Modelling the demographic history of human North African genomes points to a recent soft split divergence between populations

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• dc.contributor.author Serradell Noguera, Jose Miguel
• dc.contributor.author Lorenzo Salazar, Jose M.
• dc.contributor.author Flores, Carlos
• dc.contributor.author Lao Grueso, Oscar, 1976-
• dc.contributor.author Comas, David, 1969-
• dc.date.accessioned 2024-09-19T06:05:57Z
• dc.date.available 2024-09-19T06:05:57Z
• dc.date.issued 2024
• dc.description.abstract Background: North African human populations present a complex demographic scenario due to the presence of an autochthonous genetic component and population substructure, plus extensive gene flow from the Middle East, Europe, and sub-Saharan Africa. Results: We conducted a comprehensive analysis of 364 genomes to construct detailed demographic models for the North African region, encompassing its two primary ethnic groups, the Arab and Amazigh populations. This was achieved through an Approximate Bayesian Computation with Deep Learning (ABC-DL) framework and a novel algorithm called Genetic Programming for Population Genetics (GP4PG). This innovative approach enabled us to effectively model intricate demographic scenarios, utilizing a subset of 16 whole genomes at > 30X coverage. The demographic model suggested by GP4PG exhibited a closer alignment with the observed data compared to the ABC-DL model. Both point to a back-to-Africa origin of North African individuals and a close relationship with Eurasian populations. Results support different origins for Amazigh and Arab populations, with Amazigh populations originating back in Epipaleolithic times, while GP4PG supports Arabization as the main source of Middle Eastern ancestry. The GP4PG model includes population substructure in surrounding populations (sub-Saharan Africa and Middle East) with continuous decaying gene flow after population split. Contrary to ABC-DL, the best GP4PG model does not require pulses of admixture from surrounding populations into North Africa pointing to soft splits as drivers of divergence in North Africa. Conclusions: We have built a demographic model on North Africa that points to a back-to-Africa expansion and a differential origin between Arab and Amazigh populations.
• dc.description.sponsorship This work was supported by the Spanish Ministry of Science and Innovation and by “ERF A way of making Europe” (grant numbers RTC-2017–6471–1 AEI/FEDER, UE, PID2019-106485 GB-I00, and PID2022-138755NB-I00), Fundación CajaCanarias and Fundación Bancaria “La Caixa” (2018PATRI20), and “Unidad María de Maeztu” (CEX2018-000792-M) funded by the MCIN and the AEI (https://doi.org/10.13039/501100011033). J.M.S was supported with a Formació de Personal Investigador fellowship from Generalitat de Catalunya (FI_B100135).
• dc.format.mimetype application/pdf
• dc.identifier.citation Serradell JM, Lorenzo-Salazar JM, Flores C, Lao O, Comas D. Modelling the demographic history of human North African genomes points to a recent soft split divergence between populations. Genome Biol. 2024 Jul 30;25(1):201. DOI: 10.1186/s13059-024-03341-4
• dc.identifier.doi http://dx.doi.org/10.1186/s13059-024-03341-4
• dc.identifier.issn 1474-7596
• dc.identifier.uri http://hdl.handle.net/10230/61155
• dc.language.iso eng
• dc.publisher BioMed Central
• dc.relation.ispartof Genome Biol. 2024 Jul 30;25(1):201
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PID2019-106485 GB-I00
• dc.relation.projectID info:eu-repo/grantAgreement/ES/3PE/PID2022-138755NB-I00
• dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/CEX2018-000792-M
• dc.rights © The Author(s) 2024. 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data ma
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Deep learning
• dc.subject.keyword Demographic history
• dc.subject.keyword Genetic programming
• dc.subject.keyword Human population genetics
• dc.subject.keyword North Africa
• dc.subject.keyword Whole-genome sequences
• dc.title Modelling the demographic history of human North African genomes points to a recent soft split divergence between populations
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion