© 2006 Society of Systematic Biologists
Accurate Branch Length Estimation in Partitioned Bayesian Analyses Requires Accommodation of Among-Partition Rate Variation and Attention to Branch Length Priors
Edited by Allan Baker: Associate Editor
1 Department of Ecology and Evolutionary Biology, University of Connecticut 75 N. Eagleville Road, U-3043, Storrs, Connecticut 06269, USA E-mail: david.marshall@uconn.edu (D.C.M.) E-mail: chris.simon@uconn.edu (C.S.)
2 School of Biological Sciences, Victoria University of Wellington Wellington, New Zealand
3 Landcare Research Private Bag 92170, Auckland, New Zealand E-mail: BuckleyT@landcareresearch.co.nz
Received December 14, 2005; Revised March 1, 2006; Accepted September 5, 2006
| The first 150 words of the full text of this article appear below. |
Molecular phylogenetic studies are making increasing use of partitioned Bayesian analyses via software tools like MrBayes, version 3 (Ronquist and Huelsenbeck, 2003). Data partitioning is important because, as long as the same topology/history underlies all of the partitions, it addresses some of the problems associated with the combination of data sets with heterogeneous rates (Bull et al., 1993) and eliminates the need to argue the validity of tests that have been used to judge data combinability (e.g., Huelsenbeck et al., 1994; Huelsenbeck and Bull, 1996; Yang, 1996; Cunningham, 1997; Barker and Lutzoni, 2002; Buckley et al., 2002; Dowton and Austin, 2002). In addition, new studies indicate that data partitioning and the use of mixed models often dramatically improve the fit of model to data without the cost of overparameterization (Yang, 1996; Nylander et al., 2004; Brandley
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Effect of Among-Partition Rate Variation on Estimates of Tree Length: An Example and a Simulation Study |
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Effect of Among-Partition Rate Variation on Model Selection and Nodal Support |
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Instability of APRV Analyses Under Diffuse Branch Length Priors |
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Nonidentifiability and Sensitivity of Tree Length to the Branch Length Prior |
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Examples from Published Partitioned Analyses |
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Importance of Accurate Branch Length Estimation to Studies of Divergence Times |
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How to Partition? |
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Appendix 1. Methods |
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Effect of Accommodation of APRV on Bayesian Analyses: Empirical Data
Effect of Accommodation of APRV on Bayesian Analyses: Simulated Data
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