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Paleogenomic Analysis Places Ancient Eurasian Elephant Within African Lineages

NEW YORK (GenomeWeb) – Large straight-tusked elephants that once roamed Eurasia are more closely related to African forest elephants than they are to Asian elephants, according to a new paleogenomic analysis.

Straight-tusked elephants, Palaeoloxodon antiquus, lived some 1.5 million years to 100,000 years ago. Male straight-tusked elephants could reach four meters in height and weigh as much as 13 tons, more than twice as some modern elephants. Previous morphological analyses had indicated that Palaeoloxodon were more similar to Asian elephants, Elephas maximus, than to either species of African elephants.

But, an international team of researchers has sequenced DNA isolated from four ancient Palaeoloxodon bones, and, as it reported this week in eLife, its analysis of both mitochondrial and nuclear DNA showed that Palaeoloxodon was most closely related to African forest elephants, Loxodonta cyclotis — and are even more closely related to African forest elephants than the African forest elephants are to the African savanna elephant, L. africana.

"From the study of bone morphology, people thought Palaeoloxodon was closer to the Asian elephant. But from the molecular data, we found they are much closer to the African forest elephant," said study co-author Yasuko Ishida from the University of Illinois at Urbana-Champaign in a statement.

Ishida and her colleagues attempted to extract and sequence DNA from a number of P. antiquus samples from two sites in Germany, though they focused on four in particular. Samples from Neumark-Nord and Weimar-Ehringsdorf dated to interglacial periods about 120,000 years and about 244,000 years ago, respectively.

By morphology, three of these samples were unambiguously assigned to P. antiquus, while the third came from a rock layer that dated to a time when P. antiquus was the only known elephantid there.

The researchers generated full mitochondrial genome sequences for all four samples and partial nuclear genome sequences for two samples. The sequences all harbored signs of cytosine deamination, which is common among ancient samples.

Using the four mitochondrial genome sequences they generated along with mitochondrial genome sequences from 16 woolly mammoth (Mammuthus primigenius), two E. maximus,and 13 Loxodonta individuals, the researchers pieced together a phylogenetic tree. Rather than clustering among the E. maximus, Palaeoloxodon fell near L. cyclotis, the researchers reported.

The researchers estimated that most recent common ancestor of P. antiquus and L. cyclotis lived between 1.5 million and 3.5 million years ago, while that most recent common ancestor of P. antiquus and L. africana lived between 3.9 million and 7 million years ago.

A neighbor-joining phylogenetic tree based on the shotgun nuclear genome sequences obtained from the Neumark-Nord samples similarly indicated a sister group relationship between P. antiquus and L. cyclotis.

"The strongly supported mitochondrial and nuclear DNA phylogenies clearly demonstrate that Palaeoloxodon antiquus is more closely related to Loxodonta than to Elephas," the researchers wrote in their paper.

Additionally, they noted that the Palaeoloxodon, though few in samples, formed two lineages based on the site where they were unearthed.

Though they were only able to generate a broad view and that there could be complex interactions at play, the researchers said that their findings suggest that the evolutionary history of elephantids needs to be revisited.

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