We present the first phylogenies to include all extant species of Perissodactyla (odd-toed hoofed mammals) and the recently extinct quagga (Equus quagga). Two independent data sets were examined; one based on multiple genes and analyzed using both supertree and supermatrix approaches, and a second being a supertree constructed from trees collected from the scientific literature. All methods broadly confirmed the traditional view of perissodactyl interfamily relationships, with Equidae Hippomorpha) forming the sister-group to the clade Rhinocerotidae + Tapiridae Ceratomorpha). The contentious affinity of the Sumatran rhino (Dicerorhinus sumatrensis) is resolved in favour of it forming a clade with the two Asian rhinos (genus Rhinoceros). However, no data set or tree-building method managed to satisfactorily resolve the historically contentious relationships among extant equids; little agreement appears among the different trees for this group. In general, both the supertree and supermatrix approaches performed equally well, but both were hindered by the current paucity of data (e.g. no single gene has been sequenced to date for all 17 species) and its patchy distribution within Equidae. More data, both molecular and morphological, are required for all species to resolve the poorly supported nodes.
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