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Citation for Study 10503

Citation title: "Analysis of a plastid inverted repeat supermatrix for 246 taxa improves confidence in deeper level angiosperm relationships.".

Study name: "Analysis of a plastid inverted repeat supermatrix for 246 taxa improves confidence in deeper level angiosperm relationships.".

This study is part of submission 10493 (Status: Published).

Citation

Moore M.J., Hassan N., Gitzendanner M., Bruenn R., Croley M., Vandeventer A., Horn J., Dhingra A., Brockington S.F., Latvis M., Ramdial J., Alexandre R., Piedrahita A., Xi Z., Davis C., Soltis P., & Soltis D. 2011. Analysis of a plastid inverted repeat supermatrix for 246 taxa improves confidence in deeper level angiosperm relationships. International Journal of Plant Sciences, 172(4): 541-558.

Authors

• Moore M.J. (submitter) 440-775-6876
• Hassan N.
• Gitzendanner M.
• Bruenn R.
• Croley M.
• Vandeventer A.
• Horn J.
• Dhingra A.
• Brockington S.F.
• Latvis M.
• Ramdial J.
• Alexandre R.
• Piedrahita A.
• Xi Z.
• Davis C.
• Soltis P.
• Soltis D.

Abstract

Recent studies employing complete plastid genome sequences have helped clarify the backbone phylogeny of angiosperms. However, the relatively limited taxon sampling in these studies has left several major clades poorly represented, precluding resolution of some regions of angiosperm phylogeny with strong support. Other recent work has suggested that the 25,000 bp plastid inverted repeat (IR) region may be a valuable source of characters for resolving these remaining problematic nodes. Consequently we constructed a data set of all available angiosperm IR sequences, resulting in a matrix of 24,702 aligned bases and 246 accessions, including 21 newly sequenced taxa. Maximum likelihood analyses of these data yielded a generally well-supported topology that was highly congruent with recent trees based on complete plastid genome sequences. Notably, IR analyses resolve Pentapetalae into three well-supported clades: (1) superasterids (including Santalales, Caryophyllales, Berberidopsidales, and Asteridae), (2) superrosids (including Vitales, Saxifragales, and Rosidae), and (3) Dilleniaceae, whose position as sister to remaining Pentapetalae had the highest maximum likelihood bootstrap support yet obtained for this recalcitrant clade using character-rich data sets. These results provide important new evidence for a stable, well-supported phylogenetic framework for angiosperms, and demonstrate the usefulness of IR data at deeper levels of angiosperm phylogeny.

Keywords

Angiosperm Tree of Life, plastid inverted repeat, phylogenetics, large data sets

External links

• DOI: 10.1086/658923

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10503
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref18949,
  	 author = {Michael James Moore and Nasr S.  Hassan and Matthew A.  Gitzendanner and Riva  Bruenn and Matthew  Croley and alexia  vandeventer and James  Horn and Amit  Dhingra and Samuel F Brockington and Maribeth  Latvis and Jeremy  Ramdial and Roolse  Alexandre and Ana  Piedrahita and Zhenxiang  Xi and Charles C.  Davis and Pamela S.   Soltis and Douglas E.   Soltis},
  	 title = {Analysis of a plastid inverted repeat supermatrix for 246 taxa improves confidence in deeper level angiosperm relationships.},
  	 year = {2011},
  	 keywords = {Angiosperm Tree of Life, plastid inverted repeat, phylogenetics, large data sets},
  	 doi = {10.1086/658923},
  	 url = {http://},
  	 pmid = {},
  	 journal = {International Journal of Plant Sciences},
  	 volume = {172},
  	 number = {4},
  	 pages = {541--558},
  	 abstract = {Recent studies employing complete plastid genome sequences have helped clarify the backbone phylogeny of angiosperms.  However, the relatively limited taxon sampling in these studies has left several major clades poorly represented, precluding resolution of some regions of angiosperm phylogeny with strong support.  Other recent work has suggested that the 25,000 bp plastid inverted repeat (IR) region may be a valuable source of characters for resolving these remaining problematic nodes. Consequently we constructed a data set of all available angiosperm IR sequences, resulting in a matrix of 24,702 aligned bases and 246 accessions, including 21 newly sequenced taxa.  Maximum likelihood analyses of these data yielded a generally well-supported topology that was highly congruent with recent trees based on complete plastid genome sequences.  Notably, IR analyses resolve Pentapetalae into three well-supported clades:  (1) superasterids (including Santalales, Caryophyllales, Berberidopsidales, and Asteridae), (2) superrosids (including Vitales, Saxifragales, and Rosidae), and (3) Dilleniaceae, whose position as sister to remaining Pentapetalae had the highest maximum likelihood bootstrap support yet obtained for this recalcitrant clade using character-rich data sets.  These results provide important new evidence for a stable, well-supported phylogenetic framework for angiosperms, and demonstrate the usefulness of IR data at deeper levels of angiosperm phylogeny.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 18949
  AU  - Moore,Michael James
  AU  - Hassan,Nasr S. 
  AU  - Gitzendanner,Matthew A. 
  AU  - Bruenn,Riva 
  AU  - Croley,Matthew 
  AU  - vandeventer,alexia 
  AU  - Horn,James 
  AU  - Dhingra,Amit 
  AU  - Brockington,Samuel F
  AU  - Latvis,Maribeth 
  AU  - Ramdial,Jeremy 
  AU  - Alexandre,Roolse 
  AU  - Piedrahita,Ana 
  AU  - Xi,Zhenxiang 
  AU  - Davis,Charles C. 
  AU  - Soltis,Pamela S.  
  AU  - Soltis,Douglas E.  
  T1  - Analysis of a plastid inverted repeat supermatrix for 246 taxa improves confidence in deeper level angiosperm relationships.
  PY  - 2011
  KW  - Angiosperm Tree of Life
  KW  - plastid inverted repeat
  KW  - phylogenetics
  KW  - large data sets
  UR  - http://dx.doi.org/10.1086/658923
  N2  - Recent studies employing complete plastid genome sequences have helped clarify the backbone phylogeny of angiosperms.  However, the relatively limited taxon sampling in these studies has left several major clades poorly represented, precluding resolution of some regions of angiosperm phylogeny with strong support.  Other recent work has suggested that the 25,000 bp plastid inverted repeat (IR) region may be a valuable source of characters for resolving these remaining problematic nodes. Consequently we constructed a data set of all available angiosperm IR sequences, resulting in a matrix of 24,702 aligned bases and 246 accessions, including 21 newly sequenced taxa.  Maximum likelihood analyses of these data yielded a generally well-supported topology that was highly congruent with recent trees based on complete plastid genome sequences.  Notably, IR analyses resolve Pentapetalae into three well-supported clades:  (1) superasterids (including Santalales, Caryophyllales, Berberidopsidales, and Asteridae), (2) superrosids (including Vitales, Saxifragales, and Rosidae), and (3) Dilleniaceae, whose position as sister to remaining Pentapetalae had the highest maximum likelihood bootstrap support yet obtained for this recalcitrant clade using character-rich data sets.  These results provide important new evidence for a stable, well-supported phylogenetic framework for angiosperms, and demonstrate the usefulness of IR data at deeper levels of angiosperm phylogeny.
  L3  - 10.1086/658923
  JF  - International Journal of Plant Sciences
  VL  - 172
  IS  - 4
  SP  - 541
  EP  - 558
  ER  -