Effect of nonindependent substitution on phylogenetic accuracy

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Effect of nonindependent substitution on phylogenetic accuracy. / Huelsenbeck, John P.; Nielsen, Rasmus.

In: Systematic Biology, Vol. 48, No. 2, 1999, p. 317-328.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Huelsenbeck, JP & Nielsen, R 1999, 'Effect of nonindependent substitution on phylogenetic accuracy', Systematic Biology, vol. 48, no. 2, pp. 317-328. https://doi.org/10.1080/106351599260319

APA

Huelsenbeck, J. P., & Nielsen, R. (1999). Effect of nonindependent substitution on phylogenetic accuracy. Systematic Biology, 48(2), 317-328. https://doi.org/10.1080/106351599260319

Vancouver

Huelsenbeck JP, Nielsen R. Effect of nonindependent substitution on phylogenetic accuracy. Systematic Biology. 1999;48(2):317-328. https://doi.org/10.1080/106351599260319

Author

Huelsenbeck, John P. ; Nielsen, Rasmus. / Effect of nonindependent substitution on phylogenetic accuracy. In: Systematic Biology. 1999 ; Vol. 48, No. 2. pp. 317-328.

Bibtex

@article{a64024b89ed44b9e86bc6b9064c62cfe,
title = "Effect of nonindependent substitution on phylogenetic accuracy",
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.",
keywords = "Compound Poisson process, Nonindependent substitution, Phylogenetic accuracy",
author = "Huelsenbeck, {John P.} and Rasmus Nielsen",
year = "1999",
doi = "10.1080/106351599260319",
language = "English",
volume = "48",
pages = "317--328",
journal = "Systematic Biology",
issn = "1063-5157",
publisher = "Oxford University Press",
number = "2",

}

RIS

TY - JOUR

T1 - Effect of nonindependent substitution on phylogenetic accuracy

AU - Huelsenbeck, John P.

AU - Nielsen, Rasmus

PY - 1999

Y1 - 1999

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.

KW - Compound Poisson process

KW - Nonindependent substitution

KW - Phylogenetic accuracy

U2 - 10.1080/106351599260319

DO - 10.1080/106351599260319

M3 - Journal article

C2 - 12066710

AN - SCOPUS:0033139150

VL - 48

SP - 317

EP - 328

JO - Systematic Biology

JF - Systematic Biology

SN - 1063-5157

IS - 2

ER -

ID: 222645325