Effect of nonindependent substitution on phylogenetic accuracy

John P. Huelsenbeck; Rasmus Nielsen

doi:10.1080/106351599260319

Effect of nonindependent substitution on phylogenetic accuracy

John P. Huelsenbeck^*, Rasmus Nielsen

^*Corresponding author for this work

35 Citations (Scopus)

Abstract

All current phylogenetic methods assume that DNA substitutions are independent among sites. However, ample empirical evidence suggests that the process of substitution is not independent but is, in fact, temporally and spatially correlated. The robustness of several commonly used phylogenetic methods to the assumption of independent substitution is examined. A compound Poisson process is used to model DNA substitution. This model assumes that substitution events are Poisson-distributed in time and that the number of substitutions associated with each event is geometrically distributed. The asymptotic 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 phylogenetic methods become less efficient when substitution follows a compound Poisson process.

Original language	English
Journal	Systematic Biology
Volume	48
Issue number	2
Pages (from-to)	317-328
Number of pages	12
ISSN	1063-5157
DOIs	https://doi.org/10.1080/106351599260319
Publication status	Published - 1 Jan 1999

Keywords

Compound Poisson process
Nonindependent substitution
Phylogenetic accuracy

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10.1080/106351599260319

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N2 - All current phylogenetic methods assume that DNA substitutions are independent among sites. However, ample empirical evidence suggests that the process of substitution is not independent but is, in fact, temporally and spatially correlated. The robustness of several commonly used phylogenetic methods to the assumption of independent substitution is examined. A compound Poisson process is used to model DNA substitution. This model assumes that substitution events are Poisson-distributed in time and that the number of substitutions associated with each event is geometrically distributed. The asymptotic 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 phylogenetic methods become less efficient when substitution follows a compound Poisson process.

AB - All current phylogenetic methods assume that DNA substitutions are independent among sites. However, ample empirical evidence suggests that the process of substitution is not independent but is, in fact, temporally and spatially correlated. The robustness of several commonly used phylogenetic methods to the assumption of independent substitution is examined. A compound Poisson process is used to model DNA substitution. This model assumes that substitution events are Poisson-distributed in time and that the number of substitutions associated with each event is geometrically distributed. The asymptotic 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 phylogenetic methods become less efficient when substitution follows a compound Poisson process.

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KW - Nonindependent substitution

KW - Phylogenetic accuracy

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Effect of nonindependent substitution on phylogenetic accuracy

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Keywords

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