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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.authorGONZALEZ-MARTINEZ, Santiago C.
hal.structure.identifierColorado State University [Fort Collins] [CSU]
hal.structure.identifierÉquipe 1 - Biodiversité et Adaptation dans les Hydrosystèmes [BAH]
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.issued2024-05-03
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 (LD), in particular, have become popular in conservation as they require a single sampling and provide estimates that refer to recent generations. A software program based on the LD method, 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 SNP 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 LD 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. We finally compare the N e estimates obtained with GONE for the last generations with the contemporary N e estimates obtained with the programs currentNe and NeEstimator.
dc.language.isoen
dc.publisherBlackwell
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.subject.enEffective population size
dc.subject.enGONE
dc.subject.enLinkage disequilibrium
dc.subject.enPlants
dc.subject.enconservation genomics
dc.title.enEstimation of contemporary effective population size in plant populations: Limitations of genomic datasets
dc.typeArticle de revue
dc.identifier.doi10.1111/eva.13691
dc.subject.halSciences de l'environnement
dc.subject.halSciences du Vivant [q-bio]
bordeaux.journalEvolutionary Applications
bordeaux.volume17
bordeaux.issue5
bordeaux.peerReviewedoui
hal.identifierhal-04590931
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-04590931v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Evolutionary%20Applications&rft.date=2024-05-03&rft.volume=17&rft.issue=5&rft.eissn=1752-4563&rft.issn=1752-4563&rft.au=GARGIULO,%20Roberta&DECROOCQ,%20V%C3%A9ronique&GONZALEZ-MARTINEZ,%20Santiago%20C.&PAZ%E2%80%90VINAS,%20Ivan&AURY,%20Jean%E2%80%90marc&rft.genre=article


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