Evolutionary Genomics of Sister Species Differing in Effective Population Sizes and Recombination Rates

Studies of closely related species with known ecological differences provide exceptional opportunities for understanding the genetic mechanisms of evolution. Here, we compared population genomics data between D. pulex and D. pulicaria, two reproductively compatible sister species experiencing ecological speciation, the first largely confined to intermittent ponds and the second to permanent lakes in the same geographic region. D. pulicaria has a much lower genome-wide nucleotide diversity, a smaller effective population size, higher incidence of private alleles, and substantially more linkage-disequilibrium than D. pulex.