@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.}
}
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
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- 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 -