Compound-specific radiocarbon dating and mitochondrial DNA analysis of the Pleistocene hominin from Salkhit Mongolia

Abstract

A skullcap found in the Salkhit Valley in northeast Mongolia is, to our knowledge, the only Pleistocene hominin fossil found in the country. It was initially described as an individual with possible archaic affinities, but its ancestry has been debated since the discovery. Here, we determine the age of the Salkhit skull by compound-specific radiocarbon dating of hydroxyproline to 34,950–33,900 Cal. BP (at 95% probability), placing the Salkhit individual in the Early Upper Paleolithic period. We reconstruct the complete mitochondrial genome (mtDNA) of the specimen. It falls within a group of modern human mtDNAs (haplogroup N) that is widespread in Eurasia today. The results now place the specimen into its proper chronometric and biological context and allow us to begin integrating it with other evidence for the human occupation of this region during the Paleolithic, as well as wider Pleistocene sequences across Eurasia.

The Out of East Asia model versus the African Eve model of modern human origins in light of ancient mtDNA findings

“…That R* haplotype was found to be 5000 year older than N* haplotype as discussed above is consistent with the 2 SNP difference between R and N (Figure 1) and the mtDNA mutation rate of 2.67×10 -8 substitution per site per year (5000 × 16500 × 2.67×10 -8 = 2.2 substitution) as recently used by others 46 . This suggests that the ages of the oldest R* and N* samples found so far were likely to be close to the real ages for the R and N ancestors.…”

“…These two samples all have private mutations that are rarely found in today’s samples, indicating that those rare private mutations may represent adaptive changes related to adaptation to ancient environments and may not be used to classify these two samples as non-basal N. We note that Deviese et al 46 used the molecular clock method to calculate a split time between Salkhit and basal N* to be 19000 years and thus considered the appearance of N* basal type to be at ∼50000 years ago. However, such calculation may not be realistic as it did not consider the adaptive non-neutral roles of the ancient variants.…”

“…Both the N samples were found to be basal N* and not directly ancestral to any present day haplogroups 46 . Oase1 had all N defining mutations except 8701G and 9540C and 6 extra mutations (3205A, 3462T, 4232C, 7158G, 8749C, 11016A).…”

“…Among relatively younger samples of 39500-30000 years old, two N samples were found, the 39500 year old Oase1 from Romania 9 and the 34425 year old Salkhit from Mongolia 46 . In contrast to the rarity of N, numerous samples of R subtype U were found in Europe as recently summarized by Deviese et al 46 , indicating that R* basal samples may only be expected near the time when the root of R lived, which should be close to 45000 years ago as marked by the R* sample Ust’-Ishim. If R is indeed the root of modern mtDNA, then the modern lineage should not be much older than 45000 years old.…”

A dynamic 6,000-year genetic history of Eurasia’s Eastern Steppe

“…The Eastern Steppe has been occupied since the early Upper Paleolithic (ca. 34,000 cal BP) (Devièse et al, 2019), and recent paleogenomic studies suggest that the eastern Eurasian forest-steppe zone was genetically structured during the Pre-Bronze and Early Bronze Age periods, with a strong west-east admixture cline of ancestry stretching from Botai in central Kazakhstan to Lake Baikal in southern Siberia to Devil’s Gate Cave in the Russian Far East (de Barros Damgaard et al, 2018; Jeong et al, 2018; Sikora et al, 2019; Siska et al, 2017).…”