Taxonomy versus phylogeny: evolutionary history of marsh rabbits without hopping to conclusions

Aim To evaluate whether population genetic structure reflects taxonomic recognition of the endangered L ower K eys marsh rabbit ( S ylvilagus palustris hefneri ) and the two mainland subspecies. Location Southeastern U nited S tates. Methods We inferred phylogenetic relationships, population structure and genetic diversity within S . palustris using a mitochondrial gene (cytochrome b ) and 10 microsatellite loci. Results The cytochrome b sequence data revealed taxonomy‐phylogeography incongruence, and microsatellite data revealed moderate structure ( F ST  = 0.22) with two genetic clusters recovered: one grouping the western L ower K eys, and the second grouping the eastern L ower K eys together with the mainland. Furthermore, island genetic diversity was not reduced relative to mainland populations (cyt b : π: t  = −0.6952, P  =   0.5651; h : t  = −1.2053, P  =   0.4305; microsatellite: H E : t  = −4.1201, P  =   0.1313; AR : t  = −2.3113, P  =   0.2441). Main conclusions The taxonomy‐phylogeny disparity reveals unknown aspects of the evolutionary history including an absence of contemporary dispersal barriers between the mainland subspecies and a more recent L ower K eys isolation than originally thought. Moreover, diversity patterns indicate that undocumented man‐mediated transfers may contribute to current genetic structure between eastern L ower K eys and the mainland. Although subspecies designations were not confirmed, these findings support recognition of western L ower K eys populations as a distinct population segment under the E ndangered S pecies A ct.