Data from: The hidden history of the snowshoe hare, Lepus 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 North
America, hares (Lepus 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 North America - the snowshoe hare (Lepus americanus), the white-tailed
jackrabbit (L. townsendii) and the black-tailed jackrabbit (L.
californicus) - by analyzing sequence variation at eight nuclear markers
and one mitochondrial DNA (mtDNA) locus (6 240 bp; 94 specimens). A
multilocus-multispecies coalescent-based phylogeny suggests that L.
americanus diverged ~2.7 Mya and that L. californicus and L. townsendii
split more recently (~1.2 Mya). Within L. americanus a deep history of
cryptic divergence (~2.0 Mya) was inferred, which coincides with major
speciation events in other North American 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 mtDNA divergence revealed historical mtDNA introgression
from L. californicus into the Pacific Northwest 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.