Effect of nonindependent substitution on phylogenetic accuracy

Citation
Jp. Huelsenbeck et R. Nielsen, Effect of nonindependent substitution on phylogenetic accuracy, SYST BIOL, 48(2), 1999, pp. 317-328
Citations number
38
Language
INGLESE
art.tipo
Article
Categorie Soggetti
Biology
Journal title
SYSTEMATIC BIOLOGY
ISSN journal
1063-5157 → ACNP
Volume
48
Issue
2
Year of publication
1999
Pages
317 - 328
Database
ISI
SICI code
1063-5157(199906)48:2<317:EONSOP>2.0.ZU;2-9
Abstract
All current phylogenetic methods assume that DNA substitutions are independ ent among sites. However, ample empirical evidence suggests that the proces s of substitution is not independent but is, in fact, temporally and spatia lly correlated. The robustness of several commonly used phylogenetic method s to the assumption of independent substitution is examined. A compound Poi sson process is used to model DNA substitution. This model assumes that sub stitution events are Poisson-distributed in time and that the number of sub stitutions associated, with each event is geometrically distributed. The as ymptotic properties of phylogenetic methods do not appear to change under a compound Poisson process of DNA substitution. Moreover, the rank order of the performance of different methods does not change. However, all phylogen etic methods become less efficient when substitution follows a compound Poi sson process.