@ARTICLE{TreeBASE2Ref21765,
author = {Johannes Bergsten and Anders N Nilsson and Fredrik Ronquist},
title = {Bayesian Tests of Topology Hypotheses with an example from Diving Beetles},
year = {2013},
keywords = {Bayes factor, posterior odds, model testing, steppingstone sampling, marginal likelihood, reversiblejump MCMC, Coleoptera, Dytiscidae},
doi = {},
url = {http://},
pmid = {},
journal = {Systematic Biology},
volume = {},
number = {},
pages = {},
abstract = {We review Bayesian approaches to model testing in general and to the assessment of topological hypotheses in particular. We show that standard Bayes factor tests of the monophyly of a group, or the placement of a sample sequence in a known reference tree, can be misleading. The reason for this is related to the wellknown dependency of Bayes factors on modelspecific priors. Specifically, when testing tree hypotheses it is important that each hypothesis is associated with an appropriate tree space in the prior. This can be achieved by using appropriately constrained searches or by filtering trees in the posterior sample, but in a more elaborate way than typically implemented. If it is difficult to find the appropriate tree sets to be contrasted, then the posterior model odds may be more informative than the Bayes factor. We illustrate the recommended techniques using an empirical test case addressing the issue of whether two genera of diving beetles (Coleoptera: Dytiscidae), Suphrodytes and Hydroporus, should be synonymized. Our refined Bayes factor tests, in contrast to standard analyses, show that there is strong support for Suphrodytes nesting inside Hydroporus, and the genera are therefore synonymized.}
}
Citation for Study 13927
Citation title:
"Bayesian Tests of Topology Hypotheses with an example from Diving Beetles".
Study name:
"Bayesian Tests of Topology Hypotheses with an example from Diving Beetles".
This study is part of submission 13927
(Status: Published).
Citation
Bergsten J., Nilsson A.N., & Ronquist F. 2013. Bayesian Tests of Topology Hypotheses with an example from Diving Beetles. Systematic Biology, .
Authors

Bergsten J.
(submitter)
+46 8 5195 4192

Nilsson A.N.

Ronquist F.
Abstract
We review Bayesian approaches to model testing in general and to the assessment of topological hypotheses in particular. We show that standard Bayes factor tests of the monophyly of a group, or the placement of a sample sequence in a known reference tree, can be misleading. The reason for this is related to the wellknown dependency of Bayes factors on modelspecific priors. Specifically, when testing tree hypotheses it is important that each hypothesis is associated with an appropriate tree space in the prior. This can be achieved by using appropriately constrained searches or by filtering trees in the posterior sample, but in a more elaborate way than typically implemented. If it is difficult to find the appropriate tree sets to be contrasted, then the posterior model odds may be more informative than the Bayes factor. We illustrate the recommended techniques using an empirical test case addressing the issue of whether two genera of diving beetles (Coleoptera: Dytiscidae), Suphrodytes and Hydroporus, should be synonymized. Our refined Bayes factor tests, in contrast to standard analyses, show that there is strong support for Suphrodytes nesting inside Hydroporus, and the genera are therefore synonymized.
Keywords
Bayes factor, posterior odds, model testing, steppingstone sampling, marginal likelihood, reversiblejump MCMC, Coleoptera, Dytiscidae
External links
About this resource
 Canonical resource URI:
http://purl.org/phylo/treebase/phylows/study/TB2:S13927
 Other versions:
Nexus
NeXML
 Show BibTeX reference
@ARTICLE{TreeBASE2Ref21765,
author = {Johannes Bergsten and Anders N Nilsson and Fredrik Ronquist},
title = {Bayesian Tests of Topology Hypotheses with an example from Diving Beetles},
year = {2013},
keywords = {Bayes factor, posterior odds, model testing, steppingstone sampling, marginal likelihood, reversiblejump MCMC, Coleoptera, Dytiscidae},
doi = {},
url = {http://},
pmid = {},
journal = {Systematic Biology},
volume = {},
number = {},
pages = {},
abstract = {We review Bayesian approaches to model testing in general and to the assessment of topological hypotheses in particular. We show that standard Bayes factor tests of the monophyly of a group, or the placement of a sample sequence in a known reference tree, can be misleading. The reason for this is related to the wellknown dependency of Bayes factors on modelspecific priors. Specifically, when testing tree hypotheses it is important that each hypothesis is associated with an appropriate tree space in the prior. This can be achieved by using appropriately constrained searches or by filtering trees in the posterior sample, but in a more elaborate way than typically implemented. If it is difficult to find the appropriate tree sets to be contrasted, then the posterior model odds may be more informative than the Bayes factor. We illustrate the recommended techniques using an empirical test case addressing the issue of whether two genera of diving beetles (Coleoptera: Dytiscidae), Suphrodytes and Hydroporus, should be synonymized. Our refined Bayes factor tests, in contrast to standard analyses, show that there is strong support for Suphrodytes nesting inside Hydroporus, and the genera are therefore synonymized.}
}
 Show RIS reference
TY  JOUR
ID  21765
AU  Bergsten,Johannes
AU  Nilsson,Anders N
AU  Ronquist,Fredrik
T1  Bayesian Tests of Topology Hypotheses with an example from Diving Beetles
PY  2013
KW  Bayes factor
KW  posterior odds
KW  model testing
KW  steppingstone sampling
KW  marginal likelihood
KW  reversiblejump MCMC
KW  Coleoptera
KW  Dytiscidae
UR  http://dx.doi.org/
N2  We review Bayesian approaches to model testing in general and to the assessment of topological hypotheses in particular. We show that standard Bayes factor tests of the monophyly of a group, or the placement of a sample sequence in a known reference tree, can be misleading. The reason for this is related to the wellknown dependency of Bayes factors on modelspecific priors. Specifically, when testing tree hypotheses it is important that each hypothesis is associated with an appropriate tree space in the prior. This can be achieved by using appropriately constrained searches or by filtering trees in the posterior sample, but in a more elaborate way than typically implemented. If it is difficult to find the appropriate tree sets to be contrasted, then the posterior model odds may be more informative than the Bayes factor. We illustrate the recommended techniques using an empirical test case addressing the issue of whether two genera of diving beetles (Coleoptera: Dytiscidae), Suphrodytes and Hydroporus, should be synonymized. Our refined Bayes factor tests, in contrast to standard analyses, show that there is strong support for Suphrodytes nesting inside Hydroporus, and the genera are therefore synonymized.
L3 
JF  Systematic Biology
VL 
IS 
ER 