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Ancestral Inference in Population Genetics Models with Selection (with Discussion)

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  • Matthew Stephens
  • Peter Donnelly

Abstract

A new algorithm is presented for exact simulation from the conditional distribution of the genealogical history of a sample, given the composition of the sample, for population genetics models with general diploid selection. The method applies to the usual diffusion approximation of evolution at a single locus, in a randomly mating population of constant size, for mutation models in which the distribution of the type of a mutant does not depend on the type of the progenitor allele; this includes any model with only two alleles. The new method is applied to ancestral inference for the two‐allele case, both with genic selection and heterozygote advantage and disadvantage, where one of the alleles is assumed to have resulted from a unique mutation event. The paper describes how the method could be used for inference when data are also available at neutral markers linked to the locus under selection. It also informally describes and constructs the non‐neutral Fleming–Viot measure‐valued diffusion.

Suggested Citation

  • Matthew Stephens & Peter Donnelly, 2003. "Ancestral Inference in Population Genetics Models with Selection (with Discussion)," Australian & New Zealand Journal of Statistics, Australian Statistical Publishing Association Inc., vol. 45(4), pages 395-430, December.
    • Handle: RePEc:bla:anzsta:v:45:y:2003:i:4:p:395-430
    DOI: 10.1111/1467-842X.00295
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    Cited by:

    1. Etheridge, Alison M. & Griffiths, Robert C. & Taylor, Jesse E., 2010. "A coalescent dual process in a Moran model with genic selection, and the lambda coalescent limit," Theoretical Population Biology, Elsevier, vol. 78(2), pages 77-92.
    2. Wakeley, John & Sargsyan, Ori, 2009. "The conditional ancestral selection graph with strong balancing selection," Theoretical Population Biology, Elsevier, vol. 75(4), pages 355-364.
    3. Griffiths, Robert C. & Jenkins, Paul A. & Lessard, Sabin, 2016. "A coalescent dual process for a Wright–Fisher diffusion with recombination and its application to haplotype partitioning," Theoretical Population Biology, Elsevier, vol. 112(C), pages 126-138.

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