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Syst Biol. 2011 Jan;60(1):60-73. doi: 10.1093/sysbio/syq074. Epub 2010 Nov 15.

Quantifying the impact of dependent evolution among sites in phylogenetic inference.

Author information

1
Department of Integrative Biology, University of California, Berkeley, 3060 Valley Life Sciences Building #3140, Berkeley, CA 94720-3140, USA. nasrallah@berkeley.edu

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 biologically 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 independence-assuming methods is reduced by the dependence among sites; for proteins this reduction is relatively mild, but for RNA this reduction may be substantial. We introduce the concept of effective sequence length and its utility for considering information content in phylogenetics.

PMID:
21081481
PMCID:
PMC2997629
DOI:
10.1093/sysbio/syq074
[Indexed for MEDLINE]
Free PMC Article

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