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Estimation of contemporary effective population size in plant populations: limitations of genomic datasets

hal.structure.identifierRoyal Botanic Gardens [Kew]
dc.contributor.authorGARGIULO, Roberta
hal.structure.identifierBiologie du fruit et pathologie [BFP]
dc.contributor.authorDECROOCQ, Véronique
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorGONZÁLEZ-MARTÍNEZ, Santiago
hal.structure.identifierColorado State University [Pueblo] [CSUPueblo]
dc.contributor.authorPAZ-VINAS, Ivan
hal.structure.identifierInstitut de Biologie François JACOB [JACOB]
dc.contributor.authorAURY, Jean‐marc
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLESUR KUPIN, Isabelle
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPLOMION, Christophe
hal.structure.identifierBotanique et Modélisation de l'Architecture des Plantes et des Végétations [UMR AMAP]
dc.contributor.authorSCHMITT, Sylvain
hal.structure.identifierEcologie des Forêts Méditerranéennes [URFM]
dc.contributor.authorSCOTTI, Ivan
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorHEUERTZ, Myriam
dc.date.issued2023-07-19
dc.identifier.issn1752-4563
dc.description.abstractEnEffective population size ( N e ) is a pivotal evolutionary parameter with crucial implications in conservation practice and policy. Genetic methods to estimate N e have been preferred over demographic methods because they rely on genetic data rather than time-consuming ecological monitoring. Methods based on linkage disequilibrium, in particular, have become popular in conservation as they require a single sampling and provide estimates that refer to recent generations. A recently developed software based on linkage disequilibrium, GONE, looks particularly promising to estimate contemporary and recent-historical N e (up to 200 generations in the past). Genomic datasets from non-model species, especially plants, may present some constraints to the use of GONE, as linkage maps and reference genomes are seldom available, and SNPs genotyping is usually based on reduced-representation methods. In this study, we use empirical datasets from four plant species to explore the limitations of plant genomic datasets when estimating N e using the algorithm implemented in GONE, in addition to exploring some typical biological limitations that may affect N e estimation using the linkage disequilibrium method, such as the occurrence of population structure. We show how accuracy and precision of N e estimates potentially change with the following factors: occurrence of missing data, limited number of SNPs/individuals sampled, and lack of information about the location of SNPs on chromosomes, with the latter producing a significant bias, previously unexplored with empirical data.
dc.language.isoen
dc.publisherBlackwell
dc.subject.enconservation genomics
dc.subject.eneffective population size
dc.subject.enGONE
dc.subject.enlinkage disequilibrium
dc.subject.enplants
dc.title.enEstimation of contemporary effective population size in plant populations: limitations of genomic datasets
dc.typeArticle de revue
dc.identifier.doi10.1101/2023.07.18.549323
dc.subject.halSciences du Vivant [q-bio]/Génétique/Génétique des populations [q-bio.PE]
bordeaux.journalEvolutionary Applications
bordeaux.volume17
bordeaux.issue5
bordeaux.peerReviewedoui
hal.identifierhal-04230362
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-04230362v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Evolutionary%20Applications&rft.date=2023-07-19&rft.volume=17&rft.issue=5&rft.eissn=1752-4563&rft.issn=1752-4563&rft.au=GARGIULO,%20Roberta&DECROOCQ,%20V%C3%A9ronique&GONZ%C3%81LEZ-MART%C3%8DNEZ,%20Santiago&PAZ-VINAS,%20Ivan&AURY,%20Jean%E2%80%90marc&rft.genre=article


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