Phylogeny and new sectional classification for the Cape Clade of the genus <i>Indigofera</i> (Fabaceae: Indigofereae)

Abstract The genus Indigofera in the Greater Cape Floristic Region (GCFR) comprises a diverse assortment of species. Almost 90% of the region's Indigofera species belong to the Cape Clade, while the remaining species are scattered among the other three globally distributed Indigofera clades. As a prelude to a species‐level revision, we aimed to revise the sectional classification of the Cape Clade, making use of molecular and morphological data. We present near‐complete sampled phylogenies representing ca. 95% of species within the GCFR, using the nuclear ITS region and three plastid regions. Ancestral state reconstructions identified several morphological characters that, as unique suites of traits, can help to distinguish different sections/subsections, rather than single diagnostic traits. A total‐evidence phylogeny based on both morphology and molecular data strongly supports the recognition of eight sections within the Cape Clade. Indigofera sect. Brachypodae , sect. Digitatae , sect. Juncifoliae , sect. Oligophyllae and sect. Productae are maintained and refined from previous sectional classifications. Indigofera cytisoides , I. merxmuelleri and I. nudicaulis are circumscribed into three new monospecific sections ( I. sect. Cytisoidae , sect. Merxmuelleranae , sect. Nudicaules ), based on suites of unique morphological characters. Indigofera sect. Digitatae and sect. Brachypodae are the most diverse sections, and are each further divided into four subsections.