The first analysis of nuclear DNA from Sima de los Huesos hominins, conducted by Dr. Matthias Meyer of the Max Planck Institute for Evolutionary Anthropology and co-authors, provides evidence of their relationship to Neanderthals.

The Sima de los Huesos, or the Pit of Bones, is a cave site in Atapuerca Mountains, Spain, dated to around 430,000 years ago (Middle Pleistocene). It preserves a large collection of fossils attributed to an enigmatic species — the Sima de los Huesos hominin.

The site has been excavated continuously since 1984. After thirty years, archaeologists have recovered nearly 7,000 fossils corresponding to all skeletal regions of at least 28 individuals.

“A unique assemblage of 28 hominin individuals, found in Sima de los Huesos, has recently been dated to approximately 430,000 years ago,” explained Dr. Meyer and his colleagues from Spain, Canada, Germany and the United Kingdom.

“An interesting question is how these Middle Pleistocene hominins were related to those who lived in the Late Pleistocene epoch, in particular to Neanderthals in western Eurasia and to Denisovans, a sister group of Neanderthals so far known only from southern Siberia,” they said.

Previous analyses of the Sima de los Huesos hominins in 2013 showed that their maternally inherited mitochondrial DNA (mtDNA) was distantly related to Denisovans, a recently-discovered early human species.

The new results, appearing in the journal Nature, show that the hominins were indeed early Neanderthals.

“We recover nuclear DNA sequences from two specimens, which show that the Sima de los Huesos hominins were related to Neanderthals rather than to Denisovans, indicating that the population divergence between Neanderthals and Denisovans predates 430,000 years ago,” the scientists said.

“These results provide important anchor points in the timeline of human evolution,” said team member Dr. Svante Pääbo, also from the Max Planck Institute for Evolutionary Anthropology.

“They are consistent with a rather early divergence of 550,000 to 750,000 years ago of the modern human lineage from archaic humans.”

“The recovery of a small part of the nuclear genome from the Sima de los Huesos hominins is not just the result of our continuous efforts in pushing for more sensitive sample isolation and genome sequencing technologies,” Dr. Meyer said.

“This work would have been much more difficult without the special care that was taken during excavation.”

“We have hoped for many years that advances in molecular analysis techniques would one day aid our investigation of this unique assembly of fossils,” added team member Dr. Juan-Luis Arsuaga, of the Complutense University in Madrid, Spain. “We have thus removed some of the specimens with clean instruments and left them embedded in clay to minimize alterations of the material that might take place after excavation.”

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Matthias Meyer et al. Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature, published online March 14, 2016; doi: 10.1038/nature17405