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The Cretaceous-Palaeogene (K-Pg) extinction of the non-avian dinosaurs (66 Ma) led to a 25 million year gap of megaherbivores (>1000 kg) before the evolution of megaherbivorous mammals in the Late Eocene (40 Ma). The botanical consequences of this 'Palaeocene megaherbivore gap' (PMHG) remain poorly explored. We hypothesize that the absence of megaherbivores should result in changes in the diversification and trait evolution of associated plant lineages. We used phylogenetic time- and trait-dependent diversification models with palms (Arecaceae) and show that the PMHG was characterized by speciation slowdowns, decreased evolution of armature and increased evolution of megafaunal (≥4 cm) fruits. This suggests that the absence of browsing by megaherbivores during the PMHG may have led to a loss of defence traits, but the absence of megaherbivorous seed dispersers did not lead to a loss of megafaunal fruits. Instead, increases in PMHG fruit sizes may be explained by simultaneously rising temperatures, rainforest expansion, and the subsequent radiation of seed-dispersing birds and mammals. We show that the profound impact of the PMHG on plant diversification can be detected even with the overwriting of adaptations by the subsequent Late Eocene opening up of megaherbivore-associated ecological opportunities. Our study provides a quantitative, comparative framework to assess diversification and adaptation during one of the most enigmatic periods in angiosperm history.

Background and Aims: Flowering phenology is arguably the most striking angiosperm phenophase. Although the response of species to climate change and the environmental correlates of the communities have received much attention, the interspecific evolution of flowering phenology has hardly been investigated. I explored this in the wind-pollinated dioecious Restionaceae (restios) of the hyperdiverse Cape flora, to disentangle the effects of phylogeny, traits, and biotic and abiotic environments on flowering time shifts., Methods: I recorded the flowering times of 347 of the 351 species, mapped these over a 98 % complete phylogeny and inferred the evolutionary pattern and abiotic correlates of flowering time shifts. The patterns and biotic/abiotic correlates of restio community mean flowering time were explored using 934 plots., Key Results: Restios flower throughout the year, with large spring and smaller autumn peaks. Species flowering time is evolutionarily labile, poorly explained by either the environment or traits of the species, with half of all sister species allochronic. Community mean flowering time is related to elevation, temperature and rainfall., Conclusions: Flowering time shifts may result from assortative mating and allochronic speciation, possibly leading to non-adaptive radiation. However, community mean flowering time may be environmentally selected. Diversification of flowering time may be non-adaptive, but species could be filtered through survival in suitable communities., (© The Author(s) 2020. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

With the realization that much of the biological diversity on Earth has been generated by discrete evolutionary radiations, there has been a rapid increase in research into the biotic (key innovations) and abiotic (key environments) circumstances in which such radiations took place. Here we focus on the potential importance of population genetic structure and trait genetic architecture in explaining radiations. We propose a verbal model describing the stages of an evolutionary radiation: first invading a suitable adaptive zone and expanding both spatially and ecologically through this zone; secondly, diverging genetically into numerous distinct populations; and, finally, speciating. There are numerous examples of the first stage; the difficulty, however, is explaining how genetic diversification can take place from the establishment of a, presumably, genetically depauperate population in a new adaptive zone. We explore the potential roles of epigenetics and transposable elements (TEs), of neutral process such as genetic drift in combination with trait genetic architecture, of gene flow limitation through isolation by distance (IBD), isolation by ecology and isolation by colonization, the possible role of intra-specific competition, and that of admixture and hybridization in increasing the genetic diversity of the founding populations. We show that many of the predictions of this model are corroborated. Most radiations occur in complex adaptive zones, which facilitate the establishment of many small populations exposed to genetic drift and divergent selection. We also show that many radiations (especially those resulting from long-distance dispersal) were established by polyploid lineages, and that many radiating lineages have small genome sizes. However, there are several other predictions which are not (yet) possible to test: that epigenetics has played a role in radiations, that radiations occur more frequently in clades with small gene flow distances, or that the ancestors of radiations had large fundamental niches. At least some of these may be testable in the future as more genome and epigenome data become available. The implication of this model is that many radiations may be hard polytomies because the genetic divergence leading to speciation happens within a very short time, and that the divergence history may be further obscured by hybridization. Furthermore, it suggests that only lineages with the appropriate genetic architecture will be able to radiate, and that such a radiation will happen in a meta-population environment. Understanding the genetic architecture of a lineage may be an essential part of accounting for why some lineages radiate, and some do not., (© 2020 Cambridge Philosophical Society.)

New Guinea is the world's largest tropical island and has fascinated naturalists for centuries 1,2 . Home to some of the best-preserved ecosystems on the planet 3 and to intact ecological gradients-from mangroves to tropical alpine grasslands-that are unmatched in the Asia-Pacific region 4,5 , it is a globally recognized centre of biological and cultural diversity 6,7 . So far, however, there has been no attempt to critically catalogue the entire vascular plant diversity of New Guinea. Here we present the first, to our knowledge, expert-verified checklist of the vascular plants of mainland New Guinea and surrounding islands. Our publicly available checklist includes 13,634 species (68% endemic), 1,742 genera and 264 families-suggesting that New Guinea is the most floristically diverse island in the world. Expert knowledge is essential for building checklists in the digital era: reliance on online taxonomic resources alone would have inflated species counts by 22%. Species discovery shows no sign of levelling off, and we discuss steps to accelerate botanical research in the 'Last Unknown' 8 .

Plants use roots to access soil resources, so differences in root traits and their ecological consequences could be a mechanism of species coexistence and niche divergence. Current views of the evolution of root diversity are informed by large-scale evolutionary analyses based on taxonomically coarse sampling and led to the 'root trait phylogenetic conservatism hypothesis'. Here we test this hypothesised conservatism among closely related species, and whether root variation plays an ecological role. We collected root architectural traits for the species-rich Cape rushes (Restionaceae) in the field and from herbaria. We used machine learning to interpolate missing data. Using model-based clustering we classified root syndromes. We modelled the proportion of the syndromes along environmental gradients using assemblages and environmental data of 735 plots. We fitted trait evolutionary models to test for the conservatism hypothesis. We recognised five root syndromes. Responses to environmental gradients are syndrome specific and thus these represent ecomorphs. Trait evolutionary models reveal an evolutionary lability in these ecomorphs. This could present the mechanistic underpinning of the taxonomic radiation of this group which has been linked to repeated habitat shifts. Our results challenge the perspective of strong phylogenetic conservatism and root trait evolution may more generally drive diversification., (© 2020 The Authors. New Phytologist © 2020 New Phytologist Trust.)

Understanding how and why rates of evolutionary diversification vary is a key issue in evolutionary biology, ecology, and biogeography. Evolutionary rates are the net result of interacting processes summarized under concepts such as adaptive radiation and evolutionary stasis. Here, we review the central concepts in the evolutionary diversification literature and synthesize these into a simple, general framework for studying rates of diversification and quantifying their underlying dynamics, which can be applied across clades and regions, and across spatial and temporal scales. Our framework describes the diversification rate ( d ) as a function of the abiotic environment ( a ), the biotic environment ( b ), and clade-specific phenotypes or traits ( c ); thus, d ~ a,b,c . We refer to the four components ( a - d ) and their interactions collectively as the "Evolutionary Arena." We outline analytical approaches to this framework and present a case study on conifers, for which we parameterize the general model. We also discuss three conceptual examples: the Lupinus radiation in the Andes in the context of emerging ecological opportunity and fluctuating connectivity due to climatic oscillations; oceanic island radiations in the context of island formation and erosion; and biotically driven radiations of the Mediterranean orchid genus Ophrys . The results of the conifer case study are consistent with the long-standing scenario that low competition and high rates of niche evolution promote diversification. The conceptual examples illustrate how using the synthetic Evolutionary Arena framework helps to identify and structure future directions for research on evolutionary radiations. In this way, the Evolutionary Arena framework promotes a more general understanding of variation in evolutionary rates by making quantitative results comparable between case studies, thereby allowing new syntheses of evolutionary and ecological processes to emerge., Competing Interests: None declared., (© 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)

The Cape flora is compositionally biased, being dominated by a few fynbos clades (such as Iridaceae, Ericaceae, Proteaceae and Restionaceae) that make up major part of the distinct heathland vegetation in the Cape Floristic Region. Uncertainty exists concerning what excluded the subtropical to tropical palm-dominated woodland/forest vegetation that was the dominant component in the CFR in the Paleocene and allowed the fynbos clades, which are largely derived from outside Africa, to establish and radiate. Two filters have been proposed. The first postulates that the establishment of the Mediterranean climate driven by the late Miocene initiation of the cold-water Benguela Upwelling System (BUS) eliminated the African lineages and allowed the establishment and radiation of sclerophyllous plant clades ("the Mediterranean climate model", MCM). Alternatively, the "oligotrophic soils model" (OSM) postulates that the oligotrophic soils, gradually exhumed by post-Gondwanan Late Cretaceous - early Cenozoic erosion, acted as a filter excluding the African lineages. In this study, we re-calibrate the fynbos clade Phylica (Rhamnaceae), the genus initially used to test the MCM, using new fossil data to test if the crown age precedes the Late Miocene. Our results indicate that we cannot significantly reject a crown age of Phylica consistent with the MCM. We compare the MCM and OSM model for the Cape fynbos flora by compiling the crown ages of 22 fynbos clades. We show that crown ages are not clustered in time around the initiation of the BUS but, are dispersed throughout the Cenozoic. This suggests that oligotrophic soils, rather than summer drought, acted as a filter. Consequently, we argue that the fynbos clades radiated separately in expanding edaphically controlled heathland patches in the Cape mountains as sandstone exhumation after the Gondwanan break-up progressed., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Background and Aims: Heteroblasty is a non-reversible morphological change associated with life stage change and has been linked to predictable environmental variation. It is present in several clades from mediterranean-type climates, such as African Restionaceae (restios). These have heteroblastic shoots: juvenile shoots are thin, branched and sterile (sterile shoots); adult shoots are thicker and less branched, and bear inflorescences (reproductive shoots). Ten per cent of the restios retain juvenile-like, sterile shoots as adults (neoteny). We hypothesize (1) that the two shoot types differ in ecophysiological attributes, and (2) that these shoot types (and the neoteny) are associated with different environments., Methods: We measured shoot mass per surface area (SMA), maximum photosynthetic capacity per biomass (Amass) and chlorenchyma to ground tissue ratio (CGR) of both shoot types in 14 restio species. We also calculated environmental niche overlap between neotenous and non-neotenous species using an improved multidimensional overlap function based on occurrence data, and linked shoot types with environments using a phylogenetic generalized linear model., Key Results: Sterile shoots showed higher Amass, lower SMA and higher CGR than reproductive shoots. Neotenous and non-neotenous species overlapped ecologically less than expected by chance: neotenous species favoured more mesic, non-seasonal conditions., Conclusions: We associate sterile shoot morphology with acquisitive ecophysiological strategies and reproductive shoots with conservative strategies. The heteroblastic switch optimizes carbon efficiency in the juvenile phase (by sterile shoots) in the mesic post-fire conditions. The adult shoots present a compromise between a more conservative strategy favourable under harsher conditions and reproductive success. Heteroblasty in seasonally arid, oligotrophic ecosystems with predictable, fire-driven shifts in water and nutrient availability might play a role in the success of restios and other species-rich lineages in mediterranean-type ecosystems. It may represent a previously unrecognized adaptation in mediterranean clades sharing similar conditions, contributing to their ecological and taxonomic dominance., (© The Author(s) 2018. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Conservation biology aims at identifying areas of rich biodiversity. Currently recognized global biodiversity hotspots are spatially too coarse for conservation management and identification of hotspots at a finer scale is needed. This might be achieved by identification of areas of endemism. Here, we identify areas of endemism in Iran, a major component of the Irano-Anatolian biodiversity hotspot, and address their ecological correlates. Using the extremely diverse sunflower family (Asteraceae) as our model system, five consensus areas of endemism were identified using the approach of endemicity analysis. Both endemic richness and degree of endemicity were positively related to topographic complexity and elevational range. The proportion of endemic taxa at a certain elevation (percent endemism) was not congruent with the proportion of total surface area at this elevation, but was higher in mountain ranges. While the distribution of endemic richness (i.e., number of endemic taxa) along an elevational gradient was hump-shaped peaking at mid-elevations, the percentage of endemism gradually increased with elevation. Patterns of endemic richness as well as areas of endemism identify mountain ranges as main centres of endemism, which is likely due to high environmental heterogeneity and strong geographic isolation among and within mountain ranges. The herein identified areas can form the basis for defining areas with conservation priority in this global biodiversity hotspot.

Poaceae (the grasses) is arguably the most successful plant family, in terms of its global occurrence in (almost) all ecosystems with angiosperms, its ecological dominance in many ecosystems, and high species richness. We suggest that the success of grasses is best understood in context of their capacity to colonize, persist, and transform environments (the "Viking syndrome"). This results from combining effective long-distance dispersal, efficacious establishment biology, ecological flexibility, resilience to disturbance and the capacity to modify environments by changing the nature of fire and mammalian herbivory. We identify a diverse set of functional traits linked to dispersal, establishment and competitive abilities. Enhanced long-distance dispersal is determined by anemochory, epizoochory and endozoochory and is facilitated via the spikelet (and especially the awned lemma) which functions as the dispersal unit. Establishment success could be a consequence of the precocious embryo and large starch reserves, which may underpin the extremely short generation times in grasses. Post-establishment genetic bottlenecks may be mitigated by wind pollination and the widespread occurrence of polyploidy, in combination with gametic self-incompatibility. The ecological competitiveness of grasses is corroborated by their dominance across the range of environmental extremes tolerated by angiosperms, facilitated by both C 3 and C 4 photosynthesis, well-developed frost tolerance in several clades, and a sympodial growth form that enabled the evolution of both annual and long-lived life forms. Finally, absence of investment in wood (except in bamboos), and the presence of persistent buds at or below ground level, provides tolerance of repeated defoliation (whether by fire, frost, drought or herbivores). Biotic modification of environments via feedbacks with herbivory or fire reinforce grass dominance leading to open ecosystems. Grasses can be both palatable and productive, fostering high biomass and diversity of mammalian herbivores. Many grasses have a suite of architectural and functional traits that facilitate frequent fire, including a tufted growth form, and tannin-like substances in leaves which slow decomposition. We mapped these traits over the phylogeny of the Poales, spanning the grasses and their relatives, and demonstrated the accumulation of traits since monocots originated in the mid-Cretaceous. Although the sympodial growth form is a monocot trait, tillering resulting in the tufted growth form most likely evolved within the grasses. Similarly, although an ovary apparently constructed of a single carpel evolved in the most recent grass ancestor, spikelets and the awned lemma dispersal units evolved within the grasses. Frost tolerance and C 4 photosynthesis evolved relatively late (late Palaeogene), and the last significant trait to evolve was probably the production of tannins, associated with pyrophytic savannas. This fits palaeobotanical data, suggesting several phases in the grass success story: from a late Cretaceous origin, to occasional tropical grassland patches in the later Palaeogene, to extensive C 3 grassy woodlands in the early-middle Miocene, to the dramatic expansion of the tropical C 4 grass savannas and grasslands in the Pliocene, and the C 3 steppe grasslands during the Pleistocene glacial periods. Modern grasslands depend heavily on strongly seasonal climates, making them sensitive to climate change., (© 2017 Cambridge Philosophical Society.)

The modern vegetation of East Africa is a complex mosaic of rainforest patches; small islands of tropic-alpine vegetation; extensive savannas, ranging from almost pure grassland to wooded savannas; thickets; and montane grassland and forest. Here I trace the evolution of these vegetation types through the Cenozoic. Paleogene East Africa was most likely geomorphologically subdued and, as the few Eocene fossil sites suggest, a woodland in a seasonal climate. Woodland rather than rainforest may well have been the regional vegetation. Mountain building started with the Oligocene trap lava flows in Ethiopia, on which rainforest developed, with little evidence of grass and none of montane forests. The uplift of the East African Plateau took place during the middle Miocene. Fossil sites indicate the presence of rainforest, montane forest and thicket, and wooded grassland, often in close juxtaposition, from 17 to 10 Ma. By 10 Ma, marine deposits indicate extensive grassland in the region and isotope analysis indicates that this was a C 3 grassland. In the later Miocene rifting, first of the western Albertine Rift and then of the eastern Gregory Rift, added to the complexity of the environment. The building of the high strato-volcanos during the later Mio-Pliocene added environments suitable for tropic-alpine vegetation. During this time, the C 3 grassland was replaced by C 4 savannas, although overall the extent of grassland was reduced from the mid-Miocene high to the current low level. Lake-level fluctuations during the Quaternary indicate substantial variation in rainfall, presumably as a result of movements in the intertropical convergence zone and the Congo air boundary, but the impact of these fluctuations on the vegetation is still speculative. I argue that, overall, there was an increase in the complexity of East African vegetation complexity during the Neogene, largely as a result of orogeny. The impact of Quaternary climatic fluctuation is still poorly understood., (© 2017 Wiley Periodicals, Inc.)

The enormous species richness in the Cape Floristic Region (CFR) of Southern Africa is the result of numerous radiations, but the temporal progression and possible mechanisms of these radiations are still poorly understood. Here, we explore the macroevolutionary dynamics of the Restionaceae, which include 340 species that are found in all vegetation types in the Cape flora and are ecologically dominant in fynbos. Using an almost complete (i.e., 98%) species-level time calibrated phylogeny and models of diversification dynamics, we show that species diversification is constant through the Cenozoic, with no evidence of an acceleration with the onset of the modern winter-wet climate, or a recent density-dependent slowdown. Contrary to expectation, species inhabiting the oldest (montane) and most extensive (drylands) habitats did not undergo higher diversification rates than species in the younger (lowlands) and more restricted (wetland) habitats. We show that the rate of habitat transitions is more closely related to the speciation rate than to time, and that more than a quarter of all speciation events are associated with habitat transitions. This suggests that the unbounded Restionaceae diversification resulted from numerous, parallel, habitat shifts, rather than persistence in a habitat stimulating speciation. We speculate that this could be one of the mechanisms resulting in the hyperdiverse Cape flora., (© 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.)

High-resolution information on climatic conditions is essential to many applications in environmental and ecological sciences. Here we present the CHELSA (Climatologies at high resolution for the earth's land surface areas) data of downscaled model output temperature and precipitation estimates of the ERA-Interim climatic reanalysis to a high resolution of 30 arc sec. The temperature algorithm is based on statistical downscaling of atmospheric temperatures. The precipitation algorithm incorporates orographic predictors including wind fields, valley exposition, and boundary layer height, with a subsequent bias correction. The resulting data consist of a monthly temperature and precipitation climatology for the years 1979-2013. We compare the data derived from the CHELSA algorithm with other standard gridded products and station data from the Global Historical Climate Network. We compare the performance of the new climatologies in species distribution modelling and show that we can increase the accuracy of species range predictions. We further show that CHELSA climatological data has a similar accuracy as other products for temperature, but that its predictions of precipitation patterns are better.

Cortaderia (Poaceae; Danthonioideae) is a medium-sized genus of C3 tussock grasses, widespread in the temperate to tropic-alpine regions of South America. It is particularly important in the subalpine and alpine zones of the Andes. We revised the classification of the genus, and recognize 17 species grouped into five informal groups. We describe one new species, Cortaderia echinata H.P.Linder, from Peru. We provide a key to the groups and the species, complete nomenclature for each species including new lectotypes, and notes on the ecology, distribution and diagnostic morphological and anatomical characters.

Premise of the Study: Whole-genome duplication (WGD) in angiosperms has been hypothesized to be advantageous in unstable environments and/or to increase diversification rates, leading to radiations. Under the first hypothesis, floras in stable environments are predicted to have lower proportions of polyploids than highly, recently disturbed floras, whereas species-rich floras would be expected to have higher than expected proportions of polyploids under the second. The South African Cape flora is used to discriminate between these two hypotheses because it features a hyperdiverse flora predominantly generated by a limited number of radiations (Cape clades), against a backdrop of climatic and geological stability., Methods: We compiled all known chromosome counts for species in 21 clades present in the Cape (1653 species, including 24 Cape clades), inferred ploidy levels for these species by inspection or derived from the primary literature, and compared Cape to non-Cape ploidy levels in these clades (17,520 species) using G tests., Key Results: The Cape flora has anomalously low proportions of polyploids compared with global levels. This pattern is consistently observed across nearly half the clades and across global latitudinal gradients, although individual lineages seem to be following different paths to low levels of WGD and to differing degrees., Conclusions: This pattern shows that the diversity of the Cape flora is the outcome of primarily diploid radiations and supports the hypothesis that WGD may be rare in stable environments., (© 2016 Botanical Society of America.)

Grasses, by their high productivity even under very low pCO2, their ability to survive repeated burning and to tolerate long dry seasons, have transformed the terrestrial biomes in the Neogene and Quaternary. The expansion of grasslands at the cost of biodiverse forest biomes in Madagascar is often postulated as a consequence of the Holocene settlement of the island by humans. However, we show that the Malagasy grass flora has many indications of being ancient with a long local evolutionary history, much predating the Holocene arrival of humans. First, the level of endemism in the Madagascar grass flora is well above the global average for large islands. Second, a survey of many of the more diverse areas indicates that there is a very high spatial and ecological turnover in the grass flora, indicating a high degree of niche specialization. We also find some evidence that there are both recently disturbed and natural stable grasslands: phylogenetic community assembly indicates that recently severely disturbed grasslands are phylogenetically clustered, whereas more undisturbed grasslands tend to be phylogenetically more evenly distributed. From this evidence, it is likely that grass communities existed in Madagascar long before human arrival and so were determined by climate, natural grazing and other natural factors. Humans introduced zebu cattle farming and increased fire frequency, and may have triggered an expansion of the grasslands. Grasses probably played the same role in the modification of the Malagasy environments as elsewhere in the tropics., (© 2016 The Authors.)

In the most comprehensive study to date we explored the phylogeny and evolution of the genus Asparagus, with emphasis on the southern African species. We included 211 accessions, representing 77 (92%) of the southern African, 6 (17%) of the tropical African, 10 (56%) of the strictly European and 6 (9%) of the Eurasian species. We analyzed DNA sequences from three plastid regions (trnH-psbA, trnD-T, ndhF) and from the nuclear region phytochrome C (PHYC) with parsimony and maximum likelihood methods, and recovered a monophyletic Asparagus. The phylogeny conflicts with all previous infra-generic classifications. It has many strongly supported clades, corroborated by morphological characters, which may provide a basis for a revised taxonomy. Additionally, the phylogeny indicates that many of the current species delimitations are problematic. Using biogeographic analyses that account for phylogenetic uncertainty (S-DIVA) and take into account relative branch lengths (Lagrange) we confirm the origin of Asparagus in southern Africa, and find no evidence that the dispersal of Asparagus follow the Rand flora pattern. We find that all truly dioecious species of Asparagus share a common origin, but that sexual dimorphism has arisen independently several times., (Copyright © 2015 Elsevier Inc. All rights reserved.)

We used a very large dataset (>40% of all species) from the endemic-rich Cape Floristic Region (CFR) to explore the impact of different weighting techniques, coefficients to calculate similarity among the cells, and clustering approaches on biogeographical regionalisation. The results were used to revise the biogeographical subdivision of the CFR. We show that weighted data (down-weighting widespread species), similarity calculated using Kulczinsky's second measure, and clustering using UPGMA resulted in the optimal classification. This maximized the number of endemic species, the number of centres recognized, and operational geographic units assigned to centres of endemism (CoEs). We developed a dendrogram branch order cut-off (BOC) method to locate the optimal cut-off points on the dendrogram to define candidate clusters. Kulczinsky's second measure dendrograms were combined using consensus, identifying areas of conflict which could be due to biotic element overlap or transitional areas. Post-clustering GIS manipulation substantially enhanced the endemic composition and geographic size of candidate CoEs. Although there was broad spatial congruence with previous phytogeographic studies, our techniques allowed for the recovery of additional phytogeographic detail not previously described for the CFR.

Mountains are often more species-rich than lowlands. This could be the result of migration from lowlands to mountains, of a greater survival rate in mountains, or of a higher diversification rate in mountains. We investigated this question in the globally distributed family Ericaceae, which includes c. 4426 species ranging from sea level to > 5000 m. We predict that the interaction of low specific leaf area (SLA) and montane habitats is correlated with increased diversification rates. A molecular phylogeny of Ericaceae based on rbcL and matK sequence data was built and dated with 18 fossil calibrations and divergence time estimates. We identified radiations using bamm and correlates of diversification rate changes using binary-state speciation and extinction (BiSSE) and multiple-state speciation and extinction (MuSSE) analyses. Analyses revealed six largely montane radiations. Lineages in mountains diversified faster than nonmountain lineages (higher speciation rate, but no difference in extinction rate), and lineages with low SLA diversified faster than high-SLA lineages. Further, habitat and trait had a positive interactive effect on diversification. Our results suggest that the species richness in mountains is the result of increased speciation rather than reduced extinction or increased immigration. Increased speciation in Ericaceae was facilitated by low SLA., (© 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.)

Recent developments in phylogenetic methods have made it possible to reconstruct evolutionary radiations from extant taxa, but identifying the triggers of radiations is still problematic. Here, we propose a conceptual framework to explore the role of variables that may impact radiations. We classify the variables into extrinsic conditions vs intrinsic traits, whether they provide background conditions, trigger the radiation, or modulate the radiation. We used three clades representing angiosperm phylogenetic and structural diversity (Ericaceae, Fagales and Poales) as test groups. We located radiation events, selected variables potentially associated with diversification, and inferred the temporal sequences of evolution. We found 13 shifts in diversification regimes in the three clades. We classified the associated variables, and determined whether they originated before the relevant radiation (backgrounds), originated simultaneously with the radiations (triggers), or evolved later (modulators). By applying this conceptual framework, we establish that radiations require both extrinsic conditions and intrinsic traits, but that the sequence of these is not important. We also show that diversification drivers can be detected by being more variable within a radiation than conserved traits that only allow occupation of a new habitat. This framework facilitates exploration of the causative factors of evolutionary radiations., (© 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.)

Climate is a main predictor of biodiversity on a global scale, yet how climate availability affects niche evolution remains poorly explored. Here we assess how intercontinental climate differences may affect the evolution of climate niches and suggest three possible processes: niche truncation along major environmental gradients, intercontinental differences in available climate causing differences in selective regimes, and niche shifts associated with long-distance dispersals leading to a pattern of punctuated evolution. Using the globally distributed danthonioid grasses, we show significant niche differentiation among continents and several instances of niche truncation. The comparison of inferred selective regimes with differences in available climatic space among continents demonstrates adaptation resulting from opportunistic evolution toward available climatic space. Our results suggest that niche evolution in this clade is punctuated, consistent with accelerated niche evolution after long-distance dispersal events. Finally, we discuss how intrinsic constraints (genetic, developmental, or functional) and biotic interactions could have interacted with these three processes during range expansion. Integrating these mechanisms could improve predictions for invasive taxa and long-term evolutionary responses of expanding clades to climate change.

Mediterranean-type ecosystems (MTEs) are remarkable in their species richness and endemism, but the processes that have led to this diversity remain enigmatic. Here, we hypothesize that continent-dependent speciation and extinction rates have led to disparity in diversity between the five MTEs of the world: the Cape, California, Mediterranean Basin, Chile, and Western Australia. To test this hypothesis, we built a phylogenetic tree for 280 Rhamnaceae species, estimated divergence times using eight fossil calibrations, and used Bayesian methods and simulations to test for differences in diversification rates. Rhamnaceae lineages in MTEs generally show higher diversification rates than elsewhere, but speciation and extinction dynamics show a pattern of continent-dependence. We detected high speciation and extinction rates in California and significantly lower extinction rates in the Cape and Western Australia. The independent colonization of four of five MTEs may have occurred conterminously in the Oligocene/Early Miocene, but colonization of the Mediterranean Basin happened later, in the Late Miocene. This suggests that the in situ radiations of these clades were initiated before the onset of winter rainfall in these regions. These results indicate independent evolutionary histories of Rhamnaceae in MTEs, possibly related to the intensity of climate oscillations and the geological history of the regions., (© 2015 The Author(s).)

Background and Aims: The ability of plant lineages to reach all continents contributes substantially to their evolutionary success. This is exemplified by the Poaceae, one of the most successful angiosperm families, in which most higher taxa (tribes, subfamilies) have global distributions. Due to the old age of the ocean basins relative to the major angiosperm radiations, this is only possible by means of long-distance dispersal (LDD), yet the attributes of lineages with successful LDD remain obscure. Polyploid species are over-represented in invasive floras and in the previously glaciated Arctic regions, and often have wider ecological tolerances than diploids; thus polyploidy is a candidate attribute of successful LDD., Methods: The link between polyploidy and LDD was explored in the globally distributed grass subfamily Danthonioideae. An almost completely sampled and well-resolved species-level phylogeny of the danthonioids was used, and the available cytological information was assembled. The cytological evolution in the clade was inferred using maximum likelihood (ML) as implemented in ChromEvol. The biogeographical evolution in the clade was reconstructed using ML and Bayesian approaches., Key Results: Numerous increases in ploidy level are demonstrated. A Late Miocene-Pliocene cycle of polyploidy is associated with LDD, and in two cases (the Australian Rytidosperma and the American Danthonia) led to secondary polyploidy. While it is demonstrated that successful LDD is more likely in polyploid than in diploid lineages, a link between polyploidization events and LDD is not demonstrated., Conclusions: The results suggest that polyploids are more successful at LDD than diploids, and that the frequent polyploidy in the grasses might have facilitated the extensive dispersal among continents in the family, thus contributing to their evolutionary success., (© The Author 2014. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Fire has been proposed as a factor explaining the exceptional plant species richness found in Mediterranean regions. A fire response trait that allows plants to cope with frequent fire by either reseeding or resprouting could differentially affect rates of species diversification. However, little is known about the generality of the effects of differing fire response on species evolution. We study this question in the Restionaceae, a family that radiated in Southern Africa and Australia. These radiations occurred independently and represent evolutionary replicates. We apply Bayesian approaches to estimate trait-specific diversification rates and patterns of climatic niche evolution. We also compare the climatic heterogeneity of South Africa and Australia. Reseeders diversify faster than resprouters in South Africa, but not in Australia. We show that climatic preferences evolve more rapidly in reseeder lineages than in resprouters and that the optima of these climatic preferences differ between the two strategies. We find that South Africa is more climatically heterogeneous than Australia, independent of the spatial scale we consider. We propose that rapid shifts between states of the fire response trait promote speciation by separating species ecologically, but this only happens when the landscape is sufficiently heterogeneous., (© 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.)

· Temperature is considered an important determinant of biodiversity distribution patterns. Grasses (Poaceae) occupy among the warmest and coldest environments on earth but the role of cold tolerance evolution in generating this distribution is understudied. We studied cold tolerance of Danthonioideae (c. 280 species), a major constituent of the austral temperate grass flora. · We determined differences in cold tolerance among species from different continents grown in a common winter garden and assessed the relationship between measured cold tolerance and that predicted by species ranges. We then used temperatures in current ranges and a phylogeny of 81% of the species to study the timing and mode of cold tolerance evolution across the subfamily. · Species ranges generally underestimate cold tolerance but are still a meaningful representation of differences in cold tolerance among species. We infer cold tolerance evolution to have commenced at the onset of danthonioid diversification, subsequently increasing in both pace and extent in certain lineages. Interspecific variation in cold tolerance is better accounted for by spatial than phylogenetic distance. · Contrary to expectations, temperature - low temperature in particular - appears not to limit the distribution of this temperate clade. Competition, time or dispersal limitation could explain its relative absence from northern temperate regions., (© 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.)

Background and Aims: Species in plant communities segregate along fine-scale hydrological gradients. Although this phenomenon is not unique to fynbos, this community regenerates after fire and therefore provides an opportunity to study the ecological genesis of hydrological niche segregation., Methods: Following wildfires at two field sites where we had previously mapped the vegetation and monitored the hydrology, seeds were moved experimentally in >2500 intact soil cores up and down soil-moisture gradients to test the hypothesis that hydrological niche segregation is established during the seedling phase of the life cycle. Seedling numbers and growth were then monitored and they were identified using DNA bar-coding, the first use of this technology for an experiment of this kind., Key Results: At the site where niche segregation among Restionaceae had previously been found, the size of seedlings was significantly greater, the wetter the location into which they were moved, regardless of the soil moisture status of their location of origin, or of the species. Seedling weight was also significantly greater in a competition treatment where the roots of other species were excluded. No such effects were detected at the control site where niche segregation among Restionaceae was previously found to be absent., Conclusions: The finding that seedling growth on hydrological gradients in the field is affected by soil moisture status and by root competition shows that hydrological niche segregation could potentially originate in the seedling stage. The methodology, applied at a larger scale and followed-through for a longer period, could be used to determine whether species are differently affected by soil moisture.

The origin of species-rich insect-plant food webs has traditionally been explained by diversifying antagonistic coevolution between plant defences and herbivore counter-defences. However, recent studies combining paleoclimatic reconstructions with time-calibrated phylogenies suggest that variation in global climate determines the distribution, abundance and diversity of plant clades and, hence, indirectly influences the balance between speciation and extinction in associated herbivore groups. Extant insect communities tend to be richest on common plant species that have many close relatives. This could be explained either by climate-driven diffuse cospeciation between plants and insects, or by elevated speciation and reduced extinction in herbivore lineages associated with expanding host taxa (resources). Progress in paleovegetation reconstructions in combination with the rapidly increasing availability of fossil-calibrated phylogenies provide means to discern between these alternative hypotheses. In particular, the 'Diffuse cospeciation' scenario predicts closely matching main diversification periods in plants and in the insects that feed upon them, while the 'Resource abundance-dependent diversification' hypothesis predicts that both positive and negative responses of insect diversity are lagged in relation to host-plant availability. The dramatic Cenozoic changes in global climate provide multiple possibilities for studying the mechanisms by which climatic shifts may drive diversity dynamics in plants and insect herbivores., (© 2012 Blackwell Publishing Ltd/CNRS.)

Plants flowering together may influence each other's pollination and fecundity over a range of physical distances. Their effects on one another can be competitive, neutral, or facilitative. We manipulated the floral neighborhood of the high-alpine cushion plant Eritrichium nanum in the Swiss Alps and measured the effects of co-flowering neighbors on both the number of seeds produced and the degree of inbreeding and outbreeding in the offspring, as deduced from nuclear microsatellite markers. Seed set of E. nanum did not vary significantly with the presence or absence of two Saxifraga species growing as near neighbors, but it was higher in E. nanum cushions growing at low conspecific density than in those growing at high density. In addition, floral neighborhood had no detectable effect on the degree of selfing of E. nanum, but seeds from cushions growing at low conspecific density were more highly outbred than seeds from cushions at high density. Thus, there was no evidence of either competition or facilitation between E. nanum and Saxifraga spp. as mediated by pollinators at the spatial scale of our experimental manipulation. In contrast, the greater fecundity of E. nanum cushions at low density was consistent with reduced intraspecific competition for pollinators and might also represent a beneficial effect of highly outbred seeds as brought about by more long-distance pollinator flights under low-density conditions.

Hygroscopically active awns or "bristles" have long intrigued scientists. Experimental evidence shows that they are important for diaspore burial in the correct orientation, thereby increasing successful seed germination and seedling survival. Despite these ecological advantages, 38 of the 280 species of grasses in Danthonioideae lack awns. We provide the first study of awns in a phylogenetic context and show that although the awnless state has arisen ca. 25 times independently, the ecological disadvantage of not having an awn also applies in an evolutionary context. Only in Tribolium and Schismus have awnless ancestors diversified to form a clade of primarily awnless descendents. Several of the awnless species in these genera are annual and we find a significant correlation between the evolution of awns and the evolution of life history. A suite of other diaspore traits accompany the awned or awnless states. We interpret the awn as being the visible constituent of a compound "burial syndrome," the two ecological extremes of which may explain the correlation between awns and life history and provide an explanation why awnless species in Tribolium and Schismus persist., (© 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.)

Anthropogenic alteration of biotic distributions and disturbance regimes has dramatically changed the evolutionary context for the differentiation of species traits. Some of the most striking examples in recent centuries have been on islands where flightless birds, which evolved in the absence of mammalian carnivores, have been decimated following the widespread introduction of exotic predators. Until now, no equivalent case has been reported for plants. Here, we make use of robust analytical tools and an exceptionally well-sampled molecular phylogeny to show that a majority of New Zealand danthonioid grasses (Poaceae) may have adapted to the relaxed vertebrate herbivore pressure during the late Cenozoic through the development of a distinctive and unusual habit: abscission of old leaves. This feature occurs in only about 3 per cent of the world's roughly 11,000 grass species and has been empirically shown to increase plant productivity but to reduce protection against mammal grazing. This result suggests that release from a selective pressure can lead to species radiations. This seemingly anachronistic adaptation may represent an overlooked factor contributing to the severe decline in the geographical extent and species diversity of New Zealand's indigenous grasslands following the introduction of herbivorous terrestrial mammals in the 19th century.

Background: The best documented survival responses of organisms to past climate change on short (glacial-interglacial) timescales are distributional shifts. Despite ample evidence on such timescales for local adaptations of populations at specific sites, the long-term impacts of such changes on evolutionary significant units in response to past climatic change have been little documented. Here we use phylogenies to reconstruct changes in distribution and flowering ecology of the Cape flora--South Africa's biodiversity hotspot--through a period of past (Neogene and Quaternary) changes in the seasonality of rainfall over a timescale of several million years., Results: Forty-three distributional and phenological shifts consistent with past climatic change occur across the flora, and a comparable number of clades underwent adaptive changes in their flowering phenology (9 clades; half of the clades investigated) as underwent distributional shifts (12 clades; two thirds of the clades investigated). Of extant Cape angiosperm species, 14-41% have been contributed by lineages that show distributional shifts consistent with past climate change, yet a similar proportion (14-55%) arose from lineages that shifted flowering phenology., Conclusions: Adaptive changes in ecology at the scale we uncover in the Cape and consistent with past climatic change have not been documented for other floras. Shifts in climate tolerance appear to have been more important in this flora than is currently appreciated, and lineages that underwent such shifts went on to contribute a high proportion of the flora's extant species diversity. That shifts in phenology, on an evolutionary timescale and on such a scale, have not yet been detected for other floras is likely a result of the method used; shifts in flowering phenology cannot be detected in the fossil record.

Fire may have been a crucial component in the evolution of the Cape flora of South Africa, a region characterized by outstanding levels of species richness and endemism. However, there is, to date, no critical assessment of the age of the modern fire regime in this biome. Here, we exploit the presence of two obligate post-fire flowering clades in the orchid genus Disa, in conjunction with a robust, well-sampled and dated molecular phylogeny, to estimate the age by which fire must have been present. Our results indicate that summer drought (winter rainfall), the fire regime and the fynbos vegetation are several million years older than currently suggested. Summer drought and the fynbos vegetation are estimated to date back to at least the Early Miocene (ca 19.5 Ma). The current fire regime may have been established during a period of global cooling that followed the mid-Miocene Climatic Optimum (ca 15 Ma), which led to the expansion of open habitats and increased aridification. The first appearance of Disa species in the grassland biome, as well as in the subalpine habitat, is in striking agreement with reliable geological and palaeontological evidence of the age of these ecosystems, thus corroborating the efficacy of our methods. These results change our understanding of the historical mechanisms underlying botanical evolution in southern Africa, and confirm the potential of using molecular phylogenies to date events for which other information is lacking or inconclusive.

Ranunculus is distributed in all continents and especially species-rich in the meridional and temperate zones. To reconstruct the biogeographical history of the genus, a molecular phylogenetic analysis of the genus based on nuclear and chloroplast DNA sequences has been carried out. Results of biogeographical analyses (DIVA, Lagrange, Mesquite) combined with molecular dating suggest multiple colonizations of all continents and disjunctions between the northern and the southern hemisphere. Dispersals between continents must have occurred via migration over land bridges, or via transoceanic long-distance dispersal, which is also inferred from island endemism. In southern Eurasia, isolation of the western Mediterranean and the Caucasus region during the Messinian was followed by range expansions and speciation in both areas. In the Pliocene and Pleistocene, radiations happened independently in the summer-dry western Mediterranean-Macaronesian and in the eastern Mediterranean-Irano-Turanian regions, with three independent shifts to alpine humid climates in the Alps and in the Himalayas. The cosmopolitan distribution of Ranunculus is caused by transoceanic and intracontinental dispersal, followed by regional adaptive radiations., (Copyright © 2010 Elsevier Inc. All rights reserved.)

• Ecologists still puzzle over how plant species manage to coexist with one another while competing for the same essential resources. The classic answer for animal communities is that species occupy different niches, but how plants do this is more difficult to determine. We previously found niche segregation along fine-scale hydrological gradients in European wet meadows and proposed that the mechanism might be a general one, especially in communities that experience seasonal saturation. • We quantified the hydrological niches of 96 species from eight fynbos communities in the biodiversity hotspot of the Cape Floristic Region, South Africa and 99 species from 18 lowland wet meadow communities in the UK. Niche overlap was computed for all combinations of species. • Despite the extreme functional and phylogenetic differences between the fynbos and wet meadow communities, an identical trade-off (i.e. specialization of species towards tolerance of aeration and/or drying stress) was found to cause segregation along fine-scale hydrological gradients. • This study not only confirms the predicted generality of hydrological niche segregation, but also emphasizes its importance for structuring plant communities. Eco-hydrological niche segregation will have implications for conservation in habitats that face changing hydrology caused by water abstraction and climate change., (© The Authors (2010). Journal compilation © New Phytologist Trust (2010).)

Premise of the Study: The succulent biome is highly fragmented throughout the Old and New World. The resulting disjunctions on global and regional scales have been explained by various hypotheses. To evaluate these, we used Thamnosma, which is restricted to the succulent biome and has trans-Atlantic and trans-African disjunctions. Its three main distribution centers are in southern North America, southern and eastern Africa including Socotra., Methods: We conducted parsimony, maximum likelihood, and Bayesian phylogenetic analyses based on chloroplast and nuclear sequence data. We applied molecular clock calculations using the programs BEAST and MULTIDIVTIME and biogeographic reconstructions using S-DIVA and Lagrange., Key Results: Our data indicate a weakly supported paraphyly of the New World species with respect to a palaeotropical lineage, which is further subdivided into a southern African and a Horn of Africa group. The disjunctions in Thamnosma are mostly dated to the Miocene., Conclusions: We conclude that the Old-New World disjunction of Thamnosma is likely the result of long-distance dispersal. The Miocene closure of the arid corridor between southern and eastern Africa may have caused the split within the Old World lineage, thus making a vicariance explanation feasible. The colonization of Socotra is also due to long-distance dispersal. All recent Thamnosma species are part of the succulent biome, and the North American species may have been members of the arid Neogene Madro-Tertiary Geoflora. Phylogenetic niche conservatism, rare long-distance dispersal, and local differentiation account for the diversity among species of Thamnosma.

The speciation process that underlies recent, rapid radiations of plants is controversial, and suggested mechanisms range from pollinator or ecological niche differentiation to allopatry and nonadaptive divergence. Phylogenetic approaches to locating the most appropriate speciation models have been constrained by the low levels of molecular divergence between recently diverged species, which are typical of recent, rapid radiations. In this issue of Molecular Ecology, Rymer et al. (2010) used coalescence analyses of sequence data and genome scans of Amplified Fragment Length Polymorphism (AFLP) loci to demonstrate that in a species complex in the irid genus Gladiolus, a member of the hyper diverse Cape flora of southern Africa, speciation is a gradual process. Older divergences are genetically more differentiated, and show a greater difference in flowering time and floral morphology, than taxa that diverged more recently. There is no evidence of any abrupt events. Gene flow is limited by shifts in flowering time and floral morphology; thus, by pre-zygotic rather than by post-zygotic mechanisms, these evolved together with the occupation of somewhat different habitats. This research gives the first critical insight into how the remarkable diversity in a diversity hotspot could have arisen. More importantly, it demonstrates that the speciation process in recent, rapid radiations is tractable and can be investigated with suitable genetic tools., (© 2010 Blackwell Publishing Ltd.)

Variation in floral shape is of major interest to evolutionary and pollination biologists, plant systematists and developmental geneticists. Quantifying this variation has been difficult due to the three-dimensional (3D) complexity of angiosperm flowers. By combining 3D geometric representations of flowers obtained by micro-computed tomography scanning with geometric morphometric methods, well established in zoology and anthropology, floral shape variation can be analyzed quantitatively, allowing for powerful interpretation and visualization of the resulting patterns of variation., (2010 Elsevier Ltd. All rights reserved.)

Rytidosperma s.l., wallaby grasses and allies, is in dire need of a single, unanimously accepted generic taxonomy. Motivated by the desire to establish a generic classification that complies with phylogeny, we investigated how much phylogenetic signal is contained within a plastid (cpDNA) tree, given that the nrDNA tree (ITS) was uninformative and that a phylogenetic hypothesis based on a single genome may not be reliable. We find that the plastid tree is significantly different from a morphological cladogram and show that this is the result of homoplasy in the morphological dataset. Treated individually, several morphological characters fit the plastid tree very well. Similarly, we find a good fit of the plastid tree with ecological and distribution characters and with biogeographical patterns in the Southern Hemisphere. We conclude that a significant level of the species phylogeny is resolved by the plastid tree and are confident it can form a sound basis for a reconsideration of generic limits. None of the currently recognised seven genera in the Rytidosperma clade is monophyletic. Therefore, we propose combining the segregate genera in Australasia within a broadly construed Rytidosperma, including all the species from Australia, New Guinea, New Zealand and South America., (2009 Elsevier Inc. All rights reserved.)

The numerous disjunct plant distributions between Macaronesia and eastern Africa-Arabia suggest that these could be the relicts of a once continuous vegetation belt along the southern Tethys, which has been fragmented by Upper Miocene-Pliocene aridification. We tested this vicariance hypothesis with a phylogenetic analysis of Campylanthus (Plantaginaceae), based on nuclear and plastid DNA sequence data. Our results indicate a basal split within Campylanthus giving rise to Macaronesian and Eritreo-Arabian lineages in the Pliocene/Upper Miocene. This is consistent with the vicariance hypothesis, thus obviating the need to postulate trans-Saharan long-distance dispersal. The biogeography of Campylanthus may parallel patterns in other plant groups and the implications for our understanding of the biogeography of northern and eastern Africa, and Arabia are discussed., (Copyright (c) 2009 Elsevier Inc. All rights reserved.)

We explore the potential impact of conflicting gene trees on inferences of evolutionary history above the species level. When conflict between gene trees is discovered, it is common practice either to analyze the data separately or to combine the data having excluded the conflicting taxa or data partitions for those taxa (which are then recoded as missing). We demonstrate an alternative approach, which involves duplicating conflicting taxa in the matrix, such that each duplicate is represented by one partition only. This allows the combination of all available data in standard phylogenetic analyses, despite reticulations. We show how interpretation of contradictory gene trees can lead to conflicting inferences of both morphological evolution and biogeographic history, using the example of the pampas grasses, Cortaderia. The characteristic morphological syndrome of Cortaderia can be inferred as having arisen multiple times (chloroplast DNA [cpDNA]) or just once (nuclear ribosomal DNA [nrDNA]). The distributions of species of Cortaderia and related genera in Australia/New Guinea, New Zealand, and South America can be explained by few (nrDNA) or several (cpDNA) dispersals between the southern continents. These contradictions can be explained by past hybridization events, which have linked gains of complex morphologies with unrelated chloroplast lineages and have erased evidence of dispersals from the nuclear genome. Given the discrepancies between inferences based on the gene trees individually, we urge the use of approaches such as ours that take multiple gene trees into account.

This paper explores the relative impacts of reduction and polymerization on the evolution of reproductive structures in the small but morphologically diverse family Centrolepidaceae. Centrolepidaceae are closely related to Restionaceae and belong to the large order Poales, which also includes the grasses. In the largest genus of Centrolepidaceae, Centrolepis, the reproductive structures are viewed either as highly unusual aggregations of reduced flowers (the pseudanthial interpretation) or as unique flowers evolved through extreme reduction in the androecium, usually accompanied by a drastic increase in carpel number and elaboration of the entire gynoecium. Comparative data are here presented on gynoecia of all three genera of Centrolepidaceae; these data strongly support the latter (euanthial) interpretation. The combined phenomenon of carpel multiplication and decrease in stamen number is unexpected in a predominantly wind-pollinated lineage. Applying a pseudanthial interpretation would create a considerable morphological gap with reproductive structures of other Poales, whereas accepting a euanthial concept allows an almost continuous morphological series with related taxa.

The composition of isolated floras has long been thought to be the result of relatively rare long-distance dispersal events. However, it has recently become apparent that the recruitment of lineages may be relatively easy and that many dispersal events from distant but suitable habitats have occurred, even at an infraspecific level. The evolution of the flora on the high mountains of Africa has been attributed to the recruitment of taxa not only from the African lowland flora or the Cape Floristic Region, but also to a large extent from other areas with temperate climates. We used the species rich, pan-temperate genera Carex, Ranunculus and Alchemilla to explore patterns in the number of recruitment events and region of origin. Molecular phylogenetic analyses, parametric bootstrapping and ancestral area optimizations under parsimony indicate that there has been a high number of colonization events of Carex and Ranunculus into Africa, but only two introductions of Alchemilla. Most of the colonization events have been derived from Holarctic ancestors. Backward dispersal out of Africa seems to be extremely rare. Thus, repeated colonization from the Northern Hemisphere in combination with in situ radiation has played an important role in the composition of the flora of African high mountains.

How and why organisms are distributed as they are has long intrigued evolutionary biologists. The tendency for species to retain their ancestral ecology has been demonstrated in distributions on local and regional scales, but the extent of ecological conservatism over tens of millions of years and across continents has not been assessed. Here we show that biome stasis at speciation has outweighed biome shifts by a ratio of more than 25:1, by inferring ancestral biomes for an ecologically diverse sample of more than 11,000 plant species from around the Southern Hemisphere. Stasis was also prevalent in transocean colonizations. Availability of a suitable biome could have substantially influenced which lineages establish on more than one landmass, in addition to the influence of the rarity of the dispersal events themselves. Conversely, the taxonomic composition of biomes has probably been strongly influenced by the rarity of species' transitions between biomes. This study has implications for the future because if clades have inherently limited capacity to shift biomes, then their evolutionary potential could be strongly compromised by biome contraction as climate changes.

Like island-endemic taxa, whose origins are expected to postdate the appearance of the islands on which they occur, biome-endemic taxa should be younger than the biomes to which they are endemic. Accordingly, the ages of biome-endemic lineages may offer insights into biome history. In this study, we used the ages of multiple lineages to explore the origin and diversification of two southern African biomes whose remarkable floristic richness and endemism has identified them as global biodiversity hotspots (succulent karoo and fynbos). We used parsimony optimization to identify succulent karoo- and fynbos-endemic lineages across 17 groups of plants, for which dated phylogenies had been inferred using a relaxed Bayesian (BEAST) approach. All succulent karoo-endemic lineages were less than 17.5 My old, the majority being younger than 10 My. This is largely consistent with suggestions that this biome is the product of recent radiation, probably triggered by climatic deterioration since the late Miocene. In contrast, fynbos-endemic lineages showed a broader age distribution, with some lineages originating in the Oligocene, but most being more recent. Also, in groups having both succulent karoo- and fynbos-endemic lineages, there was a tendency for the latter to be older. These patterns reflect the greater antiquity of fynbos, but also indicate considerable recent speciation, probably through a combination of climatically-induced refugium fragmentation and adaptive radiation.

The large daisy tribe Gnaphalieae occurs in extra-tropical habitats worldwide, but is most diverse in southern Africa and in Australia. We explore the age and evolutionary history of the tribe by means of a phylogenetic hypothesis based on Bayesian analysis of plastid and nuclear DNA sequences, maximum likelihood reconstruction of ancestral areas, and relaxed Bayesian dating. Early diversification occurred in southern Africa in the Eocene-Oligocene, resulting in a grade of mostly Cape-centred lineages which subsequently began speciating in the Miocene, consistent with diversification times for many Cape groups. Gnaphalieae from other geographic regions are embedded within a southern African paraphylum, indicating multiple dispersals out of southern Africa since the Oligocene to Miocene which established the tribe in the rest of the world. Colonisation of Australia via direct long-distance trans-oceanic dispersal in the Miocene resulted in the radiation which produced the Australasian gnaphalioid flora. The similarly diverse regional gnaphalioid floras of Australasia and southern Africa thus exhibit very different temporal species accumulation histories. An examination of the timing and direction of trans-Indian Ocean dispersal events in other angiosperms suggests a role for the West Wind Drift in long-distance dispersal eastwards from southern Africa.

The spatial and temporal patterns of plant species radiations are largely unknown. I used a nonlinear regression to estimate speciation and extinction rates from all relevant dated clades. Both are surprisingly high. A high species richness can be the result of either little extinction, thus preserving the diversity that dates from older radiations (a 'mature radiation'), or a 'recent and rapid radiation'. The analysis of radiations from different regions (Andes, New Zealand, Australia, southwest Africa, tropics and Eurasia) revealed that the diversity of Australia may be largely the result of mature radiations. This is in sharp contrast to New Zealand, where the flora appears to be largely the result of recent and rapid radiations. Mature radiations are characteristic of regions that have been climatically and geologically stable throughout the Neogene, whereas recent and rapid radiations are more typical of younger (Pliocene) environments. The hyperdiverse Cape and Neotropical floras are the result of the combinations of mature as well as recent and rapid radiations. Both the areas contain stable environments (the Amazon basin and the Cape Fold Mountains) as well as dynamic landscapes (the Andes and the South African west coast). The evolution of diversity can only be understood in the context of the local environment.

Phylogeny reconstruction is challenging when branch lengths vary and when different genetic loci show conflicting signals. The number of DNA sequence characters required to obtain robust support for all the nodes in a phylogeny becomes greater with denser taxon sampling. We test the usefulness of an approach mixing densely sampled, variable non-coding sequences (trnL-F; rpl16; atpB-rbcL; ITS) with sparsely sampled, more conservative protein coding and ribosomal sequences (matK; ndhF; rbcL; 26S), for the grass subfamily Danthonioideae. Previous phylogenetic studies of Danthonioideae revealed extensive generic paraphyly, but were often impeded by insufficient character and taxon sampling and apparent inter-gene conflict. Our variably-sampled supermatrix approach allowed us to represent 79% of the species with up to c. 9900 base pairs for taxa representing the major clades. A 'taxon duplication' approach for taxa with conflicting phylogenetic signals allowed us to combine the data whilst representing the differences between chloroplast and nuclear encoded gene trees. This approach efficiently improves resolution and support whilst maximising representation of taxa and their sometimes composite evolutionary histories, resulting in a phylogeny of the Danthonioideae that will be useful both for a wide range of evolutionary studies and to inform forthcoming realignment of generic delimitations in the subfamily.

We construct a species-level phylogeny for the Pentaschistis clade based on chloroplast DNA, from the following regions: trnL-F, trnT-L, atpB-rbcL, rpL16, and trnD-psbA. The clade comprises 82 species in three genera, Pentaschistis, Pentameris, and Prionanthium. We demonstrate that Prionanthium is nested in Pentaschistis and that this clade is sister to a clade of Pentameris plus Pentaschistis tysonii. Forty-three of the species in the Pentaschistis clade have multicellular glands and we use ancestral character state reconstruction to show that they have been gained twice or possibly once, and lost several times. We suggest that the maintenance, absence, loss, and gain of glands are correlated with leaf anatomy type, and additionally that there is a difference in the degree of diversification of lineages that have these different character combinations. We propose that both glands and sclerophyllous leaves act as defense systems against herbivory, and build a cost/benefit model in which multicellular glands or sclerophyllous leaves are lost when the alternative defense system evolves. We also investigate the association between leaf anatomy type and soil nutrient type on which species grow. There is little phylogenetic constraint in soil nutrient type on members of the Pentaschistis clade, with numerous transitions between oligotrophic and eutrophic soils. However, only orthophyllous-leaved species diversify on eutrophic soils. We suggest that the presence of these glands enables the persistence of orthophyllous lineages and therefore diversification of the Pentaschistis clade on eutrophic as well as oligotrophic soils.

Phylogenetic relationships were inferred for the African subtribe Disinae (Orchidoideae, Orchidaceae), which include the large genus Disa and the small genus Schizodium. One nuclear (ITS) gene region and two plastid (trnLF and matK) gene regions were sequenced for 136 ingroup, representing 70% of all known Disinae species, as well as for 7 outgroup taxa. The combined data matrix contained 4094 characters and was analysed using parsimony and Bayesian inference. Our results show that the generic status of Schizodium can no longer be supported, as it is deeply embedded within the genus Disa. Furthermore, the currently recognised subgenera do not reflect the phylogenetic relationships and should be rejected. Several of the currently recognised sections are monophyletic, others contain misplaced elements, while some are polyphyletic. Morphological divergence, rather than convergence, has hampered previous attempts at a phylogenetic classification of the Disinae. On the basis of our molecular phylogenetic hypothesis, we propose a monotypic subtribe Disinae and a subdivision of the genus Disa into 18 sections.