Genomics of Elephants and their Extinct Relatives

Elephantid lineages first appeared in Africa about 9 million years ago giving rise to the African and Asian elephants that survive until today as well as their extinct relatives, some of which disappeared just a few thousand years ago. Morphological and genetic analyses have shown that present-day elephants comprise two genera: the African Loxodonta, which is commonly argued to include two species, the savanna (L. africana) and forest (L. cyclotis) elephant, and the Asian Elephas (Elephas maximus). Extinct woolly mammoths (Mammuthus primigenius) have been genetically shown to be most closely related to the Asian elephant, while other taxa such as the straight-tusked European elephant (Paleoloxodon antiquus) have not been sequenced to date. We generated genome-wide data from 15 Proboscideans, including new high-coverage genomes from 7 elephants (2 forest, 2 savanna, 2 Asian and 1 straight-tusked) as well as low to medium coverage genomes from another 8 proboscideans (4 woolly mammoths, 1 Columbian mammoth, 1 straight-tusked elephant, and 2 mastodons (Mammut americanum, a non-elephant outgroup). We analyzed this dataset to document the evolutionary relationships among the different lineages and reconstruct admixture events, demographic changes and natural selection. Using complete genome sequences, we were able to establish the phylogeny of elephantids and resolve the topology of P. antiquus. We also discovered signals of inter-species gene flow, such as between woolly and Columbian mammoths, and between forest and savanna elephants, revealing a complex history of admixture within the elephantid family.

Eleftheria Palkopoulou, Swapan Mallick, Jacob Enk, Emil Karpinski, Nadin Rohland, Ross MacPhee, Grant Zazula, Matthias Meyer, Kurt Alt, Harald Meller, Stefan Claesson, the Elephant Genome Sequencing Consortium, Hendrik Poinar, Michael Hofreiter, David Reich