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Citation for Study 12201

Citation title: "Incorporating indels as phylogenetic characters: Impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora)".

Study name: "Incorporating indels as phylogenetic characters: Impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora)".

This study is part of submission 12201 (Status: Published).

Citation

Luan P., Yu L., Ryder O.A., Davis H., & Zhang Y. 2012. Incorporating indels as phylogenetic characters: Impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora). Molecular Phylogenetics and evolution, .

Authors

• Luan P.
• Yu L.
• Ryder O.A.
• Davis H.
• Zhang Y.

Abstract

Insertion and deletion events (indels) provide a suite of markers complementary to nucleotide substitutions with enormous potential for molecular phylogenetics. Most previous studies explored the impact of indel inclusion on phylogenetic inferences by analyzing either computer simulation data or a small number of genes from experimental work. Using many more indel characters than those in previous studies, we here for the first time address this issue in the context of Arctoidea phylogeny. Our analyses, based on 6843 indel characters from 22 nuclear intron loci of 16 species of Arctoidea, demonstrate that when the indels were not taken into consideration (?removal of indels? and ?missing data coding scheme?), the Ursidae/Pinnipedia monophyly tree and the Pinnipedia/ Musteloidea monophyly tree were both recovered, whereas inclusion of indels by using three different indel coding schemes, i.e., indels as the fifth state, simple indel coding, and modified complex indel coding, give identical phylogenetic tree topologies supporting the Ursidae/Pinnipedia monophyly, whatever the tree-building method was used. In addition, comparison of indel incorporation methods revealed that the coding of indels as 5th state, simple indel coding and modified complex indel coding are all advantageous over treating indels as missing data. This is the first report of the impact of indel coding on phylogenetic reconstruction at the family level in Carnivora, which indicates that indels should be taken into account when additional nuclear intron genes are used in the future phylogenetic analysis.

Keywords

Insertion/deletion events; Arctoidea; Indel coding; Phylogenetic analyses

External links

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S12201
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref20281,
  	 author = {Pengtao  Luan and Li  Yu and Oliver A. Ryder and Heidi A.  Davis and Yaping  Zhang},
  	 title = {Incorporating indels as phylogenetic characters: Impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora)},
  	 year = {2012},
  	 keywords = {Insertion/deletion events; Arctoidea; Indel coding; Phylogenetic analyses},
  	 doi = {},
  	 url = {http://},
  	 pmid = {},
  	 journal = {Molecular Phylogenetics and evolution},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {Insertion and deletion events (indels) provide a suite of markers complementary to nucleotide substitutions with enormous potential for molecular phylogenetics. Most previous studies explored the impact of indel inclusion on phylogenetic inferences by analyzing either computer simulation data or a small number of genes from experimental work. Using many more indel characters than those in previous studies, we here for the first time address this issue in the context of Arctoidea phylogeny. Our analyses, based on 6843 indel characters from 22 nuclear intron loci of 16 species of Arctoidea, demonstrate that when the indels were not taken into consideration (?removal of indels? and ?missing data coding scheme?), the Ursidae/Pinnipedia monophyly tree and the Pinnipedia/ Musteloidea monophyly tree were both recovered, whereas inclusion of indels by using three different indel coding schemes, i.e., indels as the fifth state, simple indel coding, and modified complex indel coding, give identical phylogenetic tree topologies supporting the Ursidae/Pinnipedia monophyly, whatever the tree-building method was used. In addition, comparison of indel incorporation methods revealed that the coding of indels as 5th state, simple indel coding and modified complex indel coding are all advantageous over treating indels as missing data. This is the first report of the impact of indel coding on phylogenetic reconstruction at the family level in Carnivora, which indicates that indels should be taken into account when additional nuclear intron genes are used in the future phylogenetic analysis.
  }
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 20281
  AU  - Luan,Pengtao 
  AU  - Yu,Li 
  AU  - Ryder,Oliver A.
  AU  - Davis,Heidi A. 
  AU  - Zhang,Yaping 
  T1  - Incorporating indels as phylogenetic characters: Impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora)
  PY  - 2012
  KW  - Insertion/deletion events; Arctoidea; Indel coding; Phylogenetic analyses
  UR  - http://dx.doi.org/
  N2  - Insertion and deletion events (indels) provide a suite of markers complementary to nucleotide substitutions with enormous potential for molecular phylogenetics. Most previous studies explored the impact of indel inclusion on phylogenetic inferences by analyzing either computer simulation data or a small number of genes from experimental work. Using many more indel characters than those in previous studies, we here for the first time address this issue in the context of Arctoidea phylogeny. Our analyses, based on 6843 indel characters from 22 nuclear intron loci of 16 species of Arctoidea, demonstrate that when the indels were not taken into consideration (?removal of indels? and ?missing data coding scheme?), the Ursidae/Pinnipedia monophyly tree and the Pinnipedia/ Musteloidea monophyly tree were both recovered, whereas inclusion of indels by using three different indel coding schemes, i.e., indels as the fifth state, simple indel coding, and modified complex indel coding, give identical phylogenetic tree topologies supporting the Ursidae/Pinnipedia monophyly, whatever the tree-building method was used. In addition, comparison of indel incorporation methods revealed that the coding of indels as 5th state, simple indel coding and modified complex indel coding are all advantageous over treating indels as missing data. This is the first report of the impact of indel coding on phylogenetic reconstruction at the family level in Carnivora, which indicates that indels should be taken into account when additional nuclear intron genes are used in the future phylogenetic analysis.
  
  L3  - 
  JF  - Molecular Phylogenetics and evolution
  VL  - 
  IS  - 
  ER  -