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No Evidence for Phylostratigraphic Bias Impacting Inferences on Patterns of Gene Emergence and Evolution

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dc.contributor.author Domazet-Lošo, Tomislav
dc.contributor.author Carvunis, Anne-Ruxandra
dc.contributor.author Albà Soler, Mar
dc.contributor.author Šestak, Martin Sebastijan
dc.contributor.author Bakarić, Robert
dc.contributor.author Neme, Rafik
dc.contributor.author Tautz, Diethard
dc.date.accessioned 2017-05-23T08:06:07Z
dc.date.available 2017-05-23T08:06:07Z
dc.date.issued 2017
dc.identifier.citation Domazet-Lošo T, Carvunis A-R, Albà Soler M, Šestak MS, Bakarić R, Neme R, Tautz D. No Evidence for Phylostratigraphic Bias Impacting Inferences on Patterns of Gene Emergence and Evolution. Molecular Biology and Evolution. 2017;34(4):843-56. DOI: 10.1093/molbev/msw284
dc.identifier.issn 0737-4038
dc.identifier.uri http://hdl.handle.net/10230/32144
dc.description.abstract Phylostratigraphy is a computational framework for dating the emergence of DNA and protein sequences in a phylogeny. It has been extensively applied to make inferences on patterns of genome evolution, including patterns of disease gene evolution, ontogeny and de novo gene origination. Phylostratigraphy typically relies on BLAST searches along a species tree, but new simulation studies have raised concerns about the ability of BLAST to detect remote homologues and its impact on phylostratigraphic inferences. Here, we re-assessed these simulations. We found that, even with a possible overall BLAST false negative rate between 11–15%, the large majority of sequences assigned to a recent evolutionary origin by phylostratigraphy is unaffected by technical concerns about BLAST. Where the results of the simulations did cast doubt on previously reported findings, we repeated the original analyses but now excluded all questionable sequences. The originally described patterns remained essentially unchanged. These new analyses strongly support phylostratigraphic inferences, including: genes that emerged after the origin of eukaryotes are more likely to be expressed in the ectoderm than in the endoderm or mesoderm in Drosophila, and the de novo emergence of protein-coding genes from non-genic sequences occurs through proto-gene intermediates in yeast. We conclude that BLAST is an appropriate and sufficiently sensitive tool in phylostratigraphic analysis that does not appear to introduce significant biases into evolutionary pattern inferences.
dc.description.sponsorship We thank the following funding organizations for support of our work: TD-L: City of Zagreb and Adris Foundation grants; A-RC: National Institute of Health (NIH) grant K99 GM108865; MA: grant BFU2015-65235-P from MINECO/FEDER, EU; DT: ERC grant NewGenes, 322564.
dc.format.mimetype application/pdf
dc.language.iso eng
dc.publisher Oxford University Press
dc.relation.ispartof Molecular Biology and Evolution. 2017;34(4):843-56
dc.rights © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.uri http://creativecommons.org/licenses/by-nc/4.0/
dc.title No Evidence for Phylostratigraphic Bias Impacting Inferences on Patterns of Gene Emergence and Evolution
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1093/molbev/msw284
dc.subject.keyword Genome analysis
dc.subject.keyword Phylostratigraphy
dc.subject.keyword BLAST
dc.subject.keyword Gene age estimation
dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/BFU2015-65235-P
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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