Genetics 590

The Evolution and Population Genetics Seminar will cover the topic of "Selection and Coalescents" during Autumn Quarter of 1997.

The weekly references will be available to be copied in the copy room of the Genetics Department, J205 Health Sciences Building.

I will be leading the seminar, which will involve readings and student presentations. The first session will assign them. The seminar meets on Tuesdays at 12:30pm (that's just after noon, not just after midnight). It is scheduled for room J182 HSB, unless too many people register.

This will be a working seminar, where we all read readings and actually try to understand the equations. The course will presuppose knowledge of elementary statistics and evolutionary genetics.

Joe Felsenstein (joe@genetics.washington.edu)

Topics and Dates

Date	Topic
9/30	Organization meeting and coalescent refresher
10/7	Hudson and Takahata and balancing selection
10/14	Hudson et. al. on selection and coalescents
10/21	Hudson-Kreitman-Aguadé test
10/28	McDonald-Kreitman test
11/4	Fu and Li's method; Tajima's method
11/11	HOLIDAY (Armistice Day and Admission Day)
11/18	Krone and Neuhauser's method
11/25	(Joe will be out of town) (continued)
11/2	Joe's proposed method
11/9	cleanup

References for the sessions

(This list is subject to change)

General References: Hudson, R. R. 1990. Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology 7: 1-44.; Avise, J. C. 1994. Molecular markers, natural history, and evolution. Chapman and Hall, New York and London.; Ohta, T. 1996. The current significance and standing of neutral and nearly neutral theories. Bioessays 18: 673-677 (discussion, p. 683); Kreitman, M. 1996. The neutral theory is dead. Long live the neutral theory. Bioessays 18: 678-683.
September 30 session: Kingman, J.F.C. 1982. On the genealogy of large populations. Journal of Applied Probability A 19: 27-43.; Kingman, J. F. C. 1982. The coalescent. Stochastic Processes and Their Applications 13: 245-248.; Felsenstein, J. 1971. The rate of loss of multiple alleles in finite haploid populations. Theoretical Population Biology 2: 391-403.
October 7 session: Gyllensten, U. B. and H. A. Erlich. 1989. Ancient roots for polymorphism at the HLA-DQ alpha locus in primates. Proceedings of the National Academy of Science, U.S.A. 86: 9986-90.; Klein. J, Y. Satta, C. O'hUigin, and N. Takahata. 1993. The molecular descent of the major histocompatibility complex. Annual Review of Immunology 11: 269-95.; Takahata, N., Y. Satta, and J. Klein. 1992. Polymorphism and balancing selection at major histocompatibility complex loci. Genetics 130: 925-38.; Takahata, N. 1990. A simple genealogical structure of strongly balanced allelic lines and trans-species evolution of polymorphism. Proceedings of the National Academy of Sciences, U.S.A. 87: 2419-23.
October 14 session: Kaplan, N. L., T. Darden, and R. R. Hudson. 1988. The coalescent process in models with selection. Genetics 120: 819-829.; Hudson, R. R. and N. L. Kaplan. 1988. The coalescent process in models with selection and recombination. Genetics 120: 831-840.
October 21 session: Hudson, R. R., M. Kreitman, and M. Aguadé. 1987. A test of neutral molecular evolution based on nucleotide data. Genetics. 116: 153-159.; Hey, J. 1991. The structure of genealogies and the distribution of fixed differences between DNA sequence samples from natural populations. Genetics 128: 831-40.
October 28 session: McDonald, J. H., and M. Kreitman. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.; Kliman, R. M. and J. Hey. 1993. Reduced natural selection associated with low recombination in Drosophila melanogaster. Molecular Biology and Evolution 10: 1239-58.
November 4 session: Fu, Y-X, and W.-H. Li. 1993. Statistical tests of neutrality of mutations. Genetics 133: 693-709.; Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.; Fu, Y-X. 1997. Tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-925.
November 18 session: Neuhauser, C., and S. M. Krone. 1997. The genealogy of samples in models with selection. Genetics 145: 519-534.; Krone, S. M. and C. Neuhauser. 1997. Ancestral processes with selection. Theoretical Population Biology 51: 210-237.
Other references we're thinking about: Hudson, R. R. 1983. Testing the constant-rate neutral allele model with protein sequence data. Evolution 37: 203-217.; Hey, J. and R. M. Kliman. 1993. Population genetics and phylogenetics of DNA sequence variation at multiple loci within the Drosophila melanogaster species complex. Molecular Biology and Evolution 10: 804-22.