Complete Generic Level Phylogenetic Analyses of Palms (Arecaceae) with Comparisons of Supertree and Supermatrix Approaches
William J. Baker1,6, Vincent Savolainen1,2, Conny B. Asmussen-Lange3, Mark W. Chase1, John Dransfield1, FÃ©lix Forest1, Madeline M. Harley1, Natalie W. Uhl4 and Mark Wilkinson5
1Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK;
2Imperial College London, Silwood Park Campus, Buckhurst Road, Ascot, Berkshire, SL5 7PY, UK; 3Department of Ecology, University of Copenhagen, Rolighedsvej 21, DK-1958 Frederiksberg C, Denmark;
4Plant Biology, 412 Mann Library Building, Cornell University, Ithaca, NY 14853, USA;
5Department of Zoology, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
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.