Ancient hominid bone serves up DNA stunner

Scientists have recovered the oldest known DNA from a member of the human evolutionary family. This find raises surprising questions about relationships among far-flung populations of ancient hominids.

A nearly complete sample of mitochondrial DNA was extracted from a 400,000-year-old leg bone previously found in a cave in northern Spain. The DNA shows an unexpected hereditary link to the Denisovans, Neandertals’ genetic cousins that lived in East Asia at least 44,000 years ago, say paleogeneticist Matthias Meyer of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and his colleagues.

Their report, which quadruples the age of the oldest hominid DNA, appears December 4 in Nature.

The fossil bone was unearthed in three parts, one in 1994 and the other two in 1999. The same site — Sima de los Huesos, or pit of bones — has yielded the remains of at least 28 individuals. Many researchers classify these fossils as Homo heidelbergensis, a species thought to have been an ancestor of Neandertals and perhaps Homo sapiens as well.

Ancient mitochondrial DNA recovered by Meyer’s team raises questions about how genetic ties were forged between H. heidelbergensis in Western Europe and presumably later-evolving Denisovans. Mitochondrial DNA passes down solely from mother to child. Hominids’ ancient relationships are difficult to pin down partly because so few bones are available. The Denisovans, for instance, are represented today only by a finger bone and two teeth excavated in a Siberian cave.

“The Denisovan connection is fascinating, but I’m cautious about how to interpret it,” remarks paleoanthropologist John Hawks of the University of Wisconsin–Madison. Because so many years and miles separate the Sima and Denisovan populations, it’s hard to sort out the population movements and interactions that resulted in shared mitochondrial DNA segments, Hawks says.

Meyer suspects that the Sima hominids belonged to a population that was closely related to both Neandertals and Denisovans. If the Sima hominids’ ancestors mated with members of another hominid species — possibly Homo erectus or an as-yet-undiscovered population —mitochondrial DNA variants could have entered the Sima DNA and later reached the Denisovans via interbreeding with the same species, Meyer speculates.

Another possibility is that Denisovan ancestors occupied a vast expanse of Asia and Europe before the Sima population evolved, says paleogeneticist Carles Lalueza-Fox of the Institute of Evolutionary Biology in Barcelona. Hominid fossils found in two caves near Sima de los Huesos, dating to between 1.3 million and 800,000 years ago, may represent descendants of that intercontinental population, Lalueza-Fox suggests. Sima hominids thus could have received genetic contributions from those groups that partly matched DNA separately inherited by the Denisovans far to the east.

If so, Neandertals probably originated as a small, isolated European population around 250,000 years ago, Lalueza-Fox proposes.

Paleoanthropologist Chris Stringer of the Natural History Museum in London regards the ancient Sima individuals as early Neandertals. Mitochondrial DNA commonalities between the Denisovans and the Sima fossil may have been inherited from well-traveled H. heidelbergensis groups, Stringer says. These genetic sequences could eventually have been lost in Neandertals and modern humans, he hypothesizes, if women who carried the sequences had no surviving children, no daughters or daughters who had no further daughters.

“We really need nuclear DNA to solve the evolutionary puzzle at Sima de los Huesos,” Meyer says. Nuclear DNA, a legacy of both parents, is much tougher to retrieve from ancient bones than mitochondrial DNA.