI QH 455.H64 1991.

Hoelzel, A.R. (ed.). 1998. Molecular Genetic Analysis of Populations: A Practical Approach.   * ISBN: 0199636354 •

Holsinger, K.E. 1995. Population biology for policy makers. Bioscience Suppl. 10-20.

Hudson, R.R. 1990. Gene genealogies and the coalescent process. Oxford Surv. Evol Biol. 7: 1-44.

Huelsenbeck, J.P., J.J. Bull, and C.W. Cunningham. 1996. Combining data in phylogenetic analysis. TREE 11: 152-158.

Hurst, L.D. 1999. The evolution of genetic anatomy. TREE 14: 108-112.

Jarne, P. and P.J.L. Lagoda. 1996. Microsatellites, from molecules to populations and back. TREE 11: 424-429.

Kendrew, J.C. 1994. The Encyclopedia of Molecular Biology . Blackwell Science, Oxford
        * UW Science Library REF section CALL #: QH506 .E53 1994 •

Li, W. 1997. Molecular Evolution. Sinauer Associates, Sunderland, MA. •

+  Luikart, G., and P.R. England. 1999. Statistical analysis of microsatellite data. TREE 14: 253-256.

Choice Maddison, W.P. 1996. Molecular approaches and the growth of phylogenetic biology. Ch. 3 (pp. 47-64) In Molecular Zoology, Advances, Strategies and Protocols (J. D. Ferraris, and S.R. Palumbi, eds.). John Wiley and Sons, New York.

Maddison, W.P. 1997. Gene trees in species trees. Syst. Biol. 46: 523-536. •

Maddison, W.P., and D.R. Maddison. 1992. MacClade: Analysis of Phylogeny and Character Evolution. Sinauer Associates, Sunderland, MA. * McD has the book and software•

+  McDonald, D.B., and W.K. Potts. 1994. Cooperative display and relatedness among males in a lek-mating bird. Science 266: 1030-1032. •

McDonald, D.B., and W.K. Potts. 1997. Microsatellite DNA as a genetic marker at several scales. pp. 29-49 In Avian Molecular Evolution and Systematics (D. Mindell, ed.). Academic Press, New York. •

+  McDonald, D.B., W.K. Potts, J.W. Fitzpatrick, and G.E. Woolfenden. 1999. Contrasting genetic structures in sister species of North American scrub-jays. Proc. Royal Soc. London B. 266: 1117-1125. •

+  Milligan, B.G., J. Leebens-Mack, and A.E. Strand. 1994. Conservation genetics beyond the maintenance of marker diversity. Mol. Ecol. 3: 423-435.

Miyamoto, M.M., and J. Cracraft. 1991. Phylogenetic Analysis of DNA Sequences. Oxford University Press, Oxford. •

Moritz, C. 1994. Defining "evolutionary significant units" for conservation. TREE 9: 373-375.

Moritz-Craig; Faith-Daniel-P. 1998. Comparative phylogeography and the identification of genetically divergent areas for conservation. Molecular-Ecology 7: 419-429.

Mueller, U.G., and L.L. Wolfenbarger. 1999. AFLP genotyping and fingerprinting. TREE 14: 389-394.

Nei, M. 1975. Molecular Population Genetics and Evolution. American Elsevier Pub. Co., NY QH 455 .N44

Nei, M 1984. Molecular Evolutionary Genetics. Columbia University Press/New York.

Nelson, G., and N. Platnick. 1981. Systematics and Biogeography: Cladistics and Vicariance. Columbia Univ. Press, N.Y.

Pagel, M. 1999. Inferring the historical patterns of biological evolution. Nature 401: 877-884.

+  Palumbi, S.R. 1996. Nucleic acids II: the polymerase chain reaction. Ch. 7 (pp. 205-221) In Molecular Systematics (2nd ed., D.M. Hillis, C. Moritz, and B.K. Mable, eds.). Sinauer Assoc. Sunderland, MA. On Reserve

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

Petit, R.J., A. ElMousadik, and O. Pons. 1997. Identifying populations for conservation on the basis of genetic markers. Conserv. Biol. 12: 844-855.

+  Piertney, S.B., AD.C. MacColl, P.J. Bacon, and J.F. Dallas. 1999. Local genetic structure in red grouse (Lagopus lagopus scoticus): evidence from microsatellite DNA markers. Mol. Ecol. 7: 1645-1654.

(Suggested supplement to the above)  Piertney, S.B., A.D.C. MacColl, P.J. Bacon, P.A. Racey, X. Lambin, and J.F. Dallas. 2000. Matrilineal genetic structure and female-mediated gene flow in red grouse (Lagopus lagopus scoticus): An analysis using mitochondrial DNA. Evol. 54: 279-289.

Poinar, G., Jr. 1999. Ancient DNA. Am. Sci. 87: 446-457. *

Choice Pope, T.R. 1995. Socioecology, population fragmentation, and patterns of genetic loss in endangered primates. 1995. Ch. 5 (pp. 119-159) In Conservation Genetics: Case Histories from Nature (J.C. Avise, and J.L. Hamrick, eds.). Chapman & Hall, New York.

+  Queller, D.C., J.E. Strassmann, and C.R. Hughes. 1993. Microsatellites and kinship. TREE 8: 285-288.

Rieger, R, A. Michaelis, and M.M. Green. 1991. Glossary of Genetics : Classical and Molecular, 5th edn. Springer-Verlag, Berlin * UW Science Library REF section CALL #: QH427.R54 1991 •

Roughgarden, J. 1979. Theory of Population Genetics and Evolutionary Ecology: An Introduction. MacMillan, N.Y.

Rousset, F., and M. Raymond. 1997. Statistical analyses of population genetic data: new tools, old concepts. TREE 12: 313-317.

Russell, P.J. Genetics, 3rd Edition. Harper, Collins, New York. * UW Science library call # QH 430.R87 1992. •

Schaal-B-A; Hayworth-D-A; Olsen-K-M; Rauscher-J-T; Smith-W-A. 1998. Phylogeographic studies in plants: Problems and prospects. Mol. Ecol. 7: 465-474.

Schlötterer, C. 1998. Are microsatellites really simple sequences? Curr. Biol. 8: R132-R134.

Schonewald-Cox, C.M., S.M. Chambers, B. MacBryde, and L. Thomas (eds.). 1983. Genetics and Conservation. Benjamin/Cummings, Menlo Park, Calif. * QH75.G45 1983 •

Sibley, C.G., and J.E. Ahlquist. 1990. Phylogeny and Classification of Birds. Yale University Press, New Haven , CT. * Sci Ref QL696.5 .S53 1991

Slatkin, M. 1985. Gene flow in natural populations. Ann. Rev. Ecol. Syst. 16: 393-430

Smouse-Peter-E. 1998. To tree or not to tree. Mol. Ecol. 7: 399-412.

+  Sugg, D.W., R.K. Chesser, F.S. Dobson, and J.L. Hoogland. 1996. Population genetics meets behavioral ecology. TREE 11: 338-342. * Pop. gen. structure ƒ •

Swofford, D.L. 1996. PAUP: Phylogenetic Analysis Using Parsimony (and Other Methods), version 4.0. Sinauer Associates, Sunderland MA. •

Choice Swofford, D.L., G.J. Olsen, P.J. Waddell, and D.M. Hillis. 1996 Ch. 11 (pp. 407-514) In Molecular Systematics (2nd ed., D.M. Hillis, C. Moritz, and B.K. Mable, eds.). Sinauer Assoc. Sunderland, MA.

Wallace, B. 1981. Basic Population Genetics. Columbia University Press, NY.  * QH 455.W34 •

Waser, P.M., and C. Strobeck. 1998. Genetic signatures of interpopulation dispersal. TREE 13: 43-44.

Choice  Wayne, R.K. 1995. Conservation genetics in the canidae. Ch. 4 (pp. 75-118 In Conservation Genetics: Case Histories from Nature (J.C. Avise, and J.L. Hamrick, eds.). Chapman & Hall, New York.

Weir, Bruce S. 1996. Genetic Data Analysis II: Methods for discrete population genetic data (2nd. ed.). Sinauer Assoc., Sunderland, Massachusetts.

+  Westemeier et al. 1998. Tracking the long-term decline and recovery of an isolated population. Science 282: 1695-1698.

William, J., O. Ballard, and M. Kreitman. 1995. Is mitochondrial DNA a strictly neutral marker? TREE 10: 485-488.

Wright, S. 1978. Evolution and the Genetics of Populations, Vol. 4: Variability Within and Among Natural Populations. University of Chicago Press, Chicago.
    * QH 341.W79 v.4 •

Zhang, D.-X., and G.M. Hewitt. 1996. Nuclear integrations: challenges for mitochondrial DNA markers. TREE 6: 247-251.

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