Abstract
Purifying selection at many linked sites alters patterns of molecular evolution, reducing overall diversity and distorting the shapes of genealogies. Recombination attenuates these effects; however, purifying selection can significantly distort genealogies even for substantial recombination rates. Here, we show that when selection and/or recombination are sufficiently strong, the genealogy at any single site can be described by a time-dependent effective population size, Ne(t), which has a simple analytic form. Our results illustrate how recombination reduces distortions in genealogies and allow us to quantitatively describe the shapes of genealogies in the presence of strong purifying selection and recombination. We also analyze the effects of a distribution of selection coefficients across the genome.