Model-based detection of whole-genome duplications in a phylogeny

Show simple item record Zwaenepoel, Arthur Van de Peer, Yves 2021-09-21T06:49:16Z 2021-09-21T06:49:16Z 2020-09
dc.description.abstract Ancient whole-genome duplications (WGDs) leave signatures in comparative genomic data sets that can be harnessed to detect these events of presumed evolutionary importance. Current statistical approaches for the detection of ancient WGDs in a phylogenetic context have two main drawbacks. The first is that unwarranted restrictive assumptions on the “background” gene duplication and loss rates make inferences unreliable in the face of model violations. The second is that most methods can only be used to examine a limited set of a priori selected WGD hypotheses and cannot be used to discover WGDs in a phylogeny. In this study, we develop an approach for WGD inference using gene count data that seeks to overcome both issues. We employ a phylogenetic birth–death model that includes WGD in a flexible hierarchical Bayesian approach and use reversible-jump Markov chain Monte Carlo to perform Bayesian inference of branch-specific duplication, loss, and WGD retention rates across the space of WGD configurations. We evaluate the proposed method using simulations, apply it to data sets from flowering plants, and discuss the statistical intricacies of model-based WGD inference. en_ZA
dc.description.department Biochemistry en_ZA
dc.description.department Genetics en_ZA
dc.description.department Microbiology and Plant Pathology en_ZA
dc.description.librarian hj2021 en_ZA
dc.description.sponsorship PhD fellowship of the Research Foundation Flanders (FWO) and the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Program. en_ZA
dc.description.uri en_ZA
dc.identifier.citation 2020, 'Model-based detection of whole-genome duplications in a phylogeny', Molecular Biology and Evolution, vol. 37, no. 9, pp. 2734–2746, en_ZA
dc.identifier.issn 0737-4038 (print)
dc.identifier.issn 1537-1719 (online)
dc.identifier.other 10.1093/molbev/msaa111
dc.language.iso en en_ZA
dc.publisher Oxford University Press en_ZA
dc.rights © The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. en_ZA
dc.subject Whole-genome duplication (WGD) en_ZA
dc.subject Genome duplication en_ZA
dc.subject Phylogenetics en_ZA
dc.subject Gene content evolution en_ZA
dc.subject Bayesian inference en_ZA
dc.subject Reversible-jump MCMC en_ZA
dc.title Model-based detection of whole-genome duplications in a phylogeny en_ZA
dc.type Article en_ZA

Files in this item

This item appears in the following Collection(s)

Show simple item record