In popular culture, genetics is seen as a tool for predicting your future health. But increasingly, scientists use it to understand the past, as two recent papers from the lab of HMS associate professor of genetics David Reich demonstrate.

In one study, the sequenced genome of an ancient finger bone taken from a Siberian cave showed that modern humans are not related to the ancient cave dwellers. In the other, researchers found that Africa has two, not one, species of elephant—a finding that raises issues for conservationists.

Forest elephants (shown) in Africa have been confirmed as a new species of elephant, distinct from the larger savanna elephant. Photo by Nicholas Georgiadis.

The Elephants in the Room

In the elephant study, Reich and colleagues at the University of Illinois and the University of York in Britain used genetic analysis to prove that the African savanna elephant and the smaller African forest elephant have been largely separated over several million years and thus comprise separate species.

The researchers, whose findings appeared online in PLoS Biology on Dec. 21, compared the DNA of modern elephants from Africa and Asia to DNA from two extinct species: the woolly mammoth and the mastodon. This study was the first genomic comparison of the mastodon, the Asian elephant, the African forest elephant, the African savanna elephant and the woolly mammoth.

David Reich. Photo by Stephanie Mitchell/Harvard news staff

Limited to DNA samples from only a single elephant in each species, the researchers still had enough data to traverse millions of years of evolution to the time when these elephant species diverged.

“We had a major challenge to extract DNA sequences from two fossils—mammoths and mastodons— and line them up with DNA from modern elephants over hundreds of sections of the genome,” said research scientist Nadin Rohland of the Department of Genetics at Harvard Medical School.

“The divergence of the two species took place around the time of the divergence of the Asian elephant and woolly mammoths,” said Michi Hofreiter of the University of York. “The split between African savanna and forest elephants is almost as old as the split between humans and chimpanzees. This result amazed us all.”

Many naturalists consider African savanna elephants and African forest elephants as two populations of the same species, despite the significant size differences. The savanna elephant weighs between six and seven tons, roughly double the weight of the forest elephant.

DNA analysis revealed a wide range of genetic diversity within each species. The savanna elephant and woolly mammoth have very low genetic diversity, Asian elephants have medium diversity, and forest elephants have very high diversity.

All African elephants have been conserved as one species since 1950. These new findings suggest that the forest elephant should become a bigger priority for conservation.

Tooth and Finger

For the hominin study, Reich teamed up with a group of researchers led by Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology. Reporting in the Dec. 23 issue of Nature, the group described sequencing the nuclear genome from a 30,000 year old finger bone of an extinct hominin that was excavated by archaeologists in southern Siberia, Russia, in 2008. A team at Harvard Medical School led the population-genetics analysis of the fossil.

The researchers found that the individual was female and came from a group of hominins that shared an ancient origin with Neandertals, but subsequently diverged. They call this group of hominins Denisovans. Analysis revealed that Denisovans were genetically similar to modern-day Papua New Guinean populations, suggesting that there was interbreeding between Denisovans and the ancestors of Melanesians.

In addition, a Denisovan tooth found in the same cave shows a morphology distinct from Neandertals and modern humans that resembles much older hominin forms.

“The fact that Denisovans were discovered in Southern Siberia but contributed genetic material to modern human populations from New Guinea suggests that Denisovans may have been widespread in Asia during the Late Pleistocene,” said Reich.

For more information, students may contact David Reich at reich@genetics.med.harvard.edu.

Conflict Disclosure: The authors declare no conflicts of interest.

Funding Sources: For the PLoS Biology study: The Max Planck Society, Burroughs Wellcome Career Development Award in the Biomedical Science, the Broad Institute. For the Nature study: The Max Planck Society, the Krekeler Foundation, the National Institutes of Health, the National Science Foundation; the authors are solely responsible for the content of this work.