Aug 16, 2016

Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps

Genetics
Guy S JacobsToomas Kivisild

Abstract

During a selective sweep, characteristic patterns of linkage disequilibrium can arise in the genomic region surrounding a selected locus. These have been used to infer past selective sweeps. However, the recombination rate is known to vary substantially along the genome for many species. We here investigate the effectiveness of current (Kelly's [Formula: see text] and [Formula: see text]) and novel statistics at inferring hard selective sweeps based on linkage disequilibrium distortions under different conditions, including a human-realistic demographic model and recombination rate variation. When the recombination rate is constant, Kelly's [Formula: see text] offers high power, but is outperformed by a novel statistic that we test, which we call [Formula: see text] We also find this statistic to be effective at detecting sweeps from standing variation. When recombination rate fluctuations are included, there is a considerable reduction in power for all linkage disequilibrium-based statistics. However, this can largely be reversed by appropriately controlling for expected linkage disequilibrium using a genetic map. To further test these different methods, we perform selection scans on well-characterized HapMap data, finding tha...Continue Reading

Mentioned in this Paper

Fluctuation
HapMap
Genome
Chromosome Map
Dysequilibrium Syndrome
Genetics, Population
Recombination, Genetic
Theoretical Study
Cell Differentiation Process
Mathematical Formula

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