Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan Plateau

Zhang, Dongju; Xia, Huan; Chen, Fahu; Li, Bo; Slon, Viviane; Cheng, Tianyu; Yang, Ruowei; Jacobs, Zenobia; Dai, Qingyan; Massilani, Diyendo; Shen, Xiaoqiang; Wang, Jian; Feng, Xiaotian; Cao, Peng; Yang, Melinda A.; Yao, Juanting; Yang, Jinman; Madsen, David B.; Han, Yuanyuan; Ping, Wanjing; Liu, Feng; Perreault, Charles; Chen, Xiaoshan; Meyer, Matthias; Kelso, Janet; Pääbo, Svante; Fu, Qiaomei

doi:10.1126/science.abb6320

Cited by 162 publications

(87 citation statements)

References 113 publications

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“…Beyond reconstructing the occupational history of Denisova Cave, our results have wider implications for understanding the human past. First, fragments of Denisovan mtDNA recovered from the middle Middle Palaeolithic layers deposited in Denisova Cave after 80 ka consistently show the highest similarity to the mtDNA of Denisova 3 and Denisova 4, as do mtDNA fragments retrieved from sediments at Baishiya Karst Cave on the northeastern flank of the Tibetan Plateau that are broadly contemporaneous in age (70-45 ka) 27 . This pattern suggests that this lineage was the most abundant mtDNA type carried by Denisovans after 80 ka.…”

Section: Discussionmentioning

confidence: 93%

Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave

Zavala

Jacobs

Vernot

et al. 2021

Nature

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Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals1–4. The dozen hominin remains recovered from the deposits also include Neanderthals5,6 and the child of a Neanderthal and a Denisovan7, which suggests that Denisova Cave was a contact zone between these archaic hominins. However, uncertainties persist about the order in which these groups appeared at the site, the timing and environmental context of hominin occupation, and the association of particular hominin groups with archaeological assemblages5,8–11. Here we report the analysis of DNA from 728 sediment samples that were collected in a grid-like manner from layers dating to the Pleistocene epoch. We retrieved ancient faunal and hominin mitochondrial (mt)DNA from 685 and 175 samples, respectively. The earliest evidence for hominin mtDNA is of Denisovans, and is associated with early Middle Palaeolithic stone tools that were deposited approximately 250,000 to 170,000 years ago; Neanderthal mtDNA first appears towards the end of this period. We detect a turnover in the mtDNA of Denisovans that coincides with changes in the composition of faunal mtDNA, and evidence that Denisovans and Neanderthals occupied the site repeatedly—possibly until, or after, the onset of the Initial Upper Palaeolithic at least 45,000 years ago, when modern human mtDNA is first recorded in the sediments.

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Section: Discussionmentioning

confidence: 93%

Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave

Zavala

Jacobs

Vernot

et al. 2021

Nature

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“…Currently, existing archaeological evidence generally supports two settlement scenarios. The archaeological sites from middle to late Holocene ( 62 – 65 ) indicate that year-round large-scale settlements of people on the plateau started after 3.6 ka facilitated by the advent of agriculture, while analyses on the mobility of hunter-gatherers ( 66 – 68 ) suggest that permanent inhabitation (most likely on a smaller scale) may have occurred more distantly in the past. Our estimate of the Denisovan East Asian-specific admixture time (48 ka) from tract lengths surrounding the EPAS1 gene is larger than most estimates of when modern humans permanently settled in the Tibetan Plateau, suggesting that the admixture most likely occurred outside of this region.…”

Section: Discussionmentioning

confidence: 99%

The history and evolution of the Denisovan- EPAS1 haplotype in Tibetans

Zhang

Witt

Bañuelos

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Recent studies suggest that admixture with archaic hominins played an important role in facilitating biological adaptations to new environments. For example, interbreeding with Denisovans facilitated the adaptation to high-altitude environments on the Tibetan Plateau. Specifically, the EPAS1 gene, a transcription factor that regulates the response to hypoxia, exhibits strong signatures of both positive selection and introgression from Denisovans in Tibetan individuals. Interestingly, despite being geographically closer to the Denisova Cave, East Asian populations do not harbor as much Denisovan ancestry as populations from Melanesia. Recently, two studies have suggested two independent waves of Denisovan admixture into East Asians, one of which is shared with South Asians and Oceanians. Here, we leverage data from EPAS1 in 78 Tibetan individuals to interrogate which of these two introgression events introduced the EPAS1 beneficial sequence into the ancestral population of Tibetans, and we use the distribution of introgressed segment lengths at this locus to infer the timing of the introgression and selection event. We find that the introgression event unique to East Asians most likely introduced the beneficial haplotype into the ancestral population of Tibetans around 48,700 (16,000–59,500) y ago, and selection started around 9,000 (2,500–42,000) y ago. Our estimates suggest that one of the most convincing examples of adaptive introgression is in fact selection acting on standing archaic variation.

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“…The recovery of genome-wide data from multiple animal species from a single Pleistocene soil sample opens a new avenue compared to what has previously been learned from sediment DNA (Ardelean et al, 2020; Slon et al, 2017; Willerslev et al, 2003; Zhang et al, 2020). Using this data we were able to make inferences about the genetic ancestry and history of three past mammalian populations that lived in the Southern Caucasus ∼25 ka.…”

Section: Discussionmentioning

confidence: 99%

“…A ground-breaking study showed DNA preservation in clay-rich sediments for at least 240 ky. (Slon et al, 2017), and used targeted enrichment to recover sufficient numbers of fragments to reconstruct mtDNA phylogenies of Neanderthals and Denisovans. A recent study similarly recovered Denisovan mitochondrial DNA from sediments deposited ∼100 kya and ∼60 kya from Baishiya Karst Cave (BKC) on the Tibetan Plateau (Zhang et al, 2020).…”

Section: Introductionmentioning

confidence: 98%

Genome-scale sequencing and analysis of human, wolf and bison DNA from 25,000 year-old sediment

Gelabert

Sawyer

Bergström

et al. 2021

Preprint

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SummaryArchaeological sediments have been shown to preserve ancient DNA, but so far have not yielded genome-scale information of the magnitude of skeletal remains. We retrieved and analysed human and mammalian low-coverage nuclear and high-coverage mitochondrial genomes from Upper Palaeolithic sediments from Satsurblia cave, western Georgia, dated to 25,000 years ago. First, a human female genome with substantial basal Eurasian ancestry, which was an ancestry component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe. Second, a wolf genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage that diverged from the ancestors of modern wolves and dogs before these diversified. Third, a bison genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the late Pleistocene genetic histories of these three species, and demonstrate that sediment DNA can be used not only for species identification, but also be a source of genome-wide ancestry information and genetic history.HighlightsWe demonstrate for the first time that genome sequencing from sediments is comparable to that of skeletal remainsA single Pleistocene sediment sample from the Caucasus yielded three low-coverage mammalian ancient genomesWe show that sediment ancient DNA can reveal important aspects of the human and faunal pastEvidence of an uncharacterized human lineage from the Caucasus before the Last Glacial Maximum∼0.01-fold coverage wolf and bison genomes are both basal to present-day diversity, suggesting reshaping of population structure in both species

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Denisovan DNA in Late Pleistocene sediments from Baishiya Karst Cave on the Tibetan Plateau

Cited by 162 publications

References 113 publications

Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave

Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave

The history and evolution of the Denisovan- EPAS1 haplotype in Tibetans

Genome-scale sequencing and analysis of human, wolf and bison DNA from 25,000 year-old sediment

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