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Citation for Study 1483

Citation title: "Phylogeny of Symplocos Based on DNA Sequences of the Chloroplast trnC-trnD Intergenic Region".

This study was previously identified under the legacy study ID S1427 (Status: Published).

Citation

Fritsch P., Cruz B., Almeda F., Wang Y., & Shi S. 2006. Phylogeny of Symplocos Based on DNA Sequences of the Chloroplast trnC-trnD Intergenic Region. Systematic Botany, null.

Authors

• Fritsch P.
• Cruz B.
• Almeda F.
• Wang Y.
• Shi S.

Abstract

Phylogenetic analysis of 74 species of Symplocos was conducted with DNA sequence data from the chloroplast trnC-trnD intergenic region. Maximum parsimony and Bayesian inference trees are consistent with those of a previous study based on combined data from the nuclear ribosomal ITS region and the chloroplast regions rpl16, matK, and trnL-trnF. The inclusion of 21 phylogenetically informative indel characters from trnC-trnD resulted in greater maximum parsimony resolution and clade support than with these characters excluded. A combined five-gene region (trnC-trnD, ITS, rpl16, matK, and trnL-trnF) analysis based on a data set with complete sequence data is almost completely concordant with that of the combined four-gene data set, and displays higher resolution and overall clade support (in some cases 20 to > 30 bootstrap percentage points). The data indicate monophyly for only one subgenus (Epigenia) and four sections (Barberina, Cordyloblaste, Neosymplocos, and Urbaniocharis) of Symplocos; the other three subgenera (Symplocos, Hopea, and Microsymplocos) and tested sections (Bobua, Palaeosymplocos, and Symplocastrum) will require recircumscription to accord with the principle of monophyly. Supermatrix and supertree analyses were conducted to provide phylogenetic estimates based on all 107 available Symplocos samples with sequence data from at least two of the five gene regions. The supermatrix consensus tree is completely consistent with that from the combined five-gene estimate based on complete sequence data, whereas the supertree consensus differs from these trees in two regions of the topology. The supermatrix consensus also displays greater clade resolution than the supertree consensus. The aligned trnC-trnD data set exhibits a lower percentage of parsimony-informative characters than those based on matK and rpl16 sequences. The length, organization, and relative sequencing ease of trnC-trnD in Symplocos nonetheless confirm the utility of this region for phylogenetic estimation in flowering plants, as previously described.

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1483
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref15478,
  	 author = {P. K.  Fritsch and Boni C.  Cruz and Frank  Almeda and Y. J.  Wang and Suhua  Shi},
  	 title = {Phylogeny of Symplocos Based on DNA Sequences of the Chloroplast trnC-trnD Intergenic Region},
  	 year = {2006},
  	 keywords = {},
  	 doi = {},
  	 url = {},
  	 pmid = {},
  	 journal = {Systematic Botany},
  	 volume = {},
  	 number = {},
  	 pages = {},
  	 abstract = {Phylogenetic analysis of 74 species of Symplocos was conducted with DNA sequence data from the chloroplast trnC-trnD intergenic region. Maximum parsimony and Bayesian inference trees are consistent with those of a previous study based on combined data from the nuclear ribosomal ITS region and the chloroplast regions rpl16, matK, and trnL-trnF. The inclusion of 21 phylogenetically informative indel characters from trnC-trnD resulted in greater maximum parsimony resolution and clade support than with these characters excluded. A combined five-gene region (trnC-trnD, ITS, rpl16, matK, and trnL-trnF) analysis based on a data set with complete sequence data is almost completely concordant with that of the combined four-gene data set, and displays higher resolution and overall clade support (in some cases 20 to > 30 bootstrap percentage points). The data indicate monophyly for only one subgenus (Epigenia) and four sections (Barberina, Cordyloblaste, Neosymplocos, and Urbaniocharis) of Symplocos; the other three subgenera (Symplocos, Hopea, and Microsymplocos) and tested sections (Bobua, Palaeosymplocos, and Symplocastrum) will require recircumscription to accord with the principle of monophyly. Supermatrix and supertree analyses were conducted to provide phylogenetic estimates based on all 107 available Symplocos samples with sequence data from at least two of the five gene regions. The supermatrix consensus tree is completely consistent with that from the combined five-gene estimate based on complete sequence data, whereas the supertree consensus differs from these trees in two regions of the topology. The supermatrix consensus also displays greater clade resolution than the supertree consensus. The aligned trnC-trnD data set exhibits a lower percentage of parsimony-informative characters than those based on matK and rpl16 sequences. The length, organization, and relative sequencing ease of trnC-trnD in Symplocos nonetheless confirm the utility of this region for phylogenetic estimation in flowering plants, as previously described.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 15478
  AU  - Fritsch,P. K. 
  AU  - Cruz,Boni C. 
  AU  - Almeda,Frank 
  AU  - Wang,Y. J. 
  AU  - Shi,Suhua 
  T1  - Phylogeny of Symplocos Based on DNA Sequences of the Chloroplast trnC-trnD Intergenic Region
  PY  - 2006
  KW  - 
  UR  - 
  N2  - Phylogenetic analysis of 74 species of Symplocos was conducted with DNA sequence data from the chloroplast trnC-trnD intergenic region. Maximum parsimony and Bayesian inference trees are consistent with those of a previous study based on combined data from the nuclear ribosomal ITS region and the chloroplast regions rpl16, matK, and trnL-trnF. The inclusion of 21 phylogenetically informative indel characters from trnC-trnD resulted in greater maximum parsimony resolution and clade support than with these characters excluded. A combined five-gene region (trnC-trnD, ITS, rpl16, matK, and trnL-trnF) analysis based on a data set with complete sequence data is almost completely concordant with that of the combined four-gene data set, and displays higher resolution and overall clade support (in some cases 20 to > 30 bootstrap percentage points). The data indicate monophyly for only one subgenus (Epigenia) and four sections (Barberina, Cordyloblaste, Neosymplocos, and Urbaniocharis) of Symplocos; the other three subgenera (Symplocos, Hopea, and Microsymplocos) and tested sections (Bobua, Palaeosymplocos, and Symplocastrum) will require recircumscription to accord with the principle of monophyly. Supermatrix and supertree analyses were conducted to provide phylogenetic estimates based on all 107 available Symplocos samples with sequence data from at least two of the five gene regions. The supermatrix consensus tree is completely consistent with that from the combined five-gene estimate based on complete sequence data, whereas the supertree consensus differs from these trees in two regions of the topology. The supermatrix consensus also displays greater clade resolution than the supertree consensus. The aligned trnC-trnD data set exhibits a lower percentage of parsimony-informative characters than those based on matK and rpl16 sequences. The length, organization, and relative sequencing ease of trnC-trnD in Symplocos nonetheless confirm the utility of this region for phylogenetic estimation in flowering plants, as previously described.
  L3  - 
  JF  - Systematic Botany
  VL  - 
  IS  - 
  ER  -