The enigmatic tropical alpine flora on the African sky islands is young, disturbed, and unsaturated.

Tropical alpine floras are renowned for high endemism, spectacular giant rosette plants testifying to convergent adaptation to harsh climates with nightly frosts, and recruitment dominated by long-distance dispersal from remote areas. In contrast to the larger, more recent (late Miocene onward) and contiguous expanses of tropical alpine habitat in South America, the tropical alpine flora in Africa is extremely fragmented across small patches on distant mountains of variable age (Oligocene onward). How this has affected the colonization and diversification history of the highly endemic but species-poor afroalpine flora is not well known. Here we infer phylogenetic relationships of ∼20% of its species using novel genome skimming data and published matrices and infer a timeframe for species origins in the afroalpine region using fossil-calibrated molecular clocks. Although some of the mountains are old, and although stem node ages may substantially predate colonization, most lineages appear to have colonized the afroalpine during the last 5 or 10 My. The accumulation of species increased exponentially toward the present. Taken together with recent reports of extremely low intrapopulation genetic diversity and recent intermountain population divergence, this points to a young, unsaturated, and dynamic island scenario. Habitat disturbance caused by the Pleistocene climate oscillations likely induced cycles of colonization, speciation, extinction, and recolonization. This study contributes to our understanding of differences in the histories of recruitment on different tropical sky islands and on oceanic islands, providing insight into the general processes shaping their remarkable floras.

Leaps and bounds: geographical and ecological distance constrained the colonisation of the Afrotemperate by Erica.

BACKGROUND: The coincidence of long distance dispersal (LDD) and biome shift is assumed to be the result of a multifaceted interplay between geographical distance and ecological suitability of source and sink areas. Here, we test the influence of these factors on the dispersal history of the flowering plant genus Erica (Ericaceae) across the Afrotemperate. We quantify similarity of Erica climate niches per biogeographic area using direct observations of species, and test various colonisation scenarios while estimating ancestral areas for the Erica clade using parametric biogeographic model testing. RESULTS: We infer that the overall dispersal history of Erica across the Afrotemperate is the result of infrequent colonisation limited by geographic proximity and niche similarity. However, the Drakensberg Mountains represent a colonisation sink, rather than acting as a "stepping stone" between more distant and ecologically dissimilar Cape and Tropical African regions. Strikingly, the most dramatic examples of species radiations in Erica were the result of single unique dispersals over longer distances between ecologically dissimilar areas, contradicting the rule of phylogenetic biome conservatism. CONCLUSIONS: These results highlight the roles of geographical and ecological distance in limiting LDD, but also the importance of rare biome shifts, in which a unique dispersal event fuels evolutionary radiation.

Evolution of leaf anatomy in arid environments - A case study in southern African Tetraena and Roepera (Zygophyllaceae).

The dry biomes of southern Africa (Desert, Nama Karoo and Succulent Karoo) are home to a rich and diverse xerophytic flora. This flora includes two morphologically diverse clades of Zygophyllaceae, Tetraena and Roepera (Zygophylloideae), which inhabit some of the most arid habitats in the region. Using a plastid phylogeny of Zygophylloideae we assess whether the evolution of putatively adaptive traits (leaf shape, vasculature, mode of water storage and photosynthetic type: C3 versus C4) coincides with the successful colonisation of environments with different drought regimes within southern Africa. Our results show general niche conservatism within arid habitats in Tetraena, but niche shifts from arid to more mesic biomes with longer and/or cooler growing season (Fynbos and Thicket) in Roepera. However, these distinct broad-scale biogeographical patterns are not reflected in leaf anatomy, which seems to vary at more local scales. We observed considerable variability and multiple convergences to similar leaf anatomies in both genera, including shifts between "all cell succulence" leaf types and leaf types with distinct chlorenchyma and hydrenchyma. Our survey of C4 photosynthesis in the Zygophylloideae showed that the C4 pathway is restricted to Tetraena simplex, which also having an annual life history and a widespread distribution, is rather atypical for this group.

The evolution of dwarf shrubs in alpine environments: a case study of Alchemilla in Africa.

BACKGROUND AND AIMS: Alpine and arctic environments worldwide, including high mountains, are dominated by short-stature woody plants (dwarf shrubs). This conspicuous life form asserts considerable influence on local environmental conditions above the treeline, creating its own microhabitat. This study reconstructs the evolution of dwarf shrubs in Alchemilla in the African tropical alpine environment, where they represent one of the largest clades and are among the most common and abundant plants. METHODS: Different phylogenetic inference methods were used with plastid and nuclear DNA sequence markers, molecular dating (BEAST and RelTime), analyses of diversification rate shifts (MEDUSA and BAMM) and ancestral character and area reconstructions (Mesquite). KEY RESULTS: It is inferred that African Alchemilla species originated following long-distance dispersal to tropical East Africa, but that the evolution of dwarf shrubs occurred in Ethiopia and in tropical East Africa independently. Establishing a timeframe is challenging given inconsistencies in age estimates, but it seems likely that they originated in the Pleistocene, or at the earliest in the late Miocene. The adaptation to alpine-like environments in the form of dwarf shrubs has apparently not led to enhanced diversification rates. Ancestral reconstructions indicate reversals in Alchemilla from plants with a woody base to entirely herbaceous forms, a transition that is rarely reported in angiosperms. CONCLUSIONS: Alchemilla is a clear example of in situ tropical alpine speciation. The dwarf shrub life form typical of African Alchemilla has evolved twice independently, further indicating its selective advantage in these harsh environments. However, it has not influenced diversification, which, although recent, was not rapid.

Back to Gondwanaland: can ancient vicariance explain (some) Indian Ocean disjunct plant distributions?

Oceans, or other wide expanses of inhospitable environment, interrupt present day distributions of many plant groups. Using molecular dating techniques, generally incorporating fossil evidence, we can estimate when such distributions originated. Numerous dating analyses have recently precipitated a paradigm shift in the general explanations for the phenomenon, away from older geological causes, such as continental drift, in favour of more recent, long-distance dispersal (LDD). For example, the 'Gondwanan vicariance' scenario has been dismissed in various studies of Indian Ocean disjunct distributions. We used the gentian tribe Exaceae to reassess this scenario using molecular dating with minimum (fossil), maximum (geological), secondary (from wider analyses) and hypothesis-driven age constraints. Our results indicate that ancient vicariance cannot be ruled out as an explanation for the early origins of Exaceae across Africa, Madagascar and the Indian subcontinent unless a strong assumption is made about the maximum age of Gentianales. However, both the Gondwanan scenario and the available evidence suggest that there were also several, more recent, intercontinental dispersals during the diversification of the group.

When do different C4 leaf anatomies indicate independent C4 origins? Parallel evolution of C4 leaf types in Camphorosmeae (Chenopodiaceae).

Broad-scale phylogenetic studies give first insights in numbers, relationships, and ages of C4 lineages. They are, however, generally limited to a model that treats the evolution of the complex C4 syndrome in different lineages as a directly comparable process. Here, we use a resolved and well-sampled phylogenetic tree of Camphorosmeae, based on three chloroplast and one nuclear marker and on leaf anatomical traits to infer a more detailed picture of C4 leaf-type evolution in this lineage. Our ancestral character state reconstructions allowed two scenarios: (i) Sedobassia is a derived C3/C4 intermediate, implying two independent gains of C4 in Bassia and Camphorosma; or (ii) Sedobassia is a plesiomorphic C3/C4 intermediate, representing a syndrome ancestral to the Bassia/Camphorosma/Sedobassia lineage. In Bassia, a kochioid leaf type (Bassia muricata and/or Bassia prostrata type) is ancestral. At least three independent losses of water-storage tissue occurred, resulting in parallel shifts towards an atriplicoid leaf type. These changes in leaf anatomy are adaptations to different survival strategies in steppic or semi-desert habitats with seasonal rainfall. In contrast, Camphorosma shows a fixed C4 anatomy differing from Bassia types in its continuous Kranz layer, which indeed points to an independent origin of the full C4 syndrome in Camphorosma, either from an independent C3 or from a common C3/C4 intermediate ancestor, perhaps similar to its C3/C4 intermediate sister genus Sedobassia. The enlarged bundle sheath cells of Sedobassia might represent an important early step in C4 evolution in Camphorosmeae.

Do pollinator distributions underlie the evolution of pollination ecotypes in the Cape shrub Erica plukenetii?

BACKGROUND AND AIMS: According to the Grant-Stebbins model of pollinator-driven divergence, plants that disperse beyond the range of their specialized pollinator may adapt to a new pollination system. Although this model provides a compelling explanation for pollination ecotype formation, few studies have directly tested its validity in nature. Here we investigate the distribution and pollination biology of several subspecies of the shrub Erica plukenetii from the Cape Floristic Region in South Africa. We analyse these data in a phylogenetic context and combine these results with information on pollinator ranges to test whether the evolution of pollination ecotypes is consistent with the Grant-Stebbins model. METHODS AND KEY RESULTS: Pollinator observations showed that the most common form of E. plukenetii with intermediate corolla length is pollinated by short-billed Orange-breasted sunbirds. Populations at the northern fringe of the distribution are characterized by long corollas, and are mainly pollinated by long-billed Malachite sunbirds. A population with short corollas in the centre of the range was mainly pollinated by insects, particularly short-tongued noctuid moths. Bird exclusion in this population did not have an effect on fruit set, while insect exclusion reduced fruit set. An analysis of floral scent across the range, using coupled gas chromatography-mass spectrometry, showed that the scent bouquets of flowers from moth-pollinated populations are characterized by a larger number of scent compounds and higher emission rates than those in bird-pollinated populations. This was also reflected in clear separation of moth- and bird-pollinated populations in a two-dimensional phenotype space based on non-metric multidimensional scaling analysis of scent data. Phylogenetic analyses of chloroplast and nuclear DNA sequences strongly supported monophyly of E. plukenetii, but not of all the subspecies. Reconstruction of ancestral character states suggests two shifts from traits associated with short-billed Orange-breasted sunbird pollination: one towards traits associated with moth pollination, and one towards traits associated with pollination by long-billed Malachite sunbirds. The latter shift coincided with the colonization of Namaqualand in which Orange-breasted sunbirds are absent. CONCLUSIONS: Erica plukenetii is characterized by three pollination ecotypes, but only the evolutionary transition from short- to long-billed sunbird pollination can be clearly explained by the Grant-Stebbins model. Corolla length is a key character for both ecotype transitions, while floral scent emission was important for the transition from bird to moth pollination.

Redefining the megagenus Erica L. (Ericaceae): the contributions of E. G. H. Oliver and I. M. Oliver (née Nitzsche) to taxonomy and nomenclature.

The megagenus Erica L. (Ericaceae), as it is recognised today, includes 851 species of evergreen shrubs or small trees, the majority of which are endemic to the Cape Floristic Region of South Africa. From the first descriptions in Linnaeus's Genera plantarum, a succession of authors ascribed the steadily accumulating numbers of known species to various of a total of 72 different genera. Until the latter half of the twentieth century, so called 'minor genera' such as Philippia Klotzsch and Blaeria L. were still recognised for many African species. The now uncontroversial inclusive circumscription of Erica, and a substantial proportion of its currently recognised species diversity, was conceptualised, described, and illustrated by the South African botanists E. G. H. ('Ted') Oliver and Inge M. Oliver in a succession of works published from 1964 to the present day. We review the historical development of generic delimitation in Erica sens. lat., focusing on the contribution of the Olivers to the current state of systematic knowledge of the genus, and presenting an overview and complete lists of literature and of taxa that they authored.

Curating an online checklist for Erica L. (Ericaceae): contributing to and supporting global conservation through the World Flora Online.

To support the work of the Global Conservation Consortium for Erica and update the Erica checklist in the World Flora Online (WFO), we have curated the taxonomic backbone in the WFO by expanding it to include updated nomenclatural information from the International Plant Name Index, missing names present in the World Checklist of Vascular Plants (WCVP), the Botanical Database of Southern Africa (BODATSA), and from the "International register of heather names" database, a data source not readily available online. The result is the most robust database of Erica names to date, including 851 species, 111 subspecies, 244 varieties, and 2787 synonyms, which is a reliable reference for initiatives such as the Erica identification aid, conservation prioritisation, and gap analyses. We disambiguate common orthographic variants within the database and present an overview of these. We also comment on the correct orthography of E.heleophila Guthrie & Bolus and E.michellensis Dulfer and the validity of E.tegetiformis E.G.H.Oliv. are discussed, and the use of E.adunca Benth. for a South African species rather than E.triceps Link, which is here regarded as insufficiently known and of uncertain application, is clarified.

Genus Erica: An identification aid version 4.00.

Species identification is fundamental to all aspects of biology and conservation. The process can be challenging, particularly in groups including many closely related or similar species. The problem is confounded by the absence of an up-to-date taxonomic revision, but even with such a resource all but professional botanists may struggle to recognise key species, presenting a substantial barrier to vital work such as surveys, threat assessments, and seed collection for ex situ conservation. Genus Erica: An Identification Aid is a tool to help both amateurs and professionals identify (using a limited number of accessible characteristics) and find information about the 851 species and many subspecific taxa of the genus Erica. We present an updated version 4.00, with new features including integrating distribution data from GBIF and iNaturalist, links to taxonomic resources through World Flora Online, and a probability function for identifications, that is freely available for PCs. It remains a work in progress: We discuss routes forward for collaboratively improving this resource.

Spatial decoupling of taxon richness, phylogenetic diversity and threat status in the megagenus Erica (Ericaceae).

Estimates of the number of vascular plant species currently under threat of extinction are shockingly high, with the highest extinction rates reported for narrow-range, woody plants, especially in biodiversity hotspots with Mediterranean and tropical climates. The large genus Erica is a prime example, as a large proportion of its 851 species, all shrubs or small trees, are endemic to the Cape Floristic Region (CFR) of South Africa. Almost two hundred are known to be threatened and a further hundred are 'Data Deficient'. We need to target conservation efforts and research to fill the most problematic knowledge gaps. This can be especially challenging in large genera, such as Erica, with numerous threatened species that are closely related. One approach involves combining knowledge of phylogenetic diversity with that of IUCN threat status to identify the most Evolutionarily Distinct and Globally Endangered (EDGE) species. We present an expanded and improved phylogenetic hypothesis for Erica (representing 65% of described species diversity) and combine this with available threat and distribution data to identify species and geographic areas that could be targeted for conservation effort to maximise preservation of phylogenetic diversity (PD). The resulting 39 EDGE taxa include 35 from the CFR. A further 32 high PD, data deficient taxa are mostly from outside the CFR, reflecting the low proportion of assessed taxa outside South Africa. The most taxon-rich areas are found in the south-western CFR. They are not the most phylogenetically diverse, but do include the most threatened PD. These results can be cross-referenced to existing living and seed-banked ex situ collections and used to target new and updated threat assessments and conservation action.

An approach to identify putative hybrids in the 'coalescent stochasticity zone', as exemplified in the African plant genus Streptocarpus (Gesneriaceae).

The inference of phylogenetic relationships is often complicated by differing evolutionary histories of independently-inherited markers. The causes of the resulting gene tree incongruence can be challenging to identify, often relying on coalescent simulations dependent on unverifiable assumptions. We investigated alternative techniques using the South African rosulate species of Streptocarpus as a study group. Two independent gene trees - from the nuclear ITS region and from three concatenated plastid regions (trnL-F, rpl20-rps12 and trnC-D) - displayed widespread, strongly supported incongruence. We investigated the causes by detecting genetic exchange across morphological borders using morphological optimizations and genetic exchange across species boundaries using the genealogical sorting index. Incongruence between gene trees was associated with ancestral shifts in growth form (in four species) but not in pollination syndrome, suggesting introgression limited by reproductive barriers. Genealogical sorting index calculations showed polyphyly of two additional species, while individuals of all others were significantly associated. In one case the association was stronger according to the internal transcribed spacer data than according to the plastid data, which, given the smaller effective population size of the plastid, may also indicate introgression. These approaches offer alternative ways to identify potential hybridization events where incomplete lineage sorting cannot be rejected using simulations.

Erica L. (Ericaceae): homonyms amongst published names for African species and proposed replacement names.

In support of ongoing taxonomic work on the large and complex flowering plant genus Erica (Ericaceae), we document nineteen pairs of homonyms representing currently used illegitimate names. We provide replacements for thirteen names and new typifications for five. We relegate five names to synonymy: Ericaaemula Guthrie & Bolus under Ericadistorta Bartl.; Ericaarmata Klotzsch ex Benth. under Ericaumbrosa H. A. Baker; Ericacapensis T.M. Salter under Ericaturbiniflora Salisb.; Ericalanata Andrews under Ericaflaccida Link; and Ericatomentosa Salisb. under Ericavelutina Bartl. Finally, we suggest conservation of Ericaaristata Andrews. The new names are: Ericaadelopetala E.C. Nelson & E.G.H. Oliv. replacing Ericainsignis E.G.H. Oliv.; Ericabombycina E.C. Nelson & Pirie replacing Ericaniveniana E.G.H. Oliv.; Ericaconcordia E.C. Nelson & E.G.H. Oliv. replacing Ericaconstantia Nois. ex Benth.; Ericadidymocarpa E.C. Nelson & E.G.H. Oliv. replacing Ericarugata E.G.H. Oliv.; Ericagalantha E.C. Nelson & E.G.H. Oliv. replacing Ericaperlata Benth.; Ericamallotocalyx E.C. Nelson & E.G.H. Oliv. replacing Ericaflocciflora Benth.; Ericanotoporina E.C. Nelson & E.G.H. Oliv. replacing E.autumnalis L.Bolus; Ericaoliveranthus E.C. Nelson & Pirie replacing Ericatenuis Salisb.; Ericaoraria E.C. Nelson & E.G.H. Oliv. replacing Ericaspectabilis Klotzsch ex Benth.; Ericaoresbia E.C. Nelson & E.G.H. Oliv. replacing Ericademissa Klotzsch ex Benth.; Ericapoculiflora E.C. Nelson & E.G.H. Oliv. replacing Ericastenantha Klotzsch ex Benth.; Ericarhodella E.C. Nelson & E.G.H. Oliv. replacing Ericarhodantha Guthrie & Bolus; Ericasupranubia E.C. Nelson & Pirie replacing Ericapraecox Klotzsch.

A broader model for C4 photosynthesis evolution in plants inferred from the goosefoot family (Chenopodiaceae s.s.).

C(4) photosynthesis is a fascinating example of parallel evolution of a complex trait involving multiple genetic, biochemical and anatomical changes. It is seen as an adaptation to deleteriously high levels of photorespiration. The current scenario for C(4) evolution inferred from grasses is that it originated subsequent to the Oligocene decline in CO(2) levels, is promoted in open habitats, acts as a pre-adaptation to drought resistance, and, once gained, is not subsequently lost. We test the generality of these hypotheses using a dated phylogeny of Amaranthaceae s.l. (including Chenopodiaceae), which includes the largest number of C(4) lineages in eudicots. The oldest chenopod C(4) lineage dates back to the Eocene/Oligocene boundary, representing one of the first origins of C(4) in plants, but still corresponding with the Oligocene decline of atmospheric CO(2). In contrast to grasses, the rate of transitions from C(3) to C(4) is highest in ancestrally drought resistant (salt-tolerant and succulent) lineages, implying that adaptation to dry or saline habitats promoted the evolution of C(4); and possible reversions from C(4) to C(3) are apparent. We conclude that the paradigm established in grasses must be regarded as just one aspect of a more complex system of C(4) evolution in plants in general.

A densely sampled ITS phylogeny of the Cape flagship genus Erica L. suggests numerous shifts in floral macro-morphology.

Erica L. is the largest of the 'Cape' clades that together comprise around half of the disproportionately high species richness of the Cape Floristic Region (CFR) of South Africa. Around 840 species of Erica are currently recognised, C.680 of which are found in the CFR, the rest distributed across the rest of Southern Africa, the highlands of Tropical Africa and Madagascar, and Europe. Erica is taxonomically well documented, but very little is known about species-level relationships. We present the first densely sampled phylogenetic analysis of Erica, using nuclear ribosomal DNA sequences (internal transcribed spacers; ITS) of c. 45% of the species from across the full geographic range of the genus, both Calluna and Daboecia (Ericeae; monotypic genera and putative sister groups of Erica), and further Ericoideae outgroups. Our results show both morphological and geographic coherence of some clades, but numerous shifts in floral macro-morphology as represented by variation in individual morphological characters and pollination syndromes. European Ericeae is a paraphyletic grade subtending a monophyletic African/Malagasy Erica. Given the limited resolution of this single gene tree, more data are needed for further conclusions. Clades are identified that will serve as an effective guide for targeted sampling from multiple linkage groups.

Chromosome-level reference genome of the soursop (Annona muricata): A new resource for Magnoliid research and tropical pomology.

The flowering plant family Annonaceae includes important commercially grown tropical crops, but development of promising species is hindered by a lack of genomic resources to build breeding programs. Annonaceae are part of the magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades remain unclear. To provide resources to breeders and evolutionary researchers, we report a chromosome-level genome assembly of the soursop (Annona muricata). We assembled the genome using 444.32 Gb of DNA sequences (676× sequencing depth) from PacBio and Illumina short-reads, in combination with 10× Genomics and Bionano data (v1). A total of 949 scaffolds were assembled to a final size of 656.77 Mb, with a scaffold N50 of 3.43 Mb (v1), and then further improved to seven pseudo-chromosomes using Hi-C sequencing data (v2; scaffold N50: 93.2 Mb, total size in chromosomes: 639.6 Mb). Heterozygosity was very low (0.06%), while repeat sequences accounted for 54.87% of the genome, and 23,375 protein-coding genes with an average of 4.79 exons per gene were annotated using de novo, RNA-seq and homology-based approaches. Reconstruction of the historical population size showed a slow continuous contraction, probably related to Cenozoic climate changes. The soursop is the first genome assembled in Annonaceae, supporting further studies of floral evolution in magnoliids, providing an essential resource for delineating relationships of ancient angiosperm lineages. Both genome-assisted improvement and conservation efforts will be strengthened by the availability of the soursop genome. As a community resource, this assembly will further strengthen the role of Annonaceae as model species for research on the ecology, evolution and domestication potential of tropical species in pomology and agroforestry.

A plastid tree can bring order to the chaotic generic taxonomy of Rytidosperma Steud. s.l. (Poaceae).

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.

Reticulation, data combination, and inferring evolutionary history: an example from Danthonioideae (Poaceae).

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.

Diversification in evolutionary arenas-Assessment and synthesis.

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.

A novel supermatrix approach improves resolution of phylogenetic relationships in a comprehensive sample of danthonioid grasses.

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.