The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees

R. Alexander Pyron, Frank T. Burbrink, Guarino R. Colli, Adrian Nieto Montes de Oca, Laurie J. Vitt, Caitlin A. Kuczynski, John J Wiens

Research output: Contribution to journalArticle

220 Citations (Scopus)

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 5814. 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), neither bootstrap nor SHL support values for terminal species are related to their incompleteness, and that most 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.

Original languageEnglish (US)
Pages (from-to)329-342
Number of pages14
JournalMolecular Phylogenetics and Evolution
Volume58
Issue number2
DOIs
StatePublished - Feb 2011
Externally publishedYes

Fingerprint

new subfamily
Snakes
Phylogeny
snake
snakes
phylogeny
bootstrapping
Colubridae
Cytochromes b
taxonomy
methodology
Vertebrates
cytochrome b
Radiation
complement
vertebrates
comparison
method
cytochrome
vertebrate

Keywords

  • Bootstrapping
  • Colubroidea
  • Combined analysis
  • Phylogenetic methods
  • Snakes
  • Supermatrix

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics

Cite this

The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees. / Pyron, R. Alexander; Burbrink, Frank T.; Colli, Guarino R.; de Oca, Adrian Nieto Montes; Vitt, Laurie J.; Kuczynski, Caitlin A.; Wiens, John J.

In: Molecular Phylogenetics and Evolution, Vol. 58, No. 2, 02.2011, p. 329-342.

Research output: Contribution to journalArticle

Pyron, R. Alexander ; Burbrink, Frank T. ; Colli, Guarino R. ; de Oca, Adrian Nieto Montes ; Vitt, Laurie J. ; Kuczynski, Caitlin A. ; Wiens, John J. / The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees. In: Molecular Phylogenetics and Evolution. 2011 ; Vol. 58, No. 2. pp. 329-342.
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