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Citation for Study 10045

Citation title: "Complete Generic Level Phylogenetic Analyses of Palms (Arecaceae) with Comparisons of Supertree and Supermatrix Approaches".

This study was previously identified under the legacy study ID S2385 (Status: Published).

Citation

Baker W.J., Savolainen V., Asmussen-lange C., Chase M., Dransfied J., Forest F., Harley M., Uhl N., & Wilkinson M. 2009. Complete Generic Level Phylogenetic Analyses of Palms (Arecaceae) with Comparisons of Supertree and Supermatrix Approaches. Systematic Biology, 58(2): 240-256.

Authors

• Baker W.J. +44 20 8332 5224
• Savolainen V.
• Asmussen-lange C.
• Chase M.
• Dransfied J.
• Forest F.
• Harley M.
• Uhl N.
• Wilkinson M.

Abstract

Supertree and supermatrix methods have great potential in the quest to build the Tree of Life and yet they remain controversial, with most workers opting for one approach or the other, but rarely both. Here we employed both methods to construct phylogenetic trees of all genera of palms (Arecaceae/Palmae), an iconic angiosperm family of great economic importance. We assembled a supermatrix consisting of 16 partitions, comprising DNA sequence data, plastid RFLP data and morphological data for all genera, from which a highly resolved and well-supported phylogenetic tree was built despite abundant missing data. To construct supertrees, we used variants of MRP analysis based on input trees generated directly from subsamples of the supermatrix. All supertrees were highly resolved. Standard MRP with bootstrap weighted matrix elements performed most effectively in this case, generating trees with greatest congruence with the supermatrix tree and fewest clades unsupported by any input tree. Non-independence due to input trees based on combinations of data partitions was an acceptable trade-off for improvements in supertree performance. Irreversible MRP and the use of strictly independent input trees only provided no obvious benefits. Contrary to previous claims, we found that unsupported clades are not infrequent under some MRP implementations with up to 13% of clades lacking support from any input tree in some irreversible MRP supertrees. To build a formal synthesis, we assessed the cross-corroboration between supermatrix trees and the variant supertrees using semi-strict consensus, enumerating shared clades and compatible clades. The semi-strict consensus of the supermatrix tree and the most congruent supertree contained 160 clades (of a maximum of 204), 137 of which were present in both trees. The relationships recovered by these trees strongly support the current phylogenetic classification of palms. We evaluate two composite supertree support measures (rQS and V) and conclude that it is more informative to report numbers of input trees that support or conflict with a given supertree clade. This study demonstrates that supertree and supermatrix methods can provide effective, explicit and complimentary mechanisms for synthesising disjointed phylogenetic evidence while emphasising the need for further refinement of supertree methods. KEY WORDS Palmae; Arecaceae; supertree; supermatrix; phylogeny; matrix representation with parsimony (MRP); congruence.

External links

• DOI: 10.1093/sysbio/syp021

About this resource

• Canonical resource URI: http://purl.org/phylo/treebase/phylows/study/TB2:S10045
• Other versions: Nexus NeXML
• Show BibTeX reference

  		@ARTICLE{TreeBASE2Ref18536,
  	 author = {William John Baker and Vincent  Savolainen and Conny B.  Asmussen-Lange and Mark W.  Chase and J.  Dransfied and Felix  Forest and Madeline M.  Harley and N. W.  Uhl and Mark  Wilkinson},
  	 title = {Complete Generic Level Phylogenetic Analyses of Palms (Arecaceae) with Comparisons of Supertree and Supermatrix Approaches},
  	 year = {2009},
  	 keywords = {},
  	 doi = {10.1093/sysbio/syp021},
  	 url = {},
  	 pmid = {},
  	 journal = {Systematic Biology},
  	 volume = {58},
  	 number = {2},
  	 pages = {240--256},
  	 abstract = {Supertree and supermatrix methods have great potential in the quest to build the Tree of Life and yet they remain controversial, with most workers opting for one approach or the other, but rarely both. Here we employed both methods to construct phylogenetic trees of all genera of palms (Arecaceae/Palmae), an iconic angiosperm family of great economic importance. We assembled a supermatrix consisting of 16 partitions, comprising DNA sequence data, plastid RFLP data and morphological data for all genera, from which a highly resolved and well-supported phylogenetic tree was built despite abundant missing data. To construct supertrees, we used variants of MRP analysis based on input trees generated directly from subsamples of the supermatrix. All supertrees were highly resolved. Standard MRP with bootstrap weighted matrix elements performed most effectively in this case, generating trees with greatest congruence with the supermatrix tree and fewest clades unsupported by any input tree. Non-independence due to input trees based on combinations of data partitions was an acceptable trade-off for improvements in supertree performance. Irreversible MRP and the use of strictly independent input trees only provided no obvious benefits. Contrary to previous claims, we found that unsupported clades are not infrequent under some MRP implementations with up to 13% of clades lacking support from any input tree in some irreversible MRP supertrees. To build a formal synthesis, we assessed the cross-corroboration between supermatrix trees and the variant supertrees using semi-strict consensus, enumerating shared clades and compatible clades. The semi-strict consensus of the supermatrix tree and the most congruent supertree contained 160 clades (of a maximum of 204), 137 of which were present in both trees. The relationships recovered by these trees strongly support the current phylogenetic classification of palms. We evaluate two composite supertree support measures (rQS and V) and conclude that it is more informative to report numbers of input trees that support or conflict with a given supertree clade. This study demonstrates that supertree and supermatrix methods can provide effective, explicit and complimentary mechanisms for synthesising disjointed phylogenetic evidence while emphasising the need for further refinement of supertree methods. KEY WORDS Palmae; Arecaceae; supertree; supermatrix; phylogeny; matrix representation with parsimony (MRP); congruence.}
  }
  		

• Show RIS reference

  		TY  - JOUR
  ID  - 18536
  AU  - Baker,William John
  AU  - Savolainen,Vincent 
  AU  - Asmussen-Lange,Conny B. 
  AU  - Chase,Mark W. 
  AU  - Dransfied,J. 
  AU  - Forest,Felix 
  AU  - Harley,Madeline M. 
  AU  - Uhl,N. W. 
  AU  - Wilkinson,Mark 
  T1  - Complete Generic Level Phylogenetic Analyses of Palms (Arecaceae) with Comparisons of Supertree and Supermatrix Approaches
  PY  - 2009
  UR  - http://dx.doi.org/10.1093/sysbio/syp021
  N2  - Supertree and supermatrix methods have great potential in the quest to build the Tree of Life and yet they remain controversial, with most workers opting for one approach or the other, but rarely both. Here we employed both methods to construct phylogenetic trees of all genera of palms (Arecaceae/Palmae), an iconic angiosperm family of great economic importance. We assembled a supermatrix consisting of 16 partitions, comprising DNA sequence data, plastid RFLP data and morphological data for all genera, from which a highly resolved and well-supported phylogenetic tree was built despite abundant missing data. To construct supertrees, we used variants of MRP analysis based on input trees generated directly from subsamples of the supermatrix. All supertrees were highly resolved. Standard MRP with bootstrap weighted matrix elements performed most effectively in this case, generating trees with greatest congruence with the supermatrix tree and fewest clades unsupported by any input tree. Non-independence due to input trees based on combinations of data partitions was an acceptable trade-off for improvements in supertree performance. Irreversible MRP and the use of strictly independent input trees only provided no obvious benefits. Contrary to previous claims, we found that unsupported clades are not infrequent under some MRP implementations with up to 13% of clades lacking support from any input tree in some irreversible MRP supertrees. To build a formal synthesis, we assessed the cross-corroboration between supermatrix trees and the variant supertrees using semi-strict consensus, enumerating shared clades and compatible clades. The semi-strict consensus of the supermatrix tree and the most congruent supertree contained 160 clades (of a maximum of 204), 137 of which were present in both trees. The relationships recovered by these trees strongly support the current phylogenetic classification of palms. We evaluate two composite supertree support measures (rQS and V) and conclude that it is more informative to report numbers of input trees that support or conflict with a given supertree clade. This study demonstrates that supertree and supermatrix methods can provide effective, explicit and complimentary mechanisms for synthesising disjointed phylogenetic evidence while emphasising the need for further refinement of supertree methods. KEY WORDS Palmae; Arecaceae; supertree; supermatrix; phylogeny; matrix representation with parsimony (MRP); congruence.
  L3  - 10.1093/sysbio/syp021
  JF  - Systematic Biology
  VL  - 58
  IS  - 2
  SP  - 240
  EP  - 256
  ER  -