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 lower genome-wide nucleotide diversity, a smaller effective population size, higher incidence of private alleles, and substantially more linkage-disequilibrium than D. pulex. Functional enrichment analysis revealed that positively selected genes in D. pulicaria are enriched in potentially aging-related categories such as cellular homeostasis, which may explain the extended lifespan in D. pulicaria. We also found that opsin-related genes, which may mediate photoperiodic responses, are under different selection pressures in these two species. Additionally, genes involved in mitochondrial functions, ribosomes, and responses to environmental stimuli are found to be under positive selection in both species. Our results provide insights into the physiological traits that differ within this regionally sympatric sister-species pair that occupies unique microhabitats.