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Citation for Study 2155

Citation title: "A nuclear ribosomal DNA phylogeny of Acer inferred with maximum likelihood, splits graphs, and motif analyses of 606 sequences".

This study was previously identified under the legacy study ID S2159 (Status: Published).

Citation

Grimm G., Renner S.S., Stamatakis A., & Hemleben V. 2006. A nuclear ribosomal DNA phylogeny of Acer inferred with maximum likelihood, splits graphs, and motif analyses of 606 sequences. Evolutionary Bioinformatics, 2: 279-294.

Authors

• Grimm G.
• Renner S.S. 011-49-(0)89-17861250
• Stamatakis A.
• Hemleben V.

Abstract

The internal transcribed spacer (ITS) region of nuclear ribosomal DNA is a biparentally inherited, multi-copy marker that is widely used to infer phylogenetic relationships among closely related taxa. In a strict sense, sequences in ITS data sets are not homologous unless one was to sequence tandem repeats at a specified position in the nucleolus organizer region. We use maximum likelihood (ML) and splits graphs analyses to extract phylogenetic information from 584 (mostly cloned) ITS sequences, representing 81 species and subspecies of Acer, plus both species of its sister genus Dipteronia. Analyses of motifs and clade-specific substitution biases compared Acer to several hundred ITS sequences of Sapindales from GenBank, representing Anacardiaceae, Burseraceae, Meliaceae, Rutaceae, and Sapindaceae. Taxon sampling within the genus involved multiple accessions of representatives from all morphological groups, including all known polyploid maple taxa. Because of the large size of the matrices, we used RAxML-VI-HPC for tree inference under the best-fit GTR+ model. Results obtained with the full 584-sequence matrix were compared with those from reduced matrices of consensus sequences that used ambiguity coding to account for within-species/subspecies variation. Neighbor-nets and bipartition networks were used to visualize conflict among character state patterns. Species clusters observed in the trees and networks agree well with morphology-based classifications; of de Jongs (1994) 16 sections, nine are supported in neighbor-net and bipartition networks, and ten by sequence motifs and the ML tree; of his 19 series, 14 are supported in networks, motifs, and the ML tree. Within-taxon ITS divergence did not differ between diploid and polyploid species or subspecies, and there was little evidence of differentiated parental ITS haplotypes, suggesting that concerted evolution in Acer acts rapidly.

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S2155
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref15626,
  	 author = {Guido W  Grimm and Susanne S Renner and Alexandros  Stamatakis and Vera  Hemleben},
  	 title = {A nuclear ribosomal DNA phylogeny of Acer inferred with maximum likelihood, splits graphs, and motif analyses of 606 sequences},
  	 year = {2006},
  	 keywords = {},
  	 doi = {},
  	 url = {},
  	 pmid = {},
  	 journal = {Evolutionary Bioinformatics},
  	 volume = {2},
  	 number = {},
  	 pages = {279--294},
  	 abstract = {The internal transcribed spacer (ITS) region of nuclear ribosomal DNA is a biparentally inherited, multi-copy marker that is widely used to infer phylogenetic relationships among closely related taxa. In a strict sense, sequences in ITS data sets are not homologous unless one was to sequence tandem repeats at a specified position in the nucleolus organizer region. We use maximum likelihood (ML) and splits graphs analyses to extract phylogenetic information from 584 (mostly cloned) ITS sequences, representing 81 species and subspecies of Acer, plus both species of its sister genus Dipteronia. Analyses of motifs and clade-specific substitution biases compared Acer to several hundred ITS sequences of Sapindales from GenBank, representing Anacardiaceae, Burseraceae, Meliaceae, Rutaceae, and Sapindaceae. Taxon sampling within the genus involved multiple accessions of representatives from all morphological groups, including all known polyploid maple taxa. Because of the large size of the matrices, we used RAxML-VI-HPC for tree inference under the best-fit GTR+ model. Results obtained with the full 584-sequence matrix were compared with those from reduced matrices of consensus sequences that used ambiguity coding to account for within-species/subspecies variation. Neighbor-nets and bipartition networks were used to visualize conflict among character state patterns. Species clusters observed in the trees and networks agree well with morphology-based classifications; of de Jongs (1994) 16 sections, nine are supported in neighbor-net and bipartition networks, and ten by sequence motifs and the ML tree; of his 19 series, 14 are supported in networks, motifs, and the ML tree. Within-taxon ITS divergence did not differ between diploid and polyploid species or subspecies, and there was little evidence of differentiated parental ITS haplotypes, suggesting that concerted evolution in Acer acts rapidly.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 15626
  AU  - Grimm,Guido W 
  AU  - Renner,Susanne S
  AU  - Stamatakis,Alexandros 
  AU  - Hemleben,Vera 
  T1  - A nuclear ribosomal DNA phylogeny of Acer inferred with maximum likelihood, splits graphs, and motif analyses of 606 sequences
  PY  - 2006
  UR  - 
  N2  - The internal transcribed spacer (ITS) region of nuclear ribosomal DNA is a biparentally inherited, multi-copy marker that is widely used to infer phylogenetic relationships among closely related taxa. In a strict sense, sequences in ITS data sets are not homologous unless one was to sequence tandem repeats at a specified position in the nucleolus organizer region. We use maximum likelihood (ML) and splits graphs analyses to extract phylogenetic information from 584 (mostly cloned) ITS sequences, representing 81 species and subspecies of Acer, plus both species of its sister genus Dipteronia. Analyses of motifs and clade-specific substitution biases compared Acer to several hundred ITS sequences of Sapindales from GenBank, representing Anacardiaceae, Burseraceae, Meliaceae, Rutaceae, and Sapindaceae. Taxon sampling within the genus involved multiple accessions of representatives from all morphological groups, including all known polyploid maple taxa. Because of the large size of the matrices, we used RAxML-VI-HPC for tree inference under the best-fit GTR+ model. Results obtained with the full 584-sequence matrix were compared with those from reduced matrices of consensus sequences that used ambiguity coding to account for within-species/subspecies variation. Neighbor-nets and bipartition networks were used to visualize conflict among character state patterns. Species clusters observed in the trees and networks agree well with morphology-based classifications; of de Jongs (1994) 16 sections, nine are supported in neighbor-net and bipartition networks, and ten by sequence motifs and the ML tree; of his 19 series, 14 are supported in networks, motifs, and the ML tree. Within-taxon ITS divergence did not differ between diploid and polyploid species or subspecies, and there was little evidence of differentiated parental ITS haplotypes, suggesting that concerted evolution in Acer acts rapidly.
  L3  - 
  JF  - Evolutionary Bioinformatics
  VL  - 2
  IS  - 
  SP  - 279
  EP  - 294
  ER  -