Estimates of <i>α</i> due to temporally fluctuating recombination rates and variable BGS effects.

<p>Results based on forward population genetic simulations of 10,000 diploid individuals (<i>N</i>), a chromosome segment of 1 Mb containing 100 genes, and two types of mutations: neutral and deleterious (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004434#s4" target="_blank">Materials and Methods</a> for details). Cycles of fluctuating recombination followed phases of moderately high recombination for 1<i>N</i> generations (<i>H</i>_rec phase) and moderately low recombination for 3<i>N</i> generations (<i>L</i>_rec phase). Estimates of <i>α</i> at negatively selected sites obtained following the models proposed by Eyre-Walker and Keightley <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004434#pgen.1004434-EyreWalker2" target="_blank">[91]</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004434#pgen.1004434-Keightley3" target="_blank">[95]</a> every 0.1<i>N</i> generations. Blue and red lines indicate estimates of <i>α</i> assuming constant population size and variable population sizes, respectively. Continuous and dashed lines indicate estimates of <i>α</i> with and without correction for the effect of polymorphism to divergence, respectively.