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Citation for Study 1507

Citation title: "Phylogenetic Relationships of Horned Lizards (Phrynosoma) Based on Nuclear and Mitochondrial Data: Evidence for a Misleading Mitochondrial Gene Tree".

This study was previously identified under the legacy study ID S1451 (Status: Published).

Citation

Leache A., & Mcguire J. 2006. Phylogenetic Relationships of Horned Lizards (Phrynosoma) Based on Nuclear and Mitochondrial Data: Evidence for a Misleading Mitochondrial Gene Tree. Molecular Phylogenetics and Evolution, 39(3): 628-644.

Authors

• Leache A.
• Mcguire J.

Abstract

It has proven remarkably difficult to obtain a well-resolved and strongly supported phylogeny for horned lizards (Phrynosoma) because of incongruence between morphological and mitochondrial DNA sequence data. We infer the phylogenetic relationships among all 17 extant Phrynosoma species using >5.1 kb of mtDNA (12S rRNA, 16s rRNA, ND1, ND2, ND4, Cyt b, and associated tRNA genes), and >2,2 kb from three nuclear genes (RAG-1, BDNF, and GAPD) for most taxa. We conduct separate and combined phylogenetic analyses of these data using maximum parsimony, maximum likelihood, and Bayesian methods. The phylogenetic relationships inferred from the mtDNA data are congruent with previous mtDNA analyses based on fewer characters and provide strong support for most branches. However, we detected strong incongruence between the mtDNA and nuclear data using comparisons of branch support and Shimodaira-Hasegawa tests, with the (P. platyrhinos + P. goodei) clade identified as the primary source of this conflict. Our analysis of a P. mcallii x P. goodei hybrid suggests that this incongruence is caused by reticulation via introgressive hybridization. Our preferred phylogeny based on an analysis of the combined data (excluding the introgressed mtDNA data) provides a new framework for interpreting character evolution and biogeography within Phrynosoma. In the context of this improved phylogeny we propose a phylogenetic taxonomy highlighting four clades: 1) TAPAJA, containing the viviparous short-horned lizards P. ditmarsi, P. hernandesi, P. douglasii, and P. orbiculare; 2) ANOTA, containing species with prominent cranial horns (P. solare, P. mcallii, and the P. coronatum group); 3) DOLIOSAURUS, containing three species lacking antipredator blood-squirting (P. modestum, P. platyrhinos, and P. goodei); and 4) BREVICAUDA, containing two viviparous species with extremely short tails that lack blood-squirting (P. braconnieri and P. taurus).

External links

• DOI: 10.1016/j.ympev.2005.12.016

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1507
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref16280,
  	 author = {Adam D.  Leache and Jimmy A.  McGuire},
  	 title = {Phylogenetic Relationships of Horned Lizards (Phrynosoma) Based on Nuclear and Mitochondrial Data: Evidence for a Misleading Mitochondrial Gene Tree},
  	 year = {2006},
  	 keywords = {},
  	 doi = {10.1016/j.ympev.2005.12.016},
  	 url = {},
  	 pmid = {},
  	 journal = {Molecular Phylogenetics and Evolution},
  	 volume = {39},
  	 number = {3},
  	 pages = {628--644},
  	 abstract = {It has proven remarkably difficult to obtain a well-resolved and strongly supported phylogeny for horned lizards (Phrynosoma) because of incongruence between morphological and mitochondrial DNA sequence data. We infer the phylogenetic relationships among all 17 extant Phrynosoma species using >5.1 kb of mtDNA (12S rRNA, 16s rRNA, ND1, ND2, ND4, Cyt b, and associated tRNA genes), and >2,2 kb from three nuclear genes (RAG-1, BDNF, and GAPD) for most taxa. We conduct separate and combined phylogenetic analyses of these data using maximum parsimony, maximum likelihood, and Bayesian methods. The phylogenetic relationships inferred from the mtDNA data are congruent with previous mtDNA analyses based on fewer characters and provide strong support for most branches. However, we detected strong incongruence between the mtDNA and nuclear data using comparisons of branch support and Shimodaira-Hasegawa tests, with the (P. platyrhinos + P. goodei) clade identified as the primary source of this conflict. Our analysis of a P. mcallii x P. goodei hybrid suggests that this incongruence is caused by reticulation via introgressive hybridization. Our preferred phylogeny based on an analysis of the combined data (excluding the introgressed mtDNA data) provides a new framework for interpreting character evolution and biogeography within Phrynosoma. In the context of this improved phylogeny we propose a phylogenetic taxonomy highlighting four clades: 1) TAPAJA, containing the viviparous short-horned lizards P. ditmarsi, P. hernandesi, P. douglasii, and P. orbiculare; 2) ANOTA, containing species with prominent cranial horns (P. solare, P. mcallii, and the P. coronatum group); 3) DOLIOSAURUS, containing three species lacking antipredator blood-squirting (P. modestum, P. platyrhinos, and P. goodei); and 4) BREVICAUDA, containing two viviparous species with extremely short tails that lack blood-squirting (P. braconnieri and P. taurus).}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 16280
  AU  - Leache,Adam D. 
  AU  - McGuire,Jimmy A. 
  T1  - Phylogenetic Relationships of Horned Lizards (Phrynosoma) Based on Nuclear and Mitochondrial Data: Evidence for a Misleading Mitochondrial Gene Tree
  PY  - 2006
  KW  - 
  UR  - 
  N2  - It has proven remarkably difficult to obtain a well-resolved and strongly supported phylogeny for horned lizards (Phrynosoma) because of incongruence between morphological and mitochondrial DNA sequence data. We infer the phylogenetic relationships among all 17 extant Phrynosoma species using >5.1 kb of mtDNA (12S rRNA, 16s rRNA, ND1, ND2, ND4, Cyt b, and associated tRNA genes), and >2,2 kb from three nuclear genes (RAG-1, BDNF, and GAPD) for most taxa. We conduct separate and combined phylogenetic analyses of these data using maximum parsimony, maximum likelihood, and Bayesian methods. The phylogenetic relationships inferred from the mtDNA data are congruent with previous mtDNA analyses based on fewer characters and provide strong support for most branches. However, we detected strong incongruence between the mtDNA and nuclear data using comparisons of branch support and Shimodaira-Hasegawa tests, with the (P. platyrhinos + P. goodei) clade identified as the primary source of this conflict. Our analysis of a P. mcallii x P. goodei hybrid suggests that this incongruence is caused by reticulation via introgressive hybridization. Our preferred phylogeny based on an analysis of the combined data (excluding the introgressed mtDNA data) provides a new framework for interpreting character evolution and biogeography within Phrynosoma. In the context of this improved phylogeny we propose a phylogenetic taxonomy highlighting four clades: 1) TAPAJA, containing the viviparous short-horned lizards P. ditmarsi, P. hernandesi, P. douglasii, and P. orbiculare; 2) ANOTA, containing species with prominent cranial horns (P. solare, P. mcallii, and the P. coronatum group); 3) DOLIOSAURUS, containing three species lacking antipredator blood-squirting (P. modestum, P. platyrhinos, and P. goodei); and 4) BREVICAUDA, containing two viviparous species with extremely short tails that lack blood-squirting (P. braconnieri and P. taurus).
  L3  - 10.1016/j.ympev.2005.12.016
  JF  - Molecular Phylogenetics and Evolution
  VL  - 39
  IS  - 3
  SP  - 628
  EP  - 644
  ER  -