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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.

Background and AimsAccording 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 ResultsPollinator 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 plukenetiiis 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.

Plant phylogenetics has been revolutionised in the genomic era, with target capture acting as the primary workhorse of most recent research in the new field of phylogenomics. Target capture (aka Hyb-Seq) allows researchers to sequence hundreds of genomic regions (loci) of their choosing, at relatively low cost per sample, from which to derive phylogenetically informative data. Although this highly flexible and widely applicable method has rightly earned its place as the field’s de facto standard, it does not come without its challenges. In particular, users have to specify which loci to sequence—a surprisingly difficult task, especially when working with non-model groups, as it requires pre-existing genomic resources in the form of assembled genomes and/or transcriptomes. In the absence of taxon-specific genomic resources, target sets exist that are designed to work across broad taxonomic scales. However, the highly conserved loci that they target may lack informativeness for difficult phylogenetic problems, such as that presented by the rapid radiation of Erica in southern Africa. We designed a target set for Erica phylogenomics intended to maximise informativeness and minimise paralogy while maintaining universality by including genes from the widely used Angiosperms353 set. Comprising just over 300 genes, the targets had excellent recovery rates in roughly 90 Erica species as well as outgroups from Calluna , Daboecia , and Rhododendron , and had high information content as measured by parsimony informative sites and Quartet Internode Resolution Probability (QIRP) at shallow nodes. Notably, QIRP was positively correlated with intron content, while including introns in targets—rather than recovering them via exon-flanking “bycatch”—substantially improved intron recovery. Overall, our results show the value of building a custom target set, and we provide a suite of open-source tools that can be used to replicate our approach in other groups (https://github.com/SethMusker/TargetVet).

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.

The evolutionary history of the exclusively grapevine (Vitis spp.) infecting, grapevine leafroll-associated virus 3 (GLRaV-3) has not been studied extensively, partly due to limited available sequence data. In this study we trace the evolutionary history of GLRaV-3, focussing on isolate GH24, a newly discovered variant. GH24 was discovered through the use of next-generation sequencing (NGS) and the whole genome sequence determined and validated with Sanger sequencing. We assembled an alignment of all 13 available whole genomes of GLRaV-3 isolates and all other publicly available GLRaV-3 sequence data. Using multiple recombination detection methods we identified a clear signal for recombination in one whole genome sequence and further evidence for recombination in two more, including GH24. We inferred phylogenetic trees and networks and estimated the ages of common ancestors of GLRaV-3 clades by means of relaxed clock models calibrated with asynchronous sampling dates. Our results generally confirm previously identified variant groups as well as two new groups (VII and VIII). Higher order groups were defined as supergroups designated A to D. Supergroup A includes variant groups I-V and supergroup B group VI and its related unclassified isolates. Supergroups C and D are less well known, including the newly identified groups VII (including isolate GH24) and VIII respectively. The inferred node ages suggest that the origins of the major groups of GLRaV-3, including isolate GH24, may have occurred prior to worldwide cultivation of grapevines, whilst the current diversity represents closely related isolates that diverged from common ancestors within the last century.

The plant genus Erica L. (heathers; anjavidy in Malagasy) has 35 recognised species in Madagascar, but there has not been a taxonomic revision since 1927 and there are few identification resources. We review available data for Malagasy Erica (previously treated as Philippia ), summarise diagnostic species descriptions and incorporate them into the Erica Identification Aid. There is clearly variation in current species concepts that requires further study. Malagasy Erica most likely represent a single clade also encompassing species from the Mascarenes, but resolution is poor and most species remain unsequenced. Erica is found in several of Madagascar’s ecosystems, including the high-altitude “ericoid thickets” where diversity is highest, but it is absent from the extensive dry western areas. Habitats include the ericoid thickets, shrubland–grassland mosaics in the central highlands and on the eastern coast, and Uapaca bojeri (tapia) savanna. Many Erica species are likely to be part of dynamic ecosystems with infrequent fire regimes. The palaeorecord indicates a more widespread ericoid shrub vegetation during the last glacial period. There may be both wind- and insect-pollinated species. Erica is mainly used as fuelwood in Madagascar, but local uses as tools and medicine have also been reported. Estimates suggest at least one-fifth of the species may be threatened, but formal assessments are lacking. Taxonomic revision of the group, coupled with phylogenomic, ecological and ethnobotanic studies, is an urgent priority.

Targeted high-throughput sequencing using hybrid-enrichment offers a promising source of data for inferring multiple, meaningfully resolved, independent gene trees suitable to address challenging phylogenetic problems in species complexes and rapid radiations. The targets in question can either be adopted directly from more or less universal tools, or custom made for particular clades at considerably greater effort. We applied custom made scripts to select sets of homologous sequence markers from transcriptome and WGS data for use in the flowering plant genus Erica (Ericaceae). We compared the resulting targets to those that would be selected both using different available tools (Hyb-Seq; MarkerMiner), and when optimising for broader clades of more distantly related taxa (Ericales; eudicots). Approaches comparing more divergent genomes (including MarkerMiner, irrespective of input data) delivered fewer and shorter potential markers than those targeted for Erica . The latter may nevertheless be effective for sequence capture across the wider family Ericaceae. We tested the targets delivered by our scripts by obtaining an empirical dataset. The resulting sequence variation was lower than that of standard nuclear ribosomal markers (that in Erica fail to deliver a well resolved gene tree), confirming the importance of maximising the lengths of individual markers. We conclude that rather than searching for “one size fits all” universal markers, we should improve and make more accessible the tools necessary for developing “made to measure” ones.

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. The Evolutionary Arena (EvA) framework for comparative studies on evolutionary radiations, stasis, and biodiversity decline. EvA conceptualizes context‐dependent species diversification in concert with lineage‐specific traits and abiotic and biotic environmental conditions. In this concept paper, we synthesize recent progress in diversification research into a heuristic framework into which relevant processes can be grouped and parameterized (e.g., here for the conifers).

The megagenus Erica L. (Ericaceae) comprises 851 species across its global distribution, with an extraordinary focus of diversity in the Cape Floristic Region (CFR) of South Africa where almost 700 species are endemic. The genus is remarkable for both its morphological diversity and the large number of species and subspecific taxa occurring in small populations, often in specialised habitats, putting them at high risk of extinction. Despite significant taxonomic work over the past century, part of this diversity remains undescribed. The sheer size of the genus, its morphological, ecological and geographical variability, and the absence of a modern, consolidated revision make alpha taxonomy challenging. By combining traditional taxonomic methods, standard DNA sequencing methods building on openly available data matrices, and an openly available specialised taxonomic tool for the genus, we present an integrative, reproducible approach to alpha taxonomy in Erica . This approach provided support for the recognition of three new species from the Western Cape in South Africa and aided in ruling out two further putative new species, confirming one as a natural hybrid and the other as a morphological variation within an existing species. We describe the three new species Erica arida R.D.Hoekstra, Erica hessequae R.D.Hoekstra and Erica inopina J.H.J.Vlok.

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.