The hidden history of the snowshoe hare, L epus americanus : extensive mitochondrial DNA introgression inferred from multilocus genetic variation

Hybridization drives the evolutionary trajectory of many species or local populations, and assessing the geographic extent and genetic impact of interspecific gene flow may provide invaluable clues to understand population divergence or the adaptive relevance of admixture. In N orth A merica, hares ( L epus spp.) are key species for ecosystem dynamics and their evolutionary history may have been affected by hybridization. Here we reconstructed the speciation history of the three most widespread hares in N orth A merica – the snowshoe hare ( L epus americanus ), the white‐tailed jackrabbit ( L . townsendii ) and the black‐tailed jackrabbit ( L . californicus ) – by analysing sequence variation at eight nuclear markers and one mitochondrial DNA (mt DNA ) locus (6240 bp; 94 specimens). A multilocus–multispecies coalescent‐based phylogeny suggests that L . americanus diverged ~2.7 Ma and that L . californicus and L . townsendii split more recently (~1.2 Ma). Within L . americanus, a deep history of cryptic divergence (~2.0 Ma) was inferred, which coincides with major speciation events in other N orth A merican species. While the isolation‐with‐migration model suggested that nuclear gene flow was generally rare or absent among species or major genetic groups, coalescent simulations of mt DNA divergence revealed historical mt DNA introgression from L . californicus into the P acific N orthwest populations of L . americanus . This finding marks a history of past reticulation between these species, which may have affected other parts of the genome and influence the adaptive potential of hares during climate change.