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.

We present the first plastome phylogeny encompassing all 77 monocot families, estimate branch support, and infer monocot-wide divergence times and rates of species diversification. METHODS:We conducted maximum likelihood analyses of phylogeny and BAMM studies of diversification rates based on 77 plastid genes across 545 monocots and 22 outgroups. We quantified how branch support and ascertainment vary with gene number, branch length, and branch depth.KEY RESULTS: Phylogenomic analyses shift the placement of 16 families in relation to earlier studies based on four plastid genes, add seven families, date the divergence between monocots and eudicots+Ceratophyllum at 136 Mya, successfully place all mycoheterotrophic taxa examined, and support recognizing Taccaceae and Thismiaceae as separate families and Arecales and Dasypogonales as separate orders. Only 45% of interfamilial divergences occurred after the Cretaceous. Net species diversification underwent four large-scale accelerations in PACMAD-BOP Poaceae, Asparagales sister to Doryanthaceae, Orchidoideae-Epidendroideae, and Araceae sister to Lemnoideae, each associated with specific ecological/morphological shifts. Branch ascertainment and support across monocots increase with gene number and branch length, and decrease with relative branch depth. Analysis of entire plastomes in Zingiberales quantifies the importance of non-coding regions in identifying and supporting short, deep branches. CONCLUSIONS:We provide the first resolved, well-supported monocot phylogeny and timeline spanning all families, and quantify the significant contribution of plastomescale data to resolving short, deep branches. We outline a new functional model for the evolution of monocots and their diagnostic morphological traits from submersed aquatic ancestors, supported by convergent evolution of many of these traits in aquatic Hydatellaceae (Nymphaeales).

The megadiverse genus Carex (c. 2000 species, Cyperaceae) has a nearly cosmopolitan distribution, displaying an inverted latitudinal richness gradient with higher species diversity in cold‐temperate areas of the Northern Hemisphere. Despite great expansion in our knowledge of the phylogenetic history of the genus and many molecular studies focusing on the biogeography of particular groups during the last few decades, a global analysis of Carex biogeography and diversification is still lacking. For this purpose, we built the hitherto most comprehensive Carex‐dated phylogeny based on three markers (ETS–ITS–matK), using a previous phylogenomic Hyb‐Seq framework, and a sampling of two‐thirds of its species and all recognized sections. Ancestral area reconstruction, biogeographic stochastic mapping, and diversification rate analyses were conducted to elucidate macroevolutionary biogeographic and diversification patterns. Our results reveal that Carex originated in the late Eocene in E Asia, where it probably remained until the synchronous diversification of its main subgeneric lineages during the late Oligocene. E Asia is supported as the cradle of Carex diversification, as well as a “museum” of extant species diversity. Subsequent “out‐of‐Asia” colonization patterns feature multiple asymmetric dispersals clustered toward present times among the Northern Hemisphere regions, with major regions acting both as source and sink (especially Asia and North America), as well as several independent colonization events of the Southern Hemisphere. We detected 13 notable diversification rate shifts during the last 10 My, including remarkable radiations in North America and New Zealand, which occurred concurrently with the late Neogene global cooling, which suggests that diversification involved the colonization of new areas and expansion into novel areas of niche space.

AimOrchidaceae is the most species-rich angiosperm family and has one of the broadest distributions. Until now, the lack of a well-resolved phylogeny has prevented analyses of orchid historical biogeography. In this study, we use such a phylogeny to estimate the geographical spread of orchids, evaluate the importance of different regions in their diversification and assess the role of long-distance dispersal (LDD) in generating orchid diversity. LocationGlobal. MethodsAnalyses use a phylogeny including species representing all five orchid subfamilies and almost all tribes and subtribes, calibrated against 17 angiosperm fossils. We estimated historical biogeography and assessed the importance of different regions for rates of speciation, extinction and net species diversification. We evaluated the impact of particular LDD events on orchid diversity by asking how many species evolved in the new range subsequent to those events. ResultsOrchids appear to have arisen in Australia 112Ma (95% higher probability distribution: 102.0-120.0Ma), then spread to the Neotropics via Antarctica by 90Ma (HPD: 79.7-99.5Ma), when all three continents were in close contact and apostasioids split from the ancestor of all other orchids. Ancestors of vanilloids, cypripedioids and orchidoids+epidendroids appear to have originated in the Neotropics 84-64Ma. Repeated long- and short-distance dispersal occurred through orchid history: stochastic mapping identified a mean total of 74 LDD events or 0.8Ma(-1). Across orchid history, Southeast Asia was the most important source and maximally accelerated net diversification; across epidendroids, the Neotropics maximally accelerated diversification. Main conclusionsOur analysis provides the first biogeographical history of the orchids, implicating Australia, the Neotropics and Antarctica in their origin. LDD and life in the Neotropics - especially the Andes - had profound effects on their spread and diversification; >97% of all orchid species are restricted to individual continents

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Aim Across angiosperm families, the area occupied by a family is strongly correlated with its richness. We explore the causes of this area‐richness correlation using the cosmopolitan family, Cyperaceae Juss., as a model. We test the hypothesis that, despite a proposed tropical origin, temperate lineages in the family diversified at elevated rates. We test the hypothesis that the area‐richness correlation is maintained within intrafamilial clades, and that this relationship could be described as a function of niche space. We also test the hypothesis that the partitioning of geographical and ecological space, not the extent of this space, is the factor most closely associated with clade richness. Location Cosmopolitan. Methods We use molecular data from four genes sequenced in 384 taxa to develop a chronogram of Cyperaceae. We then develop a model of ancestral ranges and measure rates of diversification throughout the history of the family. Integrating data from over 4,800,000 digitized herbarium records, we characterize the range and niche of more than 4500 species and test for correlations of the species richness maintained within clades with range size, range partitioning, range overlap, niche, clade age and rate of diversification. Results Cyperaceae originated in South America in the late Cretaceous and subsequently dispersed throughout the globe. Of three increases in diversification rate, two occurred in the temperate Northern Hemisphere. The variable most closely associated with clade richness is the partitioning of geographical space by species within each clade. Main conclusions We show that species‐rich clades in Cyperaceae are not only more widespread, occupy more niche space, and diversify more quickly, but also exhibit patterns that are consistent with the partitioning of geographical and ecological space as a major correlate to diversification.

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.

With approximately 2000 species, tribe Cariceae (Cyperaceae) comprises a morphologically distinctive cosmopolitan clade, with holocentric chromosomes (N = 6 to 56), complex biogeographical patterns, and habitat diversity ranging from rainforests to deserts. Such a remarkable combination of characteristics should make Cariceae an ideal model for studying the evolution of biodiversity, although they also obscure their relationships in Cyperaceae, complicating attempts to identify the contributing factors to diversity of Cariceae. Recent molecular studies place Cariceae in a strongly supported clade consisting of tribes Dulichieae, Scirpeae s.s, and the enigmatic monotypic genus Khaosokia, although relationships in this clade are unresolved. Using the plastid genes matK and ndhF and a greatly improved taxonomic sampling covering 16 of 17 genera and 55% of the species outside Cariceae, our analyses firmly position Dulichieae and Khaosokia (79% and 85% bootstrap support) as successive sisters to a clade consisting of five major lineages (Calliscirpus, Trichophorum + Oreobolopsis + Cypringlea, Cariceae, Scirpus + Eriophorum, and Amphiscirpus + Phylloscirpus + Zameioscirpus), the first four of which receive good to strong support (> 80% bootstrap support). Cariceae are sister to the Trichophorum clade, although topological tests cannot exclude either Calliscirpus or a Scirpus clade + Zameioscirpus clade as sister to the tribe. Trichophorum appears to be paraphyletic and Eriophorum is firmly nested in Scirpus. There appears to be a trend in the increase of chromosome numbers in Scirpus and Eriophorum and a trend in the reduction and proliferation of the inflorescence throughout the major Cariceae-Dulichieae-Scirpeae clades.