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dc.contributor.author Siu Ting, Karen
dc.contributor.author Torres-Sánchez, María
dc.contributor.author San Mauro, Diego
dc.contributor.author Wilcockson, David
dc.contributor.author Wilkinson, Mark
dc.contributor.author Pisani, Davide
dc.contributor.author O'Connell, Mary J.
dc.contributor.author Creevey, Christopher
dc.date.accessioned 2020-02-25T03:08:56Z
dc.date.available 2020-02-25T03:08:56Z
dc.date.issued 2019-06-01
dc.identifier.citation Siu Ting , K , Torres-Sánchez , M , San Mauro , D , Wilcockson , D , Wilkinson , M , Pisani , D , O'Connell , M J & Creevey , C 2019 , ' Inadvertent paralog inclusion drives artefactual topologies and timetree estimates in phylogenomics ' Molecular Biology and Evolution , vol. 36 , no. 6 , pp. 1344-1356 . https://doi.org/10.1093/molbev/msz067 en
dc.identifier.issn 0737-4038
dc.identifier.other PURE: 29224529
dc.identifier.other PURE UUID: 585f5a3e-fdd3-4345-9225-bd45fa718d04
dc.identifier.other Scopus: 85066456060
dc.identifier.other handle.net: http://hdl.handle.net/2160/585f5a3e-fdd3-4345-9225-bd45fa718d04
dc.identifier.uri http://hdl.handle.net/2160/47587
dc.description.abstract Increasingly, large phylogenomic datasets include transcriptomic data from non-model organisms. This has allowed controversial and unexplored evolutionary relationships in the tree of life to be addressed but also increases the risk of inadvertent inclusion of paralogs in the analysis. While this may be expected to result in decreased phylogenetic support it is not clear if it could also drive highly supported artefactual relationships. Many groups, including the hyper-diverse Lissamphibia, are especially susceptible to these issues due to ancient gene duplication events, small numbers of sequenced genomes and because transcriptomes are increasingly applied to resolve historically conflicting taxonomic hypotheses. We tested the potential impact of paralog inclusion on the topologies and timetree estimates of the Lissamphibia using published and de novo sequencing data including 18 amphibian species, from which 2,656 single-copy gene families were identified. A novel paralog filtering approach resulted in four differently curated datasets, which were used for phylogenetic reconstructions using Bayesian inference, maximum likelihood and quartet-based supertrees. We found that paralogs drive strongly supported conflicting hypotheses within the Lissamphibia (Batrachia and Procera) and older divergence time estimates even within groups where no variation in topology was observed. All investigated methods, except Bayesian inference with the CAT-GTR model, were found to be sensitive to paralogs, but with filtering convergence to the same answer (Batrachia) was observed. This is the first large-scale study to address the impact of orthology selection using transcriptomic data and emphasises the importance of quality over quantity particularly for understanding relationships of poorly sampled taxa en
dc.format.extent 13 en
dc.language.iso eng
dc.relation.ispartof Molecular Biology and Evolution en
dc.rights en
dc.subject phylogenomics en
dc.subject orthology en
dc.subject paralogy en
dc.subject lissamphibia en
dc.subject timetree en
dc.title Inadvertent paralog inclusion drives artefactual topologies and timetree estimates in phylogenomics en
dc.type /dk/atira/pure/researchoutput/researchoutputtypes/contributiontojournal/article en
dc.description.version publishersversion en
dc.description.version publishersversion en
dc.identifier.doi https://doi.org/10.1093/molbev/msz067
dc.contributor.institution Department of Biological, Environmental and Rural Sciences en
dc.description.status Peer reviewed en


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