Molecular systematics and incongruent gene trees of Urophylleae (Rubiaceae)

Abstract

The phylogeny of the Pantropical tribe Urophylleae is poorly understood. Earlier phylogenetic work has identified major evolutionary lineages within the group, each geographically restricted to a single continent, but relationships among taxa within these lineages are so far largely unresolved. This study uses parsimony and Bayesian phylogenetic analyses of chloroplast DNA (cpDNA) and nuclear ribosomal DNA (nrDNA) to resolve phylogenetic relationships within Urophylleae. The results show that there are conflicts between cpDNA and nrDNA regarding species-level relationships within Pauridiantha, Urophyllum, and Amphidasya, which provides evidence of a complex genetic history. Different types of tests are used to explore the magnitude of the incongruence and locate the exact nodes in the two gene trees that are in conflict. This approach makes it possible to use the topology from the combined analysis, despite the separate datasets being strongly incongruent, since areas of the tree that are free from conflict can be identified. Based on the results presented in this study, Urophylleae is indicated to consist of Temnopteryx, Raritebe, Amphidasya, Urophyllum s.l., Pauridiantha s.l., and Pentaloncha. Several genera are shown to be nested inside Pauridiantha, two of which have already been included in Pauridiantha based on other data (Pamplethantha, Commitheca), and two which are included in this genus here (Poecilocalyx, Stelechantha). Likewise, three genera are shown to be ingroups in Urophyllum (Pravinaria, Maschalocorymbus, Pleiocarpidia), and are therefore subsumed under this genus. New combinations under Pauridiantha are proposed for three species in Poecilocalyx and three species in Stelechantha, as well as new combinations under Urophyllum for two species in Pravinaria and 17 species in Pleiocarpidia. For one of the latter species a new name is presented to avoid homonymy.

Target capture data resolve recalcitrant relationships in the coffee family (Rubioideae, Rubiaceae)

“… Khan et al (2008) was the first phylogenetic study based on molecular to include Temnopteryx , and they showed that it belongs to Rubioideae although they did not resolve its position within the subfamily. In subsequent work based on molecular data ( Smedmark et al, 2008 , 2010 ; Smedmark and Bremer, 2011 ; Yang et al, 2016 ), Temnopteryx has been resolved as sister to the (remaining) tribe Urophylleae, although not always with high support. Here we instead find Temnopteryx strongly supported as sister to the remaining members of the SCOUT-clade ( Figures 1 , 2 ).…”

A synopsis of the endemic plant genera of Borneo

“…and Pleiocarpidia K.Schum.) were in fact nested within it (Smedmark et al , Smedmark and Bremer using plastid and nuclear ribosomal regions). Nevertheless, because these aforementioned genera were noted to have corolla throat hairs inserted directly on the throat wall, whereas those of Crobylanthe are instead inserted on scale‐like excrescences, this suggests that it is still sufficiently distinct from Urophyllum and we tentatively accept it as a genus here.…”

“…Further work on Urophyllum and its allied genera suggested that some of the characters indicated by Bremekamp () to segregate the related genera were not very reliable in doing so (Wong ), while molecular phylogenetic analyses demonstrated that several genera separated from Urophyllum by corolla throat hair form (i.e. Pravinaria , Praravinia , Maschalocorymbus and Pleiocarpidia ) were in fact nested within it (Smedmark et al 2008, Smedmark and Bremer using plastid and nuclear ribosomal regions). However, since these sampled genera were noted to have corolla throat hairs inserted directly on the throat wall, whereas those of Rhaphidura are inserted on a ring in the corolla throat and it has not yet been included in a molecular phylogenetic study, we tentatively continue to accept it as a genus here.…”

“…Stichianthus is closely related to Urophyllum (tropical and subtropical Asia) but is unique in its cauliflorous uniflowered inflorescences that span the length of the internode (Valeton , Bremekamp ). Stichianthus is placed in the Urophylleae (Robbrecht ) but has not yet been included in any phylogenetic study of this tribe (Smedmark and Bremer ).…”

Notes on the threatened lowland forests of Mt Cameroon and their endemics including Drypetes njonji sp. nov., with a key to species of Drypetes sect. Stipulares (Putranjivaceae)

“…Dawson (2002) now Pauridiantha arcuata (S.E. Dawson) Smedmark & B. Bremer (2011) extending to Mt Kupe and the Bakossi Mts , Psychotria elephantina Lachenaud & Cheek (Cheek & Lachenaud 2013) extending to Korup (Lachenaud 2019), and also Ancistrocladus grandiflorus Cheek (Cheek 2000), subsequently found to extend to the Rumpi Hills.…”