After developing techniques for extracting and analysing DNA from ancient (c. 40,000 years ago) Neanderthal and Denisovan specimens the Max Planck team have now taken a giant leap backwards in time in extracting and analysing an almost complete mitochondrial genome sequence of a 400,000-year-hominin. The specimen is from Sima de los Huesos, a unique cave site in Northern Spain. The results show that it is related to the mitochondrial genome of Denisovans, extinct relatives of Neandertals in Asia. DNA this old has until recently been retrieved only from the permafrost.
The result itself is of great interest but it is the development of the techniques for extracting and analysing – without any contamination – and with sufficient confidence, the entire MtDNA sequence in such old specimens that is quite revolutionary. Archaeological evidence – and particularly of of such age – is subject to a great deal of subjective interpretation. But dating techniques and now DNA extraction techniques are removing much of this subjectivity and they are now providing the anchor points around which the evolutionary narrative must be built. And this narrative is now of a much more complex story of hominin expansions and admixture than has generally been thought. Ancient and presumed extinct hominin species are now showing themselves within us.
“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 Neandertals and Denisovans. It is tremendously exciting” says Svante Pääbo, director at the Max Planck Institute for Evolutionary Anthropology.
Matthias Meyer, Qiaomei Fu, Ayinuer Aximu-Petri, Isabelle Glocke, Birgit Nickel, Juan-Luis Arsuaga, Ignacio Martínez, Ana Gracia, José María Bermúdez de Castro, Eudald Carbonell, Svante Pääbo. A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature, 2013; DOI: 10.1038/nature12788
Abstract: Excavations of a complex of caves in the Sierra de Atapuerca in northern Spain have unearthed hominin fossils that range in age from the early Pleistocene to the Holocene1. One of these sites, the ‘Sima de los Huesos’ (‘pit of bones’), has yielded the world’s largest assemblage of Middle Pleistocene hominin fossils, consisting of at least 28 individuals dated to over 300,000 years ago. The skeletal remains share a number of morphological features with fossils classified asHomo heidelbergensis and also display distinct Neanderthal-derived traits. Here we determine an almost complete mitochondrial genome sequence of a hominin from Sima de los Huesos and show that it is closely related to the lineage leading to mitochondrial genomes of Denisovans, an eastern Eurasian sister group to Neanderthals. Our results pave the way for DNA research on hominins from the Middle Pleistocene.
The most impressive aspect of the new paper is most likely the technical challenges that the researchers must’ve overcome to achieve this result. The cave bear DNA showed that this was possible, but human DNA adds an additional complication in the form of contamination by a closely related species, us.
But, the new evolutionary result which will interest those of us not interested in the minutiae of biomolecules will no doubt be the fact that the Sima hominin’s mtDNA formed a clade with the much more recent Denisova girl.
Until now, we knew that Neandertal mtDNA grouped together and so did modern human mtDNA. The two groups shared a Middle Pleistocene common ancestor and a much more distant common ancestor (~1 million years) with the mtDNA found in Denisova. The new Sima specimen shares descent from Denisova. This is important because it shows that whatever archaic human population the Denisovan mtDNA belonged to also extended to western Europe. And, surprisingly, the Sima specimen did not group with Neandertals, as might be expected because of the incipient Neanderthaloid morphology of the Sima hominins which has been a matter of controversy as it pushes back the evolutionary lineage of H. neandertalensis deeper into the Middle Pleistocene that some researchers accept.
Before this paper, it was believed that H. heidelbergensis evolved somewhere (perhaps Near East or Africa), a subset of it evolved to H. sapiens in Africa, and a different subset evolved in Eurasia, leading up to H. neandertalensis in the west, and unknown forms in the east, of which the Denisova girl was a matrilineal descendant. The next question is: when did Neandertals and Neandertal mtDNA appear in Europe?
Sima de los Huesos, the “bone pit”, is a cave site in Northern Spain that has yielded the world’s largest assembly of Middle Pleistocene hominin fossils, consisting of at least 28 skeletons, which have been excavated and pieced together over the course of more than two decades by a Spanish team of paleontologists led by Juan-Luis Arsuaga. The fossils are classified as Homo heidelbergensis but also carry traits typical of Neandertals. Until now it had not been possible to study the DNA of these unique hominins.
Matthias Meyer and his team from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have developed new techniques for retrieving and sequencing highly degraded ancient DNA. They then joined forces with Juan-Luis Arsuaga and applied the new techniques to a cave bear from the Sima de los Huesos site. After this success, the researchers sampled two grams of bone powder from a hominin thigh bone from the cave. They extracted its DNA and sequenced the genome of the mitochondria or mtDNA, a small part of the genome that is passed down along the maternal line and occurs in many copies per cell. The researchers then compared this ancient mitochondrial DNA with Neandertals, Denisovans, present-day humans, and apes.
From the missing mutations in the old DNA sequences the researchers calculated that the Sima hominin lived about 400,000 years ago. They also found that it shared a common ancestor with the Denisovans, an extinct archaic group from Asia related to the Neandertals, 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 Neandertal mtDNAs is unexpected since its skeletal remains carry Neandertal-derived features”, says Matthias Meyer. Considering their age and Neandertal-like features, the Sima hominins were likely related to the population ancestral to both Neandertals and Denisovans. Another possibility is that gene flow from yet another group of hominins brought the Denisova-like mtDNA into the Sima hominins or their ancestors.