Clock-dated phylogeny for 48% of the 700 species of Crotalaria (Fabaceae–Papilionoideae) resolves sections worldwide and implies conserved flower and leaf traits throughout its pantropical range

BACKGROUND: With some 700 species, the pantropical Crotalaria is among the angiosperm’s largest genera. We sampled 48% of the species from all sections (and representatives of the 15 remaining Crotalarieae genera) for nuclear and plastid DNA markers to infer changes in climate niches, flower morphology, leaf type, and chromosome numbers. RESULTS: Crotalaria is monophyletic and most closely related to African Bolusia (five species) from which it diverged 23 to 30 Ma ago. Ancestral state reconstructions reveal that leaf and flower types are conserved in large clades and that leaf type is uncorrelated to climate as assessed with phylogenetically-informed analyses that related compound vs. simple leaves to the mean values of four Bioclim parameters for 183 species with good occurrence data. Most species occur in open habitats <1000 m alt., and trifoliolate leaves are the ancestral condition, from which unifoliolate and simple leaves each evolved a few times, the former predominantly in humid, the latter mainly in dry climates. Based on chromosome counts for 36% of the 338 sequenced species, most polyploids are tetraploid and belong to a neotropical clade. CONCLUSIONS: An unexpected finding of our study is that in Crotalaria, simple leaves predominate in humid climates and compound leaves in dry climates, which points to a different adaptive value of these morphologies, regardless of whether these two leaf types evolved rarely or frequently in our focal group. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12862-017-0903-5) contains supplementary material, which is available to authorized users.