Empirical and hierarchical Bayesian estimation of ancestral states

J. Huelsenbeck, J.P. Bollback, Systematic Biology 50 (2001) 351–366.

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Abstract
Several methods have been proposed to infer the states at the ancestral nodes on a phylogeny. These methods assume a specific tree and set of branch lengths when estimating the ancestral character state. Inferences of the ancestral states, then, are conditioned on the tree and branch lengths being true. We develop a hierarchical Bayes method for inferring the ancestral states on a tree. The method integrates over uncertainty in the tree, branch lengths, and substitution model parameters by using Markov chain Monte Carlo. We compare the hierarchical Bayes inferences of ancestral states with inferences of ancestral states made under the assumption that a specific tree is correct. We find that the methods are correlated, but that accommodating uncertainty in parameters of the phylogenetic model can make inferences of ancestral states even more uncertain than they would be in an empirical Bayes analysis.
Publishing Year
Date Published
2001-05-01
Journal Title
Systematic Biology
Volume
50
Issue
3
Page
351 - 366
IST-REx-ID

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Huelsenbeck J, Bollback JP. Empirical and hierarchical Bayesian estimation of ancestral states. Systematic Biology. 2001;50(3):351-366. doi:10.1080/10635150119871
Huelsenbeck, J., & Bollback, J. P. (2001). Empirical and hierarchical Bayesian estimation of ancestral states. Systematic Biology, 50(3), 351–366. https://doi.org/10.1080/10635150119871
Huelsenbeck, John, and Jonathan P Bollback. “Empirical and Hierarchical Bayesian Estimation of Ancestral States.” Systematic Biology 50, no. 3 (2001): 351–66. https://doi.org/10.1080/10635150119871.
J. Huelsenbeck and J. P. Bollback, “Empirical and hierarchical Bayesian estimation of ancestral states,” Systematic Biology, vol. 50, no. 3, pp. 351–366, 2001.
Huelsenbeck J, Bollback JP. 2001. Empirical and hierarchical Bayesian estimation of ancestral states. Systematic Biology. 50(3), 351–366.
Huelsenbeck, John, and Jonathan P. Bollback. “Empirical and Hierarchical Bayesian Estimation of Ancestral States.” Systematic Biology, vol. 50, no. 3, Oxford University Press, 2001, pp. 351–66, doi:10.1080/10635150119871.

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