Entrance to the Goyet Caves in Belgium. Credit: © Mateja Hajdinjak

A new genetic study has revealed the regional diversity that existed in northwestern Europe shortly before Neanderthals disappeared.

A new genetic study provides the most detailed picture to date of late Neanderthal diversity in northwestern Europe.

By analysing ancient DNA from remains found in Belgium and France, an international team led by researchers from the Max Planck Institute for Evolutionary Anthropology in Leipzig was able to reconstruct the genetic relationships of 27 Neanderthals who lived shortly before Neanderthals disappeared around 40,000 years ago.

The researchers analysed the genomes of Neanderthals from ten archaeological sites, focusing particularly on the Meuse Basin in Belgium, an area with a high concentration of late Neanderthal sites (ie those Neanderthals who lived towards the end of Neanderthal existence).

The dataset includes a new, high-coverage genome from an individual from Goyet Cave who lived around 45,000 years ago.

First author Alba Bossoms Mesa, a doctoral researcher at the Max Planck Institute for Evolutionary Anthropology, said: “Until now, we only had four high-quality Neanderthal genomes and a limited number of lower-quality ones, so most questions about the regional diversity of Neanderthals have been difficult to address.

“By generating genetic data from multiple individuals from the region of present-day Belgium and France, we can now examine late Neanderthal populations in much greater detail.”

Neanderthal femur fragment (Goyet Q56-1), from which a new high-coverage genome was sequenced. Credit: © E Dewamme, Royal Belgian Institute of Natural Sciences. CC BY.

A connected but diverse population

Previous high-quality genomes had shown that some Neanderthal groups, particularly those in the Altai region of Siberia, lived in small, genetically isolated communities, with evidence of mating among close relatives.

In contrast, in this new study the researchers found no evidence for recent mating between close relatives among these late Neanderthals of northwestern Europe.

Instead, these Neanderthals were part of a larger and more well-connected regional population, quite different to what previously seen for Neanderthals in Siberia.

Senior author Benjamin M Peter, a group leader at the Max Planck Institute for Evolutionary Anthropology, said: “Our results show that the picture emerging from one region cannot simply be applied to all Neanderthals.

“The late Neanderthals from northwestern Europe appear to have been part of a connected regional population, rather than small, isolated groups with frequent mating between close relatives.”

The study also reveals a more complex population history of Neanderthals than previously recognised.

Senior author Mateja Hajdinjak, a group leader at the Max Planck Institute for Evolutionary Anthropology, said: “The genetic data show both connection and complexity.

“Most late Neanderthals from northwestern Europe are closely related at the population level, but some lineages point to much deeper and more diverse Neanderthal history.”

The Neanderthals in this study lived at a time when early modern humans were already present in parts of Europe.

While genetic evidence indicates that Neanderthals contributed genetic material to early modern humans, the researchers found no evidence of recent gene flow in the opposite direction.

Bossoms Mesa said: “Our results add to a striking asymmetry. We repeatedly find Neanderthal ancestry in early modern humans, but so far, we have not found clear evidence of recent modern human ancestry in late Neanderthals.”

Rethinking Neanderthal extinction

The disappearance of Neanderthals has often been linked to small population size, inbreeding, and the accumulation of harmful genetic variants.

The new study tested this theory by comparing measures of genetic diversity and genetic load in Neanderthal genomes from different time periods and regions.

Although all Neanderthals had very limited genetic diversity, the researchers found no evidence that the late Neanderthals carried an increasing burden of harmful mutations, and when they compared the high-quality genome of the Goyet Neanderthal, her genome did not show lower diversity than earlier Neanderthals.

These results do not rule out the possibility of demographic vulnerability; however, they challenge the idea that Neanderthals disappeared mainly because their genomes steadily deteriorated.

Instead, late Neanderthals in Belgium and France appear to have been part of a connected, genetically diverse regional population during a period of profound ecological and demographic change.

Co-author Janet Kelso, a group leader at the Max Planck Institute for Evolutionary Anthropology, said: “This study highlights the power of ancient DNA to reveal variation within Neanderthals on a much finer scale than was previously possible.

“Rather than viewing late Neanderthals as a single declining population, we are beginning to recognise a more complex picture of regional diversity, connectivity, and population history.”

The study is published in Nature.