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Variation in species richness across the tree of life, accompanied by the incredible variety of ecological and morphological characteristics found in nature, has inspired many studies to link traits with species diversification. Angiosperms are a highly diverse group that has fundamentally shaped life on earth since the Cretaceous, and illustrate how species diversification affects ecosystem functioning. Numerous traits and processes have been linked to differences in species richness within this group, but we know little about how these interact and their relative importance. Here, we synthesized data from 152 studies that used state-dependent speciation and extinction (SSE) models on angiosperm clades. Intrinsic traits related to reproduction and morphology were often linked to diversification but a set of universal drivers did not emerge as traits did not have consistent effects across clades. Importantly, dataset properties were correlated to SSE model results - trees that were larger, older, or less well-sampled tended to yield trait-dependent outcomes. We compared these properties to recommendations for SSE model use and provide a set of best practices to follow when designing studies and reporting results. Finally, we argue that SSE model inferences should be considered in a larger context incorporating species’ ecology, demography and genetics.

The present-day ubiquity of angiosperm-insect pollination has led to the hypothesis that these two groups coevolved early in their evolutionary history. However, recent fossil discoveries and fossil-calibrated molecular dating analyses challenge the notion that early diversifications of angiosperms and insects were inextricably linked. In this article, we examine (i) the discrepancies between dates of emergence for angiosperms and major clades of insects; (ii) the long history of gymnosperm-insect pollination modes, which likely shaped early angiosperm-insect pollination mutualisms; and (iii) how the K-Pg (Cretaceous-Paleogene) mass extinction event was vital in propelling modern angiosperm-insect mutualisms. We posit that the early diversifications of angiosperms and their insect pollinators were largely decoupled until the end of the Cretaceous.

SummaryPollination is a fundamental process driving the speciation of angiosperms (flowering plants). Most contemporary angiosperms are insect pollinated, but abiotic pollination by wind or water and vertebrate pollination by birds or mammals occurs in many lineages. We model the evolution of pollination across angiosperms and quantify the timing and environmental associations of pollination shifts.We use a robust dated phylogeny and trait-independent species-level sampling across all families of angiosperms to model the evolution of pollination modes. Data on the pollination system or syndrome of 1160 species were collated from primary literature.Angiosperms were ancestrally insect pollinated, and insects have pollinated angiosperms for approximately 86% of angiosperm evolutionary history. Wind pollination evolved at least 42 times, with few reversals back to animal pollination. Transitions between insect and vertebrate pollination were more frequent: vertebrate pollination evolved at least 39 times from an insect pollinated ancestor with at least 26 reversals. The probability of wind pollination increases with habitat openness (measured by Leaf Area Index) and with distance from the equator.Our reconstruction of pollination across angiosperms sheds light on a key question in angiosperm macroevolution, highlighting the long history of interactions between insect pollinators and angiosperms still vital to global biodiversity today.

Premise of the StudyRecent studies of floral disparity in the asterid order Ericales have shown that flowers vary strongly among families and that disparity is unequally distributed between the three flower modules (perianth, androecium, gynoecium). However, it remains unknown whether these patterns are driven by heterogeneous rates of morphological evolution or other factors.MethodsHere, we compiled a dataset of 33 floral characters scored for 414 extant ericalean species sampled from 346 genera and all 22 families. We conducted ancestral state reconstructions using an equal rates Markov models for each trait. We used the rates estimated during the ancestral state reconstruction for comparing evolutionary rates between flower modules, creating a “rate profile” of ericalean flowers.Key ResultsThe androecium exhibits the highest evolutionary rates across most characters, whereas most perianth and gynoecium characters evolve slower. High and low rates of morphological evolution can result in high floral disparity in Ericales. Analyses of an angiosperm-wide floral dataset reveal that this pattern appears to be conserved across most major angiosperm clades.ConclusionsElevated rates of morphological evolution in the androecium of Ericales may explain the higher disparity reported for this floral module. We discuss the implications of heterogenous morphological rates of evolution among floral modules from a functional perspective. Comparing rates of morphological evolution through rate profiles proves to be a powerful tool in understanding floral evolution.

Determining the link between genomic and phenotypic evolution is a fundamental goal in evolutionary biology. Insights into this link can be gained by using a phylogenetic approach to test for correlations between rates of molecular and morphological evolution. However, there has been persistent uncertainty about the relationship between these rates, partly because conflicting results have been obtained using various methods that have not been examined in detail. We carried out a simulation study to evaluate the performance of five statistical methods for detecting correlated rates of evolution. Our simulations explored the evolution of molecular sequences and morphological characters under a range of conditions. Of the methods tested, Bayesian relaxed-clock estimation of branch rates was able to detect correlated rates of evolution correctly in the largest number of cases. This was followed by correlations of root-to-tip distances, Bayesian model selection, independent sister-pairs contrasts, and likelihood-based model selection. As expected, the power to detect correlated rates increased with the amount of data, both in terms of tree size and number of morphological characters. Likewise, the performance of all five methods improved when there was greater rate variation among lineages. We then applied these methods to a data set from flowering plants and did not find evidence of a correlation in evolutionary rates between genomic data and morphological characters. The results of our study have practical implications for phylogenetic analyses of combined molecular and morphological data sets, and highlight the conditions under which the links between genomic and phenotypic rates of evolution can be evaluated quantitatively.

Summary Cleistogamous flowers never fully bloom and are thought to have evolved as a means to promote self-fertilisation. A new study reveals that this curious feature arose more frequently in flowers with bilateral symmetry.

International audience; Species diversity can vary dramatically across lineages due to differences in speciation and extinction rates. Here, we explore the effects of several plant traits on diversification, finding that most traits have opposing effects on diversification. For example, outcrossing may increase the efficacy of selection and adaptation but also decrease mate availability, two processes with contrasting effects on lineage persistence. Such opposing trait effects can manifest as differences in diversification rates that depend on ecological context, spatiotemporal scale, and associations with other traits. The complexity of pathways linking traits to diversification suggests that the mechanistic underpinnings behind their correlations may be difficult to interpret with any certainty, and context dependence means that the effects of specific traits on diversification are likely to differ across multiple lineages and timescales. This calls for taxonomically and context-controlled approaches to studies that correlate traits and diversification. © 2023

Premise Significant paleobotanical discoveries in recent decades have considerably improved our understanding of the early evolution of angiosperms and their flowers. However, our ability to test the systematic placement of fossil flowers on the basis of phylogenetic analyses has remained limited, mainly due to the lack of an adequate, angiosperm-wide morphological data set for extant taxa. Earlier attempts to place fossil flowers phylogenetically were, therefore, forced to make prior qualitative assessments of the potential systematic position of fossils and to restrict phylogenetic analyses to selected angiosperm subgroups. Methods We conduct angiosperm-wide molecular backbone analyses of 10 fossil flower taxa selected from the Cretaceous record. Our analyses make use of a floral trait data set built within the framework of the eFLOWER initiative. We provide an updated version of this data set containing data for 28 floral and two pollen traits for 792 extant species representing 372 angiosperm families. Results We find that some fossils are placed congruently with earlier hypotheses while others are found in positions that had not been suggested previously. A few take up equivocal positions, including the stem branches of large clades. Conclusions Our study provides an objective approach to test for the phylogenetic position of fossil flowers across angiosperms. Such analyses may provide a complementary tool for paleobotanical studies, allowing for a more comprehensive understanding of fossil phylogenetic relationships in angiosperms. Ongoing work focused on extending the sampling of extant taxa and the number of floral traits will further improve the applicability and accuracy of our approach.

The Early Cretaceous (145–100 million years ago (Ma)) witnessed the rise of flowering plants (angiosperms), which ultimately lead to profound changes in terrestrial plant communities. However, palaeobotanical evidence shows that the transition to widespread angiosperm-dominated biomes was delayed until the Palaeocene (66–56 Ma). Important aspects of the timing and geographical setting of angiosperm diversification during this period, and the groups involved, remain uncertain. Here we address these aspects by constructing and dating a new and complete family-level phylogeny, which we integrate with 16 million geographic occurrence records for angiosperms on a global scale. We show substantial time lags (mean, 37–56 Myr) between the origin of families (stem age) and the diversification leading to extant species (crown ages) across the entire angiosperm tree of life. In turn, our results show that families with the shortest lags are overrepresented in temperate and arid biomes compared with tropical biomes. Our results imply that the diversification and ecological expansion of extant angiosperms was geographically heterogeneous and occurred long after most of their phylogenetic diversity originated during the Cretaceous Terrestrial Revolution. A new study of the divergence time of angiosperm families shows that although most angiosperm families originated during the middle Cretaceous (~100–90 million years ago), the diversification of families into extant diversity was delayed until the Palaeocene (~66–56 million years ago), this time lag being geographically heterogeneous, and longer in tropical than in temperate and arid biomes.

Fossil flowers are essential to infer past angiosperm evolutionary processes. The assignment of fossil flowers to extant clades has traditionally relied on morphological similarity and on apomorphies shared with extant taxa. The use of explicit phylogenetic analyses to establish their affinity has so far remained limited. In this study, we built a comprehensive framework to investigate the phylogenetic placement of 24 exceptionally preserved fossil flowers. For this, we assembled a new species-level dataset of 30 floral traits for 1201 extant species that were sampled to represent the stem and crown nodes of all angiosperm families. We explored multiple analytical approaches to integrate the fossils into the phylogeny, including different phylogenetic estimation methods, topological-constrained analyses, and a total evidence approach combining molecular and morphological data of extant and fossil species. Our results were widely consistent across approaches, with minor differences in the support of fossils at different phylogenetic positions. The placement of some fossils is in agreement with previously suggested relationships, but for others, a new placement is indicated. We also identified fossils that are well constrained within particular extant families, whereas others showed high phylogenetic uncertainty. Finally, we present recommendations for future total evidence analyses, regarding the selection of fossils and appropriate methodologies, and provide some perspectives on how to integrate fossils into the investigation of divergence times and the temporal evolution of morphological traits.

Pseudanthia are widespread and have long been postulated to be a key innovation responsible for some of the angiosperm radiations. The aim of our study was to analyze macroevolutionary patterns of these flower-like inflorescences and their potential correlation with diversification rates in Apiaceae subfamily Apioideae. In particular, we were interested to investigate evolvability of pseudanthia and evaluate their potential association with changes in the size of floral display.The framework for our analyses consisted of a time-calibrated phylogeny of 1734 representatives of Apioideae and a morphological matrix of inflorescence traits encoded for 847 species. Macroevolutionary patterns in pseudanthia were inferred using Markov models of discrete character evolution and stochastic character mapping, and a principal component analysis was used to visualize correlations in inflorescence architecture. The interdependence between net diversification rates and the occurrence of pseudocorollas was analyzed with trait-independent and trait-dependent approaches.Pseudanthia evolved in 10 major clades of Apioideae with at least 36 independent origins and 46 reversals. The morphospace analysis recovered differences in color and compactness between floral and hyperfloral pseudanthia. A correlation between pseudocorollas and size of inflorescence was also strongly supported. Contrary to our predictions, pseudanthia are not responsible for variation in diversification rates identified in this subfamily.Our results suggest that pseudocorollas evolve as an answer to the trade-off between enlargement of floral display and costs associated with production of additional flowers. The high evolvability and architectural differences in apioid pseudanthia may be explained on the basis of adaptive wandering and evolutionary developmental biology.

Telopea speciosissima, the New South Wales waratah, is an Australian endemic woody shrub in the family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, and are significant from a horticultural perspective. Here, we report the first chromosome-level genome for T. speciosissima. Combining Oxford Nanopore long-reads, 10x Genomics Chromium linked-reads and Hi-C data, the assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 97.8% of Embryophyta BUSCOs "Complete". We present a new method in Diploidocus (https://github.com/slimsuite/diploidocus) for classifying, curating and QC-filtering scaffolds, which combines read depths, k-mer frequencies and BUSCO predictions. We also present a new tool, DepthSizer (https://github.com/slimsuite/depthsizer), for genome size estimation from the read depth of single-copy orthologues and estimate the genome size to be approximately 900 Mb. The largest 11 scaffolds contained 94.1% of the assembly, conforming to the expected number of chromosomes (2n = 22). Genome annotation predicted 40,158 protein-coding genes, 351 rRNAs and 728 tRNAs. We investigated CYCLOIDEA (CYC) genes, which have a role in determination of floral symmetry, and confirm the presence of two copies in the genome. Read depth analysis of 180 "Duplicated" BUSCO genes using a new tool, DepthKopy (https://github.com/slimsuite/depthkopy), suggests almost all are real duplications, increasing confidence in the annotation and highlighting a possible need to revise the BUSCO set for this lineage. The chromosome-level T. speciosissima reference genome (Tspe_v1) provides an important new genomic resource of Proteaceae to support the conservation of flora in Australia and further afield.

AimClimate shapes the composition and function of plant communities globally, but it remains unclear how this influence extends to floral traits. Flowering phenology, or the time period in which a species flowers, has well-studied relationships with climatic signals at the species level but has rarely been explored at a cross-community and continental scale. Here, we characterise the distribution of flowering periods (months of flowering) across continental plant communities encompassing six biomes, and determine the influence of climate on community flowering period lengths.LocationAustraliaTaxonFlowering plantsMethodsWe combined plant composition and abundance data from 629 standardised floristic surveys (AusPlots) with data on flowering period from the AusTraits database and additional primary literature for 2,983 species. We assessed abundance-weighted community mean flowering periods across biomes and tested their relationship with climatic annual means and the predictability of climate conditions using regression models.ResultsCombined, temperature and precipitation (annual mean and predictability) explain 29% of variation in continental community flowering period. Plant communities with higher mean temperatures and lower mean precipitation have longer mean flowering periods. Moreover, plant communities in climates with predictable temperatures and, to a lesser extent, predictable precipitation have shorter mean flowering periods. Flowering period varies by biome, being longest in deserts and shortest in alpine and montane communities. For instance, desert communities experience low and unpredictable precipitation and high, unpredictable temperatures and have longer mean flowering periods, with desert species typically flowering at any time of year in response to rain.Main conclusionsOur findings demonstrate the role of current climate conditions in shaping flowering periods across biomes, with implications under climate change. Shifts in flowering periods across climatic gradients reflect changes in plant strategies, affecting patterns of plant growth and reproduction as well as the availability of floral resources across the landscape.

The origin of flowering plants (angiosperms) was one of the most transformative events in the history of our planet. Despite considerable interest from multiple research fields, numerous questions remain, including the age of the group as a whole. Recent studies have reported a perplexing range of estimates for the crown-group age of angiosperms, from ca. 140 Ma (Early Cretaceous) to 270 Ma (Permian). Both ends of the spectrum are now supported by both quantitative analyses of the fossil record and fossil-calibrated molecular dating analyses. Here, we first clarify and distinguish among the three ages of angiosperms: the age of their divergence with acrogymnosperms (stem age), the age(s) of emergence of their unique, distinctive features including flowers (morphological age), and the age of the most recent common ancestor of all their living species (crown age). We then demonstrate, based on recent studies, that fossil-calibrated molecular dating estimates of the crown-group age of angiosperms have little to do with either the amount of molecular data or the number of internal fossil calibrations included. Instead, we argue that this age is almost entirely conditioned by its own prior. Lastly, we discuss which future discoveries or novel types of analyses are most likely to bring more definitive answers. In the meantime, we propose that the age of angiosperms is best described as unknown (140–270 Ma) and that future work that depends on the time scale of flowering plant diversification be designed to integrate over this vexing uncertainty.

The origin of flowering plants (angiosperms) was one of the most transformative events in the history of our planet. Despite considerable interest from multiple research fields, numerous questions remain, including the age of the group as a whole. Recent studies have reported a perplexing range of estimates for the crown-group age of angiosperms, from ~140 million years (Ma; Early Cretaceous) to 270 Ma (Permian). Both ends of the spectrum are now supported by both macroevolutionary analyses of the fossil record and fossil-calibrated molecular dating analyses. Here, we first clarify and distinguish among the three ages of angiosperms: the age of their divergence with acrogymnosperms (stem age); the age(s) of emergence of their unique, distinctive features including flowers (morphological age); and the age of the most recent common ancestor of all their living species (crown age). We then demonstrate, based on recent studies, that fossil-calibrated molecular dating estimates of the crown-group age of angiosperms have little to do with either the amount of molecular data or the number of internal fossil calibrations included. Instead, we argue that this age is almost entirely conditioned by its own prior distribution (typically a calibration density set by the user in Bayesian analyses). Lastly, we discuss which future discoveries or novel types of analyses are most likely to bring more definitive answers. In the meantime, we propose that the age of angiosperms is best described as largely unknown (140–270 Ma) and that contrasting age estimates in the literature mostly reflect conflicting prior distributions. We also suggest that future work that depends on the time scale of flowering plant diversification be designed to integrate over this vexing uncertainty.

Telopea speciosissima,the New South Wales waratah, is an Australian endemic woody shrub in the family Proteaceae. Waratahs have great potential as a model clade to better understand processes of speciation, introgression and adaptation, and are significant from a horticultural perspective. Here, we report the first chromosome-level genome forT. speciosissima. Combining Oxford Nanopore long-reads, 10x Genomics Chromium linked-reads and Hi-C data, the assembly spans 823 Mb (scaffold N50 of 69.0 Mb) with 97.8 % of Embryophyta BUSCOs complete. We present a new method in Diploidocus (https://github.com/slimsuite/diploidocus) for classifying, curating and QC-filtering scaffolds, which combines read depths, k-mer frequencies and BUSCO predictions. We also present a new tool, DepthSizer (https://github.com/slimsuite/depthsizer), for genome size estimation from the read depth of single copy orthologues and estimate the genome size to be approximately 900 Mb. The largest 11 scaffolds contained 94.1 % of the assembly, conforming to the expected number of chromosomes (2n= 22). Genome annotation predicted 40,158 protein-coding genes, 351 rRNAs and 728 tRNAs. We investigatedCYCLOIDEA(CYC) genes, which have a role in determination of floral symmetry, and confirm the presence of two copies in the genome. Read depth analysis of 180 ‘Duplicated’ BUSCO genes suggest almost all are real duplications, increasing confidence in protein family analysis using annotated protein-coding genes, and highlighting a possible need to revise the BUSCO set for this lineage. The chromosome-levelT. speciosissimareference genome (Tspe_v1) provides an important new genomic resource of Proteaceae to support the conservation of flora in Australia and further afield.

Estimating time-dependent rates of speciation and extinction from dated phylogenetic trees of extant species (timetrees), and determining how and why they vary, is key to understanding how ecological and evolutionary processes shape biodiversity. Due to an increasing availability of phylogenetic trees, a growing number of process-based methods relying on the birth-death model have been developed in the last decade to address a variety of questions in macroevolution. However, this methodological progress has regularly been criticised such that one may wonder how reliable the estimations of speciation and extinction rates are. In particular, using lineages-through-time (LTT) plots, a recent study (Louca and Pennell, 2020) has shown that there are an infinite number of equally likely diversification scenarios that can generate any timetree. This has lead to questioning whether or not diversification rates should be estimated at all. Here we summarize, clarify, and highlight technical considerations on recent findings regarding the capacity of models to disentangle diversification histories. Using simulations we demonstrate the characteristics of newly-proposed “pulled rates” and their utility. We recognize that the recent findings are a step forward in understanding the behavior of macroevolutionary modelling, but they in no way suggest we should abandon diversification modelling altogether. On the contrary, the study of macroevolution using phylogenetic trees has never been more exciting and promising than today. We still face important limitations in regard to data availability and methodological shortcomings, but by acknowledging them we can better target our joint efforts as a scientific community.

Annonaceae contain important commercially grown tropical crops, but development of other promising species is hindered by a lack of genomic resources to build breeding programs. In addition, Annonaceae are part of the Magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades have remained unclear. To provide resources to both breeders and evolutionary researchers, we report the chromosome-level genome assembly of the soursop (Annona muricata). We assembled the soursop genome using a total of 444.32 Gb of DNA sequences that were generated using PacBio and Illumina short-reads, in combination with 10XGenomics, Bionano data and Hi-C sequencing. 949 scaffolds were assembled to a final size of 656.77Mb, with a scaffold N50 of 3.43 Mb. 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 of A. muricata showed a slow but regular contraction of the population, likely related to Cenozoic climate changes. The soursop is the first genome assembled in Annonaceae, supporting further studies of floral evolution in Magnoliids, and providing an essential resource for delineating relationships of major lineages at the base of the angiosperms. Both genome-assisted improvement and conservation efforts will be strengthened by the availability of the soursop genome. The genome assembly as a community resource 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.

We present a phylogenomic study ofBrosimumand the allied generaTrymatococcusandHelianthostylis, with near-complete taxon sampling. Distributed from Mexico and the Greater Antilles to the Amazon, this clade contains the underutilized crop ramón (bread nut) (Brosimum alicastrum) as well as other species valued for timber or medicinal uses. Target enrichment for 333 genes produced a well-resolved phylogenetic tree and showed thatTrymatoccocusandHelianthostylisare nested withinBrosimum. We present a revised subgeneric classification ofBrosimumbased on phylogenetic and morphological considerations, including the reduction ofTrymatococcusandHelianthostylisto subgenera. The monophyletic subgenera can be diagnosed based on stipule, pistillode, and cotyledon synapomorphies. Divergence date estimates suggest a Miocene origin forBrosimum, and ancestral area reconstruction indicated that all four subgenera originated and initially diversified in Amazonia before dispersing into other parts of South and Central America.ResumenPresentamos un estudio filogenómico del géneroBrosimumy sus aliados,TrymatococcusyHelianthostylis, y que incluye prácticamente todas las especies descritas. Su distribución va desde México y las Antillas Mayores hasta el Amazonas y comprende especies como el ramón (B. alicastrum), un cultivo infrautilizado, y otras especies empleadas como madera o en medicina. La secuenciación masiva dirigida de 333 marcadores nucleares de copia única permitió la reconstrucción de una filogenia bien resuelta, en la que se demuestra queTrymatococcusyHelianthostylisestán anidados enBrosimum. Presentamos, por lo tanto, una clasificación revisada a nivel de especies, teniendo en cuenta los resultados moleculares y las características morfológicas, y dondeTrymatococcusyHelianthostylispasan a ser subgéneros deBrosimum. Estos subgéneros monofiléticos pueden ser identificados por caracteres de las estípulas y de los pistilodios.

Contents Summary 1170 I. Introduction 1170 II. Six key questions 1172 III. Three key challenges 1177 IV. Conclusions 1181 Acknowledgements 1182 References 1183 SUMMARY: The origin and rapid diversification of angiosperms (flowering plants) represent one of the most intriguing topics in evolutionary biology. Despite considerable progress made in complementary fields over the last two decades (paleobotany, phylogenetics, ecology, evo-devo, genomics), many important questions remain. For instance, what has been the impact of mass extinctions on angiosperm diversification? Are the angiosperms an adaptive radiation? Has morphological evolution in angiosperms been gradual or pulsed? We propose that the recent and ongoing revolution in macroevolutionary methods provides an unprecedented opportunity to explore long-standing questions that probably hold important clues to understand present-day biodiversity. We present six key questions that explore the origin and diversification of angiosperms. We also identify three key challenges to address these questions: (1) the development of new integrative models that include diversification, multiple intrinsic and environmental traits, biogeography and the fossil record all at once, whilst accounting for sampling bias and heterogeneity of macroevolutionary processes through time and among lineages; (2) the need for large and standardized synthetic databases of morphological variation; and (3) continuous effort on sampling the fossil record, but with a revolution in current paleobotanical practice.

The Early Cretaceous (145-100 million years ago (Ma)) witnessed the rise of flowering plants (angiosperms), which ultimately lead to profound changes in terrestrial plant communities. However, palaeobotanical evidence shows that the transition to widespread angiosperm-dominated biomes was delayed until the Palaeocene (66-56 Ma). Important aspects of the timing and geographical setting of angiosperm diversification during this period, and the groups involved, remain uncertain. Here we address these aspects by constructing and dating a new and complete family-level phylogeny, which we integrate with 16 million geographic occurrence records for angiosperms on a global scale. We show substantial time lags (mean, 37-56 Myr) between the origin of families (stem age) and the diversification leading to extant species (crown ages) across the entire angiosperm tree of life. In turn, our results show that families with the shortest lags are overrepresented in temperate and arid biomes compared with tropical biomes. Our results imply that the diversification and ecological expansion of extant angiosperms was geographically heterogeneous and occurred long after most of their phylogenetic diversity originated during the Cretaceous Terrestrial Revolution.

Deep relationships and the sequence of divergence among major lineages of angiosperms (magnoliids, monocots and eudicots) remain ambiguous and differ depending on analytical approaches and datasets used. Complete genomes potentially provide opportunities to resolve these uncertainties, but two recently published magnoliid genomes instead deliver further conflicting signals. To disentangle key angiosperm relationships, we report a high-quality draft genome for the soursop (Annona muricata, Annonaceae). We reconstructed phylogenomic trees and show that the soursop represents a genomic mosaic supporting different histories, with scaffolds almost exclusively supporting single topologies. However, coalescent methods and a majority of genes support magnoliids as sister to monocots and eudicots, where previous whole genome-based studies remained inconclusive. This result is clear and consistent with recent studies using plastomes. The soursop genome highlights the need for more early diverging angiosperm genomes and critical assessment of the suitability of such genomes for inferring evolutionary history.

Synthesising trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Despite the well-recognised importance of traits for addressing ecological and evolutionary questions, trait-based approaches still struggle with several basic data requirements to deliver openly accessible, reproducible, and transparent science. Here, we introduce the Open Traits Network (OTN) – a decentralised alliance of international researchers and institutions focused on collaborative integration and standardisation of the exponentially increasing availability of trait data across all organisms. The OTN embraces the use of Open Science principles in trait research, particularly open data, open source, and open methodology protocols and workflows, to accelerate the synthesis of trait data across the Tree of Life. Increased efforts at all levels – from individual scientists, research networks, scientific societies, funding agencies, to publishers – are necessary to fully exploit the opportunities offered by Open Science in trait research. Democratising access to data, tools and resources will facilitate rapid advances in the biological sciences and our ability to address pressing environmental and societal demands.

Aim: Ecologically driven diversification can create spectacular diversity in both species numbers and form. However, the prediction that the match between intrinsic (e.g. functional trait) and extrinsic (e.g. climatic niche) variables may lead to evolutionary radiation has not been critically tested. Here, we test this hypothesis in the Southern Hemisphere plant family Proteaceae, which shows a spectacular diversity in open mediterranean shrublands in the Southwest Australian Floristic Region (SWAFR) and the Cape Floristic Region (CFR). Species in the Proteaceae family occupy habitats ranging from tropical rain forests to deserts and are remarkably variable in leaf morphology. Location: Southern Hemisphere. Methods: We built a phylogenetic tree for 337 Proteaceae species (21% of the total), representing all main clades, climatic tolerances and morphologies, and collected leaf functional traits (leaf area, sclerophylly, leaf shape) for 261 species and climatic niche data for 1645 species. Phylogenetic generalized least squares regression and quantitative-trait evolutionary model testing were used to investigate the evolutionary pathways of traits and climatic niches, and their effect on diversification rates. Results: We found that divergent selection may have caused lineages in open vegetation types to evolve towards trait and climatic niche optima distinct from those in closed forests. Furthermore, we show that the interaction between open habitats, dry, warm and/or mediterranean climates, and small, sclerophyllous, toothed leaves increases net diversification rates in Proteaceae. Main conclusions: Our results suggest that the evolution of specific leaf adaptations may have allowed Proteaceae to adapt to variable climatic niches and diversify extensively in open ecosystems such as those in the CFR and SWAFR. This match between morphology and environment may therefore more generally lead to evolutionary radiation.

The first molecular phylogenies of the flowering plant family Ranunculaceae were published more than twenty years ago, and have led to major changes in the infrafamilial classification. However, the current phylogeny is not yet well supported, and relationships among subfamilies and tribes of Ranunculaceae remain an open question. Eight molecular markers from the three genomes (nuclear, chloroplast and mitochondrial) were selected to investigate these relationships, including new markers for the family (two homologs of the nuclear CYCLOIDEA gene, the chloroplast gene ndhF, and the mitochondrial intron nad4-I1). The combination of multiple markers led to better resolution and higher support of phylogenetic relationships among subfamilies of Ranunculaceae, and among tribes within subfamily Ranunculoideae. Our results challenge the monophyly of Ranunculoideae as currently circumscribed due to the position of tribe Adonideae (Ranunculoideae), sister to Thalictroideae. We suggest that Thalictroideae could be merged with Ranunculoideae in an enlarged single subfamily.

In the version of this Perspective originally published, the first author of reference 39 was incorrectly listed as W. Cornwell and the publication year was incorrect. The reference should have read as follows: “Flores-Moreno, H. et al. fungaltraits aka funfun: a dynamic functional trait database for the world's fungi (GitHub, 2019); https://doi.org/10.5281/zenodo.1216257”. This has now been corrected.

Species diversity is remarkably unevenly distributed among flowering plant lineages. Despite a growing toolbox of research methods, the reasons underlying this patchy pattern have continued to perplex plant biologists for the past two decades. In this review, we examine the present understanding of transitions in flowering plant evolution that have been proposed to influence speciation and extinction. In particular, ploidy changes, transitions between tropical and nontropical biomes, and shifts in floral form have received attention and have offered some surprises in terms of which factors influence speciation and extinction rates. Mating systems and dispersal characteristics once predominated as determining factors, yet recent evidence suggests that these changes are not as influential as previously thought or are important only when paired with range shifts. Although range extent is an important correlate of speciation, it also influences extinction and brings an applied focus to diversification research. Recent studies that find that past diversification can predict present-day extinction risk open an exciting avenue for future research to help guide conservation prioritization.

Premise of research. The patterns of diversification of Mascarene taxa remain largely unknown in comparison to other insular systems. Traditional interpretations of insular radiations often assume that endemic taxa radiated after the origin of the insular habitats on which they were established. The Dombeyoideae (Malvaceae) sublineage endemic to Mauritius and Reunion in the Mascarenes is an ideal model to test for the signature of insular diversification.Methodology. We combined molecular sequences for a dense sample of Mascarene dombeyoids together with African, Malagasy, and Asian outgroup species. We estimated divergence times based on two calibration schemes (including or excluding geological calibration). Comparative phylogenetic methods were used to study the diversification rates and the evolution of the floral disparity in the Mascarene clade.Pivotal results. Excluding geological constraints resulted in drastically older age estimates than when we included such calibrations. Diversification patter...

Background and aims Although dioecy, which characterizes only 6 % of angiosperm species, has been considered an evolutionary dead end, recent studies have demonstrated that this is not necessarily the case. Moraceae (40 genera, 1100 spp., including Ficus, 750 spp.) are particularly diverse in breeding systems (including monoecy, gynodioecy, androdioecy and dioecy) and thus represent a model clade to study macroevolution of dioecy. Methods Ancestral breeding systems of Ficus and Moraceae were inferred. To do so, a new dated phylogenetic tree of Ficus and Moraceae was first reconstructed by combining a revised 12-fossil calibration set and a densely sampled molecular data set of eight markers and 320 species. Breeding system evolution was then reconstructed using both parsimony and model-based (maximum likelihood and Bayesian) approaches with this new time scale. Key results The crown group ages of Ficus and Moraceae were estimated in the Eocene (40.6-55.9 Ma) and Late Cretaceous (73.2-84.7 Ma), respectively. Strong support was found for ancestral dioecy in Moraceae. Although the ancestral state of Ficus remained particularly sensitive to model selection, the results show that monoecy and gynodioecy evolved from dioecy in Moraceae, and suggest that gynodioecy probably evolved from monoecy in Ficus. Conclusions Dioecy was found not to be an evolutionary dead end in Moraceae. This study provides a new time scale for the phylogeny and a new framework of breeding system evolution in Ficus and Moraceae.

The staggering diversity of angiosperms and their flowers has fascinated scientists for centuries. However, the quantitative distribution of floral morphological diversity (disparity) among lineages and the relative contribution of functional modules (perianth, androecium and gynoecium) to total floral disparity have rarely been addressed. Focusing on a major angiosperm order (Ericales), we compiled a dataset of 37 floral traits scored for 381 extant species and nine fossils. We conducted morphospace analyses to explore phylogenetic, temporal and functional patterns of disparity. We found that the floral morphospace is organized as a continuous cloud in which most clades occupy distinct regions in a mosaic pattern, that disparity increases with clade size rather than age, and that fossils fall in a narrow portion of the space. Surprisingly, our study also revealed that among functional modules, it is the androecium that contributes most to total floral disparity in Ericales. We discuss our findings in the light of clade history, selective regimes as well as developmental and functional constraints acting on the evolution of the flower and thereby demonstrate that quantitative analyses such as the ones used here are a powerful tool to gain novel insights into the evolution and diversity of flowers.

A recommendation of: Emmanuelle Jousselin, Marianne Elias Testing host-plant driven speciation in phytophagous insects : a phylogenetic perspective https://arxiv.org/abs/1910.09510v1

An early Eocene (52 ± 2 Ma) flora from the Mwadui kimberlite pipe in Tanzania includes ten leaf morphotypes, small seeds, fossil wood putatively related to Cynometra (Detarieae, Fabaceae), and a sparse palynoflora. The leaf flora is characterised by microphyllous and notophyllous entire margined leaves that are suggested to be related to the Euphorbiaceae and Fabaceae, although many cannot be firmly placed in modern families. The wood is the oldest member of Cynometroxylon and confirms that the Detarieae were diverse by the early Paleogene. The palynoflora is dominated by Ailanthipites daedaleus and Triporopollenites mwaduiensis with lesser amounts of small tricolpate ( Tricolpites ) and monosulcate ( Lilliacidites ) grains together with spores ( Cyathidites spp., Triporoletes laevigatus ) and freshwater algal cysts. Other components of the palynoresidue include abundant charcoalified tracheids and fungal hyphae. The low diversity and sparse palynoflora suggests a restricted catchment with little input from the regional vegetation. The sediments accumulated in a freshwater lacustrine environment with palynological input from the crater walls that were covered by low diversity vegetation. This is supported by the leaf floras. Although the leaf floras are more diverse with nine morphotypes identified, the small leaves (microphyll to notophyll) suggest a water-limited palaeoenvironment. This is supported by the low diversity and abundance of fern and bryophyte spores. The presence of a single wood taxon not only indicates that there were large trees around the crater-lake but that the aboreal component was of low diversity. These observations suggest an open woodland-like setting, while the taxonomic affinities of the wood ( Cynometra ) suggest a humid microclimate possibly with marked wet–dry seasonal contrasts.

Molecular dating has now become a common tool for many biologists and considerable methodological improvements have been made over the last few years. However, the practice of estimating divergence times using molecular data is highly variable among researchers and it is not straightforward for a newcomer to the field to know how to start. Here I provide a brief overview of the current state-of-the-art of molecular dating practice. I review some of the important choices that must be made when conducting a divergence time analysis, including how to select and use calibrations and which relaxed clock model and program to use, with a focus on some practical aspects. I then provide some guidelines for the interpretation of results and briefly review some alternatives to molecular dating for obtaining divergence times. Last, I present some promising developments for the future of the field, related to the improvement of the calibration process.

Dating the Tree of Life has now become central to relating patterns of biodiversity to key processes in Earth history such as plate tectonics and climate change. Regions with a Mediterranean climate have long been noted for their exceptional species richness and high endemism. How and when these biota assembled can only be answered with a good understanding of the sequence of divergence times for each of their components. A critical aspect of dating by using molecular sequence divergence is the incorporation of multiple suitable age constraints. Here, we show that only rigorous phylogenetic analysis of fossil taxa can lead to solid calibration and, in turn, stable age estimates, regardless of which of 3 relaxed clock-dating methods is used. We find that Proteaceae, a model plant group for the Mediterranean hotspots of the Southern Hemisphere with a very rich pollen fossil record, diversified under higher rates in the Cape Floristic Region and Southwest Australia than in any other area of their total distribution. Our results highlight key differences between Mediterranean hotspots and indicate that Southwest Australian biota are the most phylogenetically diverse but include numerous lineages with low diversification rates.

Aim The flowering plant family Proteaceae is putatively of Gondwanan age, with modern and fossil lineages found on all southern continents. Here we test whether the present distribution of Proteaceae can be explained by vicariance caused by the break-up of Gondwana. Location Africa, especially southern Africa, Australia, New Zealand, South America, New Caledonia, New Guinea, Southeast Asia, Sulawesi, Tasmania. Methods We obtained chloroplast DNA sequence data from the rbcL gene, the rbcL-atpB spacer, and the atpB gene from leaf samples of forty-five genera collected from the field and from living collections. We analysed these data using Bayesian phylogenetic and molecular dating methods, with five carefully selected fossil calibration points to obtain age estimates for the nodes within the family. Results Four of eight trans-continental disjunctions of sister groups within our sample of the Proteaceae post-date the break-up of Gondwana. These involve independent lineages, two with an Africa-Australia disjunction, one with an Africa–South America disjunction, and one with a New Zealand–Australasia disjunction. The date of the radiation of the bird-pollinated Embothriinae corresponds approximately to the hypothesized date of origin of nectar-feeding birds in Australia. Main conclusions The findings suggest that disjunct distributions in Proteaceae result from both Gondwanan vicariance and transoceanic dispersal. Our results imply that ancestors of some taxa dispersed across oceans rather than rafting with Gondwanan fragments as previously thought. This finding agrees with other studies of Gondwanan plants in dating the divergence of Australian, New Zealand and New Caledonian taxa in the Eocene, consistent with the existence of a shared, ancestral Eocene flora but contrary to a vicariance scenario based on accepted geological knowledge.

Proteoideae (27 genera, 655 species) are one of the largest clades in the early-diverging eudicot family Proteaceae and are distributed in Australia, New Caledonia, and Africa. New palynological observations using scanning and transmission electron microscopy are reported for 15 genera and 49 species, which complement previous work on the subfamily. These are integrated with an extensive review of all literature data available to provide a summary of pollen morphology and variation in each genus of Proteoideae, using a new rigorous method of character scoring. The results are discussed in the context of recent phylogenetic analyses of Proteaceae. The monophyletic Leucadendreae, comprising two Australian genera and a large clade of 10 southern African genera, appear to be relatively homogenous in pollen morphology, especially in ultrastructure of the apertural region. In addition, two other African genera, Faurea and Protea, share very similar pollen characters, some of which appear to be apomorphic, consistent with strong phylogenetic evidence for their sister group relationship. Beauprea, Eidothea, Faurea, Protea, and Stirlingia share a distinct pattern of foot layer disintegration at the apertural region and complete lack of endexine. The occurrence of the same apertural type in the early-diverging Persoonioideae suggests that it is plesiomorphic in Proteoideae and Proteaceae as a whole. This study highlights the phylogenetic potential of ultrastructural characters in Proteaceae and high levels of homoplasy and polymorphism in other characters including pollen shape and tectum sculptural patterns.

Background With 10,000 species, Magnoliidae are the largest clade of flowering plants outside monocots and eudicots. Despite an ancient and rich fossil history, the tempo and mode of diversification of Magnoliidae remain poorly known. Using a molecular data set of 12 markers and 220 species (representing >75% of genera in Magnoliidae) and six robust, internal fossil age constraints, we estimate divergence times and significant shifts of diversification across the clade. In addition, we test the sensitivity of magnoliid divergence times to the choice of relaxed clock model and various maximum age constraints for the angiosperms. Results Compared with previous work, our study tends to push back in time the age of the crown node of Magnoliidae (178.78-126.82 million years, Myr), and of the four orders, Canellales (143.18-125.90 Myr), Piperales (158.11-88.15 Myr), Laurales (165.62-112.05 Myr), and Magnoliales (164.09-114.75 Myr). Although families vary in crown ages, Magnoliidae appear to have diversified into most extant families by the end of the Cretaceous. The strongly imbalanced distribution of extant diversity within Magnoliidae appears to be best explained by models of diversification with 6 to 13 shifts in net diversification rates. Significant increases are inferred within Piperaceae and Annonaceae, while the low species richness of Calycanthaceae, Degeneriaceae, and Himantandraceae appears to be the result of decreases in both speciation and extinction rates. Conclusions This study provides a new time scale for the evolutionary history of an important, but underexplored, part of the tree of angiosperms. The ages of the main clades of Magnoliidae (above the family level) are older than previously thought, and in several lineages, there were significant increases and decreases in net diversification rates. This study is a new robust framework for future investigations of trait evolution and of factors influencing diversification in this group as well as angiosperms as a whole. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0320-6) contains supplementary material, which is available to authorized users.

Morphospaces are mathematical representations used for studying the evolution of morphological diversity and for the evaluation of evolved shapes among theoretically possible ones. Although widely used in zoology, they – with few exceptions – have been disregarded in plant science and in particular in the study of broad-scale patterns of floral structure and evolution. Here we provide basic information on the morphospace approach; we review earlier morphospace applications in plant science; and as a practical example, we construct and analyze a floral morphospace. Morphospaces are usually visualized with the help of ordination methods such as principal component analysis (PCA) or nonmetric multidimensional scaling (NMDS). The results of these analyses are then coupled with disparity indices that describe the spread of taxa in the space. We discuss these methods and apply modern statistical tools to the first and only angiosperm-wide floral morphospace published by Stebbins in 1951. Despite the incompleteness of Stebbins’ original dataset, our analyses highlight major, angiosperm-wide trends in the diversity of flower morphology and thereby demonstrate the power of this previously neglected approach in plant science.

The systematics of Malagasy Myristicaceae is revised to take into account new collections made since the work by Capuron in the 1970s, as well as improved knowledge from fieldwork and two scanning electron microscopy studies by the author. Four new species are described: Mauloutchia annickiae Sauquet, M. capuronii Sauquet, M. echinocarpa Capuron ex Sauquet, and M. sambiranensis (Capuron) Sauquet. In addition, basic information is given for each remaining Malagasy species of the family (synonymy, type specimen, updated distribution and main distinctive features). According to this treatment, Malagasy Myristicaceae now consist of four endemic genera and 15 species: Brochoneura Warb. (three species), Doyleanthus Sauquet (one species), Haematodendron Capuron (one species) and Mauloutchia (Baill.) Warb. (ten species). Two identification keys to these species are provided: one based primarily on fruit characters and one based primarily on male flower and inflorescence characters. Putative phylogenetic relationships among these species are also indicated, based on a previous combined morphological and molecular study by the author. © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society, 2004, 146, 351–368.