1. Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702, USA
2. Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
3. Center for Reproduction of Endangered Species, Zoological Society of San Diego, San Diego, California 92112, USA
4. Department of Biology, University of Maryland, College Park, Maryland 20742, USA
5. These authors contributed equally to this work

Correspondence to: Stephen J. O'Brien¹ Correspondence and requests for materials should be addressed to S.J.O. (e-mail: Email: obrien@mail.ncifcrf.gov).

Abstract

The precise hierarchy of ancient divergence events that led to the present assemblage of modern placental mammals has been an area of controversy among morphologists, palaeontologists and molecular evolutionists. Here we address the potential weaknesses of limited character and taxon sampling in a comprehensive molecular phylogenetic analysis of 64 species sampled across all extant orders of placental mammals. We examined sequence variation in 18 homologous gene segments (including nearly 10,000 base pairs) that were selected for maximal phylogenetic informativeness in resolving the hierarchy of early mammalian divergence. Phylogenetic analyses identify four primary superordinal clades: (I) Afrotheria (elephants, manatees, hyraxes, tenrecs, aardvark and elephant shrews); (II) Xenarthra (sloths, anteaters and armadillos); (III) Glires (rodents and lagomorphs), as a sister taxon to primates, flying lemurs and tree shrews; and (IV) the remaining orders of placental mammals (cetaceans, artiodactyls, perissodactyls, carnivores, pangolins, bats and core insectivores). Our results provide new insight into the pattern of the early placental mammal radiation.