DOI: 10.5061/dryad.dh63p
title: Data from: Conservation implications of the evolutionary history and genetic diversity hotspots of the snowshoe hare

description: 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.
description: 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).