Detecting archaic introgression using an unadmixed outgroup
Open accessAbstract
Human populations outside of Africa have experienced at least two bouts of introgression from archaic humans, from Neanderthals and Denisovans. In Papuans there is prior evidence of both these introgressions. Here we present a new approach to detect segments of individual genomes of archaic origin without using an archaic reference genome. The approach is based on a hidden Markov model that identifies genomic regions with a high density of single nucleotide variants (SNVs) not seen in unadmixed populations. We show using simulations that this provides a powerful approach to identifying segments of archaic introgression with a low rate of false detection, given data from a suitable outgroup population is available, without the archaic introgression but containing a majority of the variation that arose since initial separation from the archaic lineage. Furthermore our approach is able to infer admixture proportions and the times both of admixture and of initial divergence between the human and archaic populations. We apply the model to detect archaic introgression in 89 Papuans and show how the identified segments can be assigned to likely Neanderthal or Denisovan origin. We report more Denisovan admixture than previous studies and find a shift in size distribution of fragments of Neanderthal and Denisovan origin that is compatible with a difference in admixture time. Furthermore, we identify small amounts of Denisova ancestry in South East Asians and South Asians.
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The HMMArchaic method does not require a reference genome to guide detection of introgressed DNA, making it suitable for identifying DNA from super-archaic groups for which no genome information currently exists.
“Importantly, HMMArchaic differs from CP and HMM in that it does not require a reference genome to guide the detection of introgressed DNA, making it suitable for identifying DNA from super-archaic groups for which no genome information currently exists.”
From Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture (2021) · cites this paper as [34]
79% of the sites identified in PEL and 81% of the sites identified in MXL overlapped with archaic ancestry tracts identified by Skov et al. (2018).
“We also compared the archaic alleles with high PBS values with the archaic ancestry tracts identified by Skov et al. (2018) and found that 79% of the sites identified in PEL and 81% of the sites identified in MXL also overlapped with archaic ancestry tracts.”
From The Impact of Modern Admixture on Archaic Human Ancestry in Human Populations (2023) · cites this paper as Skov et al. 2018
Most studies of archaic introgression have relied on the GRCh37 human reference genome.
“However, most studies of archaic introgression have relied on the GRCh37 human reference genome [8, 10, 11, 13, 14, 20].”
From A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome (2025) · cites this paper as [20]
The Introduction discusses methods that use archaic reference genomes, which are distinct from the GRCh37 human reference genome. The Results mention using an hg19 repeat-mask track in this paper's simulations, but neither passage establishes that most archaic-introgression studies relied on GRCh37. Searches for GRCh37 and hg19 found no passage making that broader claim. (LLM, conf=0.76)
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An Extended Admixture Pulse Model Reveals the Limitations to Human–Neandertal Introgression Dating
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Ancient Genomes Illuminate the Origins and Dynamic History of East Asian Cattle
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Extended haplotype with rs41524547-G defines the ancestral origin of SCA10
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A global map for introgressed structural variation and selection in humans
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An extended admixture pulse model reveals the limitations to Human-Neandertal introgression datingPreprint
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- Authors
- Skov, L., Hui, R., Shchur, V., Hobolth, A., Scally, A., Schierup, M. H., & Durbin, R.
- Affiliations
- Aarhus University (DK)
- University of Cambridge (GB)
- Wellcome Sanger Institute (GB)
- Corresponding author
- Skov, Laurits
- Durbin, Richard
- ORCID
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2018-09-18
- Volume
- 14
- Issue
- 9
- Pages
- e1007641
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC6161914
- OpenAlex
- W2889626029
- Cited by
- 125
- References
- 29
- Citations by year
- 2026: 25 · 2025: 15 · 2024: 18 · 2023: 12 · 2022: 8 · 2021: 13 · 2020: 18 · 2019: 15 · 2018: 1
- FWCI
- 49.70
- Type
- journal article
- Language
- en
- Update notices
- new_version (2018-09-28)
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Apollo (cc-by)
- Funders
- Wellcome Trust (WT206194)
- Wellcome Trust (GB) (RG89781)
- Det Frie Forskningsråd (DK) (1323-00076)
- Det Frie Forskningsråd (6108-00385)
- Topics
- Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- archaic introgression, Neanderthal admixture, Denisovan admixture, Papuans, hidden Markov models, single nucleotide variants
- MeSH terms
- Animals, Fossils, Humans, Hybridization, Genetic, Phylogeny, Hominidae, Genome, Human, Black People, White People, Asian People, Native Hawaiian or Pacific Islander, Native Hawaiian or Other Pacific Islander, Neanderthals
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