Phylogenetic analyses and improved resolution of the family Bovidae based on complete mitochondrial genomes

Abstract

Efforts have been made to investigate the phylogeny of the family Bovidae; however, the relationships within this group still remain controversial. To further our understanding of the relationships, we sequenced the mitochondrial genome of the Himalayan goral, Naemorhedus goral, an IUCN Redlist near threatened conservation dependent species. Then we conducted molecular phylogenetic relationships of the Bovidae based on Bayesian and Maximum Likelihood methods. The results indicate that the basal divergence within the Bovidae is between the Bovinae and a strongly supported clade of the remaining Bovidae species. The two Neotragus species (the suni and pygmy antelope) clustered with the impala, Aepyceros melampus (Aepycerotinae), and together they formed the most basal of the non-Bovinae. All the genera of the Antilopinae clustered together except Neotragus, which suggested that the Antilopinae was a paraphyletic subfamily. The present study confirmed a close relationship between the genera Capricornis and Naemorhedus while supporting their designation as separate genera and suggested that the Capricornis-Naemorhedus-Ovibos clade (serows, gorals, and the muskox) should be placed in the Caprinae. Bison, Bos, and Tragelaphus (bison & cattle and kudus and nyalas) were paraphyletic. The very close relationship between Bison and Bos suggested that Bos and Bison should be integrated into a single Bos genus. Saiga and Pantholops (the Chiru or Tibetan Antelope), unique genera which have sometimes been lumped together, were placed in different groups: Saiga within the Antilopinae and Pantholops at the base of the Caprinae. Our results also supported a new taxonomy which places the three species of Hemitragus into three monospecific genera: the genus Hemitragus is restricted to the Himalayan tahr, and two new genera are created: Arabitragus for the Arabian tahr and Nilgiritragus for the Nilgiri tahr.