Evolution and Population Genetics Seminar

Genetics 590

Autumn, 1998

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

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 316 Hitchcock Hall (we are looking into getting into a room in J wing instead).

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. It is a graduate course with prerequisite Genetics 562 or permission of the instructor.

Joe Felsenstein (joe@genetics.washington.edu)

Readings and references

(Readings here are not assigned dates but are in the order that we will consider). The first topic will be considered starting on 13 October. In the future we will put the names of presenters on topics as they are assigned. The reading is indicated by an asterisk -- the other references for that topic are for additional information.

Readings during previous sessions

Sewall Wright's work on F_ST

(J. Felsenstein)

Wright, S. 1931. Evolution in Mendelian populations. Genetics 16: 97-159.

Wright, S. 1938. Size of population and breeding structure in relation to evolution. Science 87: 430-431.

* Wright, S. 1940. Breeding structure of populations in relation to speciation. Amer. Naturalist 74: 232-248

Wright, S. 1943. Isolation by distance. Genetics 28: 114-138.

* Wright, S. 1951. The genetical structure of populations Ann. Eugenics 15: 323-354.

More recent work on F_ST

(L. Dubb)

* Maynard Smith, J. 1970. Population size, polymorphism, and the rate of non-Darwinian evolution. American Naturalist 104: 231-237.

Nei, M., and M. W. Feldman. 1972. Identity of genes by descent within and between populations under mutation and migration pressures. Theoretical Population Biology 3: 460-465.

* Slatkin, M. and L. Voelm. 1991. FST in a hierarchical island model. Genetics 127: 627-629.

Rare allele methods

(B. Jones)

* Slatkin, M. 1985. Rare alleles as indicators of gene flow. Evolution 39: 53-65.

* Fu, Y.-X. 1994. Estimating effective population size or mutation rate using the frequencies of mutations of various classes in a sample of DNA sequences. Genetics 138: 1375-1386.

* Tajima, F. 1993. Statistical analysis of DNA polymorphism. Japanese Journal of Genetics 68: 567-595.

Segregating sites estimator (P. Beardsley)

* Wakeley, J. 1998. Segregating sites in Wright's island model. Theoretical Population Biology 53: 166-174

Slatkin and Maddison's "cladistic" method (S. Vignieri)

Slatkin, M. 1989. Detecting small amounts of gene flow from phylogenies of alleles. Genetics 121: 609-612.

Slatkin, M. 1991. Inbreeding coefficients and coalescence times. Genetical Research 58: 167-175.

* Slatkin, M. and W. P. Maddison. 1989, Cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123: 603-613.

* Hudson, R. R., M. Slatkin, and W. P. Maddison. 1992. Estimation of levels of gene flow from DNA sequence data. Genetics 132: 583-589.

Hudson, R. R., D. D. Boos, and N. L. Kaplan. 1992. A statistical test for detecting geographic subdivision. Molecular Biology and Evolution 9: 138-151.

Nei, M. and N. Takahata. 1993. Effective population size, genetic diversity, and coalescence time in subdivided populations. Journal of Molecular Evolution 37: 240-244.

ML gene frequencies method

(E. Anderson)

* Tufto, J., S. Engen, and K. Hindar. 1996. Inferring patterns of migration from gene frequencies under equilibrium conditions. Genetics 144: 1911-1921.

* Rannala, B. and J. A. Hartigan. 1996. Estimating gene flow in island populations. Genetical Research 67: 147-158.

Readings during future sessions

Coalescent likelihood methods (N. Chapman, S. Fogh, J. Jung)

Nath, H. B. and R. C. Griffiths. 1996. Estimation in an island model using simulation. Theoretical Population Biology 50: 227-253.

*Bahlo, M. and R. C. Griffiths. 1998. Inference from gene trees in a subdivided population. Submitted to Theoretical Population Biology, available for download by Web as a Postscript file.

* Kuhner, M. K., J. Yamato, and J. Felsenstein 1997. Applications of Metropolis-Hastings genealogy sampling. pp. 183-192 in Progress in Population Genetics and Human Evolution, ed. P. Donnelly and S. Tavare. IMA Volumes in Mathematics and its Applications, volume 87. Springer Verlag, Berlin.

* Beerli, P. B. and J. Felsenstein. 1998. Maximum likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics, submitted for publication.