Ancient Genomes and Proteomes Help Uncover Unexpected Origins and Cultural Connections – Genetic Engineering & Biotechnology News

With over 300 tombs, the Little River (Xiaohe) Cemetery, a Bronze Age burial located in the Tarim Basin in Xinjiang, Western China, contains the largest number of mummies found at any single site to date. Located on the Silk Road at the confluence of the Eastern and Western cultures, the naturally mummified human remains in boat coffins dating to circa 2,000 BCE to 200 CE have inspired speculations on their enigmatic origins.

Whereas some placed the origin of these mummies among the early farmers of the Iranian Plateau, many believed their origins to be Caucasoiddescendants of migrating Yamnaya herders from the steppes of the Black Sea region of southern Russiadue to their Western physical appearance, clothing, and agropastoral economy. This has led to global attention on these archeological remains.

To solve this enigma, an international team of scientists from Jilin University, the Institute of Vertebrate Paleontology and Paleoanthropology, the Max Planck Institute for Evolutionary Anthropology, Seoul National University of Korea, and Harvard University have generated and analyzed genome-wide data from thirteen of the earliest known Tarim Basin mummies, dating to circa 2,100 to 1,700 BCE, together with five individuals dating to circa 3,000 to 2,800 BCE, from the neighboring Dzungarian Basin.

This premiere genome-scale study of prehistoric populations in the Xinjiang Uyghur Autonomous Region is reported in an article in the journal Nature titled, The genomic origins of the Bronze Age Tarim Basin mummies.

A naturally mummified woman from burial M11 of the Xiaohe cemetery. [Wenying Li/Xinjiang Institute of Cultural Relics and Archaeology]Contrary to their expectations, the genomic study found that the Tarim Basin mummies were not newcomers to the area but rather appear to be direct descendants of Ancient North Eurasiansa once widespread Pleistocene population that had nearly disappeared by the end of the last Ice Age. This population survives only fractionally in the genomes of present-day populations, with Indigenous populations in Siberia and the Americas having the highest known proportions, at about 40%.

In contrast to present day populations, genomes of the Tarim Basin mummies show no admixture with other Holocene groups, demonstrating their genetic isolation.

Archaeogeneticists have long searched for Holocene Ancient North Eurasians populations to better understand the genetic history of Inner Eurasia. We have found one in the most unexpected place, says Choongwon Jeong, a senior author of the study and a professor of Biological Sciences at Seoul National University.

Genome analysis of the neighboring Dzungarian Basin mummies showed that they descended not only from local populations but also from Western steppe cattle herders with strong genetic links to the Early Bronze Age Yamanya. The genetic characterization of the Early Bronze Age Dzungarians also helped to clarify the ancestry of other cattle faming groups (Chemurchek) who later spread northward to the Altai mountains and into Mongolia.

These findings add to our understanding of the eastward dispersal of Yamnaya ancestry and the scenarios under which admixture occurred when they first met the populations of Inner Asia, says Chao Ning, co-lead author of the study and a professor at the School of Archaeology and Museology at Peking University.

The widespread genetic mixing all around the Tarim Basin throughout the Bronze Age make it even more remarkable that the Tarim Basin mummies exhibit no evidence of genetic admixture. Yet, they were not culturally isolated.

Typical Xiaohe boat coffin with oar. The coffin is covered with a cattle hide. [Wenying Li/Xinjiang Institute of Cultural Relics and Archaeology]Dietary proteins are trapped in calcifying dental plaque (dental calculus) and preserve a record of the individuals diet. Proteomic analysis of dental calculus from the Tarim mummies show cattle, sheep, and goat dairying was already practiced by the founding population, and that they were connected to neighboring cultures, cuisines, and technologies.

Despite being genetically isolated, the Bronze Age peoples of the Tarim Basin were remarkably culturally cosmopolitanthey built their cuisine around wheat and dairy from the West Asia, millet from East Asia, and medicinal plants like Ephedrafrom Central Asia, says Christina Warinner, a senior author of the study, a professor of Anthropology at Harvard University, and a research group leader at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

Dietary DNA is difficult to recover from dental calculus, and DNA cannot be used to easily distinguish specific dietary sources (e.g., meat vs. milk). Proteomics is more suitable for studying ancient diets in this context, explains Warinner.

One of the technical challenges of sequencing ancient genomes is DNA damage. The length of ancient DNA is short and contains specific forms of damage (cytosine deamination). We use this expected form of damage to authenticate DNA fragments as being ancient and to ensure accurate sequence calls. To analyze the ancient DNA sequences, we used software pipelines specifically designed for analyzing ultrashort fragments of ancient DNA, explains Warinner.

The new genomic and proteomic data presented in the paper builds upon decades of painstaking archaeological work that has fostered insights on the lifestyle and culture of the early inhabitants of the Tarim Basin. Warinner clarifies, We were able to contribute new genomic and proteomic data to this rich body of knowledge, including the first whole genome sequences for the Tarim Basin mummies. Together with our archaeologist colleagues and coauthors, we have been able to reconstruct a more complete and complex picture of the populations who first colonized the Tarim Basin more than 4,000 years ago.

Reconstructing the origins of the Tarim Basin mummies has had a transformative effect on our understanding of the region, and we will continue the study of ancient human genomes in other eras to gain a deeper understanding of the human migration history in the Eurasian steppes, says Yinquiu Cui, a senior author of the study and professor in the School of Life Sciences at Jilin University.

Future palaeogenomic and archeological research on subsequent Tarim Basin populations will focus on better understanding the later history of populations in the Tarim Basin and their role in the rise of Silk Road trade networks, says Warinner.

The Tarim mummy genomes provide a critical reference point for genetically modeling Holocene-era populations and reconstructing the population history of Asia, the authors conclude.

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Ancient Genomes and Proteomes Help Uncover Unexpected Origins and Cultural Connections - Genetic Engineering & Biotechnology News