Simulation-Based Evaluation of Three Methods for Local Ancestry Deconvolution of Non-model Crop Species Genomes.
admixture
crops
local ancestry inference
simulation analysis
Journal
G3 (Bethesda, Md.)
ISSN: 2160-1836
Titre abrégé: G3 (Bethesda)
Pays: England
ID NLM: 101566598
Informations de publication
Date de publication:
06 02 2020
06 02 2020
Historique:
pubmed:
22
12
2019
medline:
9
1
2021
entrez:
22
12
2019
Statut:
epublish
Résumé
Hybridizations between species and subspecies represented major steps in the history of many crop species. Such events generally lead to genomes with mosaic patterns of chromosomal segments of various origins that may be assessed by local ancestry inference methods. However, these methods have mainly been developed in the context of human population genetics with implicit assumptions that may not always fit plant models. The purpose of this study was to evaluate the suitability of three state-of-the-art inference methods (SABER, ELAI and WINPOP) for local ancestry inference under scenarios that can be encountered in plant species. For this, we developed an R package to simulate genotyping data under such scenarios. The tested inference methods performed similarly well as far as representatives of source populations were available. As expected, the higher the level of differentiation between ancestral source populations and the lower the number of generations since admixture, the more accurate were the results. Interestingly, the accuracy of the methods was only marginally affected by i) the number of ancestries (up to six tested); ii) the sample design (
Identifiants
pubmed: 31862786
pii: g3.119.400873
doi: 10.1534/g3.119.400873
pmc: PMC7003078
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
569-579Informations de copyright
Copyright © 2020 Cottin et al.
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