Genome Sciences 590
Evolution and Population Genetics Seminar
Autumn Quarter, 2004
Tuesdays in J182 Health Sciences Building
12:30pm - 1:20pm.
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 Genome 562
(Theoretical Population Genetics), Genome 541 (Computational Molecular
Biology) and Genome 570 (Phylogenetic Inference).
Students registered in the course will be required to lead or co-lead one
session. This will involve the leaders describing what is in the papers
(the important parts anyway) for about half the session, so we can discuss the
paper for the remainder of the session.
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.
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
A paper giving some useful methods that can be used to get close to
the coalescent is my own 1971 paper (which I did not think of using to
derive the coalescent):
- 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
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 chapter from my own
book Theoretical Evolutionary Genetics, which is available
free as a PDF on the web (see http://evolution.genetics.washington.edu/pgbook/pgbook.html.
The particular chapter is Chapter 10, which you can download as a PDF using
One can also get a lot of background from my book Inferring Phylogenies,
particularly chapters 26, 27, and 28.
Coalescents with population growth
Co-presenters: Joanna Kelley and Cindy Desmarais
- * Slatkin, M. and R. R. Hudson. 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations.
Genetics 129: 555-562. (PDF)
Coalescents with migration
Co-presenters: Tom Unfried and Andrew Eckert
- *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.
- 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.
- Wakeley, J. 2001. The coalescent in an island model of population
subdivision with variation among demes. Theoretical Population Biology
- 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.
- *Nordborg, M. 1997. Structured coalescent processes on different time
scales. Genetics 146: 1501-1514.
Recombination and coalescents
Co-presenters: Bertrand Servin and Garrett Hellenthal
- *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.
- Rosenberg, N. A. and M. Nordborg. 2002.
Genealogical trees, coalescent theory and the analysis of genetic polymorphisms.
Nature Reviews Genetics 3: 380-390.
- *Nordborg, M., and S. Tavaré. 2002.
Linkage disequilibrium: what history has to tell us.
Trends in Genetics 18: 83-90.
- Griffiths, R. C. 1999. The time to the ancestor along sequences with
recombination. Theoretical Population Biology 55: 137-44.
- 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.
- Wiuf, C., and J. Hein. 2000. The coalescent with gene conversion.
Genetics 155: 451-462.
- Wiuf, C., and J. Hein. 1999. Recombination as a point process along
sequences. Theoretical Population Biology 55: 248-259.
- Wiuf, C., and J. Hein. 1997. On the number of ancestors to a DNA sequence.
Genetics 147: 1459-1468.
Coalescents and speciation
Co-presenters: Yi-ling Chen and Yaowu Yuan
- * Tajima, F. 1983. Evolutionary relationship of DNA sequences in finite
populations. Genetics 105: 437-460.
- * Pamilo, P. and M. Nei. 1988.
Relationships between gene trees and species trees.
Molecular Biology and Evolution 5: 568-583.
- Takahata, N. 1989.
Gene genealogy in three related populations: consistency probability between gene and population trees.
Genetics 122: 957-66.
- * 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.
- 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:
- * 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.
- Hudson, R. R. and J. A. Coyne. 2002.
Mathematical consequences of the genealogical species concept.
Evolution 56: 1557-1565.
- Nordborg, M. 1998. On the probability of Neanderthal ancestry.
American Journal of Human Genetics 63: 1237-1240.
"Single-tree" inference methods
Presenter: Arindam Roy Choudhury
- Clement, M., D. Posada, and K. A. Crandall KA. 2000. TCS: a computer
program to estimate gene genealogies. Molecular Ecology 9:
- 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.
- * Templeton, A. R. 1998. Nested clade analyses of phylogeographic data:
testing hypotheses about gene flow and population history.
Molecular Ecology 7: 381-397.
- 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.
- 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.
- 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.
- * Avise, J. C. 1989. Gene trees and organismal histories - a phylogenetic
approach to population biology. Evolution 43: 1192-1208.
- 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.
- Slatkin, M. and W. P. Maddison. 1989. Cladistic measure of gene flow
inferred from the phylogenies of alleles. Genetics 123: 603-613.
Presenter: Matthias Ganter
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.
- Griffiths, R. C. and S. Tavaré. 1995.
Unrooted genealogical tree probabilities in the infinitely-many-sites model.
Mathematical Biosciences 127: 77-98.
- Tavaré, S., D. J. Balding, R. C. Griffiths, and P. Donnelly . 1997.
Inferring coalescence times from DNA sequence data.
Genetics 145: 505-518.
- * 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.
- 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
Co-presenters: Paul Scheet and Bill Stewart
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.
- 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.
- Bahlo, M. and R. C. Griffiths. 2000. Inference from gene trees in a
subdivided population. Theoretical Population Biology 57(2): 79-95.
- * 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.
- 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.
- * Nielsen, R. 1998. Maximum likelihood estimation of population
divergence times and population phylogenies under the infinite sites
model. Theoretical Population Biology 53: 143-51 .
Natural selection and coalescents I
Presenter: (none yet -- maybe that means me)
- Kaplan, N. L., T. Darden, R. R. Hudson. 1988.
The coalescent process in models with selection.
Genetics 120: 819-829.
- *Hudson, R. R., N. L. Kaplan. 1988.
The coalescent process in models with selection and recombination.
Genetics 120: 831-840.
- *Kaplan, N. L., R. R. Hudson, and C. H. Langley. 1989.
The "hitchhiking effect" revisited.
Genetics 123: 887-899.
- 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.
- 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.
Natural selection and coalescents II
Co-presenters: Lisa Kim and Charla Lambert
- *Neuhauser, C., and S. M. Krone. 1997. The genealogy of samples in models with
selection Genetics 145: 519-34.
- *Krone, S. M., and C. Neuhauser. 1997.
Ancestral processes with selection.
Theoretical Population Biology 51: 210-37.
- Neuhauser, C. 1999.
The ancestral graph and gene genealogy under frequency-dependent selection.
Theoretical Population Biology 56: 203-214.
- Slade, P. F. 2001.
Simulation of selected genealogies
Theoretical Population Biology 57: 35-49.
- Slade, P. F. 2001. Simulation of 'hitch-hiking' genealogies.
Jourmal of Mathematical Biology 42: 41-70
Joe Felsenstein ( joe (at) gs.washington.edu )