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Ancestral inference from haplotypes and mutations

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  • Griffiths, Robert C.
  • Tavaré, Simon

Abstract

We consider inference about the history of a sample of DNA sequences, conditional upon the haplotype counts and the number of segregating sites observed at the present time. After deriving some theoretical results in the coalescent setting, we implement rejection sampling and importance sampling schemes to perform the inference. The importance sampling scheme addresses an extension of the Ewens Sampling Formula for a configuration of haplotypes and the number of segregating sites in the sample. The implementations include both constant and variable population size models. The methods are illustrated by two human Y chromosome datasets.

Suggested Citation

  • Griffiths, Robert C. & Tavaré, Simon, 2018. "Ancestral inference from haplotypes and mutations," Theoretical Population Biology, Elsevier, vol. 122(C), pages 12-21.
    • Handle: RePEc:eee:thpobi:v:122:y:2018:i:c:p:12-21
    DOI: 10.1016/j.tpb.2018.04.006
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    References listed on IDEAS

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    1. Matthew Stephens & Peter Donnelly, 2000. "Inference in molecular population genetics," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 62(4), pages 605-635.
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    Cited by:

    1. Hobolth, Asger & Rivas-González, Iker & Bladt, Mogens & Futschik, Andreas, 2024. "Phase-type distributions in mathematical population genetics: An emerging framework," Theoretical Population Biology, Elsevier, vol. 157(C), pages 14-32.

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