The largest subunit of RNA polymerase II from the Glaucocystophyta: functional constraint and short-branch exclusion in deep eukaryotic phylogeny

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dc.contributor.authorStiller, John W.en_US
dc.contributor.authorHarrell, Leslieen_US
dc.date.accessioned2011-01-28T18:40:18Zen_US
dc.date.accessioned2011-05-17T14:35:02Z
dc.date.available2011-01-28T18:40:18Zen_US
dc.date.available2011-05-17T14:35:02Z
dc.date.issued2005-12en_US
dc.description.abstractBackground: Evolutionary analyses of the largest subunit of RNA polymerase II (RPB1) have yielded important and at times provocative results. One particularly troublesome outcome is the consistent inference of independent origins of red algae and green plants, at odds with the more widely accepted view of a monophyletic Plantae comprising all eukaryotes with primary plastids. If the hypothesis of a broader kingdom Plantae is correct, then RPB1 trees likely reflect a persistent phylogenetic artifact. To gain a better understanding of RNAP II evolution, and the presumed artifact relating to green plants and red algae, we isolated and analyzed RPB1 from representatives of Glaucocystophyta, the third eukaryotic group with primary plastids. Results: Phylogenetic analyses incorporating glaucocystophytes do not recover a monophyletic Plantae; rather they result in additional conflicts with the most widely held views on eukaryotic relationships. In particular, glaucocystophytes are recovered as sister to several amoebozoans with strong support. A detailed investigation shows that this clade can be explained by what we call "short-branch exclusion," a phylogenetic artifact integrally associated with "long-branch attraction." Other systematic discrepancies observed in RPB1 trees can be explained as phylogenetic artifacts; however, these apparent artifacts also appear in regions of the tree that support widely held views of eukaryotic evolution. In fact, most of the RPB1 tree is consistent with artifacts of rate variation among sequences and co-variation due to functional constraints related to C-terminal domain based RNAP II transcription. Conclusion: Our results reveal how subtle and easily overlooked biases can dominate the overall results of molecular phylogenetic analyses of ancient eukaryotic relationships. Sources of potential phylogenetic artifact should be investigated routinely, not just when obvious "long-branch attraction" is encountered. Originally published BMC Evolutionary Biology, Vol. 5, No. 71, Dec 2005en_US
dc.identifier.citationBMC Evolutionary Biology; 5:71 p. 1-17en_US
dc.identifier.doi10.1186/1471-2148-5-71
dc.identifier.pmidPMC1326215en_US
dc.identifier.urihttp://hdl.handle.net/10342/3125en_US
dc.language.isoen_USen_US
dc.publisherEast Carolina Universityen_US
dc.relation.urihttp://www.biomedcentral.com/1471-2148/5/71en_US
dc.rightsAuthor notified of opt-out rights by Cammie Jenningsen_US
dc.subjectRNA polymerase IIen_US
dc.subjectEvolutionary analysisen_US
dc.subjectPrimary plastidsen_US
dc.subjectGlaucocystophytaen_US
dc.titleThe largest subunit of RNA polymerase II from the Glaucocystophyta: functional constraint and short-branch exclusion in deep eukaryotic phylogenyen_US
dc.typeArticleen_US

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