Drawing inferences about the coancestry coefficient.

Journal Article (Journal Article;Review)

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.

Full Text

Duke Authors

Cited Authors

  • Samanta, S; Li, Y-J; Weir, BS

Published Date

  • June 2009

Published In

Volume / Issue

  • 75 / 4

Start / End Page

  • 312 - 319

PubMed ID

  • 19345237

Pubmed Central ID

  • PMC2722911

Electronic International Standard Serial Number (EISSN)

  • 1096-0325

Digital Object Identifier (DOI)

  • 10.1016/j.tpb.2009.03.005


  • eng

Conference Location

  • United States