Some literature about the coalescent and software
This list is far from complete, and focuses on basic papers about the coalescence that are good starting points to explore the field (in bold) and papers that describe extensions of the coalescent and also describe available program.
- Bahlo, M. and R. C. Griffiths 2000.
Inference from gene trees in a subdivided population. Theoretical Population Biology 57(2):79-95.
- Beaumont, M. 1999
Detecting Population Expansion and Decline Using Microsatellites. Genetics 153:2013-2029.
- 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(3): 763-773.
- 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 National Academy of Sciences 98(8): 4563-4568.
- Felsenstein, J., M. K. Kuhner, J. Yamato, and P. Beerli 1999.
Likelihoods on coalescents: a Monte Carlo sampling approach to
inferring parameters from population samples of molecular data. Lecture NotesÑ
Monograph Series (IMS, Hayward, CA) 33, 163-185.
- Griffths, R. C. and S. Tavare. 1994.
Sampling theory for neutral alleles in a varying
environment. Philosophical Transactions of the Royal Socety of London, Series B
(Biological Sciences) 344: 403-10.
- Hastings, W. K. 1970.
Monte Carlo sampling methods using Markov chains and their
applications. Biometrika 57: 97-109.
- Hudson, R. R. 1990.
Gene genealogies and the coalescent process. Oxford Surveys in
Evolutionary Biology 7: 1-44.
- Kingman, J. F. C. 2000.
Origins of the Coalescent: 1974-1982. Genetics 156:1461-1463.
- Krone, S. M. and C. Neuhauser. 1997.
Ancestral processes with selection. Theoretical
Population Biology 51: 210-237.
- 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: 1421-1430.
- Kuhner, M. K., J. Yamato, and J. Felsenstein. 1998.
Maximum Likelihood Estimation of Population Growth Rates Based on the Coalescent. Genetics 149(1): 429-434.
- Kuhner, M. K., J. Yamato, and J. Felsenstein. 2000.
Maximum likelihood estimation of recombination rates from population data. Genetics
- Metropolis, N., A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller. 1953.
Equation of state calculations by fast computing machines. Journal of Chemical
Physics 21: 1087-1092.
- Milot, E., H. L. Gibbs, K. A. Hobson 2000.
Phylogeography and genetic structure of northern populations of yellow warbler ) Dendroica petechia). Molecular Ecology 9: 667-681.
- Neuhauser, C., and S. M. Krone. 1997.
The genealogy of samples in models with selection. Genetics 145: 519-534.
- Nielsen, R. 2001
Mutations as Missing Data: Inferences on the Ages and Distributions of
Nonsynonymous and Synonymous Mutations. Genetics 159: 401Ð411.
- Stephens, M. and P. Donnelly 2000
Inference in molecular population genetics. Philosophical Transactions of the Royal Society Series B 354: 1-31.
- Wakeley, J., and R. Nielsen 2001
Distinguishing Migration From Isolation: A Markov Chain Monte Carlo Approach. Genetics 158: 885-896.
- Wilson, I. J., and D. J. Balding 1998
Genealogical Inference From Microsatellite Data. Genetics 150: 499-510.
Web sites and software
This section is incomplete, for more links visit
http://evolution.gs.washington.edu/lamarc/popgensoftware.html