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

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  • dc.contributor.author Mondal, Mayukh, 1989-
  • dc.contributor.author Bertranpetit, Jaume, 1952-
  • dc.contributor.author Lao Grueso, Oscar, 1976-
  • dc.date.accessioned 2019-01-22T13:47:17Z
  • dc.date.available 2019-01-22T13:47:17Z
  • dc.date.issued 2019
  • dc.description.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.
  • dc.description.sponsorship M.M was supported by the European Union through the European Regional Development Fund (Project No. 2014-2020.4.01.16-0030). For J.B, this study has been possible thanks to grant BFU2016-77961-P (AEI/FEDER, UE) awarded by the Agencia Estatal de Investigación (MINECO, Spain) and with the support of Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 702). Part of the “Unidad de Excelencia María de Maeztu”, funded by the MINECO (ref: MDM-2014-0370). O.L. was supported by a Ramón y Cajal grant from the Spanish Ministerio de Economia y Competitividad (MINECO) with reference RYC-2013-14797, a BFU2015-68759-P (MINECO/FEDER) grant and the support of Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 937).
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Mondal M, Bertranpetit J, Lao O. Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania. Nat Commun. 2019;10(1):246. DOI 10.1038/s41467-018-08089-7
  • dc.identifier.doi http://dx.doi.org/10.1038/s41467-018-08089-7
  • dc.identifier.issn 2041-1723
  • dc.identifier.uri http://hdl.handle.net/10230/36375
  • dc.language.iso eng
  • dc.publisher Nature Research
  • dc.relation.ispartof Nat Commun. 2019;10(1):246
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2016-77961-P
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2015-68759-P
  • dc.rights © The Author(s) 2019. Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by/4.0/
  • dc.subject.keyword Genetic variation
  • dc.title Approximate Bayesian computation with deep learning supports a third archaic introgression in Asia and Oceania
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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