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

AbstractWith 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., Usage notesCheng 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).摘要：随着气候变暖，诸多寒带北方物种的分布范围预计将向北迁移，并在南部边缘分布区发生破碎化。为明确南部种群丢失对物种保护的潜在影响，我们针对驱动寒带生态系统动态的关键猎物种群——雪鞋兔（Lepus americanus）开展了全分布范围的遗传多样性研究。我们对近1000只雪鞋兔的微卫星（microsatellite，8个位点）数据与线粒体DNA（mitochondrial DNA）序列变异（涵盖细胞色素b（cytochrome b）基因及控制区（control region））进行了分析。对微卫星数据的层级结构分析显示，雪鞋兔最初可划分为两个类群：寒带类群与西南类群。其中西南类群可进一步划分为大太平洋西北类群与美国落基山脉类群。从线粒体DNA获取的谱系信息与这三个高度分化、彼此分歧的雪鞋兔类群结果一致。这些类群可对应于更新世冰盖南部与东部的独立避难所中演化形成的进化显著单元（evolutionarily significant unit）。遗传多样性在该物种分布范围的中纬度区域达到峰值，而南部种群的遗传独特性最强，这与通过线粒体DNA与微卫星数据在更精细分析尺度下推断出的亚结构结果相符。令人意外的是，隶属于大太平洋西北线粒体谱系的雪鞋兔，相较于其他雪鞋兔，与黑尾长耳大野兔（Lepus californicus）的亲缘关系更近，这一现象可能源于次生渐渗（introgression）或共享的祖先多态性。鉴于南部种群的遗传独特性，且其与北部种群间的基因流极弱，寒带南部生境的破碎化与丧失可能会导致大量独特等位基因的丢失，并降低物种的演化潜力。 使用说明： 1. Cheng et al_All Samples：本数据集包含本研究中使用的907只雪鞋兔（Lepus americanus）与5只黑尾长耳大野兔（L. californicus）的样本详情，包括采集日期、经纬度以及相关的GenBank登录号（如适用）。 2. Cheng et al_microsatellites：包含853只雪鞋兔（Lepus americanus）在8个微卫星位点的基因型数据。 3. Cheng et al_STRUCTUREinput：用于STRUCTURE软件分析的输入文件，包含853只雪鞋兔（Lepus americanus）的微卫星基因型数据（原文存在笔误，原文本中“date”应为“data”）。 4. Cheng et al_BEASTinput：用于BEAST系统发育分析的细胞色素b基因Fasta格式输入文件。序列样本涵盖全分布范围的80只雪鞋兔（Lepus americanus）、1只白尾长耳大野兔（Lepus townsendii，样本编号WJ1，GenBank登录号AY292729）以及7只黑尾长耳大野兔（L. californicus，样本编号BJ1、BJ2、CA.933J、CA.939J、NM.978J、NV.981J、NV.988J）。其中2份黑尾长耳大野兔样本的序列来自GenBank，登录号分别为BJ1=AY292731与BJ2=HM222712。 5. Cheng et al_BEASTinputCR：用于基于BEAST软件实现的贝叶斯天际线图（Bayesian Skyline Plot）推断主要线粒体谱系种群历史的控制区（D-loop）Fasta格式输入文件。序列样本涵盖全分布范围的893只雪鞋兔（Lepus americanus）与1只白尾长耳大野兔（Lepus townsendii，样本编号WTJR，GenBank登录号AY292729）。