Quantifying the Impact of Dependent Evolution among Sites in Phylogenetic Inference英文文献.pdfVIP

Systematic Biology Advance Access published November 15, 2010 c The Author(s) 2010. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@ DOI:10.1093/sysbio/syq074 Quantifying the Impact of Dependent Evolution among Sites in Phylogenetic Inference CHRIS A . NASRALLAH1,, DAVID H . MATHEWS2 , AND JOHN P. HUELSENBECK1 1Department of Integrative Biology, University of California, Berkeley, 3060 Valley Life Sciences Building #3140, Berkeley, CA 94720-3140, USA; and 2 Department of Biochemistry and Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY 14642, USA; Correspondence to be sent to: Department of Integrative Biology, University of California, Berkeley, 3060 VLSB #3140, Berkeley, CA 94720-3140, USA; E-mail: nasrallah@. Received 5 August 2009; reviews returned 4 January 2010; accepted 15 September 2010 Associate Editor: Marc Suchard Abstract.—Nearly all commonly used methods of phylogenetic inference assume that characters in an alignment evolve independently of one another. This assumption is attractive for simplicity and computational tractability but is not bi- ologically reasonable for RNAs and proteins that have secondary and tertiary structures. Here, we simulate RNA and protein-coding DNA sequence data under a general model of dependence in order to assess the robustness of traditional methods of phylogenetic inference to violation of the assumption of independence among sites. We find that the accuracy of in