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Citation for Study 17936

Citation title: "Molecular systematics of teioid lizards (Teioidea/Gymnophthalmoidea: Squamata) based on the analysis of 48 loci under tree-alignment and similarity-alignment".

Study name: "Molecular systematics of teioid lizards (Teioidea/Gymnophthalmoidea: Squamata) based on the analysis of 48 loci under tree-alignment and similarity-alignment".

This study is part of submission 17936 (Status: Published).

Citation

Goicoechea N., Frost D., De la riva I., Pellegrino K.C., Sites J.W., Rodrigues M.T., & Padial J.M. 2015. Molecular systematics of teioid lizards (Teioidea/Gymnophthalmoidea: Squamata) based on the analysis of 48 loci under tree-alignment and similarity-alignment. Cladistics, .

Authors

• Goicoechea N. (submitter)
• Frost D.
• De la riva I.
• Pellegrino K.C. 55113319-00 Ext. 3310
• Sites J.W.
• Rodrigues M.T.
• Padial J.M.

Abstract

We infer phylogenetic relationships within Teioidea, a superfamily of Nearctic and Neotropical lizards, using nucleotide sequences (up to 48 genes). Phylogenetic analyses relied on parsimony under tree-alignment and similarity-alignment optimizations, with gaps treated as evidence and as absence of evidence, and maximum-likelihood under similarity-alignment with gaps as absence of evidence. All analyses produced almost completely resolved trees despite 86% of missing data. Tree-alignment produced the shortest trees, the strict consensus of which is more similar to the maximum likelihood tree than to any of the other parsimony trees, both in terms of number of clades shared, parsimony cost, and likelihood scores. Comparisons of tree costs suggest that the pattern of indels inferred by similarity-alignment drove parsimony analyses on similarity-aligned sequences away from more optimal solutions. All analyses agree in a majority of clades, although they differ from each other in unique ways, suggesting that neither the criterion of optimality, alignment, nor treatment of indels alone can explain all differences. Parsimony rejects the monophyly of Gymnophthalmidae due to the position of Alopoglossinae or Riolama, whereas maximum likelihood supports the monophyly albeit with low support value. We address nomenclatural issues raised by the clarification that both Tupinamidae Gray, 1825, and Gymnophthalmidae Fitzinger, 1826, are older names than Teiidae Gray, 1827, and the conclusion that several family-group names are invalid. We recognize three families in the arrangement (Alopoglossidae (Teiidae, Gymnophthalmidae)). Within Gymnophthalmidae we recognize Gymnophthalminae and Cercosaurinae, the latter of which is divided into the arrangement (Bachiini (Ecpleopodini, Cercosaurini)). Riolama and Rhachisaurus are allocated to Gymnophthalminae. Within Teiidae we retain the currently recognized three subfamilies in the arrangement (Callopistinae (Tupinambinae, Teiinae)). We also propose several genus-level changes to restore the monophyly of taxa.

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S17936
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref24836,
  	 author = {Noemi  Goicoechea and Darrel  Frost and Ignacio  De la Riva and Katia Cristina Machado Pellegrino and Jack W. Sites and Miguel Trefaut Rodrigues and Jose M Padial},
  	 title = {Molecular systematics of teioid lizards (Teioidea/Gymnophthalmoidea: Squamata) based on the analysis of 48 loci under tree-alignment and similarity-alignment},
  	 year = {2015},
  	 keywords = {},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {Cladistics},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {We infer phylogenetic relationships within Teioidea, a superfamily of Nearctic and Neotropical lizards, using nucleotide sequences (up to 48 genes). Phylogenetic analyses relied on parsimony under tree-alignment and similarity-alignment optimizations, with gaps treated as evidence and as absence of evidence, and maximum-likelihood under similarity-alignment with gaps as absence of evidence. All analyses produced almost completely resolved trees despite 86% of missing data. Tree-alignment produced the shortest trees, the strict consensus of which is more similar to the maximum likelihood tree than to any of the other parsimony trees, both in terms of number of clades shared, parsimony cost, and likelihood scores. Comparisons of tree costs suggest that the pattern of indels inferred by similarity-alignment drove parsimony analyses on similarity-aligned sequences away from more optimal solutions. All analyses agree in a majority of clades, although they differ from each other in unique ways, suggesting that neither the criterion of optimality, alignment, nor treatment of indels alone can explain all differences. Parsimony rejects the monophyly of Gymnophthalmidae due to the position of Alopoglossinae or Riolama, whereas  maximum likelihood supports the monophyly albeit with low support value. We address nomenclatural issues raised by the clarification that both Tupinamidae Gray, 1825, and Gymnophthalmidae Fitzinger, 1826, are older names than Teiidae Gray, 1827, and the conclusion that several family-group names are invalid. We recognize three families in the arrangement (Alopoglossidae (Teiidae, Gymnophthalmidae)). Within Gymnophthalmidae we recognize Gymnophthalminae and Cercosaurinae, the latter of which is divided into the arrangement (Bachiini (Ecpleopodini, Cercosaurini)). Riolama and Rhachisaurus are allocated to Gymnophthalminae. Within Teiidae we retain the currently recognized three subfamilies in the arrangement (Callopistinae (Tupinambinae, Teiinae)). We also propose several genus-level changes to restore the monophyly of taxa.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 24836
  AU  - Goicoechea,Noemi 
  AU  - Frost,Darrel 
  AU  - De la Riva,Ignacio 
  AU  - Pellegrino,Katia Cristina Machado
  AU  - Sites,Jack W.
  AU  - Rodrigues,Miguel Trefaut
  AU  - Padial,Jose M
  T1  - Molecular systematics of teioid lizards (Teioidea/Gymnophthalmoidea: Squamata) based on the analysis of 48 loci under tree-alignment and similarity-alignment
  PY  - 2015
  KW  - 
  UR  - http://dx.doi.org/
  N2  - We infer phylogenetic relationships within Teioidea, a superfamily of Nearctic and Neotropical lizards, using nucleotide sequences (up to 48 genes). Phylogenetic analyses relied on parsimony under tree-alignment and similarity-alignment optimizations, with gaps treated as evidence and as absence of evidence, and maximum-likelihood under similarity-alignment with gaps as absence of evidence. All analyses produced almost completely resolved trees despite 86% of missing data. Tree-alignment produced the shortest trees, the strict consensus of which is more similar to the maximum likelihood tree than to any of the other parsimony trees, both in terms of number of clades shared, parsimony cost, and likelihood scores. Comparisons of tree costs suggest that the pattern of indels inferred by similarity-alignment drove parsimony analyses on similarity-aligned sequences away from more optimal solutions. All analyses agree in a majority of clades, although they differ from each other in unique ways, suggesting that neither the criterion of optimality, alignment, nor treatment of indels alone can explain all differences. Parsimony rejects the monophyly of Gymnophthalmidae due to the position of Alopoglossinae or Riolama, whereas  maximum likelihood supports the monophyly albeit with low support value. We address nomenclatural issues raised by the clarification that both Tupinamidae Gray, 1825, and Gymnophthalmidae Fitzinger, 1826, are older names than Teiidae Gray, 1827, and the conclusion that several family-group names are invalid. We recognize three families in the arrangement (Alopoglossidae (Teiidae, Gymnophthalmidae)). Within Gymnophthalmidae we recognize Gymnophthalminae and Cercosaurinae, the latter of which is divided into the arrangement (Bachiini (Ecpleopodini, Cercosaurini)). Riolama and Rhachisaurus are allocated to Gymnophthalminae. Within Teiidae we retain the currently recognized three subfamilies in the arrangement (Callopistinae (Tupinambinae, Teiinae)). We also propose several genus-level changes to restore the monophyly of taxa.
  L3  - 
  JF  - Cladistics
  VL  - 
  IS  - 
  ER  -