Speciation with gene flow in the Daphnia pulex species complex

Divergent selection between contrasting habitats has the potential to drive adaptive divergence and the evolution of reproductive isolation in the face of initially high gene flow. This work explores the genetic divergence in a young ecological species pair, Daphnia pulex and Daphnia pulicaria, during habitat transition events, by surveying 363 individuals from 9 lakes and 8 ponds in Southern Ontario and Michigan. I conducted a phylogenetic and population genetics study using the mitochondrial NADH dehydrogenase 5 (ND5) gene, the nuclear Lactate dehydrogenase A (Ldh-A) locus, and 21 microsatellite markers. A discordant phylogenetic signal between nuclear and mitochondrial markers suggests a prolonged history of hybridization and introgression between lake and pond species. Population genetic analysis, based on nuclear markers, reflects low level of contemporary gene flow, clear genetic differentiation between pond and lake populations, and additional substructure within lakes, suggesting the existence of strong habitat isolating barriers between ponds and lake