Mining the mammalian genome for artiodactyl systematics

A total of 7,806 nucleotide positions derived from one mitochondrial and ei ght nuclear DNA segments were used to provide a robust phylogeny for member s of the order Artiodactyla. Twenty-four artiodactyl and two cetacean speci es were included, and the horse (order Perissodactyla) was used as the outg roup. Limited rate heterogeneity was observed among the nuclear genes. The partition homogeneity tests indicated no conflicting signal among the nucle ar gene fragments, so the sequence data were analyzed together and as separ ate loci. Analyses based on the individual nuclear DNA fragments and on 34 unique indels all produced phylogenies largely congruent with the topology from the combined data set. In sharp contrast to the nuclear DNA data, the mtDNA cytochrome b sequence data showed high levels of homoplasy, failed to produce a robust phylogeny, and were remarkably sensitive to taxon samplin g. The nuclear DNA data clearly support the paraphyletic nature of the Arti odactyla. Additionally, the family Suidae is diphyletic, and the nonruminat ing pigs and peccaries (Suiformes) were the most basal cetartiodactyl group . The morphologically derived Ruminantia was always monophyletic; within th is group, all taxa with paired bony structures on their skulls clustered to gether. The nuclear DNA data suggest that the Antilocaprinae account for a unique evolutionary lineage, the Cervidae and Bovidae are sister taxa, and the Giraffidae are more primitive.