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Cited by 129Forensic and Genetic ResearchPleistocene-Era Hominins and ArchaeologyGenetic diversity and population structure

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Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania

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Mondal, Mayukh, Bertranpetit, Jaume, Lao, Oscar·2019·Nature Communications
DOI 10.1038/s41467-018-08089-7PMC PMC6335398
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Abstract

Since anatomically modern humans dispersed Out of Africa, the evolutionary history of Eurasian populations has been marked by introgressions from presently extinct hominins. Some of these introgressions have been identified using sequenced ancient genomes (Neanderthal and Denisova). Other introgressions have been proposed for still unidentified groups using the genetic diversity present in current human populations. We built a demographic model based on deep learning in an Approximate Bayesian Computation framework to infer the evolutionary history of Eurasian populations including past introgression events in Out of Africa populations fitting the current genetic evidence. In addition to the reported Neanderthal and Denisovan introgressions, our results support a third introgression in all Asian and Oceanian populations from an archaic population. This population is either related to the Neanderthal-Denisova clade or diverged early from the Denisova lineage. We propose the use of deep learning methods for clarifying situations with high complexity in evolutionary genomics.

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Crossref · 10.1038/s41467-018-08089-7

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Figures

Fig. 1 Increase of Neanderthal ancestry in Asians compared to Europeans. The introgression amount is calculated by the F4 ratio test. F4 (Outgroup, Altai; Europeans, X)/F4(Outgroup, Altai; Africa, Vindjia) where Outgroup can be either Denisova or Ancestral alleles from 1000 Genome and X is either East Asian (ASN), Indian Tribal (IND) or Andamanese (AND). In the y axis to make it short we only mention F4(Outgroup, X) as the other populations remain constant for all the F4 ratio tests. In the x axis we have the amount of F4 ratio and the standard error is denoted by bars (standard error was calculated by Jackknife method using 555 blocks). The blue line signifies 0 value for F4 ratio test
Fig. 1 Increase of Neanderthal ancestry in Asians compared to Europeans. The introgression amount is calculated by the F4 ratio test. F4 (Outgroup, Altai; Europeans, X)/F4(Outgroup, Altai; Africa, Vindjia) where Outgroup can be either Denisova or Ancestral alleles from 1000 Genome and X is either East Asian (ASN), Indian Tribal (IND) or Andamanese (AND). In the y axis to make it short we only mention F4(Outgroup, X) as the other populations remain constant for all the F4 ratio tests. In the x axis we have the amount of F4 ratio and the standard error is denoted by bars (standard error was calculated by Jackknife method using 555 blocks). The blue line signifies 0 value for F4 ratio testCC BY · PubMed Central
Fig. 2 Demographic models implemented for explaining the genetic variation present in current African (A), European (E), East Asian (Ea), Andamanese (An), Indian (I), Papuan (P) and Australian (Au) populations, in relation with Altai Neanderthal (N) and Denisovan (D) archaic populations. The process of archaic introgression in Asian populations is modelled either by different introgression events from a anatomically modern human ghost population (Xn), b, c, d known archaic populations such as N and D and or e, f, g, h by an unknown archaic extinct (Xe) population. An archaic population (Xd) introgressing to Denisovans is also modelled. Turquoise arrows indicate single pulse events of archaic introgression. All models include recent continuous migrations between African and European, European and East Asian, and Papuan and Australian populations
Fig. 2 Demographic models implemented for explaining the genetic variation present in current African (A), European (E), East Asian (Ea), Andamanese (An), Indian (I), Papuan (P) and Australian (Au) populations, in relation with Altai Neanderthal (N) and Denisovan (D) archaic populations. The process of archaic introgression in Asian populations is modelled either by different introgression events from a anatomically modern human ghost population (Xn), b, c, d known archaic populations such as N and D and or e, f, g, h by an unknown archaic extinct (Xe) population. An archaic population (Xd) introgressing to Denisovans is also modelled. Turquoise arrows indicate single pulse events of archaic introgression. All models include recent continuous migrations between African and European, European and East Asian, and Papuan and Australian populationsCC BY · PubMed Central
Fig. 3 Graphical representation of the two best supported model (Model F and Model H) with mean posterior distribution of each parameter. a Mean of the posterior distributions of each parameter calculated by means of ABC-DL in model F for Africans (A), Europeans (E), East Asians (Ea), Andamanese (An), Indians (I), Papuans (P), Aboriginal Australians (Au), Altai Neanderthal (N) and Denisovan (D). The model includes an extinct hominin population (Xe) descendent from the Denisovan population. b Mean of the posterior distributions of each parameter calculated by means of ABC-DL in model H. Xe population is an admixture between Neanderthals and Denisovans which interbreeds with Asian populations and a Homo erectus-like population (Xd) that interbreeds with Denisovan. In blue, some of the recent continuous migrations between populations which were taken into consideration in the model. In turquoise, the different introgressions
Fig. 3 Graphical representation of the two best supported model (Model F and Model H) with mean posterior distribution of each parameter. a Mean of the posterior distributions of each parameter calculated by means of ABC-DL in model F for Africans (A), Europeans (E), East Asians (Ea), Andamanese (An), Indians (I), Papuans (P), Aboriginal Australians (Au), Altai Neanderthal (N) and Denisovan (D). The model includes an extinct hominin population (Xe) descendent from the Denisovan population. b Mean of the posterior distributions of each parameter calculated by means of ABC-DL in model H. Xe population is an admixture between Neanderthals and Denisovans which interbreeds with Asian populations and a Homo erectus-like population (Xd) that interbreeds with Denisovan. In blue, some of the recent continuous migrations between populations which were taken into consideration in the model. In turquoise, the different introgressionsCC BY · PubMed Central

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Research works printed but not linked: 1

  1. Prangle, D. in Handbook of Approximate Bayesian Computation (ABC) (eds Sisson, S. A., Fan, Y. & Beaumont, B.) 320 (Taylor & Francis, Abingdon, 2108).

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Metadata

Authors
Mondal, M., Bertranpetit, J., & Lao, O.
Affiliations
  • University of Tartu (EE)
  • Universitat Pompeu Fabra (ES)
Corresponding author
Bertranpetit, Jaume
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2019-01-16
Volume
10
Issue
1
Pages
246-246
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-018-08089-7
PMC
PMC6335398
OpenAlex
W2909640254
Cited by
124
References
51
Citations by year
2026: 7 · 2025: 6 · 2024: 11 · 2023: 9 · 2022: 15 · 2021: 29 · 2020: 38 · 2019: 9
FWCI
13.59
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, other-oa)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RECERCAT (Consorci de Serveis Universitaris de Catalunya) (publishedVersion, other-oa)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion, cc-by)
Funders
  • Centres de Recerca de Catalunya
  • European Commission (2014‐2020, 2020 ‘, 2014-2020.4.01.16-0030)
  • Generalitat de Catalunya (GRC 2017 SGR 937, 2017-SGR, MDM-2014-0370)
  • Ministerio de Asuntos Económicos y Transformación Digital, Gobierno de España (RYC-2013-14797, MDM-2014-0370, BFU2015-68759-P)
  • Instituto de Salud Carlos III (MDM-2014-0370, 2014/2020)
  • European Regional Development Fund (BFU2016, 2014-2020’, 2014-2020.4.01.16-0030, MDM-2014-0370, 14797, BFU2016-77961-P)
  • Agencia Estatal de Investigación (MDM-2014-0370, BFU2016-77961-P)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
  • Social Sciences › Anthropology › Pleistocene-Era Hominins and Archaeology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
Keywords
archaic introgression, Neanderthal introgression, Denisovan introgression, approximate Bayesian computation, dispersal out of Africa, human evolution

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