Genomic evidence for recurrent genetic admixture during the domestication of Mediterranean olive trees (Olea europaea L.)

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• dc.contributor.author Julca, Irene
• dc.contributor.author Marcet Houben, Marina
• dc.contributor.author Cruz, Fernando
• dc.contributor.author Gómez Garrido, Jèssica
• dc.contributor.author Gaut, Brandon S.
• dc.contributor.author Díez, Concepción M.
• dc.contributor.author Gut, Ivo Glynne
• dc.contributor.author Alioto, Tyler
• dc.contributor.author Vargas Gómez, Pablo
• dc.contributor.author Gabaldón Estevan, Juan Antonio, 1973-
• dc.date.accessioned 2020-11-12T11:43:32Z
• dc.date.available 2020-11-12T11:43:32Z
• dc.date.issued 2020
• dc.description.abstract Background: Olive tree (Olea europaea L. subsp. europaea, Oleaceae) has been the most emblematic perennial crop for Mediterranean countries since its domestication around 6000 years ago in the Levant. Two taxonomic varieties are currently recognized: cultivated (var. europaea) and wild (var. sylvestris) trees. However, it remains unclear whether olive cultivars derive from a single initial domestication event followed by secondary diversification, or whether cultivated lineages are the result of more than a single, independent primary domestication event. To shed light into the recent evolution and domestication of the olive tree, here we analyze a group of newly sequenced and available genomes using a phylogenomics and population genomics framework. Results: We improved the assembly and annotation of the reference genome, newly sequenced the genomes of twelve individuals: ten var. europaea, one var. sylvestris, and one outgroup taxon (subsp. cuspidata)-and assembled a dataset comprising whole genome data from 46 var. europaea and 10 var. sylvestris. Phylogenomic and population structure analyses support a continuous process of olive tree domestication, involving a major domestication event, followed by recurrent independent genetic admixture events with wild populations across the Mediterranean Basin. Cultivated olives exhibit only slightly lower levels of genetic diversity than wild forms, which can be partially explained by the occurrence of a mild population bottleneck 3000-14,000 years ago during the primary domestication period, followed by recurrent introgression from wild populations. Genes associated with stress response and developmental processes were positively selected in cultivars, but we did not find evidence that genes involved in fruit size or oil content were under positive selection. This suggests that complex selective processes other than directional selection of a few genes are in place. Conclusions: Altogether, our results suggest that a primary domestication area in the eastern Mediterranean basin was followed by numerous secondary events across most countries of southern Europe and northern Africa, often involving genetic admixture with genetically rich wild populations, particularly from the western Mediterranean Basin.
• dc.description.sponsorship This research has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 724173; RETVOLUTION)”. IJ was supported in part by a grant from the Peruvian Ministry of Education: “Beca Presidente de la República” (2013-III).
• dc.format.mimetype application/pdf
• dc.identifier.citation Julca I, Marcet-Houben M, Cruz F, Gómez-Garrido J, Gaut BS, Díez CM, Gut IG, Alioto TS, Vargas P, Gabaldón T. Genomic evidence for recurrent genetic admixture during the domestication of Mediterranean olive trees (Olea europaea L.). BMC Biol. 2020; 18(1):148. DOI: 10.1186/s12915-020-00881-6
• dc.identifier.doi http://dx.doi.org/10.1186/s12915-020-00881-6
• dc.identifier.issn 1741-7007
• dc.identifier.uri http://hdl.handle.net/10230/45740
• dc.language.iso eng
• dc.publisher BioMed Central
• dc.relation.ispartof BMC Biol. 2020; 18(1):148
• dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/724173
• dc.rights © The Author(s). 2020 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 Admixture
• dc.subject.keyword Domestication
• dc.subject.keyword Genome
• dc.subject.keyword Introgression
• dc.subject.keyword Olive
• dc.title Genomic evidence for recurrent genetic admixture during the domestication of Mediterranean olive trees (Olea europaea L.)
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion