Accommodating phylogenetic uncertainty in evolutionary studies

Science

Volumn 288, Issue 5475, 2000, Pages 2349-2350

  Huelsenbeck, John P ^a   Rannala, Bruce ^b   Masly, John P ^a  

^a UNIVERSITY OF ROCHESTER   (United States)

^b UNIVERSITY OF ALBERTA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; DNA SEQUENCE; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NATURAL SELECTION; PHYLOGENY; PRIORITY JOURNAL; PROBABILITY;

ANIMALS; APHIDS; BASE SEQUENCE; BAYES THEOREM; DNA, MITOCHONDRIAL; EVOLUTION; EVOLUTION, MOLECULAR; MARKOV CHAINS; MONTE CARLO METHOD; PHYLOGENY; PROBABILITY; STOCHASTIC PROCESSES;

EID: 0034733685     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.288.5475.2349     Document Type: Article

References (16)

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9. i is the true phylogeny under the specified model of DNA substitution.
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14. The joint posterior probability of ρ and μ were calculated with a program written by J.P.H. The posterior probability is formula presented where D is the aphid caste data and C is a normalizing constant. The posterior probability distribution was approximated with MCMC (11, 12). An exponential prior was placed on the rate of change (μ) and a uniform prior on ρ. The results for an exponential prior with mean 1.0 are shown. However, the posterior probability of ρ was not affected by the prior placed on μ, suggesting that the inferences of the direction of change (ρ) are robust to assumptions about the rate of evolution of the aphid caste character (μ).
15. M. H. Hasegawa, H. Kishino, T. Yano, J. Mol. Evol. 22, 160 (1985).
16. We thank D. Stern for providing the aphid data and G. Bharathan for constructive comments on the study. B.R. was supported by NIH grant R01-HG01988.