AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination

Peyrégne, Stéphane; Peter, Benjamin M.

doi:10.1186/s13059-020-02123-y

Cited by 39 publications

(29 citation statements)

References 74 publications

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“…Duplicates were removed with DeDup v.0.12.2 ( https://github.com/apeltzer/DeDup ). Contamination of the single-stranded sequences was assessed with AuthentiCT v.1.0 60 .…”

Section: Methodsmentioning

confidence: 99%

Genome of a middle Holocene hunter-gatherer from Wallacea

Carlhoff

Duli

Nägele

et al. 2021

Nature

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Much remains unknown about the population history of early modern humans in southeast Asia, where the archaeological record is sparse and the tropical climate is inimical to the preservation of ancient human DNA1. So far, only two low-coverage pre-Neolithic human genomes have been sequenced from this region. Both are from mainland Hòabìnhian hunter-gatherer sites: Pha Faen in Laos, dated to 7939–7751 calibrated years before present (yr cal bp; present taken as ad 1950), and Gua Cha in Malaysia (4.4–4.2 kyr cal bp)1. Here we report, to our knowledge, the first ancient human genome from Wallacea, the oceanic island zone between the Sunda Shelf (comprising mainland southeast Asia and the continental islands of western Indonesia) and Pleistocene Sahul (Australia–New Guinea). We extracted DNA from the petrous bone of a young female hunter-gatherer buried 7.3–7.2 kyr cal bp at the limestone cave of Leang Panninge2 in South Sulawesi, Indonesia. Genetic analyses show that this pre-Neolithic forager, who is associated with the ‘Toalean’ technocomplex3,4, shares most genetic drift and morphological similarities with present-day Papuan and Indigenous Australian groups, yet represents a previously unknown divergent human lineage that branched off around the time of the split between these populations approximately 37,000 years ago5. We also describe Denisovan and deep Asian-related ancestries in the Leang Panninge genome, and infer their large-scale displacement from the region today.

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“…Duplicates were removed with DeDup v.0.12.2 ( https://github.com/apeltzer/DeDup ). Contamination of the single-stranded sequences was assessed with AuthentiCT v.1.0 60 .…”

Section: Methodsmentioning

confidence: 99%

Genome of a middle Holocene hunter-gatherer from Wallacea

Carlhoff

Duli

Nägele

et al. 2021

Nature

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“…Using an approach that makes use of DNA deamination patterns 22 , we estimated that the overall nuclear DNA contamination was between 2.2% ± 0.5% (F6-620) and 42.4% ± 0.6% (CC7-2289). In the male specimens, we estimated contamination from polymorphisms on the X chromosome 23 to between 1.6% ± 0.1% and 3.4% ± 0.5% (Supplementary Information 2 ).…”

Section: Mainmentioning

confidence: 99%

Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry

Hajdinjak

Mafessoni

Skov

et al. 2021

Nature

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Modern humans appeared in Europe by at least 45,000 years ago1–5, but the extent of their interactions with Neanderthals, who disappeared by about 40,000 years ago6, and their relationship to the broader expansion of modern humans outside Africa are poorly understood. Here we present genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bacho Kiro Cave, Bulgaria1,2. They are the earliest Late Pleistocene modern humans known to have been recovered in Europe so far, and were found in association with an Initial Upper Palaeolithic artefact assemblage. Unlike two previously studied individuals of similar ages from Romania7 and Siberia8 who did not contribute detectably to later populations, these individuals are more closely related to present-day and ancient populations in East Asia and the Americas than to later west Eurasian populations. This indicates that they belonged to a modern human migration into Europe that was not previously known from the genetic record, and provides evidence that there was at least some continuity between the earliest modern humans in Europe and later people in Eurasia. Moreover, we find that all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed with Neanderthals and suggesting that such mixing could have been common.

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“…Estimates based on linkage disequilibrium 17 suggest that nuclear contamination is <1% in the capture dataset and ~2% in the shotgun dataset (Supplementary Section 4 ). The majority of the Zlatý kůň shotgun sequences (~3.2-fold out of ~3.8-fold total) have been generated from a single-stranded DNA library that allows for the quantification of contamination with an explicit model of DNA damage in the DNA molecules 18 . This model yielded an estimate of contamination of 0.1% (s.e.…”

Section: Mainmentioning

confidence: 99%

A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia

Prüfer

Posth

et al. 2021

Nat Ecol Evol

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Modern humans expanded into Eurasia more than 40,000 years ago following their dispersal out of Africa. These Eurasians carried ~2–3% Neanderthal ancestry in their genomes, originating from admixture with Neanderthals that took place sometime between 50,000 and 60,000 years ago, probably in the Middle East. In Europe, the modern human expansion preceded the disappearance of Neanderthals from the fossil record by 3,000–5,000 years. The genetic makeup of the first Europeans who colonized the continent more than 40,000 years ago remains poorly understood since few specimens have been studied. Here, we analyse a genome generated from the skull of a female individual from Zlatý kůň, Czechia. We found that she belonged to a population that appears to have contributed genetically neither to later Europeans nor to Asians. Her genome carries ~3% Neanderthal ancestry, similar to those of other Upper Palaeolithic hunter-gatherers. However, the lengths of the Neanderthal segments are longer than those observed in the currently oldest modern human genome of the ~45,000-year-old Ust’-Ishim individual from Siberia, suggesting that this individual from Zlatý kůň is one of the earliest Eurasian inhabitants following the expansion out of Africa.

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AuthentiCT: a model of ancient DNA damage to estimate the proportion of present-day DNA contamination

Cited by 39 publications

References 74 publications

Genome of a middle Holocene hunter-gatherer from Wallacea

Genome of a middle Holocene hunter-gatherer from Wallacea

Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry

A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia

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