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dc.contributor.authorLi, B
dc.contributor.authorLopes, JS
dc.contributor.authorFoster, PG
dc.contributor.authorEmbley, TM
dc.contributor.authorCox, CJ
dc.date.accessioned2019-04-29T14:02:33Z
dc.date.available2019-04-29T14:02:33Z
dc.date.issued2014-07
dc.date.submitted2011-06-22
dc.identifier.citationBlaise Li, João S. Lopes, Peter G. Foster, T. Martin Embley, Cymon J. Cox, Compositional Biases among Synonymous Substitutions Cause Conflict between Gene and Protein Trees for Plastid Origins, Molecular Biology and Evolution, Volume 31, Issue 7, July 2014, Pages 1697–1709, https://doi.org/10.1093/molbev/msu105en_US
dc.identifier.issn0737-4038
dc.identifier.doi10.1093/molbev/msu105
dc.identifier.urihttp://hdl.handle.net/10141/622505
dc.description.abstractArchaeplastida (=Kingdom Plantae) are primary plastid-bearing organisms that evolved via the endosymbiotic association of a heterotrophic eukaryote host cell and a cyanobacterial endosymbiont approximately 1,400 Ma. Here, we present analyses of cyanobacterial and plastid genomes that show strongly conflicting phylogenies based on 75 plastid (or nuclear plastid-targeted) protein-coding genes and their direct translations to proteins. The conflict between genes and proteins is largely robust to the use of sophisticated data- and tree-heterogeneous composition models. However, by using nucleotide ambiguity codes to eliminate synonymous substitutions due to codon-degeneracy, we identify a composition bias, and dependent codon-usage bias, resulting from synonymous substitutions at all third codon positions and first codon positions of leucine and arginine, as the main cause for the conflicting phylogenetic signals. We argue that the protein-coding gene data analyses are likely misleading due to artifacts induced by convergent composition biases at first codon positions of leucine and arginine and at all third codon positions. Our analyses corroborate previous studies based on gene sequence analysis that suggest Cyanobacteria evolved by the early paraphyletic splitting of Gloeobacter and a specific Synechococcus strain (JA33Ab), with all other remaining cyanobacterial groups, including both unicellular and filamentous species, forming the sister-group to the Archaeplastida lineage. In addition, our analyses using better-fitting models suggest (but without statistically strong support) an early divergence of Glaucophyta within Archaeplastida, with the Rhodophyta (red algae), and Viridiplantae (green algae and land plants) forming a separate lineage.en_US
dc.publisherOxford Academicen_US
dc.rightsopenAccessen_US
dc.titleCompositional Biases among Synonymous Substitutions Cause Conflict between Gene and Protein Trees for Plastid Originsen_US
dc.typeJournal Articleen_US
dc.identifier.eissn1537-1719
dc.identifier.journalMolecular Biology and Evolutionen_US
dc.identifier.volume31en_US
dc.identifier.issue7en_US
dc.identifier.startpage1697 - 1709en_US
dc.internal.reviewer-noteMolecular Biology and Evolutionen
pubs.organisational-group/Natural History Museum
pubs.organisational-group/Natural History Museum/Science Group
pubs.organisational-group/Natural History Museum/Science Group/Functional groups
pubs.organisational-group/Natural History Museum/Science Group/Functional groups/Research
pubs.organisational-group/Natural History Museum/Science Group/Functional groups/Research/LS Research
pubs.organisational-group/Natural History Museum/Science Group/Life Sciences
dc.embargoNot knownen_US
elements.import.authorLi, Ben_US
elements.import.authorLopes, JSen_US
elements.import.authorFoster, PGen_US
elements.import.authorEmbley, TMen_US
elements.import.authorCox, CJen_US
dc.description.nhmCopyright The Author 2014. 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/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com. The attached file is the published version of the article.en_US
dc.subject.nhmorigin of plastidsen_US
dc.subject.nhmphylogenyen_US
dc.subject.nhmCyanobacteriaen_US
dc.subject.nhmArchaeplastidaen_US
refterms.dateFOA2019-04-29T14:02:34Z


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