Surprising Genetic Diversity Among European Hunter-Gatherers

Given the relative homogeneity of Y-DNA haplogroups (predominantly one clade of Y-DNA I) and mtDNA haplogroups (predominantly a few kinds of mtDNA U) among European hunter-gatherers before the Neolithic Revolution arrived there, you might expect a similar lack of diversity in their autosomal DNA. This turns out not to be the reality.

The role of the Italian refuge in during the Upper Paleolithic Ice Age and the repopulation of Europe that followed when it retreated has also been more or less completely upended. It was a dead end and completely replaced in the Mesolithic era.

New ancient DNA reported in an article in Nature reveals that there were great regional variation in the DNA and even phenotypes of European hunter-gatherers, despite the loss of diversity that it suffered during the Upper Paleolithic ice age there from which it was repopulated in the Mesolithic era from relict populations in what turn out to be basically two of three small communities in addition to migration from more distant parts of Southeast Europe and West Asia. 

According to the magazine Science at the link above:

[T]he Gravettians were not a single people. New DNA evidence, published today in Nature, shows Gravettians in France and Spain were genetically distinct from groups living in what is now the Czech Republic and Italy. “What we thought was one homogenous thing in Europe 30,000 years ago is actually two distinct groups,” says Mateja Hajdinjak, a molecular biologist at the Max Planck Institute for Evolutionary Anthropology who was not part of the new study.

The Gravettian data are part of a larger trove of ancient European DNA that reveals striking genetic diversity within apparently unified prehistoric cultures. The sweeping study analyzed 116 newly sequenced genomes and hundreds of previously published ones, ranging from about 45,000 years ago, when the first modern humans reached the continent, to about 6000 B.C.E., and from the Iberian Peninsula to the western steppes of modern-day Russia. . . .

Many of the samples were in poor condition and some came from unusual contexts, like the now-submerged landscape between the British Isles and the Netherlands known as Doggerland. New analytical methods and increasingly powerful DNA sequencing tools enabled researchers to squeeze information from extremely degraded bones and teeth, including some that contained just 1% of their original genetic material. . . .

The DNA also sheds light on what happened to these ancient Europeans when the climate worsened between 25,000 and 19,000 years ago, a time known as the last glacial maximum when much of Northern and central Europe was blanketed in ice more than 1 kilometer thick. Archaeologists had assumed people including the Gravettians retreated into ice-free areas in southern Europe beginning about 26,000 years ago, then filtered back north several thousand years later as the glaciers melted. That scenario appears to hold true in the Iberian Peninsula and the south of France: People living there before the ice reached its peak persist through the worst of the cold spell, then surge back north and east as the continent warms.

But the Italian Peninsula, long thought to have been a relatively secure refuge, showed something different. Despite what looked to archaeologists like evidence of continuous occupation during and after the glacial maximum, DNA reveals the refuge was actually a dead end. “We expected Italy to be a climate refugium, but there’s a sharp and complete turnover—it’s a big surprise,” Posth says. “The Gravettian population completely disappears.” Instead, after the glacial maximum, people in Italy show genetic links to the Near East, suggesting a new population arrived from the Balkans. . . .

About 14,000 years ago, when temperatures across the continent rose sharply in the space of a few centuries, archaeologists recognized cultural changes. But they thought the changes reflected an existing population adapting to hunt in warmer, more heavily forested landscapes. Instead, DNA shows an almost complete population replacement: The people who survived the glacial maximum, known as the Magdalenians, all but vanish and are replaced by populations moving north from postglacial Italy.

The study also looked at the final era of hunter-gatherers in Europe, beginning 10,000 years ago as warming continued to transform the open steppe to dense forests and rich wetlands. Here, again, the genes revealed a surprising wrinkle: Despite broadly similar hunting and gathering lifestyles, people in Western Europe remain genetically distinct from those east of the Baltic Sea.

They even looked different: Genetic data suggest that before the arrival of farmers in northern Europe around 6000 B.C.E., hunter-gatherers in Western Europe had dark skin and light eyes. People in Eastern Europe and Russia, meanwhile, had light skin and dark eyes. Most surprising, despite the lack of geographic barriers between modern-day Germany and Russia, the two groups spent millennia not mingling. “From 14,000 years ago to 8000 years ago, they do not mix at all,” Posth says. But he acknowledges that the team’s samples don’t cover the continent completely, and the likely contact zones—in Poland and Belarus, for example—lack samples. More genetic data from those areas might show the two populations mixing locally.

The source article and its abstract are as follows:

Modern humans have populated Europe for more than 45,000 years. Our knowledge of the genetic relatedness and structure of ancient hunter-gatherers is however limited, owing to the scarceness and poor molecular preservation of human remains from that period. Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 individuals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. 

We identify a genetic ancestry profile in individuals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe, but resembles that of preceding individuals associated with the Aurignacian culture. 

This ancestry profile survived during the Last Glacial Maximum (25,000 to 19,000 years ago) in human populations from southwestern Europe associated with the Solutrean culture, and with the following Magdalenian culture that re-expanded northeastward after the Last Glacial Maximum. 

Conversely, we reveal a genetic turnover in southern Europe suggesting a local replacement of human groups around the time of the Last Glacial Maximum, accompanied by a north-to-south dispersal of populations associated with the Epigravettian culture. From at least 14,000 years ago, an ancestry related to this culture spread from the south across the rest of Europe, largely replacing the Magdalenian-associated gene pool. 

After a period of limited admixture that spanned the beginning of the Mesolithic, we find genetic interactions between western and eastern European hunter-gatherers, who were also characterized by marked differences in phenotypically relevant variants. 

Posth, C., Yu, H., Ghalichi, A. et al. Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers. 615 Nature 117–126 (March 1, 2023) (open access). https://doi.org/10.1038/s41586-023-05726-0

The paper also notes that:

A companion paper describes genome-wide data of a 23,000-year-old Solutrean-associated individual from southern Iberia that extend the evidence of genetic continuity across the LGM in southwestern Europe.

The reference to this paper is as follows:

Villalba-Mouco, V. et al. A 23,000-year-old southern-Iberian individual links human groups that lived in Western Europe before and after the Last Glacial Maximum. Nat. Ecol. Evol., https://doi.org/10.1038/s41559-023-01987-0 (2023).

The abstract to that open access paper states:

Human populations underwent range contractions during the Last Glacial Maximum (LGM) which had lasting and dramatic effects on their genetic variation. The genetic ancestry of individuals associated with the post-LGM Magdalenian technocomplex has been interpreted as being derived from groups associated with the pre-LGM Aurignacian. However, both these ancestries differ from that of central European individuals associated with the chronologically intermediate Gravettian. Thus, the genomic transition from pre- to post-LGM remains unclear also in western Europe, where we lack genomic data associated with the intermediate Solutrean, which spans the height of the LGM. Here we present genome-wide data from sites in Andalusia in southern Spain, including from a Solutrean-associated individual from Cueva del Malalmuerzo, directly dated to ~23,000 cal yr BP. The Malalmuerzo individual carried genetic ancestry that directly connects earlier Aurignacian-associated individuals with post-LGM Magdalenian-associated ancestry in western Europe. This scenario differs from Italy, where individuals associated with the transition from pre- and post-LGM carry different genetic ancestries. This suggests different dynamics in the proposed southern refugia of Ice Age Europe and posits Iberia as a potential refugium for western European pre-LGM ancestry. More, individuals from Cueva Ardales, which were thought to be of Palaeolithic origin, date younger than expected and, together with individuals from the Andalusian sites Caserones and Aguilillas, fall within the genetic variation of the Neolithic, Chalcolithic and Bronze Age individuals from southern Iberia.