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

Nicholas J. Georgiadis,Nadin Rohland,David Reich,Alfred L. Roca,Richard E. Green,David Penny,Swapan Mallick,Matthias Meyer,Michael Hofreiter

doi:10.1371/journal.pbio.1000564

Abstract

Author SummaryThe living elephants are the last survivors of a once highly successful mammalian order, the Proboscidea, which includes extinct species such as the iconic woolly mammoth (Mammuthus primigenius) and the American mastodon (Mammut americanum). Despite numerous studies, the phylogenetic relationships of the modern elephants to the woolly mammoth, as well as the taxonomic status of the African elephants of the genus Loxodonta, remain controversial. This is in large part due to the fact that both the woolly mammoth and the American mastodon (the closest outgroup to elephants and mammoths available for genetic studies) are extinct, posing considerable technical hurdles for comparative genetic analysis. We have used a combination of modern DNA sequencing and targeted PCR amplification to obtain a large data set for comparing American mastodon, woolly mammoth, Asian elephant, African savanna elephant, and African forest elephant. We unequivocally establish that the Asian elephant is the sister species to the woolly mammoth. A surprising finding from our study is that the divergence of African savanna and forest elephants—which some have argued to be two populations of the same species—is about as ancient as the divergence of Asian elephants and mammoths. Given their ancient divergence, we conclude that African savanna and forest elephants should be classified as two distinct species.

Highlights

The technology for sequencing DNA from extinct species such as mastodons and mammoths provides a powerful tool for elucidating the phylogeny of the Elephantidae, a family that originated in the Miocene and that includes Asian elephants, African elephants, and extinct mammoths [1,2,3,4,5,6,7,8]
The mitochondrial DNA (mtDNA) analysis suggested that mammoths and Asian elephants form a clade with an estimated genetic divergence time of 5.8–7.8 million years ago (Mya), while African elephants diverged from an earlier common ancestor 6.6–8.8 Mya [8]
We have used a combination of modern DNA sequencing and targeted PCR amplification to obtain a large data set for comparing American mastodon, woolly mammoth, Asian elephant, African savanna elephant, and African forest elephant

Summary

Introduction

The technology for sequencing DNA from extinct species such as mastodons (genus Mammut) and mammoths (genus Mammuthus) provides a powerful tool for elucidating the phylogeny of the Elephantidae, a family that originated in the Miocene and that includes Asian elephants (genus Elephas), African elephants (genus Loxodonta), and extinct mammoths [1,2,3,4,5,6,7,8]. Generalizing about species relationships based on mtDNA alone is especially problematic for the Elephantidae because their core social groups (‘‘herds’’) are matrilocal, with females rarely, if ever, dispersing across groups [12]. This results in mtDNA genealogies in both African [13,14] and Asian elephants [15] that exhibit deeper divergence and/or different phylogeographic patterns than the nuclear genome

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