Inferring the mode of origin of polyploid species from next-generation sequence data.

Détails

ID Serval
serval:BIB_F0BD4BFC5A57
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Institution
Titre
Inferring the mode of origin of polyploid species from next-generation sequence data.
Périodique
Molecular Ecology
Auteur(s)
Roux C., Pannell J.R.
ISSN
1365-294X (Electronic)
ISSN-L
0962-1083
Statut éditorial
Publié
Date de publication
2015
Peer-reviewed
Oui
Volume
24
Numéro
5
Pages
1047-1059
Langue
anglais
Résumé
Many eukaryote organisms are polyploid. However, despite their importance, evolutionary inference of polyploid origins and modes of inheritance has been limited by a need for analyses of allele segregation at multiple loci using crosses. The increasing availability of sequence data for nonmodel species now allows the application of established approaches for the analysis of genomic data in polyploids. Here, we ask whether approximate Bayesian computation (ABC), applied to realistic traditional and next-generation sequence data, allows correct inference of the evolutionary and demographic history of polyploids. Using simulations, we evaluate the robustness of evolutionary inference by ABC for tetraploid species as a function of the number of individuals and loci sampled, and the presence or absence of an outgroup. We find that ABC adequately retrieves the recent evolutionary history of polyploid species on the basis of both old and new sequencing technologies. The application of ABC to sequence data from diploid and polyploid species of the plant genus Capsella confirms its utility. Our analysis strongly supports an allopolyploid origin of C. bursa-pastoris about 80 000 years ago. This conclusion runs contrary to previous findings based on the same data set but using an alternative approach and is in agreement with recent findings based on whole-genome sequencing. Our results indicate that ABC is a promising and powerful method for revealing the evolution of polyploid species, without the need to attribute alleles to a homeologous chromosome pair. The approach can readily be extended to more complex scenarios involving higher ploidy levels.
Mots-clé
approximate Bayesian computation, Capsella, coalescence, disomic inheritance, polyploidization, speciation, tetrasomic inheritance
Pubmed
Web of science
Création de la notice
16/02/2015 14:01
Dernière modification de la notice
20/08/2019 16:18
Données d'usage