Phylogenetics of Perissodactyla and tests of the molecular clock

Two mitochondrial genes, the protein-coding cytochrome c oxidase subunit II (COII) gene and a portion of the 12S rRNA gene, were used for phylogenetic investigation of the mammalian order Perissodactyla. The primary objective of the study was to utilize the extensive fossil record of perissodactyls for calibrating molecular clocks and comparing estimates of divergence time s using both genes and two fossil calibration points. Secondary objectives included clarification of previously unresolved relationships within Tapiri dae and comparison of the results of separate and combined analyses of two genes. Analyses included several perissodactyl lineages representing all th ree families (Tapiridae, Equidae, and Rhinocerotidae), most extant genera, all four species of tapirs, two to four species of rhinoceros, and two spec ies of Equus. The application of a relatively recent fossil calibration poi nt and a relatively ancient calibration point produced greatly different es timates of evolutionary rates and divergence times for both genes, even tho ugh a relative rates test did not find significant rate differences among t axa. A likelihood-ratio test, however, rejected a molecular clock for both genes. Neither calibration point produced estimates of divergence times con sistent with paleontological evidence over a range of perissodactyl radiati ons. The combined analysis of both genes produces a well-resolved phylogeny with Perissodactyla that conforms to traditional views of interfamilial re lationships and supports monophyly of neotropical tapirs. Combining the dat a sets increases support for most nodes but decreases the support for a neo tropical tapir clade because the COII and 12S rRNA data sets are in conflic t for tapir relationships.