Isolation with migration models for more than two populations

Molecular Biology and Evolution

Volumn 27, Issue 4, 2010, Pages 905-920

  Hey, Jody ^a  

^a Rutgers University   (United States)

Author keywords

Coalescent; Divergence population genetics; Gene flow; Speciation

Indexed keywords

ARTICLE; CONTROLLED STUDY; EVOLUTION; GENE FLOW; GENETIC MODEL; GENETIC VARIABILITY; HUMAN; ISOLATION WITH MIGRATION MODEL; MOLECULAR PHYLOGENY; MONTE CARLO METHOD; POPULATION GENETICS; SIMULATION; BIOLOGICAL MODEL; COMPUTER SIMULATION; MIGRATION; PHYLOGENY;

COMPUTER SIMULATION; EMIGRATION AND IMMIGRATION; GENETICS, POPULATION; MODELS, GENETIC; PHYLOGENY;

EID: 77952294620     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msp296     Document Type: Article

References (42)

1. Arbogast BS, Edwards SV, Wakeley J, Beerli P, Slowinski JB. 2002. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annu Rev Ecol Syst. 33:707-740. (Pubitemid 36035155)
2. Arnold ML. 1997. Natural hybridization and evolution. New York: Oxford University Press.
3. Avise JC. 1998. The history and purview of phylogeography: A personal reflection. Mol Ecol. 7:371-379. (Pubitemid 28226686)
4. Barton NH. 2001. The role of hybridization in evolution. Mol Ecol. 10:551-568. (Pubitemid 32406342)
5. Becquet C, Przeworski M. 2007. A new approach to estimate parameters of speciation models with application to apes. Genome Res. 17:1505-1519. (Pubitemid 47529435)
6. Becquet C, Przeworski M. 2009. Learning about modes of speciation by computational approaches. Evolution 63:2547-2562.
7. Degnan JH, Salter LA. 2005. Gene tree distributions under the coalescent process. Evolution 59:24-37. (Pubitemid 40181296)
8. Dobzhansky T. 1936. Studies of hybrid sterility. II. Localization of sterility factors in Drosophila pseudoobscura hybrids. Genetics 21:113-135.
9. Dobzhansky T. 1951. Genetics and the origins of species. New York: Columbia University Press.
10. Endler JA. 1977. Geographic variation, speciation, and clines. Princeton (NJ): Princeton University Press.
11. Ewens WJ. 1979. Mathematical population genetics. New York: Springer Verlag.
12. Felsenstein J. 1981. Skepticism towards Santa Rosalia, or why are there so few kinds of animals. Evolution 35:124-138.
13. Felsenstein J. 1988. Phylogenies from molecular sequences: Inference and reliability. Annu Rev Genet. 22:521-565. (Pubitemid 19156673)
14. Felsenstein J. 2006. Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci? Mol Biol Evol. 23:691-700. (Pubitemid 43278281)
15. Gillespie JH, Langley CH. 1979. Are evolutionary rates really variable? J Mol Evol. 13:27-34.
16. Hey J. 1994. Bridging phylogenetics and population genetics with gene tree models. In: Schierwater B, Streit B, Wagner G, DeSalleR, editors. Molecular approaches to ecology and evolution. Basel (Switzerland): Birkhäuser- Verlag. p. 435-449.
17. Hey J. 2006. Recent advances in assessing gene flow between diverging populations and species. Curr Opin Genet Dev. 16:592-596. (Pubitemid 44738527)
18. Hey J. 2010. Isolation with migration models for more than two populations. Mol Biol Evol. Advance Access published December 2, 2009, doi:10.1093/molbev/msp296.
19. Hey J, Nielsen R. 2004. Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics 167:747-760. (Pubitemid 38931862)
20. Hey J, Nielsen R. 2007. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc Natl Acad Sci USA. 104:2785-2790. (Pubitemid 46327957)
21. Hoelzel AR, Hey J, Dahlheim ME, Nicholson C, Burkanov V, Black N. 2007. Evolution of population structure in a highly social top predator, the killer whale. Mol Biol Evol. 24:1407-1415. (Pubitemid 47343946)
22. Hudson RR. 1983. Properties of a neutral allele model with intragenic recombination. Theor Popul Biol. 23:183-201.
23. Hudson RR. 1992. Gene trees, species trees and the segregation of ancestral alleles. Genetics 131:509-513.
24. Kimura M. 1969. The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics 61:893-903.
25. Knowles LL, Maddison WP. 2002. Statistical phylogeography. Mol Ecol. 11:2623-2635. (Pubitemid 35436682)
26. Latter BDH. 1973. The island model of population differentiation: A general solution. Genetics 73:147-157.
27. Lucas L, Gompert Z, Ott J, Nice C. 2009. Geographic and genetic isolation in spring-associated Eurycea salamanders endemic to the Edwards Plateau region of Texas. Conserv Genet. 10:1309-1319.
28. Maddison W, Knowles L. 2006. Inferring phylogeny despite incomplete lineage sorting. Syst Biol. 55:21-30.
29. Maddison WP. 1997. Gene trees in species trees. Syst Biol. 46:523-536.
30. Maynard Smith J. 1966. Sympatric speciation. Am Nat. 100:637-650.
31. Millicent E, Thoday JM. 1961. Effects of disruptive selection. Heredity 16:199-217.
32. Muller HJ. 1940. Bearings of the Drosophila work on systematics. In: Huxley J, editor. The new systematics. Oxford: Clarendon Press. p. 185-268.
33. Nielsen R. 1998. Maximum likelihood estimation of population divergence times and population phylogenies under the infinite sites model. Theor Popul Biol. 53:143-151. (Pubitemid 28417977)
34. Nielsen R, Wakeley J. 2001. Distinguishing migration from isolation. A Markov chain Monte Carlo approach. Genetics 158:885-896.
35. Orr HA. 1995. The population genetics of speciation: The evolution of hybrid incompatibilities. Genetics 139:1805-1813.
36. Pamilo P, Nei M. 1988. Relationships between gene trees and species trees. Mol Biol Evol. 5:568-583.
37. Pinho C, Harris DJ, Ferrand N. 2008. Non-equilibrium estimates of gene flow inferred from nuclear genealogies suggest that Iberian and North African wall lizards (Podarcis spp.) are an assemblage of incipient species. BMC Evol Biol. 8:63.
38. Rannala B, Yang Z. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164:1645-1656. (Pubitemid 37102224)
39. Rice WR, Hostert EF. 1993. Laboratory experiments on speciation: What have we learned in 40 years? Evolution 47:1637-1653. (Pubitemid 2097320)
40. Tajima F. 1983. Evolutionary relationships of DNA sequences in finite populations. Genetics 105:437-460. (Pubitemid 14247444)
41. Wakeley J, Hey J. 1998. Testing speciation models with DNA sequence data. In: DeSalle R, Schierwater B, editors. Molecular approaches to ecology and evolution. Basel (Switzerland): Birkhäuser Verlag. p. 157-175.
42. Wilson IJ, Balding DJ. 1998. Genealogical inference from microsatellite data. Genetics 150:499-510. (Pubitemid 28415541)