The HKA Test Revisited | Zendy

Stephen Wright | Zendy; Brian Charlesworth | Zendy

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The HKA Test Revisited

Author(s) -

Stephen Wright,

Brian Charlesworth

Publication year - 2004

Publication title -

genetics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 2.792

H-Index - 246

eISSN - 1943-2631

pISSN - 0016-6731

DOI - 10.1534/genetics.104.026500

Subject(s) - biology , coalescent theory , genetics , locus (genetics) , test statistic , likelihood ratio test , population genetics , population , evolutionary biology , gene , statistics , statistical hypothesis testing , phylogenetic tree , mathematics , demography , sociology

We present a maximum-likelihood-ratio test of the standard neutral model, using multilocus data on polymorphism within species and divergence between species. The model is based on the Hudson-Kreitman-Aguade (HKA) test, but allows for an explicit test of selection at individual loci in a multilocus framework. We use coalescent simulations to show that the likelihood-ratio test statistic is conservative, particularly when the assumption of no recombination is violated. Application of the method to polymorphism data from 18 loci from a population of Arabidopsis lyrata provides significant evidence for a balanced polymorphism at a candidate locus thought to be linked to the centromere. The method is also applied to polymorphism data in maize, providing support for the hypothesis of directional selection on genes in the starch pathway.

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