Jul 4, 2013

Robust identification of local adaptation from allele frequencies

Genetics
Torsten Günther, Graham Coop

Abstract

Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele frequencies and neutral correlations of allele frequencies among populations due to shared population history and gene flow. Here we develop a set of methods to robustly test for unusual allele frequency patterns and correlations between environmental variables and allele frequencies while accounting for these complications based on a Bayesian model previously implemented in the software Bayenv. Using this model, we calculate a set of "standardized allele frequencies" that allows investigators to apply tests of their choice to multiple populations while accounting for sampling and covariance due to population history. We illustrate this first by showing that these standardized frequencies can be used to detect nonparametric correlations with environmental variables; these correlations are also less prone to spurious results due to outlier populations. We then demonstrate how these standardized allele frequencies can be used to construct a test to detect SNPs that deviate strongly from neutral populatio...Continue Reading

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Mentioned in this Paper

Computer Programs and Programming
School Age Population
Massively-Parallel Sequencing
Genetic Equilibrium
Alleles
Impacts, Environmental
Single Nucleotide Polymorphism
Genome, Human
Evolution, Molecular
Clupea harengus (organism)

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