Phylogenetic Analysis of the Cultivated and Wild Species of Phaseolus (Fabaceae) (1999)

The species of Phaseolus were exhaustively sampled for both ITS/5.8S DNA sequence and non-molecular data. With all related New World genera designated as outgroups, a phylogenetic analysis of combined data reveals a strongly supported monophyletic Phaseolus. Other well supported relationships include nine monophyletic species clades within Phaseolus, designated as the P vulgaris, P filiformis, P lunatus, P polystachios, P leptostachyus, P pauciflorus, P tuerckheimii, and P pedicellatus groups, and P microcarpus. Only the last of these is monotypic and consistently resolved in a sensitivity analysis as the earliest branch in the Phaseolus clade, though with poor bootstrap support. The five most commonly domesticated species in the genus arise from within the P vulgaris and P lunatus groups. The gene pools traditionally recognized for the domesticated species P vulgaris and P lunatus are not detected with ITS sequence variation. This is in spite of a very high degree of interand intra-specific ITS sequence divergence in Phaseolus. Though the genus Phaseolus has a complex taxonomic and nomenclatural history, recent circumscriptions of the genus are narrow (e.g., Verdcourt 1970) and most of the species with uncertain affinities have been relegated to Vigna. Vigna rather than Phaseolus has become the large catch-all pantropcial genus (Marechal 1982; Delgado-Salinas 1985; McVaugh 1987). In this modern circumscription, Phaseolus is strictly New World, concentrated in tropical and warm temperate North America, and diagnosed by foliage bearing hooked hairs, keel petals that are laterally and tightly coiled, and inflorescence nodes that lack extrafloral nectaries (Baudet 1977; Lackey 1978, 1981, 1983). Still retained in the genus are five economically important species: P acutifolius (tepary bean), P coccineus (scarlet runner bean), P lunatus (lima bean), P polyanthus (year bean), and P vulgaris (common bean). Little has been done to test the hypothesis of monophyly for the modern circumscription of Phaseolus. The traits supposedly diagnostic of Phaseolus occur in species of other genera (e.g., Vigna adenantha has laterally coiled keel petals, and species of Dolichos and Dipogon have inflorescence nodes lacking nectaries). A phylogenetic analysis of chloroplast DNA restriction site data suggests that Phaseolus is monophyletic (Delgado-Salinas et al. 1993). Taxon sampling, however, was not addressed, and this is a concern given that only 10 of approximately 50 species in the genus were sampled. Phaseolus is suggested to be part of a weakly supported monophyletic group of about 10 Old and New World genera that have poorly resolved relationships (Doyle and Doyle 1993; Bruneau et al. 1995). However, other studies suggest that the sister group relationships of Phaseolus include only New World genera. Analysis of chloroplast DNA restriction sites (Delgado-Salinas et al. 1993) resolved a New World clade where the genera Macroptilium and Strophostyles were sister to Phaseolus. A close relationship of Phaseolus to other New World genera is also suggested by an additional analysis of chloroplast DNA restriction sites (Vaillancourt et al. 1993-a study that focused on Vigna), a phenetic analysis of morphological data (Marechal et al. 1978, 1981), and a traditional taxonomic classification (Lackey 1981, 1983). A comprehensive phylogeny including both the wild and cultivated species of Phaseolus has been neglected, possibly because of an emphasis on the study of the domesticated species. What is known comes from phenetic and cladistic analysis of isozyme banding profiles (Jaaska 1996), phenetic analysis of morphological characters (Marechal et al. 1978), and cladistic analysis of chloroplast DNA restriction site data (Delgado-Salinas et al. 1993; Llaca et al. 1994). Yet character or taxon sampling has been insufficient to make any definitive conclusions about the infra-generic phylogenetic relationships