Ancient genomes reveal immunity adaptation in early farmers

Research from the Francis Crick Institute published today in Current Biology has revealed that diversity in genes coding for immunity may have facilitated adaptation to farming lifestyles in prehistoric periods.

Researchers at the Ancient Genomics Laboratory at the Crick studied available genome-wide DNA from 677 individuals dating to Stone Age Europe, spanning the movement of Neolithic farmers from the Near East into Europe about 8000 years ago, where they mixed with Mesolithic hunter-gatherers already in Europe.

They were interested in whether any particular genes might have coded for adaptations important to early farming groups, and looked for evidence of rapid evolution in these populations.

Since about 20% of the ancestry of descendant late Stone Age people could be traced to the local European hunter-gatherers, the researchers also asked whether any particular genes showed evidence of more hunter-gatherer ancestry.

They found that a large genetic region responsible for immune responses to diseases -- the major histocompatibility complex (MHC) -- showed both the strongest evidence of rapid evolution, and more Mesolithic hunter-gatherer ancestry than expected, suggesting that genetic variants in the MHC region already present in Europe were passed down preferentially.

It has previously been thought that the transition to farming was associated with increased natural selection on immunity variants, as people started living closer to animals and eating more animal products. This research supports this view, but also shows that diversity in immune genes may be just as important as adaptation to lifestyle.

The research team speculates that either the hunter-gatherers already had genetic adaptations against bacteria, viruses or other microorganisms in Europe, or that having many different forms of the genes was advantageous.

Tom Davy, PhD student at the Francis Crick Institute and lead author, said: "It was really exciting to see for the first time that immunity is important for the transition to farming in a prehistoric population. The later Neolithic people had far more farmer ancestry in general, so we expected to see the same at the MHC region, especially as many diseases have been linked to Neolithic periods. But we saw about 50:50 ancestry from Neolithic farmers and Mesolithic hunter-gatherers here, showing that natural selection favoured genes from the hunter-gatherers already in Europe.

"At the moment we're not quite sure whythis happened, but a proposal is that the European hunter-gatherers had genetic variations which allowed them to fight Europe-specific diseases. Or picking up a variety of genes from both hunter-gatherers and farmers was beneficial because it resulted in lots of diversity at this major group of genes, allowing people to better fight off disease."

The team also confirmed results from previous studies, showing that genes coding for skin pigmentation showed the greatest representation for Neolithic farmer ancestry, with these variations coming into Europe from the Near East. This may be to maintain vitamin D levels when sources, such as diet and exposure to sunlight, change.

Pontus Skoglund, Group Leader of the Ancient Genomics Laboratory at the Crick, said: "The shift to farming was an important transition all over the world, resulting in changing diets and exposure to infectious disease.

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Ancient genomes reveal hidden history of human adaptation

The use of ancient DNA, including samples of human remains around 45,000 years old, has shed light on a previously unknown aspect of human evolution.

Dr Yassine Souilmi, Group Leader at the University of Adelaide's Australian Centre for Ancient DNA, co-led the new study published in Nature Ecology and Evolution.

"It was widely believed the genetics of our human ancestors didn't change due to environmental pressures as much as other animals, due to our enhanced communication skills and ability to make and use tools," Dr Souilmi said.

"However, by comparing modern genomes with ancient DNA, we discovered more than 50 cases of an initially rare beneficial genetic variant becoming prevalent across all members of ancient human groups.

"In contrast to many other species, evidence for this type of adaptive genetic change has been inconsistent in humans. This discovery consequently challenges the prevailing view of human adaptation, and gives us a new and exciting insight into how humans have adapted to the novel environmental pressures they encountered as we spread across the planet."

Co-lead author Dr Ray Tobler -- an Adjunct Fellow at the University of Adelaide and a DECRA fellow at the Australian National University -- said examining ancient DNA has been critical in unlocking the secrets of human evolution.

"We believed historical mixing events between human groups might have hidden signs of genetic changes in modern human genomes," Dr Tobler said.

"We examined DNA from more than 1,000 ancient genomes, the oldest which was around 45,000 years old, to see if certain types of genetic adaptation had been more common in our history than studies of modern genomes had suggested."

Professor Christian Huber, a senior author of the research paper, is an Adjunct Fellow at the University of Adelaide and an Assistant Professor at Penn State University.

"The use of ancient genomes was crucial because they preceded major historical mixing events that have radically reshaped modern European genetic ancestry," Professor Huber said.

"This allowed the recovery of historical signs of adaptation that are invisible to standard analysis of modern genomes."

Established in 2005, the Australian Centre for Ancient DNA is a world leader in the research and development of advanced ancient DNA approaches for evolutionary, environmental and conservation applications.

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Pre-historic Wallacea: A melting pot of human genetic ancestries

The Wallacean islands have always been separated from Asia and Oceania by deep-sea waters. Yet, these tropical islands were a corridor for modern humans migrating into the Pleistocene Australia-New Guinea landmass (Sahul) and have been home to modern human groups for at least 47 thousand years. The archaeological record attests a major cultural transition across Wallacea that started around 3,500 years ago and is associated with the expansion of Austronesian-speaking farmers, who intermixed with local hunter-gatherer groups. However, previous genetic studies of modern-day inhabitants have yielded conflicting dates for this intermixing, ranging from 1,100 to nearly 5,000 years ago.

To shed light on the details of this expansion and the resulting human interactions, an international team of researchers analyzed DNA from 16 ancient individuals from different islands in Wallacea, greatly increasing the amount of ancient genomic data representing this region. "We found striking differences between regions in Wallacea and surprisingly, the ancestry of ancient individuals from the southern islands cannot be simply explained by admixture between Austronesian- and Papuan-related groups," says Sandra Oliveira, one of the study's lead authors.

Early ancestry contribution from Mainland Southeast Asia

The team identified an additional ancestry contribution from Mainland Southeast Asia, closest to present-day Austroasiatic speakers, and proposed that admixture occurred first between the Mainland Southeast Asian and Papuan-related ancestry and that gene flow from Austronesian-related groups occurred only later. "That Mainland Southeast Asian component is a great mystery to me. I suspect that we might be looking at small groups, perhaps of early farmers, who travelled a long way, left no archaeological or linguistic traces along the way, but who increased their population sizes after arrival," says Peter Bellwood, an author of the study who has conducted archaeological work in Island Southeast Asia for decades.

While the identity of the people who spread this ancestry is still unclear, the discovery of the Mainland Southeast Asian ancestry and its possible antiquity in the southern Wallacean islands has major implications for the understanding of the Neolithic dispersals into Island Southeast Asia. "This finding is very important for the archaeologists in the region," adds Toetik Koesbardiati, an Indonesian anthropologist involved in the study. He adds, "We will certainly intensify our efforts to study this migration with other lines of evidence."

Multiple admixture events throughout Wallacea

This work also revealed a closer relationship between the Austronesian-related ancestry of ancient individuals from northern Wallacea and the Pacific, compared to those from southern Wallacea -- a pattern matched by linguistic evidence. Additionally, it shed light on the timing of the Asian-Papuan genetic admixture. "Previous studies based on present-day populations have reported widely different estimates, some of which preceeded the archaeological evidence for the Austronesian expansion, while others were much more recent. Since we now have ancient individuals from different time periods we can directly show that admixture occurred in multiple pulses or continuously since at least 3,000 years ago throughout Wallacea," explains Mark Stoneking, a senior author of the study. He adds, "Future studies on older genomes might extend this date even further."

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Ancient genomes trace the origin and decline of the Scythians

 Because of their interactions and conflicts with the major contemporaneous civilizations of Eurasia, the Scythians enjoy a legendary status in historiography and popular culture. The Scythians had major influences on the cultures of their powerful neighbors, spreading new technologies such as saddles and other improvements for horse riding. The ancient Greek, Roman, Persian and Chinese empires all left a multitude of sources describing, from their perspectives, the customs and practices of the feared horse warriors that came from the interior lands of Eurasia.

Still, despite evidence from external sources, little is known about Scythian history. Without a written language or direct sources, the language or languages they spoke, where they came from and the extent to which the various cultures spread across such a huge area were in fact related to one another, remain unclear.

The Iron Age transition and the formation of the genetic profile of the Scythians

A new study published in Science Advances by an international team of geneticists, anthropologists and archeologists lead by scientists from the Archaeogenetics Department of the Max Planck Institute for the Science of Human History in Jena, Germany, helps illuminate the history of the Scythians with 111 ancient genomes from key Scythian and non-Scythian archaeological cultures of the Central Asian steppe. The results of this study reveal that substantial genetic turnovers were associated with the decline of the long-lasting Bronze Age sedentary groups and the rise of Scythian nomad cultures in the Iron Age. Their findings show that, following the relatively homogenous ancestry of the late Bronze Age herders, at the turn of the first millennium BCE, influxes from the east, west and south into the steppe formed new admixed gene pools.

The diverse peoples of the Central Asian Steppe

The study goes even further, identifying at least two main sources of origin for the nomadic Iron Age groups. An eastern source likely originated from populations in the Altai Mountains that, during the course of the Iron Age, spread west and south, admixing as they moved. These genetic results match with the timing and locations found in the archeological record and suggest an expansion of populations from the Altai area, where the earliest Scythian burials are found, connecting different renowned cultures such as the Saka, the Tasmola and the Pazyryk found in southern, central and eastern Kazakhstan respectively. Surprisingly, the groups located in the western Ural Mountains descend from a second separate, but simultaneous source. Contrary to the eastern case, this western gene pool, characteristic of the early Sauromatian-Sarmatian cultures, remained largely consistent through the westward spread of the Sarmatian cultures from the Urals into the Pontic-Caspian steppe.

The decline of the Scythian cultures associated with new genetic turnovers

The study also covers the transition period after the Iron Age, revealing new genetic turnovers and admixture events. These events intensified at the turn of the first millennium CE, concurrent with the decline and then disappearance of the Scythian cultures in the Central Steppe. In this case, the new far eastern Eurasian influx is plausibly associated with the spread of the nomad empires of the Eastern steppe in the first centuries CE, such as the Xiongnu and Xianbei confederations, as well as minor influxes from Iranian sources likely linked to the expansion of Persian-related civilization from the south.

Although many of the open questions on the history of the Scythians cannot be solved by ancient DNA alone, this study demonstrates how much the populations of Eurasia have changed and intermixed through time. Future studies should continue to explore the dynamics of these trans-Eurasian connections by covering different periods and geographic regions, revealing the history of connections between west, central and east Eurasia in the remote past and their genetic legacy in present day Eurasian populations.

From Science Daily