Phylogenomics and evolutionary history of Oreocnide (Urticaceae) shed light on recent geological and climatic events in SE Asia.

Climate change and geological events have long been known to shape biodiversity, implying that these can likewise be viewed from a biological perspective. To study whether plants can shed light on this, and how they responded to climate change there, we examined Oreocnide, a genus widely distributed in SE Asia. Based on broad geographic sampling with genomic data, we employed an integrative approach of phylogenomics, molecular dating, historical biogeography, and ecological analyses. We found that Oreocnide originated in mainland East Asia and began to diversify ∼6.06 Ma, probably in response to a distinct geographic and climatic transition in East Asia at around that time, implying that the last important geological change in mainland SE Asia might be 1 Ma older than previously suggested. Around six immigration events to the islands of Malesia followed, indicating that immigration from the mainland could be an underestimated factor in the assembly of biotic communities in the region. Two detected increases of diversification rate occurred 3.13 and 1.19 Ma, which strongly implicated climatic rather than geological changes as likely drivers of diversification, with candidates being the Pliocene intensification of the East Asian monsoons, and Pleistocene climate and sea level fluctuations. Distribution modelling indicated that Pleistocene sea level and climate fluctuations were inferred to enable inter-island dispersal followed by allopatric separation, underpinning radiation in the genus. Overall, our study, based on multiple lines of evidence, linked plant diversification to the most recent climatic and geological events in SE Asia. We highlight the importance of immigration in the assembly and diversification of the SE Asian flora, and underscore the utility of plant clades, as independent lines of evidence, for reconstructing recent climatic and geological events in the SE Asian region.

Implications of a molecular phylogenetic study of the Malagasy genus Cedrelopsis and its relatives (Ptaeroxylaceae).

Ptaeroxylaceae is an Afro-Malagasy family containing three genera, Bottegoa, Cedrelopsis, and Ptaeroxylon. Although the family is morphologically well delimited, it is currently considered part of the subfamily Spathelioideae in a broadly circumscribed orange family (Rutaceae). The Malagasy Cedrelopsis has traditionally been associated with different families of the order Sapindales and its phylogenetic placement in Rutaceae sensu lato has yet to be tested with molecular data. The present molecular phylogenetic study reaffirms the monophyly of Ptaeroxylaceae and its placement in Spathelioideae. Therefore, molecules and morphology support close affinities between Bottegoa, Cedrelopsis, and Ptaeroxylon and also their current generic circumscriptions. We report a case of an evolutionary change from one-seeded to two-seeded carpels within the Harrisonia-Cneorum-Ptaeroxylaceae clade of Spathelioideae. Finally, the sister-group relationship between the African Bottegoa and the Afro-Malagasy Ptaeroxylon-Cedrelopsis clade suggests an African origin of Cedrelopsis.

Molecular phylogenetic study of the tribe Tropidieae (Orchidaceae, Epidendroideae) with taxonomic and evolutionary implications.

The orchid tribe Tropidieae comprises three genera, Tropidia, Corymborkis and Kalimantanorchis. There are three fully mycoheterotrophic species within Tropidieae: Tropidia saprophytica, T. connata and Kalimantanorchis nagamasui. A previous phylogenetic study of K. nagamasui, based only on plastid matK data, placed K. nagamasui outside the clade of Tropidia and Corymborkis without support. In this study, we performed phylogenetic analyses using a nuclear ribosomal DNA spacer (ITS1-5.8S-ITS2), a low-copy nuclear coding gene (Xdh) and a mitochondrial intron (nad1b-c intron) to study the phylogenetic relationships within Tropidieae. We included six photosynthetic and all three fully mycoheterotrophic Tropidieae species. The resulting phylogenetic trees placed these fully mycoheterotrophic species inside the Tropidia clade with high support. In our trees, these three species do not form a monophyletic group together, because the photosynthetic T. graminea is nested amongst them. Our results also suggest that the loss of photosynthetic ability occurred at least twice in Tropidia.

Identifying clades in Asian Annonaceae: monophyletic genera in the polyphyletic Miliuseae.

The tribe Miliuseae (Annonaceae) comprises six genera distributed in Asia: Alphonsea, Mezzettia, Miliusa, Orophea, Platymitra, and Phoenicanthus. A phylogenetic study to investigate the putative monophyly of the tribe and the intergeneric relationships is presented here. Nucleotide sequences of the plastid gene rbcL, trnL intron, and trnL-trnF intergenic spacer were analyzed from 114 Annonaceae taxa, including 24 Miliuseae species and two outgroups using maximum parsimony and Bayesian inference. The two data sets (rbcL and the trnL-trnF regions) were analyzed separately and in combination. Miliuseae were found to be polyphyletic due to the position of Mezzettia and are part of a large, predominantly Asian and Central-American clade (miliusoid clade). Although intergeneric relationships were poorly resolved, all genera, except Polyalthia, were monophyletic, supporting previous generic delimitation based on morphology. A group of three Polyalthia species seems the most likely sister group of Miliusa. Several infrageneric groups of Miliusa, Orophea, and Polyalthia are supported by both molecular and morphological data. No morphological synapomorphies have yet been found for the miliusoid clade. Molecular clades within the miliusoid clade, however, can be characterized by size and the shape of the outer petals, number of ovules per carpel, and the size of the fruits.