Iceman Ötzi: Dark skin, bald head, Anatolian ancestry

A research team has used advanced sequencing technology to analyze Ötzi's genome to obtain a more accurate picture of the Iceman's appearance and genetic origins.

Ötzi's genome was decoded for the first time more than ten years ago. This was also the first time the genome of a mummy had been sequenced. The results provided important insights into the genetic makeup of prehistoric Europeans. Advances in sequencing technology have now enabled a research team from the Max Planck Institute for Evolutionary Anthropology and Eurac Research to reconstruct Ötzi's genome more accurately. The results of this recent analysis refine the Iceman's genetic picture: compared to other contemporary Europeans, Ötzi's genome has an unusually high proportion of genes in common with those of early farmers from Anatolia. And, contrary to previous findings, at the time of his death, Ötzi had advanced hair loss and may have even been bald. Furthermore, his skin was darker than previously thought. Ötzi's genes also show a predisposition to diabetes and obesity.

The genetic makeup of most present-day Europeans has resulted mainly from the admixture of three ancestral groups: western hunter-gatherers gradually merged with early farmers who migrated from Anatolia about 8,000 years ago and who were later on joined by Steppe Herders from Eastern Europe, approximately 4,900 years ago.

The initial analysis of the Iceman's genome revealed genetic traces of these Steppe Herders. However, the refined new results no longer support this finding. The reason for the inaccuracy: the original sample had been contaminated with modern DNA. Since that first study, not only have sequencing technologies advanced enormously, but many more genomes of other prehistoric Europeans have been fully decoded, often from skeletal finds. This has made it possible to compare Ötzi's genetic code with his contemporaries. The result: among the hundreds of early European people who lived at the same time as Ötzi and whose genomes are now available, Ötzi's genome has more ancestry in common with early Anatolian farmers than any of his European counterparts.

Ötzi's ancestry and appearance

The research team concludes that the Iceman came from a relatively isolated population that had very little contact with other European groups. "We were very surprised to find no traces of Eastern European Steppe Herders in the most recent analysis of the Iceman genome; the proportion of hunter-gatherer genes in Ötzi's genome is also very low. Genetically, his ancestors seem to have arrived directly from Anatolia without mixing with hunter gatherer groups," explains Johannes Krause, head of the Department of Archaeogenetics at the Max Planck Institute for Evolutionary Anthropology in Leipzig, and co-author of the study.

The study also yielded new results about Ötzi's appearance. His skin type, already determined in the first genome analysis to be Mediterranean-European, was even darker than previously thought. "It's the darkest skin tone that has been recorded in contemporary European individuals," explains anthropologist Albert Zink, study co-author and head of the Eurac Research Institute for Mummy Studies in Bolzano: "It was previously thought that the mummy's skin had darkened during its preservation in the ice, but presumably what we see now is actually largely Ötzi's original skin color. Knowing this, of course, is also important for the proper conservation of the mummy."

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The genetic origins of the world's first farmers clarified

The genetic origins of the first agriculturalists in the Neolithic period long seemed to lie in the Near East. A new study published in the journal Cell shows that the first farmers actually represented a mixture of Ice Age hunter-gatherer groups, spread from the Near East all the way to south-eastern Europe. Researchers from the University of Bern and the SIB Swiss Institute of Bioinformatics as well as from the Johannes Gutenberg University Mainz and the University of Fribourg were involved in the study. The method they developed could help reveal other human evolution patterns with unmatched resolution.

The first signs of agriculture and a sedentary lifestyle are found in the so-called 'Fertile Crescent', a region in the Near East where people began to settle down and domesticate animals and plants about 11,000 years ago. The question of the origin of agriculture and sedentism has occupied researchers for over 100 years: did farming spread from the Near East through cultural diffusion or through migration? Genetic analyses of prehistoric skeletons so far supported the idea that Europe's first farmers were descended from hunter-gatherer populations in Anatolia. While that may well be the case, this new study shows that the Neolithic genetic origins cannot clearly be attributed to a single region. Unexpected and complex population dynamics occurred at the end of the Ice Age, and led to the ancestral genetic makeup of the populations who invented agriculture and a sedentary life-style i.e. the first Neolithic farmers.

First farmers emerged from a mixing process starting 14,000 years ago

Previous analyses had suggested that the first Neolithic people were genetically different from other human groups from that time. Little was known about their origins. Nina Marchi, one of the study's first authors from the Institute of Ecology and Evolution at the University of Bern and SIB says: "We now find that the first farmers of Anatolia and Europe emerged from a population admixed between hunter-gatherers from Europe and the Near East." According to the authors, the mixing process started around 14,000 years ago, which was followed by a period of extreme genetic differentiation lasting several thousand years.

A novel approach to model population history from prehistoric skeletons

This research was made possible by combining two techniques: the production of high-quality ancient genomes from prehistoric skeletons, coupled with demographic modeling on the resulting data. The research team coined the term "demogenomic modeling" for this purpose. "It is necessary to have genome data of the best possible quality so that the latest statistical genomic methods can reconstruct the subtle demographic processes of the last 30 thousand years at high resolution," says Laurent Excoffier, one of the senior authors of the study. Laurent Excoffier is a professor at the Institute of Ecology and Evolution at the University of Bern and group leader at SIB. He initiated the project together with Joachim Burger of the Johannes Gutenberg University in Mainz and Daniel Wegmann of the University of Fribourg. Nina Marchi adds: "Simply comparing the similarity of different ancient genomes is not enough to understand how they evolved. We had to reconstruct the actual histories of the populations studied as accurately as possible. This is only possible with complex population genetic statistics."

Interdisciplinarity key to solve such ancient puzzles

Joachim Burger of the University of Mainz and second senior author emphasizes the necessity of interdisciplinarity: "It took close to ten years to gather and analyze the skeletons suitable for such a study. This was only possible by collaborating with numerous archaeologists and anthropologists, who helped us to anchor our models historically." The historical contextualisation was coordinated by Maxime Brami, who works with Burger at Johannes Gutenberg University. The young prehistorian was surprised by some of the study's findings: "Europe's first farmers seem to be descended from hunter-gatherer populations that lived all the way from the Near East to the Balkans. This was not foreseeable archaeologically."

Towards a general model of human population evolution

Genetic data from fossils (skeletons) are badly damaged and must be processed accordingly using bioinformatics, as Daniel Wegmann from the University of Fribourg and group leader at SIB explains: "The high-resolution reconstruction of the prehistory of the Europeans was only possible thanks to methods that we specifically developed to analyse ancient fossil genomes." Joachim Burger adds: "With these approaches, we have not only elucidated the origins of the world's first Neolithic populations, but we have established a general model of the evolution of human populations in Southwest Asia and Europe."

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Ancient DNA rewrites early Japanese history -- modern day populations have tripartite genetic origin

Ancient DNA extracted from human bones has rewritten early Japanese history by underlining that modern day populations in Japan have a tripartite genetic origin -- a finding that refines previously accepted views of a dual genomic ancestry.

Twelve newly sequenced ancient Japanese genomes show that modern day populations do indeed show the genetic signatures of early indigenous Jomon hunter-gatherer-fishers and immigrant Yayoi farmers -- but also add a third genetic component that is linked to the Kofun peoples, whose culture spread in Japan between the 3rd and 7th centuries.

Rapid cultural transformations

The Japanese archipelago has been occupied by humans for at least 38,000 years but Japan underwent rapid transformations only in the last 3,000 years, first from foraging to wet-rice farming, and then to a technologically advanced imperial state.

The previous, long-standing hypothesis suggested that mainland Japanese populations derive dual-ancestry from the indigenous Jomon hunter-gatherer-fishers, who inhabited the Japanese archipelago from around 16,000 to 3,000 years ago, and later Yayoi farmers, who migrated from the Asian continent and lived in Japan from around 900 BC to 300 AD.

But the 12 newly sequenced ancient Japanese genomes -- which came from the bones of people living in pre- and post-farming periods -- also identify a later influx of East Asian ancestry during the imperial Kofun period, which lasted from around 300 to 700 AD and which saw the emergence of political centralisation in Japan.

Shigeki Nakagome, Assistant Professor in Psychiatry in Trinity College Dublin's School of Medicine, led the research, which brought together an interdisciplinary team of researchers from Japan and Ireland. Professor Nakagome said:

"Researchers have been learning more and more about the cultures of the Jomon, Yayoi, and Kofun periods as more and more ancient artefacts show up, but before our research we knew relatively little about the genetic origins and impact of the agricultural transition and later state-formation phase."

"We now know that the ancestors derived from each of the foraging, agrarian, and state-formation phases made a significant contribution to the formation of Japanese populations today. In short, we have an entirely new tripartite model of Japanese genomic origins -- instead of the dual-ancestry model that has been held for a significant time."

Genomic insights into key Japanese transformations

In addition to the overarching discovery, the analyses also found that the Jomon maintained a small effective population size of around 1,000 over several millennia, with a deep divergence from continental populations dated to 20,000-15,000 years ago -- a period which saw Japan become more geographically insular through rising sea-levels.

The Japanese archipelago had become accessible through the Korean Peninsula at the beginning of the Last Glacial Maximum, some 28,000 years ago, enabling movement between. And the widening of the Korea Strait 16,000 to 17,000 years ago due to rising sea-levels may have led to the subsequent isolation of the Jomon lineage from the rest of the continent. These time frames also coincide with the oldest evidence of Jomon pottery production.

"The indigenous Jomon people had their own unique lifestyle and culture within Japan for thousands of years prior to the adoption of rice farming during the subsequent Yayoi period. Our analysis clearly finds them to be a genetically distinct population with an unusually high affinity between all sampled individuals -- even those differing by thousands of years in age and excavated from sites on different islands," explained Niall Cooke, PhD Researcher at Trinity. "These results strongly suggest a prolonged period of isolation from the rest of the continent."

The spread of agriculture is often marked by population replacement, as documented in the Neolithic transition throughout most of Europe, with only minimal contributions from hunter-gatherer populations observed in many regions. However, the researchers found genetic evidence that the agricultural transition in prehistoric Japan involved the process of assimilation, rather than replacement, with almost equal genetic contributions from the indigenous Jomon and new immigrants associated with wet-rice farming.

Several lines of archaeological evidence support the introduction of new large settlements to Japan, most likely from the southern Korean peninsula, during the Yayoi-Kofun transition. And the analyses provide strong support for the genetic exchange involved in the appearance of new social, cultural, and political traits in this state-formation phase.

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