Robust Identification of Local Adaptation from Allele Frequencies

Robust identification of local adaptation from allele frequencies.

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 robust...

Allele Frequencies and Genotype Frequencies

The Limits of Individual Identification from Sample Allele Frequencies: Theory and Statistical Analysis

It was shown recently using experimental data that it is possible under certain conditions to determine whether a person with known genotypes at a number of markers was part of a sample from which only allele frequencies are known. Using population genetic and statistical theory, we show that the power of such identification is, approximately, proportional to the number of independent SNPs divi...

Estimation of allele frequencies from high-coverage genome-sequencing projects.

A new generation of high-throughput sequencing strategies will soon lead to the acquisition of high-coverage genomic profiles of hundreds to thousands of individuals within species, generating unprecedented levels of information on the frequencies of nucleotides segregating at individual sites. However, because these new technologies are error prone and yield uneven coverage of alleles in diplo...

PopHist: inferring population history from the spectrum of allele frequencies

SUMMARY PopHist is a computer program that uses the frequency spectrum of alleles to: (a) estimate maximum likelihood parameters describing a population's history; and (b) compare alternative hypotheses about population history using likelihood ratio tests. The program uses the matrix coalescent, a method for calculating theoretical frequency spectra that can be applied to sets of unlinked site...