Estimation of contemporary effective population size in plant populations: limitations of genomic datasets
| hal.structure.identifier | Royal Botanic Gardens [Kew] | |
| dc.contributor.author | GARGIULO, Roberta | |
| hal.structure.identifier | Biologie du fruit et pathologie [BFP] | |
| dc.contributor.author | DECROOCQ, Véronique | |
| hal.structure.identifier | Biodiversité, Gènes & Communautés [BioGeCo] | |
| dc.contributor.author | GONZÁLEZ-MARTÍNEZ, Santiago | |
| hal.structure.identifier | Colorado State University [Pueblo] [CSUPueblo] | |
| dc.contributor.author | PAZ-VINAS, Ivan | |
| hal.structure.identifier | Laboratoire de Bioinformatique pour la Génomique et la Biodiversité [LBGB] | |
| dc.contributor.author | AURY, Jean-Marc | |
| hal.structure.identifier | Biodiversité, Gènes & Communautés [BioGeCo] | |
| dc.contributor.author | LESUR KUPIN, Isabelle | |
| hal.structure.identifier | Biodiversité, Gènes & Communautés [BioGeCo] | |
| dc.contributor.author | PLOMION, Christophe | |
| hal.structure.identifier | Botanique et Modélisation de l'Architecture des Plantes et des Végétations [UMR AMAP] | |
| dc.contributor.author | SCHMITT, Sylvain | |
| hal.structure.identifier | Ecologie des Forêts Méditerranéennes [URFM] | |
| dc.contributor.author | SCOTTI, Ivan | |
| hal.structure.identifier | Biodiversité, Gènes & Communautés [BioGeCo] | |
| dc.contributor.author | HEUERTZ, Myriam | |
| dc.date.issued | 2023-07-19 | |
| dc.identifier.issn | 1614-2942 | |
| dc.description.abstractEn | Effective 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.iso | en | |
| dc.publisher | Springer Verlag | |
| dc.subject.en | conservation genomics, effective population size, GONE, linkage disequilibrium, plants | |
| dc.title.en | Estimation of contemporary effective population size in plant populations: limitations of genomic datasets | |
| dc.type | Article de revue | |
| dc.identifier.doi | 10.1101/2023.07.18.549323 | |
| dc.subject.hal | Sciences du Vivant [q-bio]/Génétique/Génétique des populations [q-bio.PE] | |
| bordeaux.journal | Tree Genetics and Genomes | |
| bordeaux.page | 76 | |
| bordeaux.volume | 15 | |
| bordeaux.issue | 5 | |
| bordeaux.peerReviewed | oui | |
| hal.identifier | hal-04230362 | |
| hal.version | 1 | |
| hal.popular | non | |
| hal.audience | Internationale | |
| hal.origin.link | https://hal.archives-ouvertes.fr//hal-04230362v1 | |
| bordeaux.COinS | ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=Tree%20Genetics%20and%20Genomes&rft.date=2023-07-19&rft.volume=15&rft.issue=5&rft.spage=76&rft.epage=76&rft.eissn=1614-2942&rft.issn=1614-2942&rft.au=GARGIULO,%20Roberta&DECROOCQ,%20V%C3%A9ronique&GONZ%C3%81LEZ-MART%C3%8DNEZ,%20Santiago&PAZ-VINAS,%20Ivan&AURY,%20Jean-Marc&rft.genre=article |
Files in this item
| Files | Size | Format | View |
|---|---|---|---|
|
There are no files associated with this item. |
|||