Estimating the impact of selection on linked neutral variation.

<p>To obtain a direct estimate of the amount of linked neutral variation removed by selection, we fit a population genetic model incorporating HH and BGS effects to the estimates of neutral diversity and recombination rate in 500 kb windows across the genome. Model fit (blue), predicted neutral diversity in the absence of selection (red), and observed genetic diversity (dashed) are shown for a species with large population size (<i>Drosophila melanogaster</i>, part A) and small population size (<i>Equus ferus przewalskii</i>, part B). The magnitude of the impact of selection on linked neutral diversity is estimated as 1 – (observed neutral diversity / neutral diversity in the absence of selection). R code to replicate this figure is available at <a href="https://github.com/tsackton/linked-selection/blob/master/final_analysis/figure1.R" target="_blank">https://github.com/tsackton/linked-selection/blob/master/final_analysis/figure1.R</a>.