Sima de los Huesos: Scientists Sequence Genome of Enigmatic Hominin

Researchers from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have sequenced the mitochondrial genome of a 400,000-year-old hominin found in Sima de los Huesos, Spain.

Sima de los Huesos hominins lived in what is now Spain about 400,000 years ago. Image credit: © Kennis & Kennis / Madrid Scientific Films.

Sima de los Huesos hominins lived in what is now Spain about 400,000 years ago. Image credit: © Kennis & Kennis / Madrid Scientific Films.

Sima de los Huesos – the Pit of Bones – is a cave site in Atapuerca Mountains, northern Spain.

During 1990s, at least 28 skeletons of Middle Pleistocene hominins were found at the site by Spanish paleontologists led by Dr Juan-Luis Arsuaga from the Center for Research on Human Evolution and Behaviour.

The scientists dated the finds as being 600,000 to 300,000 years old, and assigned them as belonging to Homo heidelbergensis.

In 2010s, Dr Arsuaga teamed up with Max Planck scientists, who recently developed novel techniques for retrieving and sequencing highly degraded ancient DNA.

The team applied the new techniques to hominin remains from the Sima de los Huesos site to sequence their mitochondrial DNA (mtDNA) and then compared the genome with that of Neandertals, Denisovans, present-day humans, and apes.

The results show that the Sima de los Huesos hominin lived about 400,000 years ago and shared a common ancestor with Denisovans, an ancient human species that lived in a vast range from Siberia to Southeast Asia at the same time as Neanderthals, about 700,000 years ago.

“The fact that the mtDNA of the Sima de los Huesos hominin shares a common ancestor with Denisovan rather than Neanderthal mtDNAs is unexpected since its skeletal remains carry Neanderthal-derived features,” said Dr Matthias Meyer, the lead author of a paper published online in Nature.

“Considering their age and Neanderthal-like features, the Sima de los Huesos hominins were likely related to the population ancestral to both Neanderthals and Denisovans. Another possibility is that gene flow from yet another group of hominins brought the Denisova-like mtDNA into the Sima de los Huesos hominins or their ancestors.”

Study co-author Dr Svante Pääbo added: “our results show that we can now study DNA from human ancestors that are hundreds of thousands of years old. This opens prospects to study the genes of the ancestors of Neanderthals and Denisovans. It is tremendously exciting.”

“This unexpected result points to a complex pattern of evolution in the origin of Neanderthals and modern humans. I hope that more research will help clarify the genetic relationships of the hominins from Sima de los Huesos to Neandertals and Denisovans,” Dr Arsuaga said.


Meyer M et al. A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature, published online December 4, 2013; doi: 10.1038/nature12788