The genomic origins of the Bronze Age Tarim Basin mummies.

The identity of the earliest inhabitants of Xinjiang, in the heart of Inner Asia, and the languages that they spoke have long been debated and remain contentious1. Here we present genomic data from 5 individuals dating to around 3000-2800 BC from the Dzungarian Basin and 13 individuals dating to around 2100-1700 BC from the Tarim Basin, representing the earliest yet discovered human remains from North and South Xinjiang, respectively. We find that the Early Bronze Age Dzungarian individuals exhibit a predominantly Afanasievo ancestry with an additional local contribution, and the Early-Middle Bronze Age Tarim individuals contain only a local ancestry. The Tarim individuals from the site of Xiaohe further exhibit strong evidence of milk proteins in their dental calculus, indicating a reliance on dairy pastoralism at the site since its founding. Our results do not support previous hypotheses for the origin of the Tarim mummies, who were argued to be Proto-Tocharian-speaking pastoralists descended from the Afanasievo1,2 or to have originated among the Bactria-Margiana Archaeological Complex3 or Inner Asian Mountain Corridor cultures4. Instead, although Tocharian may have been plausibly introduced to the Dzungarian Basin by Afanasievo migrants during the Early Bronze Age, we find that the earliest Tarim Basin cultures appear to have arisen from a genetically isolated local population that adopted neighbouring pastoralist and agriculturalist practices, which allowed them to settle and thrive along the shifting riverine oases of the Taklamakan Desert.

A 3,000-year-old, basal S. enterica lineage from Bronze Age Xinjiang suggests spread along the Proto-Silk Road.

Salmonella enterica (S. enterica) has infected humans for a long time, but its evolutionary history and geographic spread across Eurasia is still poorly understood. Here, we screened for pathogen DNA in 14 ancient individuals from the Bronze Age Quanergou cemetery (XBQ), Xinjiang, China. In 6 individuals we detected S. enterica. We reconstructed S. enterica genomes from those individuals, which form a previously undetected phylogenetic branch basal to Paratyphi C, Typhisuis and Choleraesuis-the so-called Para C lineage. Based on pseudogene frequency, our analysis suggests that the ancient S. enterica strains were not host adapted. One genome, however, harbors the Salmonella pathogenicity island 7 (SPI-7), which is thought to be involved in (para)typhoid disease in humans. This offers first evidence that SPI-7 was acquired prior to the emergence of human-adapted Paratyphi C around 1,000 years ago. Altogether, our results show that Salmonella enterica infected humans in Eastern Eurasia at least 3,000 years ago, and provide the first ancient DNA evidence for the spread of a pathogen along the Proto-Silk Road.

Ancient Genomes Reveal Yamnaya-Related Ancestry and a Potential Source of Indo-European Speakers in Iron Age Tianshan.

Recent studies of early Bronze Age human genomes revealed a massive population expansion by individuals-related to the Yamnaya culture, from the Pontic Caspian steppe into Western and Eastern Eurasia, likely accompanied by the spread of Indo-European languages [1-5]. The south eastern extent of this migration is currently not known. Modern-day human populations from the Xinjiang region in northwestern China show a complex population history, with genetic links to both Eastern and Western Eurasia [6-10]. However, due to the lack of ancient genomic data, it remains unclear which source populations contributed to the Xinjiang population and what was the timing and the number of admixture events. Here, we report the first genome-wide data of 10 ancient individuals from northeastern Xinjiang. They are dated to around 2,200 years ago and were found at the Iron Age Shirenzigou site. We find them to be already genetically admixed between Eastern and Western Eurasians. We also find that the majority of the East Eurasian ancestry in the Shirenzigou individuals is-related to northeastern Asian populations, while the West Eurasian ancestry is best presented by ∼20% to 80% Yamnaya-like ancestry. Our data thus suggest a Western Eurasian steppe origin for at least part of the ancient Xinjiang population. Our findings furthermore support a Yamnaya-related origin for the now extinct Tocharian languages in the Tarim Basin, in southern Xinjiang.

Mitochondrial Genome of an 8,400-Year-Old Individual from Northern China Reveals a Novel Subclade Under C5d.

Ancient DNA studies have always refreshed our understanding of the human past that cannot be tracked by modern DNA alone. Until recently, ancient mitochondrial genomic studies in East Asia were still very limited. Here, we retrieved the whole mitochondrial genome of an 8,400-year-old individual from Inner Mongolia, China. Phylogenetic analyses show that the individual belongs to a previously undescribed clade under haplogroup C5d that most probably originated in northern Asia and may have a very low frequency in extant populations that have not yet been sampled. We further characterized the demographic history of mitochondrial haplogroups C5 and C5d and found that C5 experienced a sharp increase in population size starting around 4,000 years before present, the time when intensive millet farming was developed by populations who are associated with the Lower Xiajiadian culture and was widely adopted in northern China. We caution that people related to haplogroup C5 may have added this farming technology to their original way of life and that the various forms of subsistence may have provided abundant food sources and further contributed to the increase in population size.

Tracing the genetic history of the Chinese people: mitochondrial DNA analysis of aneolithic population from the Lajia site.

Ancient DNA analysis was conducted on the dental remains of specimens from the Lajia site, dating back 3,800-4,000 years. The Lajia site is located in Minhe county, Qinghai province, in northwestern China. Archaeological studies link Lajia to the late period of the Qijia culture, one of the most important Neolithic civilizations of the upper Yellow River region, the cradle of Chinese civilization. Excavations at the site revealed that the inhabitants died in their houses as the result of a sudden flood. The Lajia site provides a rare chance to study the putative families, all of whom died at the same instant. Possible maternal familial relationships were investigated through mitochondrial DNA (mtDNA) sequence analysis. Twelve sequences from individuals found in one house were assigned to only five haplotypes, consistent with a possible close kinship. Results from analyses of RFLP typing and HVI motifs suggest that the Lajia people belonged to the haplogroups B, C, D, M*, and M10. This study, combined with archaeological and anthropological investigations, provides a better understanding of the genetic history of the Chinese people.