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Citation for Study 10165

Citation title: "Bayesian Dating of Shallow Phylogenies with a Relaxed Clock".

This study was previously identified under the legacy study ID S2509 (Status: Published).

Citation

Brown R., & Yang Z. 2010. Bayesian Dating of Shallow Phylogenies with a Relaxed Clock. Systematic Biology, 59(2): 119-131.

Authors

• Brown R.
• Yang Z.

Abstract

Bayesian methods are increasingly being used to estimate divergence times without the restrictive assumption of a global clock. Little is known about their reliability for shallow phylogenies where DNA sequence divergence is low. We analyzed both simulated and real sequence to evaluate dating methods in phylogenies with mid-late Miocene roots. A large number of data sets (5000) with ten taxa each were simulated under a rate drift model for trees with two topologies (balanced or unbalanced) and with different sets of divergence times (characterized by long or short external branches). Data were analyzed using Bayesian Markov chain Monte Carlo methods in which the prior on divergence times was specified from a birth-death process with species sampling (BDS) or a Dirichlet distribution, using the programs MCMCTREE and MULTIDIVTIME. The programs generally performed well on shallow phylogenies, but posterior mean node ages were biased and 95% posterior intervals included true ages in fewer than 95% of trees, in some analyses. This typically occurred when the 95% prior interval did not include the true age and/or sequence lengths were less than 1Kbp. Widths of posterior intervals were also very dependent on the position of the calibrated node within the tree, particularly when sequences were short. Different divergence times priors within MCMCTREE, MULTIDIVTIME and BEAST were used to analyze mtDNA data sets from a Bovid subfamily (the Caprinae), from Asian Laudakia and North African Chalcides lizards. Posterior divergence times were quite sensitive to different BDS priors, but less sensitive to different Dirichlet priors. Our study demonstrates the impact of the prior on divergence times in shallow phylogenies and shows that: 1) prior intervals on nodes should be assessed as a prerequisite to a dating analysis, 2) greater than 1 Kbp of quite rapidly-evolving sequence may be required to obtain accurate posterior means and usefully narrow posterior intervals.

Keywords

Agamidae; Bayesian phylogenetics; Caprinae; phylogeny; posterior; prior; relaxed clock

External links

• DOI: 10.1093/sysbio/syp082

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10165
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref18656,
  	 author = {Richard P.  Brown and Ziheng  Yang},
  	 title = {Bayesian Dating of Shallow Phylogenies with a Relaxed Clock},
  	 year = {2010},
  	 keywords = {Agamidae; Bayesian phylogenetics; Caprinae; phylogeny; posterior; prior; relaxed clock},
  	 doi = {10.1093/sysbio/syp082},
  	 url = {},
  	 pmid = {},
  	 journal = {Systematic Biology},
  	 volume = {59},
  	 number = {2},
  	 pages = {119--131},
  	 abstract = {Bayesian methods are increasingly being used to estimate divergence times without the restrictive assumption of a global clock. Little is known about their reliability for shallow phylogenies where DNA sequence divergence is low. We analyzed both simulated and real sequence to evaluate dating methods in phylogenies with mid-late Miocene roots. A large number of data sets (5000) with ten taxa each were simulated under a rate drift model for trees with two topologies (balanced or unbalanced) and with different sets of divergence times (characterized by long or short external branches). Data were analyzed using Bayesian Markov chain Monte Carlo methods in which the prior on divergence times was specified from a birth-death process with species sampling (BDS) or a Dirichlet distribution, using the programs MCMCTREE and MULTIDIVTIME. The programs generally performed well on shallow phylogenies, but posterior mean node ages were biased and 95% posterior intervals included true ages in fewer than 95% of trees, in some analyses. This typically occurred when the 95% prior interval did not include the true age and/or sequence lengths were less than 1Kbp. Widths of posterior intervals were also very dependent on the position of the calibrated node within the tree, particularly when sequences were short. Different divergence times priors within MCMCTREE, MULTIDIVTIME and BEAST were used to analyze mtDNA data sets from a Bovid subfamily (the Caprinae), from Asian Laudakia and North African Chalcides lizards. Posterior divergence times were quite sensitive to different BDS priors, but less sensitive to different Dirichlet priors. Our study demonstrates the impact of the prior on divergence times in shallow phylogenies and shows that: 1) prior intervals on nodes should be assessed as a prerequisite to a dating analysis, 2) greater than 1 Kbp of quite rapidly-evolving sequence may be required to obtain accurate posterior means and usefully narrow posterior intervals.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 18656
  AU  - Brown,Richard P. 
  AU  - Yang,Ziheng 
  T1  - Bayesian Dating of Shallow Phylogenies with a Relaxed Clock
  PY  - 2010
  KW  - Agamidae; Bayesian phylogenetics; Caprinae; phylogeny; posterior; prior; relaxed clock
  UR  - 
  N2  - Bayesian methods are increasingly being used to estimate divergence times without the restrictive assumption of a global clock. Little is known about their reliability for shallow phylogenies where DNA sequence divergence is low. We analyzed both simulated and real sequence to evaluate dating methods in phylogenies with mid-late Miocene roots. A large number of data sets (5000) with ten taxa each were simulated under a rate drift model for trees with two topologies (balanced or unbalanced) and with different sets of divergence times (characterized by long or short external branches). Data were analyzed using Bayesian Markov chain Monte Carlo methods in which the prior on divergence times was specified from a birth-death process with species sampling (BDS) or a Dirichlet distribution, using the programs MCMCTREE and MULTIDIVTIME. The programs generally performed well on shallow phylogenies, but posterior mean node ages were biased and 95% posterior intervals included true ages in fewer than 95% of trees, in some analyses. This typically occurred when the 95% prior interval did not include the true age and/or sequence lengths were less than 1Kbp. Widths of posterior intervals were also very dependent on the position of the calibrated node within the tree, particularly when sequences were short. Different divergence times priors within MCMCTREE, MULTIDIVTIME and BEAST were used to analyze mtDNA data sets from a Bovid subfamily (the Caprinae), from Asian Laudakia and North African Chalcides lizards. Posterior divergence times were quite sensitive to different BDS priors, but less sensitive to different Dirichlet priors. Our study demonstrates the impact of the prior on divergence times in shallow phylogenies and shows that: 1) prior intervals on nodes should be assessed as a prerequisite to a dating analysis, 2) greater than 1 Kbp of quite rapidly-evolving sequence may be required to obtain accurate posterior means and usefully narrow posterior intervals.
  L3  - 10.1093/sysbio/syp082
  JF  - Systematic Biology
  VL  - 59
  IS  - 2
  SP  - 119
  EP  - 131
  ER  -