A comprehensive genomic history of extinct and living elephants.

Elephantids are the world's most iconic megafaunal family, yet there is no comprehensive genomic assessment of their relationships. We report a total of 14 genomes, including 2 from the American mastodon, which is an extinct elephantid relative, and 12 spanning all three extant and three extinct elephantid species including an ∼120,000-y-old straight-tusked elephant, a Columbian mammoth, and woolly mammoths. Earlier genetic studies modeled elephantid evolution via simple bifurcating trees, but here we show that interspecies hybridization has been a recurrent feature of elephantid evolution. We found that the genetic makeup of the straight-tusked elephant, previously placed as a sister group to African forest elephants based on lower coverage data, in fact comprises three major components. Most of the straight-tusked elephant's ancestry derives from a lineage related to the ancestor of African elephants while its remaining ancestry consists of a large contribution from a lineage related to forest elephants and another related to mammoths. Columbian and woolly mammoths also showed evidence of interbreeding, likely following a latitudinal cline across North America. While hybridization events have shaped elephantid history in profound ways, isolation also appears to have played an important role. Our data reveal nearly complete isolation between the ancestors of the African forest and savanna elephants for ∼500,000 y, providing compelling justification for the conservation of forest and savanna elephants as separate species.

A new Mammutidae (Proboscidea, Mammalia) from the Late Miocene of Gansu Province, China.

The "Yanghecun specimen", a proboscidean specimen represented by a mandible from Miocene of China and previously described as Gomphotheriidae, is here reviewed and described as a new genus and species of Mammutidae: Sinomammut tobieni. This taxon is a longirostrine mastodon, lacking lower tusks, and bearing a wide last molar with oblique and non-inflated lophids, broad transverse interlophids, and yoke-like wear figures. Phylogenetic analysis of Mammutidae based on dental and mandibular features recovered S. tobieni as sister group of the mastodon Mammut. The longirostrine condition and the well-developed lower incisors seem to be primitive for Mammutidae, while the brevirostry is the derived condition, probably emerged during the middle Miocene (12-11 Mya). However, two derived conditions are recognized to the lower tusks: the absence of lower tusks (S. tobieni) and the occasional presence of vestigial lower tusks (Mammut).

Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephants.

To elucidate the history of living and extinct elephantids, we generated 39,763 bp of aligned nuclear DNA sequence across 375 loci for African savanna elephant, African forest elephant, Asian elephant, the extinct American mastodon, and the woolly mammoth. Our data establish that the Asian elephant is the closest living relative of the extinct mammoth in the nuclear genome, extending previous findings from mitochondrial DNA analyses. We also find that savanna and forest elephants, which some have argued are the same species, are as or more divergent in the nuclear genome as mammoths and Asian elephants, which are considered to be distinct genera, thus resolving a long-standing debate about the appropriate taxonomic classification of the African elephants. Finally, we document a much larger effective population size in forest elephants compared with the other elephantid taxa, likely reflecting species differences in ancient geographic structure and range and differences in life history traits such as variance in male reproductive success.