Genome Sciences 590

Evolution and Population Genetics Seminar

Autumn Quarter, 2002

topic: COALESCENTS

Tuesdays in J182 Health Sciences Building
12:30pm - 1:20pm.

(the first session will be in the SECOND week of the quarter as I will be away the first week)

We will cover the theory of the coalescent in population genetics, how evolutionary forces affect it, and how it is used in inferring population and genetic parameters. Students in the course will be expected to lead one of these sessions, to do all readings, and to participate actively. The course will expend on the coverage of coalescents in Genetics 562 (Theoretical Population Genetics) and Genetics 570 (Phylogenetic Inference).

Topics

References will be listed here for each session. When a reference can be accessed by web from the UW, a link will be given here (note that it may not work from home, as you might not be recognized as being covered by the UW's subscription to an electronic journal). For the others distribution arrangements will be made in class. The references marked with asterisks (*) are the ones we will be covering most closely in each class.

October 8

Kingman's coalescent and its predecessors

I will lead this session and explain the material. The fundamental papers of Kingman, which we will not read in detail, are

• Kingman, J. F. C. 1982a. The coalescent. Stochastic Processes and Their Applications 13: 235-248. (This can be downloaded electronically from the UW)
• Kingman, J. F. C. 1982b. On the genealogy of large populations. Journal of Applied Probability 19A: 27-43.
• Kingman, J. F. C. 1982c. Exchangeability and the evolution of large populat ions. pp. 97-112 in Exchangeability in Probability and Statistics. Proceedings of the International Conference on Exchangeability in Probability and Statistics, Rome, 6th-9th April, 1981, in honour of Professor Bruno de Finetti. ed. G. Koch and F. Spizzichino. North-Holland Elsevier, Amsterdam.

Felsenstein, J. 1971. The rate of loss of multiple alleles in finite haploid populations. Theoretical Population Biology 2: 391-403.

In this session, we will use as our basic text a preliminary version of the chapter on Coalescents from my forthcoming book Inferring Phylogenies, to be published in 2003 by Sinauer Associates. Click here to download a PDF of the first part of that chapter. If your browser does not have a PDF reader plugin, you should be able to use Save As to save the garbage that appears into a file called, say chap26a.pdf and then use a PDF reader on that.

October 15

Coalescents with population growth

• Slatkin, M. and R. R. Hudson. 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129: 555-562. (PDF)

October 22

Coalescents with migration

• Slatkin, M. and W. P. Maddison. 1989. Cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123: 603-613. (PDF)
• Hudson, R. R., M. Slatkin, and W. P. Maddison. 1992. Estimation of levels of gene flow from DNA sequence data. Genetics 132: 583-589. (PDF)
• Takahata, N., and M. Slatkin. 1990. Genealogy of neutral genes in two partially isolated populations. Theoretical Population Biology 38: 331-50.
• Bahlo, M, and R, C. Griffiths. 2001. Coalescence time for two genes from a subdivided population. Journal of Mathematical Biology 43: 397-410. (PDF)
• Wakeley, J. 2001. The coalescent in an island model of population subdivision with variation among demes. Theoretical Population Biology 59(2): 133-44. (PDF)
• Barton, N. H., and I. Wilson. 1995. Genealogies and geography. Philosophical Transactions of the Royal Society of London B (Biological Sciences) 349(1327): 49-59. (PDF)
• Nordborg, M. 1997. Structured coalescent processes on different time scales. Genetics 146: 1501-1514. (PDF)

October 29

Recombination and coalescents

• Hudson, R. R., and N. L. Kaplan. 1985. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111: 147-64. (is this available online anywhere?)
• Rosenberg, N. A. and M. Nordborg. 2002. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nature Reviews Genetics 3: 380-390. (PDF)
• Nordborg, M., and S. Tavaré. 2002. Linkage disequilibrium: what history has to tell us. Trends in Genetics 18: 83-90. (PDF)
• Griffiths, R. C. 1999. The time to the ancestor along sequences with recombination. Theoretical Population Biology 55: 137-44. (PDF)
• Wiuf, C., T. Christensen, and J. Hein. 2001. A simulation study of the reliability of recombination detection methods. Molecular Biology and Evolution 18: 1929-1939. (PDF)
• Wiuf, C., and J. Hein. 2000. The coalescent with gene conversion. Genetics 155: 451-462. (PDF)
• Wiuf, C., and J. Hein. 1999. Recombination as a point process along sequences. Theoretical Population Biology 55: 248-259. (PDF)
• Wiuf, C., and J. Hein. 1997. On the number of ancestors to a DNA sequence. Genetics 147: 1459-1468. (PDF)

November 5

Coalescents and speciation

• * Tajima, F. 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics 105: 437-460. (PDF -- abstract only)
• * Pamilo, P. and M. Nei. 1988. Relationships between gene trees and species trees. Molecular Biology and Evolution 5: 568-583. (PDF)
• Takahata, N. 1989. Gene genealogy in three related populations: consistency probability between gene and population trees. Genetics 122: 957-66. (PDF)
• * Takahata, N., Y. Satta, and J. Klein. 1995. Divergence time and population size in the lineage leading to modern humans. Theoretical Population Biology 48: 198-221. (PDF -- UW does not have current subscription)
• Takahata, N. and Y. Satta. 1997. Evolution of the human lineage: Phylogenetic and demographic inferences from primate DNA sequences. Proceedings of the National Academy of Sciences, USA 94: 4811-4815. (PDF)
• * Yang, Z. 1997. On the estimation of ancestral population sizes of modern humans. Genetical Research 69: 111-116. (can be reached through UW Electronic Journals but is no way to put link here)
• Edwards, S. V., and P. Beerli. 2000. Perspective: gene divergence, population divergence, and the variance in coalescence time in phylogeographic studies. Evolution 54: 1839-1854. (PDF)
• Hudson, R. R. and J. A. Coyne. 2002. Mathematical consequences of the genealogical species concept. Evolution 56: 1557-1565. (PDF)
• Nordborg, M. 1998. On the probability of Neanderthal ancestry. American Journal of Human Genetics 63: 1237-1240. (HTML)

November 12

"Single-tree" inference methods

• Clement, M., D. Posada, and K. A. Crandall KA. 2000. TCS: a computer program to estimate gene genealogies. Molecular Ecology 9: 1657-1659. (HTML)
• Posada D., K. A. Crandall, A. R. Templeton. 2000. GeoDis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Molecular Ecology 9: 487-488. (HTML)
• * Templeton, A. R. 1998. Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Molecular Ecology 7: 381-397. (HTML)
• Templeton, A. R., C. F. Sing, A. Kessling and S. Humphries. 1988. A cladistic-analysis of phenotype associations with haplotypes inferred from restriction endonuclease mapping .2. The analysis of natural-populations. Genetics 120: 1145-1154. (PDF)
• Templeton, A. R., K. A. Crandall and C. F. Sing. 1992. A cladistic-analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA-sequence data .3. Cladogram estimation Genetics 132: 619-633. (PDF)
• Walker, D. and J. C. Avise. 1998. Principles of phylogeography as illustrated by freshwater and terrestrial turtles in the southeastern United States Annual Review of Ecology and Systematics 29: 23-58. (HTML)
• * Avise, J. C. 1989. Gene trees and organismal histories - a phylogenetic approach to population biology. Evolution 43: 1192-1208. (PDF)
• Avise, J. C., J. Arnold, R. M. Ball, E. Bermingham, T. Lamb, J. E. Neigel, C. A. Reeb and N. C. Saunders. 1987. Intraspecific phylogeography - the mitochondrial-DNA bridge between population-genetics and systematics. Annual Review of Ecology and Systematics 18: 489-522. (Not available on-line)
• * Fu, Y-X. 1994. A phylogenetic estimator of effective population size or mutation rate. Genetics 136: 685-92. (PDF)
• Slatkin, M. and W. P. Maddison. 1989. Cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123: 603-613. (PDF)

November 19

MCMC and Importance Sampling likelihood methods (I)

• Griffiths, R. C. 1989. Genealogical-tree probabilities in the infinitely-many-site model. Journal of Mathematical Biology 27: 667-80. (is this available online anywhere?)
• Griffiths, R. C., and S. Tavaré. 1994. Sampling theory for neutral alleles in a varying environment. Philosophical Transactions of the Royal Society of London B (Biological Sciences) 344: 403-10. (PDF)
• Griffiths, R. C. and S. Tavaré. 1995. Unrooted genealogical tree probabilities in the infinitely-many-sites model. Mathematical Biosciences 127: 77-98. (PDF)
• Tavaré, S., D. J. Balding, R. C. Griffiths, and P. Donnelly . 1997. Inferring coalescence times from DNA sequence data. Genetics 145: 505-518. (PDF)
• * Kuhner, M. K., J. Yamato, and J. Felsenstein. 1995. Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics 140: 1421-30. (PDF)
• Stephens, M., and P. Donnelly. 2000. Inference in molecular population genetics. Journal of the Royal Statistical Society, Series B - Statistical Methodology 62: 605-635. PDF (click there on "Article availability")
• * A reprint explaining the relationship between the Griffiths-Tavaré and Kuhner-Yamato-Felsenstein methods is available here

November 26

MCMC and Importance Sampling likelihood methods (II)

• * Kuhner, M. K., J. Yamato, and J. Felsenstein. 1998. Maximum likelihood estimation of population growth rates based on the coalescent. Genetics 149: 429-34. (PDF)
• Beerli, P. and J. Felsenstein. 1999. Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152: 763-73. (PDF)
• Bahlo, M. and R. C. Griffiths. 2000. Inference from gene trees in a subdivided population. Theoretical Population Biology 57(2): 79-95. (PDF)
• * Beerli, P. and J. Felsenstein. 2001. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proceedings of the National Academy of Sciences, USA 98: 4563-4568. (PDF)
• Griffiths, R. C., and P. Marjoram. 1996. Ancestral inference from samples of DNA sequences with recombination. Journal of Computational Biology 3: 479-502. (is this available online anywhere?)
• * Kuhner, M. K., J. Yamato, and J. Felsenstein. 2000. Maximum likelihood estimation of recombination rates from population data. Genetics 156: 1393-1401. (PDF)
• * Nielsen, R. 1998. Maximum likelihood estimation of population divergence times and population phylogenies under the infinite sites model. Theoretical Population Biology 53: 143-51 . (PDF)

December 3

Natural selection and coalescents I

• Kaplan, N. L., T. Darden, R. R. Hudson. 1988. The coalescent process in models with selection. Genetics 120: 819-829. (PDF)
• *Hudson, R. R., N. L. Kaplan. 1988. The coalescent process in models with selection and recombination. Genetics 120: 831-840. (PDF)
• *Kaplan, N. L., R. R. Hudson, and C. H. Langley. 1989. The "hitchhiking effect" revisited. Genetics 123: 887-899. (PDF)
• Kaplan, N., R. R. Hudson, and M. Iizuka. 1991. The coalescent process in models with selection, recombination and geographic subdivision. Genetical Research 57: 83-91. (can be reached through UW Electronic Journals but is no way to put link here)
• Hudson, R. R. and N. L. Kaplan. 1995. Deleterious background selection with recombination. Genetics 141: 1605-1617. (PDF)
• Hudson, R. R. and N. L. Kaplan. 1995. The coalescent process and background selection. Philosophical Transactions of the Royal Society of London B (Biological Sciences) 349: 19-23. (PDF)

December 10

Natural selection and coalescents II

• *Neuhauser, C., and S. M. Krone. 1997. The genealogy of samples in models with selection Genetics 145: 519-34. (PDF)
• *Krone, S. M., and C. Neuhauser. 1997. Ancestral processes with selection. Theoretical Population Biology 51: 210-37. (PDF)
• Neuhauser, C. 1999. The ancestral graph and gene genealogy under frequency-dependent selection. Theoretical Population Biology 56: 203-214. (PDF)
• Slade, P. F. 2001. Simulation of selected genealogies Theoretical Population Biology 57: 35-49. (PDF)
• Slade, P. F. 2001. Simulation of 'hitch-hiking' genealogies. Jourmal of Mathematical Biology 42: 41-70 (PDF)