PROGRESS AND PROSPECTSIN RECONSTRUCTINGPLANT PHYLOGENY'Michael J. Donoghue2ABSTRACT Phylogeny reconstruction has become respectable science over the last few decades, and trees are accumulatingrapidly in the literature. Botanists have been active in this effort and can already cite success stories (e.g., recognitionof streptophytes, stomatophytes, anthophytes, eudi�ots). Nevertheless, only a small number of problems have beenaddressed and some of these have resisted solution. To solve the toughest problems, especially those involving ancient,rapid radiations, various sources of data will need to be combined, including evidence from fossils. Furthermore, inview of limitations in analyzing data sets with many taxa, more attention must be paid to the consequences of differenttaxon sampling strategies and to how large, variable taxa can be represented in more inclusive studies. Over the next few years we should continue to move toward a phylogenetic system (monophyletic groups definedby ancestry, diagnosed by characters), which will entail the elimination of familiar paraphyletic taxa. We can expectincreased use of phylogenies by ecologists, molecular biologists, and others, which will force us to attend to the issueof the reliability of phylogenetic hypotheses, and will necessitate the development of a database of phylogenetic studies.Interactions with population biologists promise to be especially productive, since there are obvious mutual concernscentered on the analysis of gene trees and reticulation. Over twenty-five years have elapsed since thepublication of Willi Hennig's Phylogenetic Sys-tematics (Hennig, 1966), and for well over a de-cade botanical systematists have been conductingnumerical phylogenetic analyses. The focus of theMisouri Botanical Garden's Annual SystematicsSymposium on the "Origin and Relationships ofthe Major Plant Groups" suggests that progresshas been made, and the meeting itself documentedignificant advances in our understanding of severalof the most challenging phylogenetic questions. Theaim of this paper is to take stock, in general termns,of where things stand. Has phylogenetic analysishad a subtantial impact on our understanding oflant phylogeny, and where do we go from here?PROGRESS Although many of the ideas underlying phylo-etic analysis have a rather long history (seeaw, 1992; Donoghue & Kadereit, 1992), phy-tylo recioction has become respectable sci-ence only over the last few decades. This happycicumstance can be traced to a series of devel-optents in the logic of phylogeny reconstruction(e.g., Hennig, 1966; Farris, 1983; see Sober, 1988;Swofford & Olsen, 1990), to the availability ofcomputers and algorithms to implement this logic(e.g., Farris, 1988; Maddison & Maddison, 1992;Swofford, 1993), and to new sources of evidence,especially molecular data (e.g., Fernholm et al.,1989; Hilis & Moritz, 1990). While it is obviousthat these developments have had a significantimpact on plant systematics, it is not entirely clearhow best to measure the progress that has beenmade. There are, however, several indicators thatbear consideration.LEVEL OF ACTIVITY One measure of progress is simply the rate ofpublication of phylogenetic hypotheses. Phyloge-netic trees are undoubtedly accumulating in theliterature, but the magnitude of the effort is difficultto assess because no one has been keeping trackof such information. In a survey of 79 journalspulished in 1989, 1990, and 1991, we recentlyassembled data on 1140 articles that containedtrees (Sanderson et al., 1993). This remarkablenumber of studies (nearly a tree a day) is surelyS grateful to Bruce Baldwin, Peter Crane, Jim Doyle, David Hills, Toby Keogg, David Maddison, Wayne, Dick Olmstead, Mike Sanderson, and Li Zimmer for helful discuion d/or acce to upulishedk, as we as to Mick Richardson for inviting me to participate in the symposium. My work as been upportedb the NSF (SR8822658), the University of Arizona, and a Mel Fonation Fellowhip from the Smithonlnstitution. arttnent of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachett 02138, SANN. MIsoulR BT. GARD. 81: 405-418. 1994.
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