Synthesizing phylogenetic knowledge for ecological research

TitleSynthesizing phylogenetic knowledge for ecological research
Publication TypeJournal Article
Year of Publication2012
AuthorsBeaulieu JM, Ree RH, Cavender-Bares J, Weiblen GD, Donoghue MJ
PaginationS4 - S13
Keywordscommunity phylogenetics, ECOLOGY, Phylografter, Phylomatic, supermatrix, supertree

The demand for knowledge about the tree of life is steadily rising in ecology and other fields, but bioinformatic resources designed to meet these needs remain poorly developed. Ecologists pursuing phylogenetic insights into the organization of communities have come to rely on relatively conservative reference trees that, in general, are poorly resolved and documented. New methods for inferring very large trees by mining data from DNA sequence repositories will undoubtedly be useful in community phylogenetics but are not without limitations. Here we argue that the collective phylogenetic knowledge embodied in the literature of systematics is a valuable resource that can be tapped in assembling synthetic trees. Assembling a composite “literature-based’’ tree by the judicious grafting of clades is one way to achieve a synthesis of current knowledge, and could, under some circumstances, better represent “what we know’’ about phylogenetic relationships than results obtained from automated