Elephants were once among the most widespread megafaunal families. However, only three species exist today: two species of the genus Loxodonta, the forest elephant (Loxodonta cyclotis) and the savanna elephant (Loxodonta africana), which are restricted to Africa; and one of the genus Elephas, which is endemic to Asia (Elephas maximus). To reconstruct their evolutionary history, an international team of scientists generated 14 genomes from several living and extinct elephant species. The results appear in the Proceedings of the National Academy of Science.

The team — led by researchers at the Broad Institute of MIT and Harvard, Harvard Medical School, Uppsala University, the University of Potsdam, and McMaster University — sequenced and analyzed 14 genomes from several species: two forest, two savanna, and two Asian elephants, an 120,000-year-old straight-tusked elephant (Palaeoloxodon antiquus), four woolly mammoths (Mammuthus primigenius), one Columbian mammoth (Mammuthus columbi), and also two American mastodons (Mammut americanum), which are an extinct distant relative of the elephant family.

The detailed analysis reveals that gene flow between elephant species was a common feature of their history, contrary to previous studies which represented their relationships as simple trees. However, the behavior has virtually stopped among living elephants, adding to growing fears about the future of the few species that remain on Earth.

“Interbreeding may help explain why mammoths were so successful over such diverse environments and for such a long time, importantly this genomic data also tells us that biology is messy and that evolution doesn’t happen in an organized, linear fashion,” said co-lead author Dr. Hendrik Poinar, director of the McMaster Ancient DNA Centre and principal investigator at the Michael G. DeGroote Institute for Infectious Research.

“The combined analysis of genome-wide data from all these ancient elephants and mastodons has raised the curtain on elephant population history, revealing complexity that we were simply not aware of before.”

The DNA analysis of the ancient straight-tusked elephant, for example, showed that it was a hybrid with portions of its genetic makeup stemming from an ancient African elephant, the woolly mammoth and present-day forest elephants.

“This is one of the oldest high-quality genomes that currently exists for any species,” said co-lead author Dr. Michael Hofreiter, from the University of Potsdam in Germany.

The team also found further evidence of interbreeding among the Columbian and woolly mammoths.

Despite their vastly different habitats and sizes, the authors believe the woolly mammoths encountered Columbians mammoths at the boundary of glacial and in the more temperate ecotones of North America.

Strikingly, the researchers found no genetic evidence of interbreeding among two of the world’s three remaining species, the forest and savanna elephants, suggesting they have lived in near-complete isolation for the past 500,000 years, despite living in neighboring habitats.

“There’s been a simmering debate in the conservation communities about whether African savannah and forest elephants are two different species,” said co-lead author Professor David Reich, from the Broad Institute, the Department of Genetics at Harvard Medical School and a Howard Hughes Medical Institute Investigator.

“Our data show that these two species have been isolated for long periods of time — making each worthy of independent conservation status.”

“The findings were extremely surprising to us. The elephant population relationships could not be explained by simple splits, providing clues for understanding the evolution of these iconic species,” said study first author Dr. Eleftheria Palkopoulou, a postdoctoral scientist at Harvard Medical School.

Future studies will need to explore the diversity of both living and ancient elephants and investigate population structure changes over distance and time.

“Obtaining a technicolor picture of elephant population structure may also be of immediate value for conservation efforts,” Dr. Reich said.

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Eleftheria Palkopoulou et al. A comprehensive genomic history of extinct and living elephants. PNAS, published online February 26, 2018; doi: 10.1073/pnas.1720554115