Data from: Conservation implications of the evolutionary history and genetic diversity hotspots of the snowshoe hare

With climate warming, the ranges of many boreal species are expected to shift northward and to fragment in southern peripheral ranges. To understand the conservation implications of losing southern populations, we examined range-wide genetic diversity of the snowshoe hare (Lepus americanus), an important prey species that drives boreal ecosystem dynamics. We analysed microsatellite (8 loci) and mitochondrial DNA sequence (cytochrome b and control region) variation in almost 1000 snowshoe hares. A hierarchical structure analysis of the microsatellite data suggests initial subdivision in two groups, Boreal and southwestern. The southwestern group further splits into Greater Pacific Northwest and U.S. Rockies. The genealogical information retrieved from mtDNA is congruent with the three highly differentiated and divergent groups of snowshoe hares. These groups can correspond with evolutionarily significant units that might have evolved in separate refugia south and east of the Pleistocene ice sheets. Genetic diversity was highest at mid-latitudes of the species' range, and genetic uniqueness was greatest in southern populations, consistent with substructuring inferred from both mtDNA and microsatellite analyses at finer levels of analysis. Surprisingly, snowshoe hares in the Greater Pacific Northwest mtDNA lineage were more closely related to black-tailed jackrabbits (Lepus californicus) than to other snowshoe hares, which may result from secondary introgression or shared ancestral polymorphism. Given the genetic distinctiveness of southern populations and minimal gene flow with their northern neighbours, fragmentation and loss of southern boreal habitats could mean loss of many unique alleles and reduced evolutionary potential.Cheng et al_All SamplesSample details for 907 specimens of snowshoe hare (Lepus americanus) and 5 specimens of black-tailed jackrabbit (L. californicus) used in study. Includes collection date, latitude-longitude, and GenBank accession numbers (where relevant).Cheng et al_microsatellitesMicrosatellite genotype data for 853 specimens of snowshoe hare (Lepus americanus) at eight microsatellite lociCheng et al_STRUCTUREinputSTRUCTURE input file with microsatellite genotype date for 853 specimens of snowshoe hare (Lepus americanus)Cheng et al_BEASTinputCytBFasta input file for BEAST phylogenetic analysis, based on the CytB gene. Sequences are provided for 80 snowshoe hare (Lepus americanus) specimens collected from throughout the species' range, 1 white-tailed jackrabbit (L. townsendii: Sample ID WJ1, GenBank accession number AY292729), and 7 black-tailed jackrabbits (L. californicus: Sample ID's BJ1, BJ2, CA.933J, CA.939J, NM.978J, NV.981J, NV.988J). Sequences for two of the black-tailed jackrabbit specimens were from GenBank, with these accession numbers: BJ1 = AY292731 and BJ2 = HM222712.Cheng et al_BEASTinputCRFasta input file of control region (d-loop), for inferring demographic history of the major mtDNA lineages, using the Bayesian Skyline Plot implemented in BEAST. Sequences are provided for 893 snowshoe hare (Lepus americanus) specimens collected from throughout the species' range and 1 white-tailed jackrabbit (L. townsendii: Sample ID WTJR, GenBank accession number AY292729)