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Systematics Section / ASPT

McMahon, Michelle [1], Sanderson, MJ [1].

Multi-gene papilionoid phylogeny: a supermatrix approach.

The phylogeny of Papilionoideae (Fabaceae, c. 12000 spp.) is becoming increasingly well understood, but many relationships at the base of the tree remain uncertain. This is an especially critical region for reconstructing the evolution of the papilionaceous flower, which early in its history exhibits far more variety than it does in more familiar species-rich clades nested within papilionoids. We explored several "supermatrix" strategies for extracting sequences from GenBank and assembling them into phylogenetically suitable data sets. Our aims were (1) to develop a set of tools to facilitate the creation, management, and updating of such a supermatrix, (2) to assess the currently available sequence data that bears on deep Papilionoideae relationships, even if the data was originally obtained for other purposes, and (3) to present a tree based on the maximum amount of combinable data for the maximum number of taxa. Approximately 10,000 sequences were obtained from GenBank. Homology across genes and non-coding regions was initially assessed using "all-by-all" BLAST searches, single-linkage clustering, and a phylogenetic test of orthology, to screen out likely paralogs. Clusters with sufficient taxonomic overlap ("groves") were concatenated into a supermatrix. The resulting matrices contained organellar and nuclear sequences from many loci and from over 1000 taxa. Several strategies for clustering and combining data into groves were examined, each differing in the taxon-by-sequence composition of the supermatrix and the quantity of missing data. Initial parsimony analyses of supermatrices resulted in trees that accord well with previously published results based on single-gene analyses, add large numbers of taxa never placed in a single tree before, and may provide additional resolution among the deeper, more difficult, nodes. Based on these results, targets for future sampling efforts can be proposed.


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1 - University of California, Davis, Section of Evolution and Ecology, One Shields Ave., Davis, California, 95616, USA
2 - University of California, Davis, Section of Evolution and Ecology, One Shields Ave., Davis, California, 95616, USA

Keywords:
Papilionoideae
Fabaceae
supermatrices
Phylogeny.

Presentation Type: Oral Paper
Session: 38-7
Location: 400/Hilton
Date: Tuesday, August 16th, 2005
Time: 3:45 PM
Abstract ID:65


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