Data from: Phylogenomics and historical biogeography of the monocot order Liliales: out of Australia and through Antarctica

We present the first phylogenomic analysis of relationships among all ten families of Liliales, based on 75 plastid genes from 35 species in 29 genera, and 97 additional plastomes stratified across angiosperm lineages. We used a supermatrix approach to extend our analysis to 58 of 64 genera of Liliales, and calibrated the resulting phylogeny against 17 fossil dates to produce a new timeline for monocot evolution. Liliales diverged from other monocots 124 Mya and began splitting into separate families 113 Mya. Our data support an Australian origin for Liliales, with close relationships between three pairs of lineages (Corsiaceae/Campynemataceae, Philesiaceae/Ripogonaceae, tribes Alstroemerieae/Luzuriageae) in South America and Australia or New Zealand reflecting teleconnections of these areas via Antarctica. Long-distance dispersal (LDD) across the Pacific and Tasman Sea led to re-invasion of New Zealand by two lineages (Luzuriaga, Ripogonum); LDD allowed Campynemanthe to colonize New Caledonia after its submergence until 37 Mya. LDD permitted Colchicaceae to invade East Asia and Africa from Australia, and re-invade Africa from Australia. Periodic desert greening permitted Gloriosa and Iphigenia to colonize Southeast Asia overland from Africa, and Androcymbium–Colchicum to invade the Mediterranean from South Africa. Melanthiaceae and Liliaceae crossed the Bering land-bridge several times from the Miocene to the Pleistocene

Data from: Orchid phylogenomics and multiple drivers of their extraordinary diversification

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−1 My−1) is 6.8 times that at the Asparagales crown

XML BEAST file for divergence times estimation

XML file for divergence times estimation analysis with BEAST v1.8.0

75 chloroplast coding regions alignments in nexus format

This file contains alignments of 75 chloroplast coding regions for orchid taxa plus Mapania (Cyperaceae) generated in this stud

Making Carex monophyletic (Cyperaceae, tribe Cariceae): a new broader circumscription

Carex (Cyperaceae), with an estimated 2000 species, nearly cosmopolitan distribution and broad range of habitats, is one of the largest angiosperm genera and the largest in the temperate zone. In this article, we provide argument and evidence for a broader circumscription of Carex to add all species currently classified in Cymophyllus (monotypic), Kobresia (c. 60 species), Schoenoxiphium (c. 15 species) and Uncinia (c. 70 species) to those currently classified as Carex. Carex and these genera comprise tribe Cariceae (subfamily Cyperoideae, Cyperaceae) and form a well-supported monophyletic group in all molecular phylogenetic studies to date. Carex as defined here in the broad sense currently comprises at least four clades. Three are strongly supported (Siderostictae, core Vignea and core Carex), whereas the caricoid clade, which includes all the segregate genera, receives only weak to moderate support. The caricoid clade is most commonly split into two clades, one including a monophyletic Schoenoxiphium and two small clades of species of Carex s.s., and the other comprising Kobresia, Uncinia and mostly unispicate species of Carex s.s. Morphological variation is high in all but the Vignea clade, making it extremely difficult to define consistent synapomorphies for most clades. However, Carex s.l. as newly circumscribed here is clearly differentiated from the sister groups in tribe Scirpeae by the transition from bisexual flowers with a bristle perianth in the sister group to unisexual flowers without a perianth in Carex. The naked female flowers of Carex s.l. are at least partially enclosed in a flask-shaped prophyll, termed a perigynium. Carex s.s. is not only by far the largest genus in the group, but also the earliest published name. As a result, only 72 new combinations and 58 replacement names are required to treat all of tribe Cariceae as a single genus Carex. We present the required transfers here, with synonymy, and we argue that this broader monophyletic circumscription of Carex reflects the close evolutionary relationships in the group and serves the goal of nomenclatural stability better than other possible treatments.(c) 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179, 1-42

Making 'Carex' monophyletic (Cyperaceae, tribe Cariceae): a new broader circumscription

'Carex' (Cyperaceae), with an estimated 2000 species, nearly cosmopolitan distribution and broad range of habitats, is one of the largest angiosperm genera and the largest in the temperate zone. In this article, we provide argument and evidence for a broader circumscription of 'Carex' to add all species currently classified in 'Cymophyllus' (monotypic), 'Kobresia' (c. 60 species), 'Schoenoxiphium' (c. 15 species) and 'Uncinia' (c. 70 species) to those currently classified as 'Carex'. 'Carex' and these genera comprise tribe Cariceae (subfamily Cyperoideae, Cyperaceae) and form a wellsupported monophyletic group in all molecular phylogenetic studies to date. 'Carex' as defined here in the broad sense currently comprises at least four clades. Three are strongly supported ('Siderostictae', core 'Vignea' and core 'Carex'), whereas the caricoid clade, which includes all the segregate genera, receives only weak to moderate support. The caricoid clade is most commonly split into two clades, one including a monophyletic Schoenoxiphium and two small clades of species of 'Carex s.s.', and the other comprising 'Kobresia', 'Uncinia' and mostly unispicate species of 'Carex s.s.' Morphological variation is high in all but the 'Vignea' clade, making it extremely difficult to define consistent synapomorphies for most clades. However, 'Carex s.l.' as newly circumscribed here is clearly differentiated from the sister groups in tribe Scirpeae by the transition from bisexual flowers with a bristle perianth in the sister group to unisexual flowers without a perianth in 'Carex'. The naked female flowers of 'Carex s.l.' are at least partially enclosed in a flask-shaped prophyll, termed a perigynium. 'Carex s.s.' is not only by far the largest genus in the group, but also the earliest published name. As a result, only 72 new combinations and 58 replacement names are required to treat all of tribe Cariceae as a single genus 'Carex'. We present the required transfers here, with synonymy, and we argue that this broader monophyletic circumscription of 'Carex' reflects the close evolutionary relationships in the group and serves the goal of nomenclatural stability better than other possible treatments