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Citation for Study 14692

Citation title: "Undersampling taxa will underestimate molecular divergence dates: An example from the South American lizard clade Liolaemini ".

Study name: "Undersampling taxa will underestimate molecular divergence dates: An example from the South American lizard clade Liolaemini ".

This study is part of submission 14692 (Status: Published).

Citation

Schulte ii J.A. 2013. Undersampling taxa will underestimate molecular divergence dates: An example from the South American lizard clade Liolaemini. International Journal of Evolutionary Biology, .

Authors

• Schulte ii J.A.

Abstract

Methods for estimating divergence times from molecular data have improved dramatically over the past decade, yet there are few studies examining alternative taxon sampling effects on node age estimates. Here, using 11 time calibrations and several subsampling strategies, I investigate the effect of undersampling species diversity on node ages of the South American lizard clade Liolaemini. Penalized likelihood (PL) and Bayesian molecular dating analyses were conducted on a densely sampled (202 taxa) mtDNA-based phylogenetic hypothesis of Iguanidae, including 92 Liolaemini species. I subsampled three Liolaemini subclades using random taxon deletions and analyzed these datasets using 11 calibrations or only one or two calibrations. Using all calibrations and penalized likelihood, there was a clear trend for node age estimates to be younger the greater a clade was undersampled. This trend could be seen at both shallow and deep nodes in the tree. The most extreme case using one calibration and less than 10% of extant species diversity resulted in age estimates of Liolaemini clades to be almost half the age using all available fossil calibrations and DNA sequences. The effect of Bayesian and PL methods differed when either one or two calibrations only were used with dense taxon sampling. Bayesian node ages were always older when fewer calibrations were used, whereas PL node ages were always younger. This work reinforces two important points: 1) whenever possible authors should strongly consider adding as many taxa as possible, including numerous additional outgroups, prior to node age estimation to avoid considerable underestimation of node ages and; 2) using more, critically assessed and accurate fossil calibrations should yield improved divergence time estimates.

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About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S14692
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref22364,
  	 author = {James Allen Schulte II},
  	 title = {Undersampling taxa will underestimate molecular divergence dates: An example from the South American lizard clade Liolaemini },
  	 year = {2013},
  	 keywords = {},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {International Journal of Evolutionary Biology},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {Methods for estimating divergence times from molecular data have improved dramatically over the past decade, yet there are few studies examining alternative taxon sampling effects on node age estimates.  Here, using 11 time calibrations and several subsampling strategies, I investigate the effect of undersampling species diversity on node ages of the South American lizard clade Liolaemini. Penalized likelihood (PL) and Bayesian molecular dating analyses were conducted on a densely sampled (202 taxa) mtDNA-based phylogenetic hypothesis of Iguanidae, including 92 Liolaemini species. I subsampled three Liolaemini subclades using random taxon deletions and analyzed these datasets using 11 calibrations or only one or two calibrations. Using all calibrations and penalized likelihood, there was a clear trend for node age estimates to be younger the greater a clade was undersampled. This trend could be seen at both shallow and deep nodes in the tree. The most extreme case using one calibration and less than 10% of extant species diversity resulted in age estimates of Liolaemini clades to be almost half the age using all available fossil calibrations and DNA sequences. The effect of Bayesian and PL methods differed when either one or two calibrations only were used with dense taxon sampling. Bayesian node ages were always older when fewer calibrations were used, whereas PL node ages were always younger. This work reinforces two important points:  1) whenever possible authors should strongly consider adding as many taxa as possible, including numerous additional outgroups, prior to node age estimation to avoid considerable underestimation of node ages and; 2) using more, critically assessed and accurate fossil calibrations should yield improved divergence time estimates.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 22364
  AU  - Schulte II,James Allen
  T1  - Undersampling taxa will underestimate molecular divergence dates: An example from the South American lizard clade Liolaemini 
  PY  - 2013
  KW  - 
  UR  - http://dx.doi.org/
  N2  - Methods for estimating divergence times from molecular data have improved dramatically over the past decade, yet there are few studies examining alternative taxon sampling effects on node age estimates.  Here, using 11 time calibrations and several subsampling strategies, I investigate the effect of undersampling species diversity on node ages of the South American lizard clade Liolaemini. Penalized likelihood (PL) and Bayesian molecular dating analyses were conducted on a densely sampled (202 taxa) mtDNA-based phylogenetic hypothesis of Iguanidae, including 92 Liolaemini species. I subsampled three Liolaemini subclades using random taxon deletions and analyzed these datasets using 11 calibrations or only one or two calibrations. Using all calibrations and penalized likelihood, there was a clear trend for node age estimates to be younger the greater a clade was undersampled. This trend could be seen at both shallow and deep nodes in the tree. The most extreme case using one calibration and less than 10% of extant species diversity resulted in age estimates of Liolaemini clades to be almost half the age using all available fossil calibrations and DNA sequences. The effect of Bayesian and PL methods differed when either one or two calibrations only were used with dense taxon sampling. Bayesian node ages were always older when fewer calibrations were used, whereas PL node ages were always younger. This work reinforces two important points:  1) whenever possible authors should strongly consider adding as many taxa as possible, including numerous additional outgroups, prior to node age estimation to avoid considerable underestimation of node ages and; 2) using more, critically assessed and accurate fossil calibrations should yield improved divergence time estimates.
  L3  - 
  JF  - International Journal of Evolutionary Biology
  VL  - 
  IS  - 
  ER  -