The DOI matches its OpenAlex record; 6 of the 6 references it cites were found in a registry or an index.
Empirical and Hierarchical Bayesian Estimation of Ancestral States
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.
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Cites
Monte Carlo sampling methods using Markov chains and their applications.
Hastings, W. K. (1970) · Biometrika · doi:10.1093/biomet/57.1.97 · Cited by 15,195
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571
Evolution of Protein Molecules
JUKES, T. H., & CANTOR, C. R. (1969) · Mammalian Protein Metabolism · doi:10.1016/b978-1-4832-3211-9.50009-7 · Cited by 11,032
Dating of the human–ape splitting by a molecular clock of mitochondrial DNA.
Hasegawa, M., Kishino, H., & Yano, T.-A. (1985) · Journal of Molecular Evolution · doi:10.1007/bf02101694 · Cited by 8,687
Yang, Z. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00160154 · Cited by 2,960
A codon-based model of nucleotide substitution for protein-coding DNA sequences.
(1994) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040153 · Cited by 1,960
Cited by
PAML 4: Phylogenetic Analysis by Maximum Likelihood
Yang, Z. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm088 · Cited by 13,879
Taxon sampling and the accuracy of phylogenetic analyses
(2008) · Journal of Systematics and Evolution · doi:10.3724/sp.j.1002.2008.08016 · Cited by 553
Model misspecification and probabilistic tests of topology: evidence from empirical data sets.
Buckley, T. R. (2002) · Systematic Biology · doi:10.1080/10635150290069922 · Cited by 253
Comparative bioacoustics: a roadmap for quantifying and comparing animal sounds across diverse taxa
Odom, K. J., Araya‐Salas, M., Morano, J. L., Ligon, R. A., Leighton, G. M., Taff, C. C., Dalziell, A. H., Billings, A. C., Germain, R. R., Pardo, M., et al. (2021) · Biological Reviews · doi:10.1111/brv.12695 · Cited by 81
Accuracy of ancestral state reconstruction for non-neutral traits
Holland, B. R., Ketelaar-Jones, S., O’Mara, A. R., Woodhams, M. D., & Jordan, G. J. (2020) · Scientific Reports · doi:10.1038/s41598-020-64647-4 · Cited by 58
Metadata
- Authors
- Huelsenbeck, J. P., & Bollback, J. P.
- Venue
- Systematic Biology
- Publisher
- Oxford University Press
- Published
- 2001-05-01
- Volume
- 50
- Issue
- 3
- Pages
- 351-366
- ISSN
- 1063-5157 (ISSN-L)
- OpenAlex
- W2150215622
- Cited by
- 358
- References
- 6
- FWCI
- 5.32
- Type
- journal article
- Language
- en
- Open access
- closed
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