RAD sequencing resolves the phylogeny, taxonomy and biogeography of Trichophoreae despite a recent rapid radiation (Cyperaceae).

Trichophoreae is a nearly cosmopolitan Cyperaceae tribe that contains ~17 species displaying striking variation in size, inflorescence complexity, and perianth morphology. Although morphologically distinct, the status of its three genera (Cypringlea, Oreobolopsis and Trichophorum) is controversial because recent phylogenetic studies have suggested they might not be reciprocally monophyletic. However, previous analyses have shown conflicting topologies and consistently poor support due to an initial rapid diversification of the tribe. We analysed restriction-site associated DNA sequencing (RADseq) data from nearly all species of the clade, combined with five Sanger-based markers (matK, ndhF, rps16, ETS-1f, ITS) sampled extensively within species. This approach allowed us to resolve deep and shallow relationships within Trichophoreae for the first time, despite an anomaly zone spanning several successive short branches that produced considerable gene tree incongruence. Analyses reveal a primary phylogenetic split of the tribe into two clades roughly corresponding to an East Asian-North American disjunction that dates back to the mid-Miocene, with both clades comprised of a mixture of reduced unispicate and larger taxa with highly compound inflorescences. Morphological characters traditionally used in the circumscription of Trichophoreae genera are shown to be homoplasious. Several of these characters correlate best with climatic conditions, with the most reduced species occurring in open habitats at high latitudes and altitudes. Close relatives with highly compound inflorescences are found in temperate or subtropical forest understories. Cypringlea and Oreobolopsis are deeply nested within Trichophorum, and we merge all three genera into a more broadly circumscribed Trichophorum. We also show that Scirpus filipes is another previously unrecognized East Asian species of Trichophorum with highly compound inflorescences.