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Drawing inferences about the coancestry coefficient

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  • Samanta, Suvajit
  • Li, Yi-Ju
  • Weir, Bruce S.

Abstract

The coancestry coefficient, also known as the population structure parameter, is of great interest in population genetics. It can be thought of as the intraclass correlation of pairs of alleles within populations and it can serve as a measure of genetic distance between populations. For a general class of evolutionary models it determines the distribution of allele frequencies among populations. Under more restrictive models it can be regarded as the probability of identity by descent of any pair of alleles at a locus within a random mating population. In this paper we review estimation procedures that use the method of moments or are maximum likelihood under the assumption of normally distributed allele frequencies. We then consider the problem of testing hypotheses about this parameter. In addition to parametric and non-parametric bootstrap tests we present an asymptotically-distributed chi-square test. This test reduces to the contingency-table test for equal sample sizes across populations. Our new test appears to be more powerful than previous tests, especially for loci with multiple alleles. We apply our methods to HapMap SNP data to confirm that the coancestry coefficient for humans is strictly positive.

Suggested Citation

  • Samanta, Suvajit & Li, Yi-Ju & Weir, Bruce S., 2009. "Drawing inferences about the coancestry coefficient," Theoretical Population Biology, Elsevier, vol. 75(4), pages 312-319.
    • Handle: RePEc:eee:thpobi:v:75:y:2009:i:4:p:312-319
    DOI: 10.1016/j.tpb.2009.03.005
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    References listed on IDEAS

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    1. George Nicholson & Albert V. Smith & Frosti Jónsson & Ómar Gústafsson & Kári Stefánsson & Peter Donnelly, 2002. "Assessing population differentiation and isolation from single‐nucleotide polymorphism data," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 64(4), pages 695-715, October.
    2. Neerchal, Nagaraj K. & Morel, Jorge G., 2005. "An improved method for the computation of maximum likeliood estimates for multinomial overdispersion models," Computational Statistics & Data Analysis, Elsevier, vol. 49(1), pages 33-43, April.
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    Cited by:

    1. Leviyang, Sivan & Hamilton, Matthew B., 2011. "Properties of Weir and Cockerham’s Fst estimators and associated bootstrap confidence intervals," Theoretical Population Biology, Elsevier, vol. 79(1), pages 39-52.
    2. Tvedebrink, Torben, 2010. "Overdispersion in allelic counts and θ-correction in forensic genetics," Theoretical Population Biology, Elsevier, vol. 78(3), pages 200-210.

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