Analysis of oldest sequence from a human ancestor reveals close link with Denisovans

Image: Javier Trueba/Madrid Scientific Films

Another ancient genome, another mystery. DNA gleaned from a 400,000-year-old femur from Spain has revealed an unexpected link between Europes hominin inhabitants of the time and a cryptic population, the Denisovans, who are known to have lived much more recently in southwestern Siberia.

The DNA, which represents the oldest hominin sequence yet published, has left researchers baffled because most of them believed that the bones would be more closely linked to Neanderthals than to Denisovans. Thats not what I would have expected; thats not what anyone would have expected, says Chris Stringer, a paleoanthropologist at Londons Natural History Museum who was not involved in sequencing the femur DNA.

The fossil was excavated in the 1990s from a deep cave in a well-studied site in northern Spain called Sima de los Huesos (pit of bones). This femur and the remains of more than two dozen other hominins found at the site have previously been attributed either to early forms of Neanderthals, who lived in Europe until about 30,000 years ago, or to Homo heidelbergensis, a loosely defined hominin population that gave rise to Neanderthals in Europe and possibly humans in Africa.

But a closer link to Neanderthals than to Denisovans was not what was discovered by the team led by Svante Pbo, a molecular geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

The team sequenced most of the femurs mitochondrial genome, which is made up of DNA from the cells energy-producing structures and passed down the maternal line. The resulting phylogenetic analysis which shows branches in evolutionary history placed the DNA closer to that of Denisovans than to Neanderthals or modern humans. This really raises more questions than it answers, Pbo says.

The teams finding, published online in Nature this week (M. Meyer et al. Nature http://dx.doi.org/10.1038/nature12788; 2013), does not necessarily mean that the Sima de los Huesos hominins are more closely related to the Denisovans, a population that lived thousands of kilometres away and hundreds of thousands of years later, than to nearby Neanderthals. This is because the mitochondrial genome tells the history of just an individuals mother, and her mother, and so on.

Courtesy of Nature Magazine

Nuclear DNA, by contrast, contains material from both parents (and all of their ancestors) and typically provides a more accurate overview of a populations history. But this was not available from the femur.

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Earliest Human DNA Shows Unforeseen Mixing with Mystery Population