Journal
SYSTEMATIC BIOLOGY
Volume 60, Issue 1, Pages 60-73Publisher
OXFORD UNIV PRESS
DOI: 10.1093/sysbio/syq074
Keywords
Continuous-time Markov model; distance methods; Independence; maximum likelihood; parsimony
Categories
Funding
- National Institutes of Health [MCB-0075404, R01GM076485]
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM076485, R01GM069801] Funding Source: NIH RePORTER
Ask authors/readers for more resources
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.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available