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Citation for Study 10982

Citation title: "The Phylogeny of Advanced Snakes (Colubroidea), with Discovery of a New Subfamily and Comparison of Support Methods for Likelihood Trees".

Study name: "The Phylogeny of Advanced Snakes (Colubroidea), with Discovery of a New Subfamily and Comparison of Support Methods for Likelihood Trees".

This study is part of submission 10972 (Status: Published).

Citation

Pyron R.A., Burbrink F., Colli G., Montes de oca A.N., Vitt L.J., Kuczynski C.A., & Wiens J.J. 2010. The Phylogeny of Advanced Snakes (Colubroidea), with Discovery of a New Subfamily and Comparison of Support Methods for Likelihood Trees. Molecular Phylogenetics and Evolution, .

Authors

• Pyron R.A. (submitter) 706-489-9727
• Burbrink F.
• Colli G.
• Montes de oca A.N.
• Vitt L.J.
• Kuczynski C.A.
• Wiens J.J. 631-632-1101

Abstract

The superfamily Colubroidea (>2500 species) includes the majority of snake species and is one of the most conspicuous and well-known radiations of terrestrial vertebrates. However, many aspects of the phylogeny of the group remain contentious, and dozens of genera have yet to be included in molecular phylogenetic analyses. We present a new, large-scale, likelihood-based phylogeny for the colubroids, including 761 species sampled for up to five genes: cytochrome b (93% of 761 species sampled), ND4 (69%), ND2 (28%), c-mos (54%), and RAG-1 (13%), totaling up to 5,814 bp per species. We also compare likelihood bootstrapping and a recently proposed ultra-fast measure of branch support (Shimodaira-Hasegawa-like [SHL] approximate likelihood ratio), and find that the SHL test shows strong support for several clades that were weakly-supported by bootstrapping in this or previous analyses (e.g., Dipsadinae, Lamprophiidae). We find that SHL values are positively related to branch lengths, but show stronger support for shorter branches than bootstrapping. Despite extensive missing data for many taxa (mean = 67% per species), we find that neither bootstrap nor SHL support values for terminal species are related to their incompleteness, and that all highly incomplete taxa are placed in the expected families from previous taxonomy, typically with very strong support. The phylogeny indicates that the Neotropical colubrine genus Scaphiodontophis represents an unexpectedly ancient lineage within Colubridae. We present a revised higher-level classification of Colubroidea, which includes a new subfamily for Scaphiodontophis (Scaphiodontophiinae). Our study provides the most comprehensive phylogeny of Colubroidea to date, and suggests that SHL values may provide a useful complement to bootstrapping for estimating support on likelihood-based trees.

Keywords

bootstrapping, Colubroidea, combined analysis, phylogenetic methods, snakes, supermatrix

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10982
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref19299,
  	 author = {Robert Alexander Pyron and Frank T.  Burbrink and Guarino Rinaldi  Colli and Adrian Nieto Montes de Oca and Laurie J Vitt and Caitlin A. Kuczynski and John J. Wiens},
  	 title = {The Phylogeny of Advanced Snakes (Colubroidea), with Discovery of a New Subfamily and Comparison of Support Methods for Likelihood Trees},
  	 year = {2010},
  	 keywords = {bootstrapping, Colubroidea, combined analysis, phylogenetic methods, snakes, supermatrix},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {Molecular Phylogenetics and Evolution},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {The superfamily Colubroidea (>2500 species) includes the majority of snake species and is one of the most conspicuous and well-known radiations of terrestrial vertebrates.  However, many aspects of the phylogeny of the group remain contentious, and dozens of genera have yet to be included in molecular phylogenetic analyses.  We present a new, large-scale, likelihood-based phylogeny for the colubroids, including 761 species sampled for up to five genes: cytochrome b (93% of 761 species sampled), ND4 (69%), ND2 (28%), c-mos (54%), and RAG-1 (13%), totaling up to 5,814 bp per species.  We also compare likelihood bootstrapping and a recently proposed ultra-fast measure of branch support (Shimodaira-Hasegawa-like [SHL] approximate likelihood ratio), and find that the SHL test shows strong support for several clades that were weakly-supported by bootstrapping in this or previous analyses (e.g., Dipsadinae, Lamprophiidae).  We find that SHL values are positively related to branch lengths, but show stronger support for shorter branches than bootstrapping.  Despite extensive missing data for many taxa (mean = 67% per species), we find that neither bootstrap nor SHL support values for terminal species are related to their incompleteness, and that all highly incomplete taxa are placed in the expected families from previous taxonomy, typically with very strong support.  The phylogeny indicates that the Neotropical colubrine genus Scaphiodontophis represents an unexpectedly ancient lineage within Colubridae.  We present a revised higher-level classification of Colubroidea, which includes a new subfamily for Scaphiodontophis (Scaphiodontophiinae).  Our study provides the most comprehensive phylogeny of Colubroidea to date, and suggests that SHL values may provide a useful complement to bootstrapping for estimating support on likelihood-based trees.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 19299
  AU  - Pyron,Robert Alexander
  AU  - Burbrink,Frank T. 
  AU  - Colli,Guarino Rinaldi 
  AU  - Montes de Oca,Adrian Nieto
  AU  - Vitt,Laurie J
  AU  - Kuczynski,Caitlin A.
  AU  - Wiens,John J.
  T1  - The Phylogeny of Advanced Snakes (Colubroidea), with Discovery of a New Subfamily and Comparison of Support Methods for Likelihood Trees
  PY  - 2010
  KW  - bootstrapping
  KW  - Colubroidea
  KW  - combined analysis
  KW  - phylogenetic methods
  KW  - snakes
  KW  - supermatrix
  UR  - http://dx.doi.org/
  N2  - The superfamily Colubroidea (>2500 species) includes the majority of snake species and is one of the most conspicuous and well-known radiations of terrestrial vertebrates.  However, many aspects of the phylogeny of the group remain contentious, and dozens of genera have yet to be included in molecular phylogenetic analyses.  We present a new, large-scale, likelihood-based phylogeny for the colubroids, including 761 species sampled for up to five genes: cytochrome b (93% of 761 species sampled), ND4 (69%), ND2 (28%), c-mos (54%), and RAG-1 (13%), totaling up to 5,814 bp per species.  We also compare likelihood bootstrapping and a recently proposed ultra-fast measure of branch support (Shimodaira-Hasegawa-like [SHL] approximate likelihood ratio), and find that the SHL test shows strong support for several clades that were weakly-supported by bootstrapping in this or previous analyses (e.g., Dipsadinae, Lamprophiidae).  We find that SHL values are positively related to branch lengths, but show stronger support for shorter branches than bootstrapping.  Despite extensive missing data for many taxa (mean = 67% per species), we find that neither bootstrap nor SHL support values for terminal species are related to their incompleteness, and that all highly incomplete taxa are placed in the expected families from previous taxonomy, typically with very strong support.  The phylogeny indicates that the Neotropical colubrine genus Scaphiodontophis represents an unexpectedly ancient lineage within Colubridae.  We present a revised higher-level classification of Colubroidea, which includes a new subfamily for Scaphiodontophis (Scaphiodontophiinae).  Our study provides the most comprehensive phylogeny of Colubroidea to date, and suggests that SHL values may provide a useful complement to bootstrapping for estimating support on likelihood-based trees.
  L3  - 
  JF  - Molecular Phylogenetics and Evolution
  VL  - 
  IS  - 
  ER  -