Neanderthal DNA reveals ancient long-distance migrations

In their new study an international team led by the University of Vienna reports the discovery and extraction of ancient DNA from a tiny 5 cm long Neanderthal bone found in the Crimean peninsula, shedding light on long-distance migrations during the Late Pleistocene period 40,000 - 50,000 years ago. The Neanderthal bone, called "Star 1", after the site from which it was excavated – Starosele Cave – was found using a biomolecular method that uses ancient proteins to determine if a bone belongs to humans or animals. Ancient DNA extracted from the bone showed that it was genetically closest related to Neanderthals from the Altai region of Siberia, over 3,000 kilometers away. Climate modelling suggests that Neanderthal groups probably migrated across the vast Eurasian steppes during a time of favourable climate. The study was published in PNAS.

A site with a long history

The Crimean Peninsula rock shelter of Starosele has been studied since 1952. Until now, only post-medieval human remains had been recovered. However, using new molecular methods, researchers from the University of Vienna now examined more than 150 unidentified bone fragments from the site. Amongst these fragments they discovered a small, 5 cm fragment of what was probably a human thigh bone.

The site's four archaeological layers contain rich cultural material: levels 1, 2, and 4 are associated with stone tools from an archaeological industry called the Crimean Micoquian stone tool industry, which is linked to Neanderthals.

Revisiting the past with new techniques

Researcher Emily M. Pigott, a doctoral student at the University of Vienna and lead author on the paper, employed a palaeoproteomic method known as Zooarchaeology by Mass Spectrometry (ZooMS) to determine the species of 150 fragmented bones. While these bones could not be identified taxonomically due to their small size, by extracting the collagen peptides and analysing their mass it is possible to identify even tiny fragments to species or genus level. Of the 150 analysed bones, 93% belonged to horses and deer, with smaller numbers of mammoth and wolf remains — suggesting that Palaeolithic humans in Crimea relied heavily on horse hunting. Remarkably, one small fragment — only 49.8 mm long and 18.8 mm wide — was identified as human.

The human bone was scanned using micro-CT imaging, which revealed it was likely to have come from a thigh bone. Subsequently, it was also radiocarbon dated using the most up-to-date decontamination methods, which placed the bone between 46,000 and 44,000 years ago, securely within the Palaeolithic period.

"This was an extremely exciting discovery, especially since previous human remains at Starosele were thought to be Homo sapiens from much later periods," said Pigott. "When the radiocarbon results came back, we knew we had found a truly Palaeolithic human. It was an unforgettable moment — and it happened to be only the 46th bone I analysed with ZooMS. Across Eurasia, very few human fossils are known from this crucial period when Neanderthals disappeared and Homo sapiens replaced them, and still fewer with genetic Information".

A glimpse into Neanderthal mobility

The discovery highlights the mobility and resilience of Neanderthals, revealing that these ancient humans were more widespread in their dispersal than often previously assumed.

Co-authors Konstantina Cheshmedzhieva and Martin Kuhlwilm of the University of Vienna led the genetic analysis on the new human remains, finding that the human bone belonged to a Neanderthal, which the team named "Star 1". Surprisingly, this individual was most closely related to Neanderthals from Siberia's Altai region, more than 3,000 kilometers to the east, but also with Neanderthals that once lived in regions of Europe such as Croatia. The findings confirm previous studies suggesting that Neanderthals once dispersed over vast distances across Eurasia during the Late Pleistocene, from as far west as central Europe to central Eurasia. This work places the Crimean Peninsula at the crossroads of this Neanderthal migration corridor.

Through climate and human habitat modelling, Elke Zeller (University of Arizona, US) and Axel Timmermann (Pusan National University, South Korea) identified two favourable climatic periods (120,000 and 60,000 years ago) during which Neanderthals may have moved between Crimea, central Asia, and Europe, perhaps following migrating herds of animals.

"Our work demonstrates that by combining techniques such as ZooMS, radiocarbon dating, and ancient DNA analysis, even the smallest bone fragments can yield profound information about our evolutionary past", senior author Tom Higham from the University of Vienna summarizes. "This type of multianalytical work applied to other collections will help us uncover more hidden human remains, and bring us closer to understanding the complex story of human evolution across Eurasia. Our understanding of Neanderthals has changed so much over the last few years. Our new study confirms that they were capable of moving long distances in various directions, something we thought for many decades was restricted almost exclusively to our species."

Summary:

• When examining more than 150 unidentified bone fragments from the Crimean peninsula rockshelter of Starosele one small 5 cm fragment was identified as a small piece of a Neanderthal bone – named "Star 1" by the team. 
• The fragment was scanned using micro-CT imaging, which revealed it was likely to have come from a human thigh bone. It was also radiocarbon dated using the most up-to-date decontamination methods, which placed the bone between 46,000 and 44,000 years ago, securely within the Palaeolithic period.
• Further investigations showed, the individual was most closely related to Neanderthals from Siberia's Altai region, more than 3,000 kilometers to the east, but also with Neanderthals that once lived in regions of Europe such as Croatia.
• The findings suggest that Neanderthals must have once dispersed over vast distances across Eurasia during the Late Pleistocene; from as far west as central Europe, all the way to central Eurasia, with Crimea being at the crossroads of this pathway.
• Through climate modelling the scientists identified when humans were most likely to move, taking advantage of favourable climates. They found the so-called 'last interglacial period' around 120,000 years ago was one of these periods, and another around 60,000 years ago.

About the study:

The scientists used Mass Spectrometry (ZooMS) to identify different species among the fragmented bones. The fragment identified as human was scanned using micro-CT imaging, was radiocarbon dated and genetically analysed, revealing it belonged to a late Neanderthal. Climate modelling identified key periods when humans were most likely taking advantage of favourable climates along which they could move.

About the University of Vienna:

For over 650 years the University of Vienna has stood for education, research and innovation. Today, it is ranked among the top 100 and thus the top four per cent of all universities worldwide and is globally connected.
With degree programmes covering over 180 disciplines, and more than 10,000 employees we are one of the largest academic institutions in Europe. Here, people from a broad spectrum of disciplines come together to carry out research at the highest level and develop solutions for current and future challenges. Its students and graduates develop reflected and sustainable solutions to complex challenges using innovative spirit and curiosity.

Funding

This research was funded by the European Union (ERC grant number 101142352 "DISPERSE" awarded to TH). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union. Neither the European Union nor the granting authority can be held responsible for them. The Vienna Science and Technology Fund (WWTF) [10.47379/VRG20001] supported Prof. Kuhlwilm, along with the Life Science Compute Cluster (LiSC) of the University of Vienna. The IBS Center for Climate Physics grant IBS-R028-D1 supported Prof. Timmermann.

The Vienna authors are supported by and part of the HEAS Forschungsverbund (Human Evolution and Archaeological Sciences), of which Prof. Higham is the Director. 

Higham Lab.

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