Coalescent genealogy samplers: windows into population history

Trends in Ecology and Evolution

Volumn 24, Issue 2, 2009, Pages 86-93

  Kuhner, Mary K ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABUNDANCE; CHROMOSOME; COALESCENCE; DIVERGENCE; GENE FLOW; GROWTH RATE; POPULATION DECLINE; POPULATION ESTIMATION; POPULATION GROWTH; POPULATION SIZE;

ANIMAL; BAYES THEOREM; COMPUTER PROGRAM; GENEALOGY; HUMAN; PHYLOGENY; POPULATION DYNAMICS; REVIEW; STATISTICAL MODEL;

ANIMALS; BAYES THEOREM; GENEALOGY AND HERALDRY; HUMANS; LIKELIHOOD FUNCTIONS; PHYLOGENY; POPULATION DYNAMICS; SOFTWARE;

BISON; CETACEA;

EID: 58349112353     PISSN: 01695347     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tree.2008.09.007     Document Type: Review

References (43)

1. Kingman, J.F.C. (1982a) The coalescent. Stochastic Process. Appl. 13, 235-248
2. Kingman, J.F.C. (1982b) On the genealogy of large populations. J. Appl. Probab. 19A, 27-43
3. Griffiths R.C., and Tavare S. Sampling theory for neutral alleles in a varying environment. Proc. R. Soc. Lond. B Biol. Sci. 344 (1993) 403-410
4. Beerli P., and Felsenstein J. Maximum likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152 (1999) 763-773
5. Griffiths R.C., and Marjoram P. Ancestral inference from samples of DNA sequences with recombination. J. Comput. Biol. 3 (1996) 479-502
6. Krone S.M., and Neuhauser C. Ancestral processes with selection. Theor. Popul. Biol. 51 (1997) 210-237
7. Griffiths R.C., and Tavare S. The age of a mutation in a general coalescent tree. Stoch. Models 14 (1998) 273-295
8. Nielsen R., and Wakeley J. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158 (2001) 885-896
9. De Oliveira T., et al. Molecular epidemiology: HIV-1 and HCV sequences from Libyan outbreak. Nature 444 (2006) 836-837
10. Geraldes A., et al. Contrasting patterns of introgression at X-linked loci across the hybrid zone between subspecies of the European rabbit (Oryctolagus cuniculus). Genetics 173 (2006) 919-933
11. Shapiro B., et al. Rise and fall of the Beringian steppe bison. Science 306 (2004) 1561-1565
12. Fujimoto A., et al. Adaptive and slightly deleterious evolution in a conifer, Cryptomeria japonica. J. Mol. Evol. 67 (2008) 201-210
13. Charlesworth B. Measures of divergence between populations and the effects of forces that reduce variability. Mol. Biol. Evol. 15 (1998) 538-543
14. Thornton K. Recombination and the properties of Tajima's D in the context of approximate-likelihood calculation. Genetics 171 (2005) 2143-2148
15. Nielsen R., et al. Maximum-likelihood estimation of population divergence times and population phylogeny in models without mutation. Evolution Int. J. Org. Evolution 52 (1998) 669-677
16. Fu Y.-X. A phylogenetic estimator of effective population size or mutation rate. Genetics 136 (1994) 685-692
17. Templeton A.R., et al. Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Amblystoma tigrinum. Genetics 140 (1995) 767-782
18. Petit R. The coup de grâce for the nested clade phylogeographic analysis?. Mol. Ecol. 17 (2008) 516-518
19. Hey J., and Machado C.A. The study of structured populations - new hope for a difficult and divided science. Nat. Rev. Genet. 4 (2003) 535-543
20. Huelsenbeck J.P., and Ronquist F. MRBAYES: Bayesian inference of phylogeny. Bioinformatics 17 (2001) 754-755
21. Drummond A.J., and Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7 (2007) 214
22. Griffiths R.C., and Tavaré S. Sampling theory for neutral alleles in a varying environment. Proc. R. Soc. Lond. B Biol. Sci. 344 (1993) 403-410
23. Nielsen R., and Wakeley J. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 58 (2001) 885-896
24. Hey J., and Nielsen R. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167 (2004) 747-760
25. Hey J., and Nielsen R. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 2785-2790
26. Kuhner M.K. LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics 22 (2006) 768-770
27. Beerli P., and Felsenstein J. Maximum-likelihood estimation of effective population numbers in two populations using a coalescent approach. Genetics 152 (1999) 763-773
28. Beerli P., and Felsenstein J. Maximum likelihood estimation of a migration matrix and effective population size in n subpopulations by using a coalescent approach. Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 4563-4568
29. Felsenstein J. Accuracy of coalescent likelihood estimators: do we need more sites, more sequences, or more loci?. Mol. Biol. Evol. 23 (2006) 691-700
30. Pluzhnikov A., and Donnelly P. Optimal sequencing strategies for surveying molecular genetic diversity. Genetics 144 (1996) 1247-1262
31. Kuhner M.K., and Smith L.P. Comparing likelihood and Bayesian coalescent estimation of population parameters. Genetics 175 (2007) 155-165
32. Beerli P. Comparison of Bayesian and maximum-likelihood inference of population genetic parameters. Bioinformatics 22 (2006) 341-345
33. Biek R., et al. A virus reveals population structure and recent demographic history of its carnivore host. Science 311 (2006) 538-541
34. Thomson R., et al. Recent common ancestry of human Y chromosomes: evidence from DNA sequence data. Proc. Natl. Acad. Sci. U. S. A. 97 (2001) 7360-7365
35. Alter S.E., et al. DNA evidence for historic population size and past ecosystem impacts of gray whales. Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 15162-15167
36. Turner T.F., et al. Genetic effective size is three orders of magnitude smaller than adult census size in an abundant, estuarine-dependent marine fish (Sciaenops occellatus). Genetics 162 (2002) 1329-1339
37. Ewing G., et al. Using temporally spaced sequences to simultaneously estimate migration rates, mutation rate and population sizes in measurably evolving populations (MEPs). Genetics 168 (2004) 2407-2420
38. Yang Z. Discussion on the paper by Wilson, Weale and Balding. J. R. Stat. Soc. A 166 (2003) 188-201
39. Pritchard J.K., et al. Inference of population structure using multi-locus genotype data. Genetics 155 (2000) 945-959
40. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
41. Rambaut, A. and Drummond, A.J. (2007) Tracer v1.4 (http://beast.bio.ed.ac.uk/tracer)
42. Nylander J.A., et al. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24 (2007) 581-583
43. Felsenstein J. Inferring Phylogenies (2004), Sinauer Associates