Max Planck Research Group on Plant Foods in Hominin Dietary Ecology

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23 October 2014

Earliest modern human sequenced

A research team led by Svante Pääbo, Bence Viola and Janet Kelso from the Department of Evolutionary Genetics of the Max Planck Institute for Evolutionary Anthropology (Leipzig, Germany), with participation of Plant Foods Group researcher Domingo Carlos Salazar García, has sequenced the genome of a 45,000-year-old modern human male from western Siberia. The comparison of his genome to the genomes of people that lived later in Europe and Asia show that he lived close in time to when the ancestors of present-day people in Europe and eastern Asia went different ways. Like all present-day people outside Africa the Ust’-Ishim man carried segments of Neandertal DNA in his genome. But these segments were much longer than the ones found in present-day humans and indicate that the admixture with Neandertals took place between 50,000 and 60,000 years ago. Its diet shows higher environment plasticity, differently to what is directly observed on Neanderthals.

In 2008, a relatively complete human femur was discovered on the banks of the river Irtysh near the village of Ust’-Ishim in western Siberia. Radiocarbon dating of the bone showed it to be about 45,000 years old. “The morphology of the bone suggests that it is an early modern human, that is an individual related to populations that are the direct ancestors of people alive today” says Bence Viola, an archaeologist who analyzed it. “This individual is one of the oldest modern humans found outside the Middle East and Africa” he says.

The research team sequenced this individual’s genome to a very high quality and compared it to the genomes of present-day humans from more than 50 populations. They found that the Ust’-Ishim bone comes from a male individual who is more related to present-day people outside Africa than to Africans thus showing that he is an early representative of the modern population that left Africa. When his genome was compared to people outside Africa, he was found to be approximately equally related to people in East Asia and people that lived in Europe during the Stone Age. “The population to which the Ust’-Ishim individual belonged may have split from the ancestors of present-day West Eurasian and East Eurasian populations before, or at about the same time, when these two first split from each other”, says Svante Pääbo.  “It is very satisfying that we now have a good genome not only from Neandertals and Denisovans, but also from a very early modern human” he says. Paleoanthropologist Jean-Jacques Hublin, who was involved in the study, says that “it is possible that the Ust’-Ishim individual belonged to a population of early migrants into Europe and Central Asia, who failed to leave descendants among present-day populations”.

Since the Ust’-Ishim man lived at a time when Neandertals were still present in Eurasia, the researchers were interested in seeing whether his ancestors had already mixed with Neandertals. They found that that about 2 per cent of his DNA came from Neandertals -  similar to the proportion found in present-day East Asians and Europeans. However, the lengths of Neandertal DNA segments in his genome are much longer than the ones found in present-day humans because he lived closer in time to the admixture event so that the Neandertal segments had not had time to become as reduced in size over the generations. “This allowed us to estimate that the ancestors of the Ust’-Ishim individual mixed with Neandertals approximately about 7,000-13,000 years before this individual lived or about 50,000 to 60,000 years ago, which is close to the time of the major expansion of modern humans out of Africa and the Middle East”, says Janet Kelso, who led the computer-based analyses of the genome.

Stable isotope analysis of this early modern human suggest that he consumed freshwater resources on a regular basis, something yet to be directly observed on Neanderthals. "These results are important, since the consumption of aquatic resources portraits a wide-spectrum dietary pattern for these Eurasian pioneer early modern human populations not observed yet for Neanderthals of the region", says Domingo Carlos Salazar García. "Probably the ability to have this dietary plasticity helped them to adapt to extreme northern environments, helping them in their Eurasian 'enterprise' compared to Neanderthals, which eventually disappeared", he adds. Stable isotope analyses are useful to find out information about regular consumption of different types of dietary protein resources, differently to faunal and plant studies that, although showing what types of foods were consumed by past populations, can't define their overall proportion in the diet of the individuals.

The high quality of this 45,000-year-old genome also enabled the team to estimate the rate with which mutations accumulate in the human genome. They found that between one and two mutations per year have accumulated in the genomes of populations in Europe and Asia since the Ust’-Ishim man lived. This is similar to recent estimates from counting genetic differences between parents and children, but lower than more traditional, indirect estimates based on fossil divergences between species.

 

Original publication:

Qiaomei Fu, Heng Li, Priya Moorjani, Flora Jay, Sergey M. Slepchenko, Aleksei A. Bondarev, Philip L.F. Johnson, Ayinuer A. Petri, Kay Prüfer, Cesare de Filippo, Matthias Meyer, Nicolas Zwyns, Domingo C. Salazar-Garcia, Yaroslav V. Kuzmin, Susan G. Keates, Pavel A. Kosintsev, Dmitry I. Razhev, Michael P. Richards, Nikolai V. Peristov, Michael Lachmann, Katerina Douka, Thomas F.G. Higham, Montgomery Slatkin, Jean-Jacques Hublin, David Reich, Janet Kelso, T. Bence Viola, Svante Pääbo

The genome sequence of a 45,000-year-old modern human from western Siberia
Nature, 23 October 2014, DOI: 10.1038/nature13810

 

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