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Estimating Parameters of Speciation Models Based on Refined Summaries of the Joint Site-Frequency Spectrum

By Aurélien Tellier, Peter Pfaffelhuber, Bernhard Haubold, Lisha Naduvilezhath, Laura E. Rose, Thomas Städler, Wolfgang Stephan and Dirk Metzler

Abstract

Understanding the processes and conditions under which populations diverge to give rise to distinct species is a central question in evolutionary biology. Since recently diverged populations have high levels of shared polymorphisms, it is challenging to distinguish between recent divergence with no (or very low) inter-population gene flow and older splitting events with subsequent gene flow. Recently published methods to infer speciation parameters under the isolation-migration framework are based on summarizing polymorphism data at multiple loci in two species using the joint site-frequency spectrum (JSFS). We have developed two improvements of these methods based on a more extensive use of the JSFS classes of polymorphisms for species with high intra-locus recombination rates. First, using a likelihood based method, we demonstrate that taking into account low-frequency polymorphisms shared between species significantly improves the joint estimation of the divergence time and gene flow between species. Second, we introduce a local linear regression algorithm that considerably reduces the computational time and allows for the estimation of unequal rates of gene flow between species. We also investigate which summary statistics from the JSFS allow the greatest estimation accuracy for divergence time and migration rates for low (around 10) and high (around 100) numbers of loci. Focusing on cases with low numbers of loci and high intra-locus recombination rates we show that our methods for the estimation of divergence time and migration rates are more precise than existing approaches

Topics: Research Article
Publisher: Public Library of Science
OAI identifier: oai:pubmedcentral.nih.gov:3102651
Provided by: PubMed Central

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Citations

  1. (2007). A new approach to estimate parameters of speciation models with application to apes.
  2. (1963). Animal species and evolution.
  3. (2008). Approximately sufficient statistics and Bayesian computation.
  4. (2009). Automating approximate Bayesian computation by local linear regression.
  5. (1985). Bootstrap confidence intervals for a class of parametric problems.
  6. (2009). Composite likelihood estimation of demographic parameters.
  7. (2005). Core Team
  8. (2001). Distinguishing migration from isolation: A Markov chain Monte Carlo approach.
  9. (2005). Divergence population genetics of chimpanzees.
  10. (1998). DNA polymorphism in Lycopersicon and crossing-over per physical length.
  11. (1997). Estimating ancestral population parameters.
  12. (2010). Estimating divergence parameters with small samples from a large number of loci.
  13. (2011). Fitness effects of derived deleterious mutations in four closely related wild tomato species with spatial structure. Heredity in press: advance online publication
  14. (2005). Genealogical footprints of speciation processes in wild tomatoes: Demography and evidence for historical gene flow.
  15. (1989). Generalized linear models 2nd edition.
  16. (2002). Generating samples under a Wright-Fisher neutral model of genetic variation.
  17. (2010). How Robust Are ‘‘Isolation with Migration’’ Analyses to Violations of the IM Model? A Simulation Study.
  18. (2001). In all likelihood: Statistical modelling and inference using likelihood.
  19. (2008). Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation.
  20. (2008). Inferring selection in partially sequenced regions.
  21. (2007). Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics.
  22. (2010). Isolation with migration models for more than two populations.
  23. (2009). Learning about modes of speciation by computational approaches.
  24. (2003). Linkage disequilibrium patterns across a recombination gradient in African Drosophila melanogaster.
  25. (2002). Linkage disequilibrium: what history has to tell us.
  26. (2004). Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis.
  27. (2005). Multivariate Poisson regression with covariance structure.
  28. (2010). On optimal selection of summary statistics for Approximate Bayesian Computation. Stat Appl Genet Mol Biol 9: article number:
  29. (2006). On the failure of modern species concepts.
  30. (1988). Phylogenies from molecular sequences: inference and reliability.
  31. (2009). PopABC: a program to infer historical demographic parameters.
  32. (2008). Population genetics of speciation in two closely related wild tomatoes (Solanum section Lycopersicon).
  33. (2006). Recent advances in assessing gene flow between diverging populations and species.
  34. (2004). Speciation.
  35. (2005). Sta ¨dler T
  36. (1969). The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations.