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To understand the conservation implications of losing southern populations, we examined range\u2010wide genetic diversity of the snowshoe hare (<jats:italic>Lepus americanus<\/jats:italic>), an important prey species that drives boreal ecosystem dynamics. We analysed microsatellite (8 loci) and mitochondrial <jats:styled-content style=\"fixed-case\">DNA<\/jats:styled-content> 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 mt<jats:styled-content style=\"fixed-case\">DNA<\/jats:styled-content> 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\u2010latitudes of the species' range, and genetic uniqueness was greatest in southern populations, consistent with substructuring inferred from both mt<jats:styled-content style=\"fixed-case\">DNA<\/jats:styled-content> and microsatellite analyses at finer levels of analysis. Surprisingly, snowshoe hares in the Greater Pacific Northwest mt<jats:styled-content style=\"fixed-case\">DNA<\/jats:styled-content> lineage were more closely related to black\u2010tailed jackrabbits <jats:italic>(Lepus californicus<\/jats:italic>) 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.<\/jats:p>","DOI":"10.1111\/mec.12790","type":"journal-article","created":{"date-parts":[[2014,5,9]],"date-time":"2014-05-09T18:47:18Z","timestamp":1399661238000},"page":"2929-2942","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":35,"title":["Conservation implications of the evolutionary history and genetic diversity hotspots of the snowshoe hare"],"prefix":"10.1111","volume":"23","author":[{"given":"Ellen","family":"Cheng","sequence":"first","affiliation":[{"name":"Wildlife Biology Program Department of Ecosystem and Conservation Sciences University of Montana 32 Campus Drive Missoula MT 59812 USA"}]},{"given":"Karen E.","family":"Hodges","sequence":"additional","affiliation":[{"name":"Department of Biology University of British Columbia Okanagan 3333 University Way Kelowna BC V1V 1V7 Canada"}]},{"given":"Jos\u00e9","family":"Melo\u2010Ferreira","sequence":"additional","affiliation":[{"name":"CIBIO Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos Universidade do Porto InBIO \u2010 Laborat\u00f3rio Associado Campus Agr\u00e1rio de Vair\u00e3o 4485\u2010661 Vair\u00e3o Portugal"}]},{"given":"Paulo C.","family":"Alves","sequence":"additional","affiliation":[{"name":"Wildlife Biology Program Department of Ecosystem and Conservation Sciences University of Montana 32 Campus Drive Missoula MT 59812 USA"},{"name":"Departamento de Biologia Faculdade de Ci\u00eancias da Universidade do Porto Rua do Campo Alegre s\/n 4169\u2010007 Porto Portugal"}]},{"given":"L. 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