---
_id: '4347'
abstract:
- lang: eng
text: 'Phylogenetic trees can be rooted by a number of criteria. Here, we introduce
a Bayesian method for inferring the root of a phylogenetic tree by using one of
several criteria: the outgroup, molecular clock, and nonreversible model of DNA
substitution. We perform simulation analyses to examine the relative ability of
these three criteria to correctly identify the root of the tree. The outgroup
and molecular clock criteria were best able to identify the root of the tree,
whereas the nonreversible model was able to identify the root only when the substitution
process was highly nonreversible. We also examined the performance of the criteria
for a tree of four species for which the topology and root position are well supported.
Results of the analyses of these data are consistent with the simulation results.'
article_processing_charge: No
article_type: original
author:
- first_name: John
full_name: Huelsenbeck, John
last_name: Huelsenbeck
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
- first_name: Amy
full_name: Levine, Amy
last_name: Levine
citation:
ama: Huelsenbeck J, Bollback JP, Levine A. Inferring the root of a phylogenetic
tree. Systematic Biology. 2002;51(1):32-43. doi:10.1080/106351502753475862
apa: Huelsenbeck, J., Bollback, J. P., & Levine, A. (2002). Inferring the root
of a phylogenetic tree. Systematic Biology. Oxford University Press. https://doi.org/10.1080/106351502753475862
chicago: Huelsenbeck, John, Jonathan P Bollback, and Amy Levine. “Inferring the
Root of a Phylogenetic Tree.” Systematic Biology. Oxford University Press,
2002. https://doi.org/10.1080/106351502753475862.
ieee: J. Huelsenbeck, J. P. Bollback, and A. Levine, “Inferring the root of a phylogenetic
tree,” Systematic Biology, vol. 51, no. 1. Oxford University Press, pp.
32–43, 2002.
ista: Huelsenbeck J, Bollback JP, Levine A. 2002. Inferring the root of a phylogenetic
tree. Systematic Biology. 51(1), 32–43.
mla: Huelsenbeck, John, et al. “Inferring the Root of a Phylogenetic Tree.” Systematic
Biology, vol. 51, no. 1, Oxford University Press, 2002, pp. 32–43, doi:10.1080/106351502753475862.
short: J. Huelsenbeck, J.P. Bollback, A. Levine, Systematic Biology 51 (2002) 32–43.
date_created: 2018-12-11T12:08:23Z
date_published: 2002-02-01T00:00:00Z
date_updated: 2023-06-06T09:53:27Z
day: '01'
doi: 10.1080/106351502753475862
extern: '1'
external_id:
pmid:
- '11943091'
intvolume: ' 51'
issue: '1'
language:
- iso: eng
month: '02'
oa_version: None
page: 32 - 43
pmid: 1
publication: Systematic Biology
publication_identifier:
issn:
- 0039-7989
publication_status: published
publisher: Oxford University Press
publist_id: '1113'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Inferring the root of a phylogenetic tree
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 51
year: '2002'
...
---
_id: '3440'
abstract:
- lang: eng
text: "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.\r\n"
article_processing_charge: No
article_type: original
author:
- first_name: John
full_name: Huelsenbeck, John
last_name: Huelsenbeck
- first_name: Jonathan P
full_name: Bollback, Jonathan P
id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87
last_name: Bollback
orcid: 0000-0002-4624-4612
citation:
ama: Huelsenbeck J, Bollback JP. Empirical and hierarchical Bayesian estimation
of ancestral states. Systematic Biology. 2001;50(3):351-366. doi:10.1080/10635150119871
apa: Huelsenbeck, J., & Bollback, J. P. (2001). Empirical and hierarchical Bayesian
estimation of ancestral states. Systematic Biology. Oxford University Press.
https://doi.org/10.1080/10635150119871
chicago: Huelsenbeck, John, and Jonathan P Bollback. “Empirical and Hierarchical
Bayesian Estimation of Ancestral States.” Systematic Biology. Oxford University
Press, 2001. https://doi.org/10.1080/10635150119871.
ieee: J. Huelsenbeck and J. P. Bollback, “Empirical and hierarchical Bayesian estimation
of ancestral states,” Systematic Biology, vol. 50, no. 3. Oxford University
Press, pp. 351–366, 2001.
ista: Huelsenbeck J, Bollback JP. 2001. Empirical and hierarchical Bayesian estimation
of ancestral states. Systematic Biology. 50(3), 351–366.
mla: 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.
short: J. Huelsenbeck, J.P. Bollback, Systematic Biology 50 (2001) 351–366.
date_created: 2018-12-11T12:03:20Z
date_published: 2001-05-01T00:00:00Z
date_updated: 2023-05-15T13:54:01Z
day: '01'
doi: 10.1080/10635150119871
extern: '1'
external_id:
pmid:
- '12116580'
intvolume: ' 50'
issue: '3'
language:
- iso: eng
month: '05'
oa_version: None
page: 351 - 366
pmid: 1
publication: Systematic Biology
publication_identifier:
issn:
- 0039-7989
publication_status: published
publisher: Oxford University Press
publist_id: '2960'
quality_controlled: '1'
status: public
title: Empirical and hierarchical Bayesian estimation of ancestral states
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 50
year: '2001'
...