ArticleGenetics2013
Robust identification of local adaptation from allele frequencies.
Article in Genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 255 papers.
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Who cites it
255 citing papers in PubMed.
- Identifying adaptive variation in spatially structured populations using low-coverage whole-genome sequencing data.Molecular biology and evolution · 2026Article
- Signals of Natural Selection across Regions of Low Recombination in Wild Populations of the Purple Sea Urchin, Strongylocentrotus purpuratus.Genome biology and evolution · 2026Article
- Assessing Future Maladaptation Risk in the Keystone SpeciesEvolutionary applications · 2026Article
- A Selective Sweep Likely Linked to Xenobiotic Detoxification Identified Along Altitudinal Gradients in the Pine Processionary Moth.Genome biology and evolution · 2026Article
- Sexual selection purges mutation load, but not overall genetic diversity, decreasing vulnerability to extinction.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Similar Habitat Gradients Across Native and Invasive Ranges Elicit Divergent Evolutionary Responses.Ecology and evolution · 2026Article
- Putatively Adaptive and Genome-Wide Genetic Variation Often Rank Populations as Similarly Distinctive.Molecular ecology · 2026Article
- What has population genomics told us about the dynamics of selection and plant adaptation?Molecular biology and evolution · 2026Review
- Environmental Association Analyses in Plants and the Influence of Methodological Decisions.Molecular ecology · 2026Review
- How Robust Are Genomic Offset Predictions to Methodological Choices? Insights From Perennial Ryegrass.Molecular ecology · 2026Article
- Patterns of Local Adaptation in the Northern Leopard Frog (Evolutionary applications · 2026Article
- Bringing environment back into human evolution: why human genetics needs genome-environment association studies.Human genetics · 2026Review
- Conservation Units for Anadromous Arctic Char (Evolutionary applications · 2026Article
- Using drift coefficients as a basis for inferring times, effective population sizes, and genetic adaptations.Molecular biology and evolution · 2026Article
- Historical and contemporary genomes of an endangered rodent reveal shifts in environmentally associated genes.Science advances · 2026Article
- Identifying Adaptive Footprints in the Presence of Demographic Uncertainty.Genome biology and evolution · 2026Article
- When South Meets North: A Joint Contact Zone Coinciding With Environmental Gradients in Three Boreal Tree Species.Molecular ecology · 2026Article
- Identification of Genetic Variation Associated With Heat Tolerance in Cowpea (Vigna unguiculata L. Walp.).Molecular ecology · 2026Article
- A key regulator of missing-self innate immunity is polymorphic and under diversifying selection.Molecular biology and evolution · 2026Article
- Divergent Selection on Dispersal Targets Chemosensory and Neuronal Genes in Tribolium castaneum.Molecular ecology · 2026Article
195 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
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 population structure. This test is conceptually related to FST and is shown to be more powerful, as we account for population history. We also extend the model to next-generation sequencing of population pools-a cost-efficient way to estimate population allele frequencies, but one that introduces an additional level of sampling noise. The utility of these methods is demonstrated in simulations and by reanalyzing human SNP data from the Human Genome Diversity Panel populations and pooled next-generation sequencing data from Atlantic herring. An implementation of our method is available from http://gcbias.org.
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