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

Devièse, Thibaut, Massilani, Diyendo, Yi, Seonbok, Comeskey, Daniel, Nagel, Sarah, Nickel, Birgit, Ribechini, Erika, Lee, Jungeun, Tseveendorj, Damdinsuren, Gunchinsuren, Byambaa, Meyer, Matthias, Pääbo, Svante, Higham, Tom·2019·Nature Communications
DOI 10.1038/s41467-018-08018-8PMC PMC6353915
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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.

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Fig. 1 Map showing Upper Paleolithic sites in Mongolia. 1—Tolbor sites, 2—Dörölj, 3—Orkhon sites, 4—Chickhen sites, 5—Tsagaan Agui, 6—Rashaan Khad and 7—Salkhit. Chronometric data for these sites is listed in Supplementary Table 1. Blocks on scale bars represent 100 km
Fig. 1 Map showing Upper Paleolithic sites in Mongolia. 1—Tolbor sites, 2—Dörölj, 3—Orkhon sites, 4—Chickhen sites, 5—Tsagaan Agui, 6—Rashaan Khad and 7—Salkhit. Chronometric data for these sites is listed in Supplementary Table 1. Blocks on scale bars represent 100 kmCC BY · PubMed Central
Fig. 2 The Salkhit skullcap. In norma frontalis (1), in norma basilaris showing the first sampling for dating A (2) and the areas of sampling B, C, D and E (3) for genetic analyses and compound-specific radiocarbon dating. Blocks on scale bars represent 1 cm
Fig. 2 The Salkhit skullcap. In norma frontalis (1), in norma basilaris showing the first sampling for dating A (2) and the areas of sampling B, C, D and E (3) for genetic analyses and compound-specific radiocarbon dating. Blocks on scale bars represent 1 cmCC BY · PubMed Central
Fig. 3 Calibration of the radiocarbon measurement. The left-hand axis shows the radiocarbon concentration (F14C or fraction modern) and the bottom axis shows the calibrated age obtained using the IntCal13 calibration curve of Reimer et al.25. Figure produced using OxCal24
Fig. 3 Calibration of the radiocarbon measurement. The left-hand axis shows the radiocarbon concentration (F14C or fraction modern) and the bottom axis shows the calibrated age obtained using the IntCal13 calibration curve of Reimer et al.25. Figure produced using OxCal24CC BY · PubMed Central
Fig. 4 Py-GC/MS characterization. Blue profile—Pyrogram obtained on 450 µg of the Salkhit bone; Black profile—Pyrogram obtained on 220 µg of an uncontaminated bone (Latton, UK) used as a standard at the ORAU. The main compounds identified in both profiles are pyrolytic products of collagen51,52. The profile of the Salkhit sample also shows the presence of 3 compounds with siloxane structure (red arrows) that are reported as pyrolysis products of silicone53 leading to assess the residual presence of such material within the bone matrix
Fig. 4 Py-GC/MS characterization. Blue profile—Pyrogram obtained on 450 µg of the Salkhit bone; Black profile—Pyrogram obtained on 220 µg of an uncontaminated bone (Latton, UK) used as a standard at the ORAU. The main compounds identified in both profiles are pyrolytic products of collagen51,52. The profile of the Salkhit sample also shows the presence of 3 compounds with siloxane structure (red arrows) that are reported as pyrolysis products of silicone53 leading to assess the residual presence of such material within the bone matrixCC BY · PubMed Central
Fig. 5 Maximum parsimony phylogeny relating the Salkhit mtDNA to ancient and present-day human mtDNAs. a Subtree of the N haplogroup (Hg) phylogeny structure extracted from a global tree including all the mtDNAs diversity found in ancient and present-day anatomically modern human (Supplementary Fig. 3). The tree was obtained in MEGA6 (30, 31) and is #1 out of 3 most parsimonious trees putting in a phylogenetic network 58 ancient and 55 present-day modern human mtDNA including the Salkhit sequence. The mtDNA sequence of a Neanderthal from Altai is used as outgroup. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. b Diagnostic positions of the N haplogroup and positions of the substitutions accumulated in the Salkhit mtDNA since its divergence from the common ancestor of the N haplogroup, indicated along the branch, are obtained using mtPhyl (https://sites.google.com/site/mtphyl/home)
Fig. 5 Maximum parsimony phylogeny relating the Salkhit mtDNA to ancient and present-day human mtDNAs. a Subtree of the N haplogroup (Hg) phylogeny structure extracted from a global tree including all the mtDNAs diversity found in ancient and present-day anatomically modern human (Supplementary Fig. 3). The tree was obtained in MEGA6 (30, 31) and is #1 out of 3 most parsimonious trees putting in a phylogenetic network 58 ancient and 55 present-day modern human mtDNA including the Salkhit sequence. The mtDNA sequence of a Neanderthal from Altai is used as outgroup. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches. b Diagnostic positions of the N haplogroup and positions of the substitutions accumulated in the Salkhit mtDNA since its divergence from the common ancestor of the N haplogroup, indicated along the branch, are obtained using mtPhyl (https://sites.google.com/site/mtphyl/home)CC BY · PubMed Central

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Cited by

Metadata

Authors
Devièse, T., Massilani, D., Yi, S., Comeskey, D., Nagel, S., Nickel, B., Ribechini, E., Lee, J., Tseveendorj, D., Gunchinsuren, B., Meyer, M., Pääbo, S., & Higham, T.
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2019-01-30
Volume
10
Issue
1
ISSN
2041-1723
DOI
10.1038/s41467-018-08018-8
PMC
PMC6353915
Cited by
55
References
8
Language
en
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