Abstract
Aim To evaluate whether population genetic structure reflects taxonomic recognition of the endangered Lower Keys marsh rabbit ( Sylvilagus palustris hefneri) and the two mainland subspecies. Location Southeastern United States. 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 Lower Keys, and the second grouping the eastern Lower Keys together with the mainland. Furthermore, island genetic diversity was not reduced relative to mainland populations (cyt b: p: 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 Lower Keys isolation than originally thought. Moreover, diversity patterns indicate that undocumented man-mediated transfers may contribute to current genetic structure between eastern Lower Keys and the mainland. Although subspecies designations were not confirmed, these findings support recognition of western Lower Keys populations as a distinct population segment under the Endangered Species Act.