Estimating parameters of speciation models based on refined summaries of the joint site-frequency spectrum

PLoS ONE

Volumn 6, Issue 5, 2011, Pages

  Tellier, Aurélien ^a   Pfaffelhuber, Peter ^b   Haubold, Bernhard ^c   Naduvilezhath, Lisha ^a   Rose, Laura E ^a   Städler, Thomas ^d   Stephan, Wolfgang ^a   Metzler, Dirk ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITY OF FREIBURG   (Germany)

^c MAX PLANCK INSTITUTE FOR EVOLUTIONARY BIOLOGY   (Germany)

^d ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DNA POLYMORPHISM; EVOLUTION; GENE FLOW; LINEAR REGRESSION ANALYSIS; NONHUMAN; POPULATION MIGRATION; SPECIES DIFFERENTIATION; SPECIES DISTRIBUTION; STATISTICAL ANALYSIS; BIOLOGICAL MODEL; GENE LOCUS; GENETIC DATABASE; GENETIC RECOMBINATION; GENETICS; MIGRATION; MUTATION;

DATABASES, GENETIC; EMIGRATION AND IMMIGRATION; GENE FLOW; GENETIC LOCI; GENETIC SPECIATION; MODELS, GENETIC; MUTATION; RECOMBINATION, GENETIC;

EID: 79957579993     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0018155     Document Type: Article

References (38)

1. Hey J, (2006) On the failure of modern species concepts. Trends Ecol Evol 21: 447-450.
2. Mayr E, (1963) Animal species and evolution Cambridge, MA, USA The Belknap Press.
3. Coyne JA, Orr HA, (2004) Speciation Sunderland, MA Sinauer Associates.
4. Becquet C, Przeworski M, (2007) A new approach to estimate parameters of speciation models with application to apes. Genome Res 17: 1505-1519.
5. 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.
6. Städler T, Roselius K, Stephan W, (2005) Genealogical footprints of speciation processes in wild tomatoes: Demography and evidence for historical gene flow. Evolution 59: 1268-1279.
7. Nielsen R, Wakeley J, (2001) Distinguishing migration from isolation: A Markov chain Monte Carlo approach. Genetics 158: 885-896.
8. Wang Y, Hey J, (2010) Estimating divergence parameters with small samples from a large number of loci. Genetics 184: 363-379.
9. 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.
10. Won YJ, Hey J, (2005) Divergence population genetics of chimpanzees. Mol Biol Evol 22: 297-307.
11. Hey J, (2010) Isolation with migration models for more than two populations. Mol Biol Evol 27: 905-920.
12. Hey J, (2006) Recent advances in assessing gene flow between diverging populations and species. Curr Opin Genet Dev 16: 592-596.
13. Andolfatto P, Wall JD, (2003) Linkage disequilibrium patterns across a recombination gradient in African Drosophila melanogaster. Genetics 165: 1289-1305.
14. Arunyawat U, Stephan W, Städler T, (2007) Using multilocus sequence data to assess population structure, natural selection, and linkage disequilibrium in wild tomatoes. Mol Biol Evol 24: 2310-2322.
15. Roselius K, Stephan W, Städler T, (2005) The relationship of nucleotide polymorphism, recombination rate and selection in wild tomato species. Genetics 171: 753-763.
16. Stephan W, Langley CH, (1998) DNA polymorphism in Lycopersicon and crossing-over per physical length. Genetics 150: 1585-1593.
17. Nordborg M, Tavare S, (2002) Linkage disequilibrium: what history has to tell us. Trends Genet 18: 83-90.
18. Strasburg JL, Rieseberg LH, (2010) How Robust Are "Isolation with Migration" Analyses to Violations of the IM Model? A Simulation Study. Mol Biol Evol 27: 297-310.
19. Wakeley J, Hey J, (1997) Estimating ancestral population parameters. Genetics 145: 847-855.
20. Garrigan D, (2009) Composite likelihood estimation of demographic parameters. BMC Genet 10: 72.
21. Lopes JS, Balding D, Beaumont MA, (2009) PopABC: a program to infer historical demographic parameters. Bioinformatics 25: 2747-2749.
22. Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD, (2009) Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data. PLoS Genet 5: e1000695.
23. Städler T, Arunyawat U, Stephan W, (2008) Population genetics of speciation in two closely related wild tomatoes (Solanum section Lycopersicon). Genetics 178: 339-350.
24. Tellier A, Fischer I, Merino C, Xia H, Camus-Kulandaivelu L, et al. (2011) Fitness effects of derived deleterious mutations in four closely related wild tomato species with spatial structure. Heredity in press: advance online publication Jan 2011, doi:2010.1038/hdy.2010.2175.
25. Kimura M, (1969) The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics 61: 893-903.
26. Hudson RR, (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337-338.
27. Felsenstein J, (1988) Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet 22: 521-565.
28. R Development Core Team (2005) R: A language and environment for statistical computing Vienna, Austria R foundation for Statistical Computing.
29. McCullagh P, Nelder JA, (1989) Generalized linear models 2nd edition London, UK Chapman and Hall/CRC.
30. Karlis D, Meligkotsidou L, (2005) Multivariate Poisson regression with covariance structure. Stat Comp 15: 255-265.
31. Becquet C, Przeworski M, (2009) Learning about modes of speciation by computational approaches. Evolution 63: 2547-2562.
32. Thornton KR, (2009) Automating approximate Bayesian computation by local linear regression. BMC Genet 10: 35.
33. Joyce P, Marjoram P, (2008) Approximately sufficient statistics and Bayesian computation. Stat Appl Genet Mol Biol 7 article 26.
34. Nunes MA, Balding DJ, (2010) On optimal selection of summary statistics for Approximate Bayesian Computation. Stat Appl Genet Mol Biol 9 article number: 34.
35. Cornuet JM, Santos F, Beaumont MA, Robert CP, Marin JM, et al. (2008) Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation. Bioinformatics 24: 2713-2719.
36. Jensen JD, Thornton KR, Aquadro CF, (2008) Inferring selection in partially sequenced regions. Mol Biol Evol 25: 438-446.
37. Pawitan Y, (2001) In all likelihood: Statistical modelling and inference using likelihood Oxford, UK Oxford University Press.
38. Efron B, (1985) Bootstrap confidence intervals for a class of parametric problems. Biometrika 72: 45-58.