ArticleGenetics2006
An integrated-likelihood method for estimating genetic differentiation between populations.
Article in Genetics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Determining the phylogenetic and phylogeographic origin of highly pathogenic avian influenza (H7N3) in Mexico.PloS one · 2014Article
- Modelling the evolutionary dynamics of viruses within their hosts: a case study using high-throughput sequencing.PLoS pathogens · 2012Article
- A new method to uncover signatures of divergent and stabilizing selection in quantitative traits.Genetics · 2011Article
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Authors and funding
4 authors.
Funding
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Abstract
The aim of this article is to develop an integrated-likelihood (IL) approach to estimate the genetic differentiation between populations. The conventional maximum-likelihood (ML) and pseudolikelihood (PL) methods that use sample counts of alleles may cause severe underestimations of FST, which means overestimations of theta=4Nm, when the number of sampling localities is small. To reduce such bias in the estimation of genetic differentiation, we propose an IL method in which the mean allele frequencies over populations are regarded as nuisance parameters and are eliminated by integration. To maximize the IL function, we have developed two algorithms, a Monte Carlo EM algorithm and a Laplace approximation. Our simulation studies show that the method proposed here outperforms the conventional ML and PL methods in terms of unbiasedness and precision. The IL method was applied to real data for Pacific herring and African elephants.
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