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

ECU Author/Contributor (non-ECU co-authors, if there are any, appear on document)

Leslie Harrell (Creator)

John W. Stiller (Creator)

Institution

East Carolina University (ECU )

Web Site: http://www.ecu.edu/lib/

Abstract: Background: 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 2005

Additional Information

Publication

Other

BMC Evolutionary Biology. 5:71(December 2005) p. 1-17.

Language: English

Date: 2011

Keywords

RNA polymerase II, evolutionary analysis, primary plastids, glaucocystophyta

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