Orchid phylogenomics and multiple drivers of their extraordinary diversification

Abstract

Orchids are the most diverse family of angiosperms, with over 25 000 species, more than mammals, birds and reptiles combined. Tests of hypotheses to account for such diversity have been stymied by the lack of a fully resolved broad-scale phylogeny. Here, we provide such a phylogeny, based on 75 chloroplast genes for 39 species representing all orchid subfamilies and 16 of 17 tribes, time-calibrated against 17 angiosperm fossils. A supermatrix analysis places an additional 144 species based on three plastid genes. Orchids appear to have arisen roughly 112 million years ago (Mya); the subfamilies Orchidoideae and Epidendroideae diverged from each other at the end of the Cretaceous; and the eight tribes and three previously unplaced subtribes of the upper epidendroids diverged rapidly from each other between 37.9 and 30.8 Mya. Orchids appear to have undergone one significant acceleration of net species diversification in the orchidoids, and two accelerations and one deceleration in the upper epidendroids. Consistent with theory, such accelerations were correlated with the evolution of pollinia, the epiphytic habit, CAM photosynthesis, tropical distribution (especially in extensive cordilleras), and pollination via Lepidoptera or euglossine bees. Deceit pollination appears to have elevated the number of orchid species by one-half but not via acceleration of the rate of net diversification. The highest rate of net species diversification within the orchids (0.382 sp sp 21 My 21) is 6.8 times that at the Asparagales crown.

The complete chloroplast genome of a rare orchid species Liparis loeselii (L.)

“…2). The result indicated that L. loeselii is clustered together with D. officinale what confirmed close relationship of Liparis and Dendrobium genera reported in Givnish et al (2015). The complete plastid genome information reported in this paper provided data useful for population genomic studies, conservation works on L. loeselii as well as for phylogenetic studies within Orchidaceae.…”

Genera Pleurothallidinarum: an updated phylogenetic overview of Pleurothallidinae

“…The answer is most likely both. Givnish et al (2015) showed that Pleurothallidinae has one of the highest species diversification rates in the Orchidaceae. With just above 10 My of age, the subtribe is about one third younger than Laeliinae and Oncidiinae and has more than double the number of species.…”

Phylogenomics of Andropogoneae (Panicoideae: Poaceae) of Mainland Southeast Asia

“…A number of studies have taken advantage of this technology, using either chloroplast protein-coding genes (e.g. Givnish et al 2015;Washburn et al 2015;Barrett et al 2016) or complete chloroplast genomes (e.g. Carbonell-Caballero et al 2015;Cotton et al 2015;Burke et al 2016;McKain et al 2016b) to resolve phylogenetic relationships from as deep as across Viridiplantae (Ruhfel et al 2014) to within a species complex (e.g.…”