Tropical mountains are hot spots of biodiversity and endemism, but the evolutionary origins of their unique biotas are poorly understood. In varying degrees, local and regional extinction, long-distance colonization, and local recruitment may all contribute to the exceptional character of these communities. Also, it is debated whether mountain endemics mostly originate from local lowland taxa, or from lineages that reach the mountain by long-range dispersal from cool localities elsewhere. Here we investigate the evolutionary routes to endemism by sampling an entire tropical mountain biota on the 4,095-metre-high Mount Kinabalu in Sabah, East Malaysia. We discover that most of its unique biodiversity is younger than the mountain itself (6 million years), and comprises a mix of immigrant pre-adapted lineages and descendants from local lowland ancestors, although substantial shifts from lower to higher vegetation zones in this latter group were rare. These insights could improve forecasts of the likelihood of extinction and 'evolutionary rescue' in montane biodiversity hot spots under climate change scenarios.

The pantropical genus Begonia is the sixth-largest genus of flowering plants, including 1870 species. The sections of Begonia are used frequently as analogues to genera in other families but, despite their taxonomic utility, few of the current sections have been examined in the light of molecular phylogenetic analyses. We present herein the largest, most representative phylogeny of Begonia published to date and a subsequent provisional sectional classification of the genus. We utilised three plastid markers for 574 species and 809 accessions of Begonia and used Hillebrandia as an outgroup to produce a dated phylogeny. The relationships between some species and sections are poorly resolved, but many sections and deeper nodes receive strong support. We recognise 70 sections of Begonia including 5 new sections: Astrothrix, Ephemera, Jackia, Kollmannia, and Stellandrae; 4 sections are reinstated from synonymy: Australes, Exalabegonia, Latistigma and Pereira; and 5 sections are newly synonymised. The new sectional classification is discussed with reference to identifying characters and previous classifications.

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Aim The complex palaeogeography of the Malesian archipelago, characterized by the evolution of an ever-changing mosaic of terrestrial and marine areas throughout the Cenozoic, provides the geographic backdrop for the remarkable diversification of Malesian Begonia (> 450 species). This study aimed to investigate the origin of Malesian Begonia, the directionality of dispersal events within the Malesian archipelago and the impact of ancient water gaps on colonization patterns, and to identify drivers of diversification.Location Asia, Southeast Asia, Malesia.Methods Plastid DNA sequence data of representatives of all families of the Cucurbitales and Fagales (matK, rbcL, trnL intron, trnL-F spacer, 4076 aligned positions, 92 taxa) and a sample of all major Asian Begonia sections (ndhA intron, ndhF-rpl32 spacer, rpl32-trnL spacer, 4059 aligned positions, 112 taxa) were analysed under an uncorrelated-rates relaxed molecular clock model to estimate the age of the Begonia crown group divergence and divergence ages within Asian Begonia. Ancestral areas were reconstructed using a likelihood approach implementing a dispersal-extinction-cladogenesis model, and with a Bayesian approach to dispersal-vicariance analysis.

The Annonaceae, the largest family in the early-divergent order Magnoliales, comprises 107 genera and c. 2,400 species. Previous molecular phylogenetic studies targeting different taxa have generated large quantities of partially overlapping DNA sequence data for many species, although a large-scale phylogeny based on the maximum number of representatives has never been reconstructed. We use a supermatrix of eight chloroplast markers (rbcL, matK, ndhF, psbA-trnH, trnL-F, atpB-rbcL, trnS-G and ycf1) to reconstruct the most comprehensive tree to date, including 705 species (29%) from 105 genera (98%). This provides novel insights into the relationships of five enigmatic genera (Bocagea, Boutiquea, Cardiopetalum, Duckeanthus and Phoenicanthus). Fifteen main clades are retrieved in subfamilies Annonoideae and Malmeoideae collectively, 14 of which correspond with currently recognised tribes. Phoenicanthus cannot be accommodated in any existing tribe, however: it is retrieved as sister to a clade comprising the tribes Dendrokingstonieae, Monocarpieae and Miliuseae, and we therefore validate a new tribe, Phoenicantheae. Our results provide strong support for many previously recognised groups, but also indicate non-monophyly of several genera (Desmopsis, Friesodielsia, Klarobelia, Oxandra, Piptostigma and Stenanona). The relationships of these non-monophyletic genera—and two other genera (Froesiodendron and Melodorum) not yet sampled—are discussed, with recommendations for future research.

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Aim African-Asian disjunctions are common in palaeotropical taxa, and are typically explained by reference to three competing hypotheses: (1) 'rafting' on the Indian tectonic plate, enabling Africa-to-Asia dispersal; (2) migration via Eocene boreotropical forests; and (3) transoceanic long-distance dispersal. These hypotheses are tested using Uvaria (Annonaceae), which is distributed in tropical regions of Africa, Asia and Australasia. Recent phylogenetic reconstructions of the genus show a clear correlation with geographical provenance, indicating a probable origin in Africa and subsequent dispersal to Asia and then Australasia. Ancestral areas and migration routes are inferred and compared with estimates of divergence times in order to distinguish between the prevailing dispersal hypotheses.Location Palaeotropics.Methods Divergence times in Uvaria are estimated by analysing the sequences of four DNA regions (matK, psbA-trnH spacer, rbcL and trnL-F) from 59 Uvaria species and 77 outgroup species, using a Bayesian uncorrelated lognormal (UCLD) relaxed molecular clock. The ancestral area of Uvaria and subsequent dispersal routes are inferred using statistical dispersal-vicariance analysis (s-diva). ResultsUvaria is estimated to have originated in continental Africa 31.6 Ma [95% highest posterior density (HPD): 38.4-25.1 Ma] between the Middle Eocene and Late Oligocene. Two main migration events during the Miocene are identified: dispersal into Madagascar around 17.0 Ma (95% HPD: 22.3-12.3 Ma); and dispersal into Asia between 21.4 Ma (95% HPD: 26.7-16.7 Ma) and 16.

Friesodielsia and the closely related genera Dasymaschalon, Desmos, Exellia, Gilbertiella and Monanthotaxis (Annonaceae subfamily Annonoideae tribe Uvarieae) are taxonomically problematic, with obscure generic delimitations and poorly known phylogenetic relationships. The present study addresses the polyphyletic status of Friesodielsia, using two nuclear and five chloroplast DNA regions to resolve this taxonomic confusion by circumscribing strictly monophyletic genera across the tribe. Bayesian, maximum likelihood and maximum parsimony analyses using a broad taxon sampling (101 taxa) reveal that Friesodielsia species form five robust and morphologically distinct clades. In order to ensure strict monophyly of genera, we restrict the generic name Friesodielsia to an exclusively Asian clade, and the African species that were formerly included in the genus are transferred to Afroguatteria, Monanthotaxis and Sphaerocoryne, necessitating ten new nomenclatural combinations. Schefferomitra, a monospecific genus from New Guinea, is shown to be congeneric with Asian Friesodielsia, and the nomenclatural implications of this are discussed. Two monospecific genera, Exellia and Gilbertiella, are furthermore synonymised with Monanthotaxis, necessitating two additional nomenclatural changes. New generic descriptions are provided for Dasymaschalon (ca. 27 species), Desmos (ca. 22 species), Friesodielsia (ca. 38 species) and Monanthotaxis (ca. 94 species) to reflect these revised circumscriptions.