Phylogenomics and the rise of the angiosperms

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.

A latitudinal gradient in Darwin's naturalization conundrum at the global scale for flowering plants

Darwin's naturalization conundrum describes two seemingly contradictory hypotheses regarding whether alien species closely or distantly related to native species should be more likely to naturalize in regional floras. Both expectations have accumulated empirical support, and whether such apparent inconsistency can be reconciled at the global scale is unclear. Here, using 219,520 native and 9,531 naturalized alien plant species across 487 globally distributed regions, we found a latitudinal gradient in Darwin's naturalization conundrum. Naturalized alien plant species are more closely related to native species at higher latitudes than they are at lower latitudes, indicating a greater influence of preadaptation in harsher climates. Human landscape modification resulted in even steeper latitudinal clines by selecting aliens distantly related to natives in warmer and drier regions. Our results demonstrate that joint consideration of climatic and anthropogenic conditions is critical to reconciling Darwin's naturalization conundrum.

Phylogenomic inference of the African tribe Monodoreae (Annonaceae) and taxonomic revision of Dennettia, Uvariodendron and Uvariopsis

Monodoreae (Annonaceae) is a tribe composed of 11 genera and 90 species restricted to the tropical African rain forests. All the genera are taxonomically well circumscribed except the species rich genera Uvariodendron and Uvariopsis which lack a recent taxonomic revision. Here, we used a robust phylogenomic approach, including all the 90 currently accepted species, with several specimens per species, and based on more than 300 Annonaceae-specific nuclear genes, to infer the phylogenetic tree of the Monodoreae and test the limits between the genera and species. We recover all the genera as monophyletic, except the genus Uvariopsis for which the species Uvariopsistripetala falls outside this clade. We thus reinstate the monotypic genus Dennettia for its single species Dennettiatripetala. We also erect a new tribe, Ophrypetaleae trib. nov., to accommodate the genera Ophrypetalum and Sanrafaelia, as we recover them excluded from the Monodoreae tribe with good support. Below the genus level, the genera Isolona, Monodora, Uvariastrum, Uvariodendron and Uvariopsis show weakly supported nodes and phylogenetic conflicts, suggesting that population level processes of evolution might occur in these clades. Our results also support, at the molecular level, the description of several new species of Uvariodendron and Uvariopsis, as well as several new synonymies. Finally, we present a taxonomic revision of the genera Dennettia, Uvariodendron and Uvariopsis, which contain one, 18 and 17 species respectively. We provide a key to the 11 genera of the Monodoraeae and describe four new species to science: Uvariodendronkimbozaense Dagallier & Couvreur, sp. nov., Uvariodendronmossambicense Robson ex Dagallier & Couvreur, sp. nov., Uvariodendronpilosicarpum Dagallier & Couvreur, sp. nov. and Uvariopsisoligocarpa Dagallier & Couvreur, sp. nov., and provide provisional descriptions of three putatively new species. We also present lectotypifications and nomenclatural changes implying synonymies and new combinations (Uvariodendroncitriodorum (Le Thomas) Dagallier & Couvreur, comb. et stat. nov., Uvariodendronfuscumvar.magnificum (Verdc.) Dagallier & Couvreur, comb. et stat. nov., Uvariopsiscongensisvar.angustifolia Dagallier & Couvreur, var. nov., Uvariopsisguineensisvar.globiflora (Keay) Dagallier & Couvreur, comb. et stat. nov., and Uvariopsissolheidiivar.letestui (Pellegr.) Dagallier & Couvreur, comb. et stat. nov.).

Global models and predictions of plant diversity based on advanced machine learning techniques

Despite the paramount role of plant diversity for ecosystem functioning, biogeochemical cycles, and human welfare, knowledge of its global distribution is still incomplete, hampering basic research and biodiversity conservation. Here, we used machine learning (random forests, extreme gradient boosting, and neural networks) and conventional statistical methods (generalized linear models and generalized additive models) to test environment-related hypotheses of broad-scale vascular plant diversity gradients and to model and predict species richness and phylogenetic richness worldwide. To this end, we used 830 regional plant inventories including c. 300 000 species and predictors of past and present environmental conditions. Machine learning showed a superior performance, explaining up to 80.9% of species richness and 83.3% of phylogenetic richness, illustrating the great potential of such techniques for disentangling complex and interacting associations between the environment and plant diversity. Current climate and environmental heterogeneity emerged as the primary drivers, while past environmental conditions left only small but detectable imprints on plant diversity. Finally, we combined predictions from multiple modeling techniques (ensemble predictions) to reveal global patterns and centers of plant diversity at multiple resolutions down to 7774 km² . Our predictive maps provide accurate estimates of global plant diversity available at grain sizes relevant for conservation and macroecology.

Selecting the best candidates for resurrecting extinct-in-the-wild plants from herbaria

Resurrecting extinct species is a fascinating and challenging idea for scientists and the general public. Whereas some theoretical progress has been made for animals, the resurrection of extinct plants (de-extinction sensu lato) is a relatively recently discussed topic. In this context, the term 'de-extinction' is used sensu lato to refer to the resurrection of 'extinct in the wild' species from seeds or tissues preserved in herbaria, as we acknowledge the current impossibility of knowing a priori whether a herbarium seed is alive and can germinate. In plants, this could be achieved by germinating or in vitro tissue-culturing old diaspores such as seeds or spores available in herbarium specimens. This paper reports the first list of plant de-extinction candidates based on the actual availability of seeds in herbarium specimens of globally extinct plants. We reviewed globally extinct seed plants using online resources and additional literature on national red lists, resulting in a list of 361 extinct taxa. We then proposed a method of prioritizing candidates for seed-plant de-extinction from diaspores found in herbarium specimens and complemented this with a phylogenetic approach to identify species that may maximize evolutionarily distinct features. Finally, combining data on seed storage behaviour and longevity, as well as specimen age in the novel 'best de-extinction candidate' score (DEXSCO), we identified 556 herbarium specimens belonging to 161 extinct species with available seeds. We expect that this list of de-extinction candidates and the novel approach to rank them will boost research efforts towards the first-ever plant de-extinction.

The Herbarium 2021 Half-Earth Challenge Dataset and Machine Learning Competition

Herbarium sheets present a unique view of the world's botanical history, evolution, and biodiversity. This makes them an all-important data source for botanical research. With the increased digitization of herbaria worldwide and advances in the domain of fine-grained visual classification which can facilitate automatic identification of herbarium specimen images, there are many opportunities for supporting and expanding research in this field. However, existing datasets are either too small, or not diverse enough, in terms of represented taxa, geographic distribution, and imaging protocols. Furthermore, aggregating datasets is difficult as taxa are recognized under a multitude of names and must be aligned to a common reference. We introduce the Herbarium 2021 Half-Earth dataset: the largest and most diverse dataset of herbarium specimen images, to date, for automatic taxon recognition. We also present the results of the Herbarium 2021 Half-Earth challenge, a competition that was part of the Eighth Workshop on Fine-Grained Visual Categorization (FGVC8) and hosted by Kaggle to encourage the development of models to automatically identify taxa from herbarium sheet images.

The global loss of floristic uniqueness

Regional species assemblages have been shaped by colonization, speciation and extinction over millions of years. Humans have altered biogeography by introducing species to new ranges. However, an analysis of how strongly naturalized plant species (i.e. alien plants that have established self-sustaining populations) affect the taxonomic and phylogenetic uniqueness of regional floras globally is still missing. Here, we present such an analysis with data from native and naturalized alien floras in 658 regions around the world. We find strong taxonomic and phylogenetic floristic homogenization overall, and that the natural decline in floristic similarity with increasing geographic distance is weakened by naturalized species. Floristic homogenization increases with climatic similarity, which emphasizes the importance of climate matching in plant naturalization. Moreover, floristic homogenization is greater between regions with current or past administrative relationships, indicating that being part of the same country as well as historical colonial ties facilitate floristic exchange, most likely due to more intensive trade and transport between such regions. Our findings show that naturalization of alien plants threatens taxonomic and phylogenetic uniqueness of regional floras globally. Unless more effective biosecurity measures are implemented, it is likely that with ongoing globalization, even the most distant regions will lose their floristic uniqueness.

Areas of global importance for conserving terrestrial biodiversity, carbon and water

To meet the ambitious objectives of biodiversity and climate conventions, the international community requires clarity on how these objectives can be operationalized spatially and how multiple targets can be pursued concurrently. To support goal setting and the implementation of international strategies and action plans, spatial guidance is needed to identify which land areas have the potential to generate the greatest synergies between conserving biodiversity and nature's contributions to people. Here we present results from a joint optimization that minimizes the number of threatened species, maximizes carbon retention and water quality regulation, and ranks terrestrial conservation priorities globally. We found that selecting the top-ranked 30% and 50% of terrestrial land area would conserve respectively 60.7% and 85.3% of the estimated total carbon stock and 66% and 89.8% of all clean water, in addition to meeting conservation targets for 57.9% and 79% of all species considered. Our data and prioritization further suggest that adequately conserving all species considered (vertebrates and plants) would require giving conservation attention to ~70% of the terrestrial land surface. If priority was given to biodiversity only, managing 30% of optimally located land area for conservation may be sufficient to meet conservation targets for 81.3% of the terrestrial plant and vertebrate species considered. Our results provide a global assessment of where land could be optimally managed for conservation. We discuss how such a spatial prioritization framework can support the implementation of the biodiversity and climate conventions.

Phylogenomics resolves deep subfamilial relationships in Malvaceae s.l

Malvaceae s.l., the most diverse family within Malvales, includes well-known species of great economic importance like cotton, cacao, and durian. Despite numerous phylogenetic analyses employing multiple markers, relationships between several of its nine subfamilies, particularly within the largest lineage /Malvadendrina, remain unclear. In this study, we attempted to resolve the relationships within the major clades of Malvaceae s.l. using plastid genomes of 48 accessions representing all subfamilies. Maximum likelihood and Bayesian analyses recovered a fully resolved and well-supported topology confirming the split of the family into /Byttneriina (/Grewioideae +/Byttnerioideae) and /Malvadendrina. Within /Malvadendrina, /Helicteroideae occupied the earliest branching position, followed by /Sterculioideae, /Brownlowioideae, /Tiliodeae, and /Dombeyoideae formed a clade sister to /Malvatheca (/Malvoideae +/Bombacoideae), a grouping morphologically supported by the lack of androgynophore. Results from dating analyses suggest that all subfamilies originated during hot or warm phases in the Late Cretaceous to Paleocene. This study presents a well-supported phylogenetic framework for Malvaceae s.l. that will aid downstream revisions and evolutionary studies of this economically important plant family.

Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna

Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.

Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments.

Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate

Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments.

The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous-Paleogene (K-Pg) Mass Extinction Event

The consequences of the Cretaceous–Paleogene (K–Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic. [Allopolyploidy; Cretaceous–Paleogene (K–Pg) boundary; Fabaceae, Leguminosae; paleopolyploidy; phylogenomics; whole genome duplication events]

Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea

Natural history collections and tropical tree diversity are both treasure troves of biological and evolutionary information, but their accessibility for scientific study is impeded by a number of properties. DNA in historical specimens is generally highly fragmented, complicating the recovery of high-grade genetic material. Furthermore, our understanding of hyperdiverse, wide-spread tree assemblages is obstructed by extensive species ranges, fragmented knowledge of tropical tree diversity and phenology, and a widespread lack of species-level diagnostic characters, prohibiting the collecting of readily identifiable specimens which can be used to build, revise or strengthen taxonomic frameworks. This, in turn, delays the application of downstream conservation action. A sizable component of botanical collections are sterile-thus eluding identification and are slowing down progress in systematic treatments of tropical biodiversity. With rapid advances in genomics and bioinformatic approaches to biodiversity research, museomics is emerging as a new field breathing life into natural collections that have been built up over centuries. Using MIGseq (multiplexed ISSR genotyping by sequencing), we generated 10,000s of short loci, for both freshly collected materials and museum specimens (aged >100 years) of Lithocarpus-a widespread tropical tree genus endemic to the Asian tropics. Loci recovery from historical and recently collected samples was not affected by sample age and preservation history of the study material, underscoring the reliability and flexibility of the MIGseq approach. Phylogenomic inference and biogeographic reconstruction across insular Asia, highlights repeated migration and diversification patterns between continental regions and islands. Results indicate that co-occurring insular species at the extremity of the distribution range are not monophyletic, raising the possibility of multiple independent dispersals along the outer edge of Wallacea. This suggests that dispersal of large seeded tree genera throughout Malesia and across Wallacea may have been less affected by large geographic distances and the presence of marine barriers than generally assumed. We demonstrate the utility of MIGseq in museomic studies using non-model taxa, presenting the first range-wide genomic assessment of Lithocarpus and tropical Fagaceae as a proof-of-concept. Our study shows the potential for developing innovative genomic approaches to improve the capture of novel evolutionary signals using valuable natural history collections of hyperdiverse taxa.

Plastome phylogeography in two African rain forest legume trees reveals that Dahomey Gap populations originate from the Cameroon volcanic line

Paleo-environmental data show that the distribution of African rain forests was affected by Quaternary climate changes. In particular, the Dahomey Gap (DG) - a 200 km wide savanna corridor currently separating the West African and Central African rain forest blocks and containing relict rain forest fragments - was forested during the mid-Holocene and possibly during previous interglacial periods, whereas it was dominated by open vegetation (savanna) during glacial periods. Genetic signatures of past population fragmentation and demographic changes have been found in some African forest plant species using nuclear markers, but such events appear not to have been synchronous or shared across species. To better understand the colonization history of the DG by rain forest trees through seed dispersal, the plastid genomes of two widespread African forest legume trees, Anthonotha macrophylla and Distemonanthus benthamianus, were sequenced in 47 individuals for each species, providing unprecedented phylogenetic resolution of their maternal lineages (857 and 115 SNPs, respectively). Both species exhibit distinct lineages separating three regions: 1. Upper Guinea (UG, i.e. the West African forest block), 2. the area ranging from the DG to the Cameroon volcanic line (CVL), and 3. Lower Guinea (LG, the western part of the Central African forest block) where three lineages co-occur. In both species, the DG populations (including southern Nigeria west of Cross River) exhibit much lower genetic diversity than UG and LG populations, and their plastid lineages originate from the CVL, confirming the role of the CVL as an ancient forest refuge. Despite the similar phylogeographic structures displayed by A. macrophylla and D. benthamianus, molecular dating indicates very contrasting ages of lineage divergence (UG diverged from LG since c. 7 Ma and 0.7 Ma, respectively) and DG colonization (probably following the Mid Pleistocene Transition and the Last Glacial Maximum, respectively). The stability of forest refuge areas and repeated similar forest shrinking/expanding events during successive glacial periods might explain why similar phylogeographic patterns can be generated over contrasting timescales.

Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus Raphia (Calamoideae, Arecaceae)

Palms are conspicuous floristic elements across the tropics. In continental Africa, even though there are less than 70 documented species, they are omnipresent across the tropical landscape. The genus Raphia has 20 accepted species in Africa and one species endemic to the Neotropics. It is the most economically important genus of African palms with most of its species producing food and construction material. Raphia is divided into five sections based on inflorescence morphology. Nevertheless, the taxonomy of Raphia is problematic with no intra-generic phylogenetic study available. We present a phylogenetic study of the genus using a targeted exon capture approach sequencing of 56 individuals representing 18 out of the 21 species. Our results recovered five well supported clades within the genus. Three sections correspond to those based on inflorescence morphology. R. regalis is strongly supported as sister to all other Raphia species and is placed into a newly described section: Erectae. Overall, morphological based identifications agreed well with our phylogenetic analyses, with 12 species recovered as monophyletic based on our sampling. Species delimitation analyses recovered 17 or 23 species depending on the confidence level used. Species delimitation is especially problematic in the Raphiate and Temulentae sections. In addition, our clustering analysis using SNP data suggested that individual clusters matched geographic distribution. The Neotropical species R. taedigera is supported as a distinct species, rejecting the hypothesis of a recent introduction into South America. Our analyses support the hypothesis that the Raphia individuals from Madagascar are potentially a distinct species different from the widely distributed R. farinifera. In conclusion, our results support the infra generic classification of Raphia based on inflorescence morphology, which is shown to be phylogenetically useful. Classification and species delimitation within sections remains problematic even with our phylogenomic approach. Certain widely distributed species could potentially contain cryptic species. More in-depth studies should be undertaken using morphometrics, increased sampling, and more variable markers. Our study provides a robust phylogenomic framework that enables further investigation on the biogeographic history, morphological evolution, and other eco-evolutionary aspects of this charismatic, socially, and economically important palm genus.

Cradles and museums of generic plant diversity across tropical Africa

Determining where species diversify (cradles) and persist (museums) over evolutionary time is fundamental to understanding the distribution of biodiversity and for conservation prioritization. Here, we identify cradles and museums of angiosperm generic diversity across tropical Africa, one of the most biodiverse regions on Earth. Regions containing nonrandom concentrations of young (neo-) and old (paleo-) endemic taxa were identified using distribution data of 1719 genera combined with a newly generated time-calibrated mega-phylogenetic tree. We then compared the identified regions with the current network of African protected areas (PAs). At the generic level, phylogenetic diversity and endemism are mainly concentrated in the biogeographically complex region of Eastern Africa. We show that mountainous areas are centres of both neo- and paleo-endemism. By contrast, the Guineo-Congolian lowland rain forest region is characterized by widespread and old lineages. We found that the overlap between centres of phylogenetic endemism and PAs is high (> 85%). We show the vital role played by mountains acting simultaneously as cradles and museums of tropical African plant biodiversity. By contrast, lowland rainforests act mainly as museums for generic diversity. Our study shows that incorporating large-scale taxonomically verified distribution datasets and mega-phylogenies lead to an improved understanding of tropical plant biodiversity evolution.

Phylogeny and biogeography of the Daniellia clade (Leguminosae: Detarioideae), a tropical tree lineage largely threatened in Africa and Madagascar

The legume subfamily Detarioideae is exceptionally diverse in tropical Africa and Madagascar, compared to South America or Asia, a trend contrary to that shown by most other pantropical plant groups. We aim to elucidate the process of diversification giving rise to these high diversity levels by focussing our investigations on the Daniellia clade, which is present in both Africa and Madagascar. The Daniellia clade is an early-diverging lineage of subfamily Detarioideae (Leguminosae; pea family) and consists of three genera: Daniellia, Brandzeia and Neoapaloxylon. The species belonging to this group exhibit a wide range of habitat types. The Madagascar endemics Brandzeia (1 species) and Neoapaloxylon (3 species) occupy dry woodlands and arid succulent habitats respectively. Daniellia alsteeniana and D. oliveri are found in savannahs while the remaining eight species within Daniellia all occupy rainforest habitats. Phylogenetic analyses were generated from a dense, multi-individual species level sampling of the clade. Divergence time estimates were carried out using a molecular clock method to investigate biogeographical patterns and shifts in habitat types within the Daniellia clade, and conservation assessments were conducted to determine the levels of extinction risks these species are facing. We estimate that the Daniellia clade first emerged during the Early Eocene from an ancestor present in the rainforests of North Africa at that time, reflecting an ancestral habitat preference. There was a first major split over the course of the Eocene, giving rise to both African rainforest and Madagascan savannah lineages. With the emergence of a drier climate and vegetation type in Africa during the Eocene, it is likely that a dry-climate adapted lineage from the Daniellia clade ancestor could have dispersed through suitable savannah or woodland regions to reach Madagascar, subsequently giving rise to the savannah-adapted ancestor of Brandzeia and Neoapaloxylon in the Early Miocene. The African rainforest lineage gave rise to the genus Daniellia, which is postulated to have first diversified in the Middle Miocene, while savannah species of Daniellia emerged independently during the Pliocene, coinciding with the global rise of C4-dominated grasslands. More than half of the species in the Daniellia clade are near threatened or threatened, which highlights the need to understand the threats of anthropogenic pressures and climate change these species are facing to prioritise their conservation.

Large-scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near-simultaneous evolutionary origin of all six subfamilies

Phylogenomics is increasingly used to infer deep-branching relationships while revealing the complexity of evolutionary processes such as incomplete lineage sorting, hybridization/introgression and polyploidization. We investigate the deep-branching relationships among subfamilies of the Leguminosae (or Fabaceae), the third largest angiosperm family. Despite their ecological and economic importance, a robust phylogenetic framework for legumes based on genome-scale sequence data is lacking. We generated alignments of 72 chloroplast genes and 7621 homologous nuclear-encoded proteins, for 157 and 76 taxa, respectively. We analysed these with maximum likelihood, Bayesian inference, and a multispecies coalescent summary method, and evaluated support for alternative topologies across gene trees. We resolve the deepest divergences in the legume phylogeny despite lack of phylogenetic signal across all chloroplast genes and the majority of nuclear genes. Strongly supported conflict in the remainder of nuclear genes is suggestive of incomplete lineage sorting. All six subfamilies originated nearly simultaneously, suggesting that the prevailing view of some subfamilies as 'basal' or 'early-diverging' with respect to others should be abandoned, which has important implications for understanding the evolution of legume diversity and traits. Our study highlights the limits of phylogenetic resolution in relation to rapid successive speciation.

The commonness of rarity: Global and future distribution of rarity across land plants

A key feature of life's diversity is that some species are common but many more are rare. Nonetheless, at global scales, we do not know what fraction of biodiversity consists of rare species. Here, we present the largest compilation of global plant diversity to quantify the fraction of Earth's plant biodiversity that are rare. A large fraction, ~36.5% of Earth's ~435,000 plant species, are exceedingly rare. Sampling biases and prominent models, such as neutral theory and the k-niche model, cannot account for the observed prevalence of rarity. Our results indicate that (i) climatically more stable regions have harbored rare species and hence a large fraction of Earth's plant species via reduced extinction risk but that (ii) climate change and human land use are now disproportionately impacting rare species. Estimates of global species abundance distributions have important implications for risk assessments and conservation planning in this era of rapid global change.

The Global Naturalized Alien Flora (GloNAF) database

This dataset provides the Global Naturalized Alien Flora (GloNAF) database, version 1.2. GloNAF represents a data compendium on the occurrence and identity of naturalized alien vascular plant taxa across geographic regions (e.g. countries, states, provinces, districts, islands) around the globe. The dataset includes 13,939 taxa and covers 1,029 regions (including 381 islands). The dataset is based on 210 data sources. For each taxon-by-region combination, we provide information on whether the taxon is considered to be naturalized in the specific region (i.e. has established self-sustaining populations in the wild). Non-native taxa are marked as "alien", when it is not clear whether they are naturalized. To facilitate alignment with other plant databases, we provide for each taxon the name as given in the original data source and the standardized taxon and family names used by The Plant List Version 1.1 (http://www.theplantlist.org/). We provide an ESRI shapefile including polygons for each region and information on whether it is an island or a mainland region, the country and the Taxonomic Databases Working Group (TDWG) regions it is part of (TDWG levels 1-4). We also provide several variables that can be used to filter the data according to quality and completeness of alien taxon lists, which vary among the combinations of regions and data sources. A previous version of the GloNAF dataset (version 1.1) has already been used in several studies on, for example, historical spatial flows of taxa between continents and geographical patterns and determinants of naturalization across different taxonomic groups. We intend the updated and expanded GloNAF version presented here to be a global resource useful for studying plant invasions and changes in biodiversity from regional to global scales. We release these data into the public domain under a Creative Commons Zero license waiver (https://creativecommons.org/share-your-work/public-domain/cc0/). When you use the data in your publication, we request that you cite this data paper. If GloNAF is a major part of the data analyzed in your study, you should consider inviting the GloNAF core team (see Metadata S1: Originators in the Overall project description) as collaborators. If you plan to use the GloNAF dataset, we encourage you to contact the GloNAF core team to check whether there have been recent updates of the dataset, and whether similar analyses are already ongoing.

Pollen morphology of the African Sclerosperma (Arecaceae)

Three currently accepted Sclerosperma species appear to produce four different pollen morphologies. Sclerosperma mannii and S. walkeri pollen share the same distinct reticulate sculpture, but S. profizianum produces three different pollen types (microreticulate, fossulate, and perforate). The pollen morphology suggests that S. mannii and S. walkeri are sister taxa of the same intrageneric lineage. The pollen diversity observed in S. profizianum suggests (a) this taxon is unique regarding its pollen diversity despite being a non-heterostylous plant or (b) that circumscription of S. profizianum as a species may well be in the need of redefinition.

Sclerosperma fossils from the late Oligocene of Chilga, north-western Ethiopia

The palm family, Arecaceae, is notoriously depauperate in Africa today, and its evolutionary, paleobiogeographic, and extinction history there are not well documented by fossils. In this article we report the pollen of two new extinct species of the small genus, Sclerosperma (Arecoideae), from a late Oligocene (27-28 Ma) stratum exposed along the Guang River in Chilga Wereda of north-western Ethiopia. The pollen are triporate, and the two taxa can be distinguished from each other and from modern species using a combination of light and scanning electron microscopy, which reveals variations in the finer details of their reticulate to perforate exine sculpture. We also report a palm leaf fragment from a stratum higher in the same section that is in the Arecoideae subfamily, and most likely belongs to Sclerosperma. The implications of these discoveries for the evolutionary history of this clade of African arecoid palms is that their diversification was well underway by the middle to late Oligocene, and they were much more widespread in Africa at that time than they are now, limited to West and Central Africa. Sclerosperma exhibits ecological conservatism, as today it occurs primarily in swamps and flooded forests, and the sedimentology of the Guang River deposits at Chilga indicate a heterogeneous landscape with a high water table. The matrix containing the fossil pollen is lignite, which itself indicates standing water, and a variety of plant macrofossils from higher in the section have been interpreted as representing moist tropical forest or seasonally inundated forest communities.

Floral evolution by simplification in Monanthotaxis (Annonaceae) and hypotheses for pollination system shifts

Simplification by reduction has occurred many times independently in the floral evolution of angiosperms. These reductions have often been attributed to changes in reproductive biology. In the angiosperm plant family Annonaceae, most species have flowers with six petals, and many stamens and carpels. In the genus Monanthotaxis several deviations from this pattern have been observed, including flowers that contain three petals and three stamens only. New DNA sequences were generated for 42 specimens of Monanthotaxis. Five chloroplast markers and two nuclear markers for 72 out of 94 species of Monanthotaxis were used to reconstruct a phylogeny of the genus, which revealed several well-supported, morphologically distinct clades. The evolution of four quantitative and two qualitative floral characters was mapped onto this phylogeny, demonstrating a reduction in flower size and number of flower parts in Monanthotaxis. A large variation in stamen forms and numbers, strong correlations between petal size, stamen and carpel number, combined with a non-gradual mode of evolution and the sympatric co-occurrence of Monanthotaxis species from different clades suggest that the high diversity in the African rainforest of this genus is caused by switches in pollination systems.

A new phylogeny-based tribal classification of subfamily Detarioideae, an early branching clade of florally diverse tropical arborescent legumes

Detarioideae (81 genera, c. 760 species) is one of the six Leguminosae subfamilies recently reinstated by the Legume Phylogeny Working Group. This subfamily displays high morphological variability and is one of the early branching clades in the evolution of legumes. Using previously published and newly generated sequences from four loci (matK-trnK, rpL16, trnG-trnG2G and ITS), we develop a new densely sampled phylogeny to assess generic relationships and tribal delimitations within Detarioideae. The ITS phylogenetic trees are poorly resolved, but the plastid data recover several strongly supported clades, which also are supported in a concatenated plastid + ITS sequence analysis. We propose a new phylogeny-based tribal classification for Detarioideae that includes six tribes: re-circumscribed Detarieae and Amherstieae, and the four new tribes Afzelieae, Barnebydendreae, Saraceae and Schotieae. An identification key and descriptions for each of the tribes are also provided.

Insights on the evolutionary origin of Detarioideae, a clade of ecologically dominant tropical African trees

African tropical forests are generally considered less diverse than their Neotropical and Asian counterparts. By contrast, the Detarioideae is much more diverse in Africa than in South America and Asia. To better understand the evolution of this contrasting diversity pattern, we investigated the biogeographical and ecological origin of this subfamily, testing whether they originated in dry biomes surrounding the Tethys Seaway as currently hypothesized for many groups of Leguminosae. We constructed the largest time-calibrated phylogeny for the subfamily to date, reconstructed ancestral states for geography and biome/habitat, estimated diversification and extinction rates, and evaluated biome/habitat and geographic shifts in Detarioideae. The ancestral habitat of Detarioideae is postulated to be a primary forest (terra firme) originated in Africa-South America, in the early Palaeocene, after which several biome/habitat and geographic shifts occurred. The origin of Detarioideae is older than previous estimates, which postulated a dry (succulent) biome origin according to the Tethys Seaway hypothesis, and instead we reveal a post Gondwana and terra firme origin for this early branching clade of legumes. Detarioideae include some of the most dominant trees in evergreen forests and have likely played a pivotal role in shaping continental African forest diversity.

Correlated evolutionary rates across genomic compartments in Annonaceae

The molecular clock hypothesis is an important concept in biology. Deviations from a constant rate of nucleotide substitution have been found widely among lineages, genomes, genes and individual sites. Phylogenetic research can accommodate for these differences in applying specific models of evolution. Lineage-specific rate heterogeneity however can generate bi- or multimodal distributions of substitution rates across the branches of a tree and this may mislead phylogenetic inferences with currently available models. The plant family Annonaceae is an excellent case to study lineage-specific rate heterogeneity. The two major sister subfamilies, Annonoideae and Malmeoideae, have shown great discrepancies in branch lengths. We used high-throughput sequencing data of 72 genes, 99 spacers and 16 introns from 24 chloroplast genomes and nuclear ribosomal DNA of 23 species to study the molecular rate of evolution in Annonaceae. In all analyses, longer branch lengths and/or higher substitution rates were found for the Annonoideae compared to the Malmeoideae. The Annonaceae had wide variability in chloroplast length, ranging from minimal 175,684bp to 201,723 for Annonoideae and minimal 152,357 to 170,985bp in Malmeoideae, mostly reflecting variation in inverted-repeat length. The Annonoideae showed a higher GC-content in the conserved parts of the chloroplast genome and higher omega (d_N/d_S)-ratios than the Malmeoideae, which could indicate less stringent purifying selection, a pattern that has been found in groups with small population sizes. This study generates new insights into the processes causing lineage-specific rate heterogeneity, which could lead to improved phylogenetic methods.

Exploring the floristic diversity of tropical Africa

BACKGROUND

Understanding the patterns of biodiversity distribution and what influences them is a fundamental pre-requisite for effective conservation and sustainable utilisation of biodiversity. Such knowledge is increasingly urgent as biodiversity responds to the ongoing effects of global climate change. Nowhere is this more acute than in species-rich tropical Africa, where so little is known about plant diversity and its distribution. In this paper, we use RAINBIO - one of the largest mega-databases of tropical African vascular plant species distributions ever compiled - to address questions about plant and growth form diversity across tropical Africa.

RESULTS

The filtered RAINBIO dataset contains 609,776 georeferenced records representing 22,577 species. Growth form data are recorded for 97% of all species. Records are well distributed, but heterogeneous across the continent. Overall, tropical Africa remains poorly sampled. When using sampling units (SU) of 0.5°, just 21 reach appropriate collection density and sampling completeness, and the average number of records per species per SU is only 1.84. Species richness (observed and estimated) and endemism figures per country are provided. Benin, Cameroon, Gabon, Ivory Coast and Liberia appear as the botanically best-explored countries, but none are optimally explored. Forests in the region contain 15,387 vascular plant species, of which 3013 are trees, representing 5-7% of the estimated world's tropical tree flora. The central African forests have the highest endemism rate across Africa, with approximately 30% of species being endemic.

CONCLUSIONS

The botanical exploration of tropical Africa is far from complete, underlining the need for intensified inventories and digitization. We propose priority target areas for future sampling efforts, mainly focused on Tanzania, Atlantic Central Africa and West Africa. The observed number of tree species for African forests is smaller than those estimated from global tree data, suggesting that a significant number of species are yet to be discovered. Our data provide a solid basis for a more sustainable management and improved conservation of tropical Africa's unique flora, and is important for achieving Objective 1 of the Global Strategy for Plant Conservation 2011-2020. In turn, RAINBIO provides a solid basis for a more sustainable management and improved conservation of tropical Africa's unique flora.

Unequal Contribution of Widespread and Narrow-Ranged Species to Botanical Diversity Patterns

In conservation studies, solely widespread species are often used as indicators of diversity patterns, but narrow-ranged species can show different patterns. Here, we assess how well subsets of narrow-ranged, widespread or randomly selected plant species represent patterns of species richness and weighted endemism in Gabon, tropical Africa. Specifically, we assess the effect of using different definitions of widespread and narrow-ranged and of the information content of the subsets. Finally, we test if narrow-ranged species are overrepresented in species-rich areas. Based on distribution models of Gabonese plant species, we defined sequential subsets from narrow-ranged-to-widespread, widespread-to-narrow-ranged, and 100 randomly arranged species sequences using the range sizes of species in tropical Africa and within Gabon. Along these sequences, correlations between subsets and the total species richness and total weighted endemism patterns were computed. Random species subsets best represent the total species richness pattern, whereas subsets of narrow-ranged species best represent the total weighted endemism pattern. For species ordered according to their range sizes in tropical Africa, subsets of narrow-ranged species represented the total species richness pattern better than widespread species subsets did. However, the opposite was true when range sizes were truncated by the Gabonese national country borders. Correcting for the information content of the subset results in a skew of the sequential correlations, its direction depending on the range-size frequency distribution. Finally, we find a strong, positive, non-linear relation between weighted endemism and total species richness. Observed differences in the contribution of narrow-ranged, widespread and randomly selected species to species richness and weighted endemism patterns can be explained by the range-size frequency distribution and the use of different definitions of widespread or narrow-ranged. We call for a reconsideration of the use of widespread species as an indicator of diversity patterns, and advocate using the full ranges of species when assessing diversity patterns.

A molecular-dated phylogeny and biogeography of the monotypic legume genus Haplormosia, a missing African branch of the otherwise American-Australian Brongniartieae clade

A comprehensively sampled reassessment of the molecular phylogeny of the genistoid legumes questions the traditional placement of Haplormosia, an African monotypic genus traditionally classified within tribe Sophoreae close to the Asian-American geographically disjunct genus Ormosia. Plastid matK sequences placed Haplormosia as sister to the American-Australian tribe Brongniartieae. Despite a superficial resemblance between Haplormosia and Ormosia, a re-examination of the morphology of Haplormosia corroborates the new phylogenetic result. The reciprocally monophyletic deep divergence of the Haplormosia stem lineage from the remaining Brongniartieae is dated to ca. 52Mya, thus supporting a signature of an old single long-distance dispersal during the early Eocene. Conversely, we estimated a relatively recent long-distance dispersal rooted in the Early Miocene for the Australian Brongniartieae clade emerging from within a grade of American Brongniartieae. The Bayesian ancestral area reconstruction revealed the coming and going of neotropical ancestors during the diversification history of the Brongniartieae legumes in Africa and all over the Americas and Australia.

Bioquality Hotspots in the Tropical African Flora

Identifying areas of high biodiversity is an established way to prioritize areas for conservation [1-3], but global approaches have been criticized for failing to render global biodiversity value at a scale suitable for local management [4-6]. We assembled 3.1 million species distribution records for 40,401 vascular plant species of tropical Africa from sources including plot data, herbarium databases, checklists, and the Global Biodiversity Information Facility (GBIF) and cleaned the records for geographic accuracy and taxonomic consistency. We summarized the global ranges of tropical African plant species into four weighted categories of global rarity called Stars. We applied the Star weights to summaries of species distribution data at fine resolutions to map the bioquality (range-restricted global endemism) of areas [7]. We generated confidence intervals around bioquality scores to account for the remaining uncertainty in the species inventory. We confirm the broad significance of the Horn of Africa, Guinean forests, coastal forests of East Africa, and Afromontane regions for plant biodiversity but also reveal the variation in bioquality within these broad regions and others, particularly at local scales. Our framework offers practitioners a quantitative, scalable, and replicable approach for measuring the irreplaceability of particular local areas for global biodiversity conservation and comparing those areas within their global and regional context.

Evolution in African tropical trees displaying ploidy-habitat association: The genus Afzelia (Leguminosae)

Polyploidy has rarely been documented in rain forest trees but it has recently been found in African species of the genus Afzelia (Leguminosae), which is composed of four tetraploid rain forest species and two diploid dry forest species. The genus Afzelia thus provides an opportunity to examine how and when polyploidy and habitat shift occurred in Africa, and whether they are associated. In this study, we combined three plastid markers (psbA, trnL, ndhF), two nuclear markers (ribosomal ITS and the single-copy PEPC E7 gene), plastomes (obtained by High Throughput Sequencing) and morphological traits, with an extensive taxonomic and geographic sampling to explore the evolutionary history of Afzelia. Both nuclear DNA and morphological vegetative characters separated diploid from tetraploid lineages. Although the two African diploid species were well differentiated genetically and morphologically, the relationships among the tetraploid species were not resolved. In contrast to the nuclear markers, plastid markers revealed that one of the diploid species forms a well-supported clade with the tetraploids, suggesting historical hybridisation, possibly in relation with genome duplication (polyploidization) and habitat shift from dry to rain forests. Molecular dating based on fossil-anchored gene phylogenies indicates that extant Afzelia started diverging c. 14.5 or 20Ma while extant tetraploid species started diverging c. 7.0 or 9.4Ma according to plastid and nuclear DNA, respectively. Additional studies of tropical polyploid plants are needed to assess whether the ploidy-habitat association observed in African Afzelia would reflect a role of polyploidization in niche divergence in the tropics.

RAINBIO: a mega-database of tropical African vascular plants distributions

The tropical vegetation of Africa is characterized by high levels of species diversity but is undergoing important shifts in response to ongoing climate change and increasing anthropogenic pressures. Although our knowledge of plant species distribution patterns in the African tropics has been improving over the years, it remains limited. Here we present RAINBIO, a unique comprehensive mega-database of georeferenced records for vascular plants in continental tropical Africa. The geographic focus of the database is the region south of the Sahel and north of Southern Africa, and the majority of data originate from tropical forest regions. RAINBIO is a compilation of 13 datasets either publicly available or personal ones. Numerous in depth data quality checks, automatic and manual via several African flora experts, were undertaken for georeferencing, standardization of taxonomic names and identification and merging of duplicated records. The resulting RAINBIO data allows exploration and extraction of distribution data for 25,356 native tropical African vascular plant species, which represents ca. 89% of all known plant species in the area of interest. Habit information is also provided for 91% of these species.

A nonet of novel species of Monanthotaxis (Annonaceae) from around Africa

As part of an ongoing revision of the genus Monanthotaxis Baill. (Annonaceae), nine new species are described and one variety is reinstated to species rank. Two new species from West Africa (Monanthotaxis aquila P.H.Hoekstra, sp. nov. and Monanthotaxis atewensis P.H.Hoekstra, sp. nov.), four new species from Central Africa (Monanthotaxis couvreurii P.H.Hoekstra, sp. nov., Monanthotaxis latistamina P.H.Hoekstra, sp. nov., Monanthotaxis tripetala P.H.Hoekstra, sp. nov. and Monanthotaxis zenkeri P.H.Hoekstra, sp. nov.), one new species from Tanzania (Monanthotaxis filipes P.H.Hoekstra, sp. nov.), one new species from the area around Maputo (Monanthotaxis maputensis P.H.Hoekstra, sp. nov.), one new species from the Comoro Islands (Monanthotaxis komorensis P.H.Hoekstra, sp. nov.) and Monanthotaxis klainei (Engl.) Verdc. var. angustifolia (Boutique) Verdc. is raised to species level leading to the replacement name Monanthotaxis atopostema P.H.Hoekstra, nom. nov. (not Monanthotaxis angustifolia (Exell) Verdc.). Complete descriptions, comparisons with related species, ecological information and IUCN conservation assessments are given for the new species. Five species were classified as critical endangered, two species as endangered, one as vulnerable and one as least concern, warranting the need of further collecting and studying those species.

Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens

Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing (NGS) world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae) herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22–82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) were generated with 81.4–97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2–71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes), but at least generating vital comparative genomic data for testing (phylo)genetic, demographic and genetic hypotheses, that become increasingly more horizontal. Furthermore, NGS of historical DNA enables recovering crucial genetic information from old type specimens that to date have remained mostly unutilized and, thus, opens up a new frontier for taxonomic research as well.

Multi-locus phylogenies of the genus Barteria (Passifloraceae) portray complex patterns in the evolution of myrmecophytism

The four species of the central African genus Barteria show variation in habitat and in degree of association with ants. Whereas B. solida, restricted to submontane forests, attracts opportunistic ants to extrafloral nectar, the three other species, found in lowland rainforests (B. fistulosa, B. dewevrei) and in littoral scrub (B. nigritana), possess stem domatia of varying shapes and degrees of specialisation, hosting either non-specific arboreal ants (B. nigritana, some B. dewevrei) or two large species of ants of the genus Tetraponera Smith, 1852 that are specific to some species of Barteria (B. fistulosa, some B. dewevrei). We aimed to investigate whether this variation represents an evolutionary trend toward increasing specialisation of mutualism or the reduction or loss of myrmecophytic traits. For this, we determined phylogenetic relationships within the genus using DNA sequences (primarily nuclear ITS) and microsatellite genotypes (11 loci) on a large sample of individuals, mostly from Cameroon and Gabon. The two types of markers support an initial dichotomy that groups B. dewevrei with B. nigritana and B. fistulosa with B. solida respectively. Within these pairs, species do not appear reciprocally monophyletic. At microsatellite loci, B. nigritana forms a clade embedded within B. dewevrei; and within both B. solida and B. fistulosa, geographical populations show levels of differentiation similar to that observed between populations of B. solida and B. fistulosa. Geographic distance alone does not account for genetic differentiation between species, which indicates reproductive isolation. Divergence in each of the two pairs implies evolutionary transitions in habitat and in myrmecophytism. Specialised mutualism with specific ant species of the genus Tetraponera has been lost in species found in more marginal habitats.

Legume diversity patterns in West Central Africa: influence of species biology on distribution models

OBJECTIVES

Species Distribution Models (SDMs) are used to produce predictions of potential Leguminosae diversity in West Central Africa. Those predictions are evaluated subsequently using expert opinion. The established methodology of combining all SDMs is refined to assess species diversity within five defined vegetation types. Potential species diversity is thus predicted for each vegetation type respectively. The primary aim of the new methodology is to define, in more detail, areas of species richness for conservation planning.

METHODOLOGY

Using Maxent, SDMs based on a suite of 14 environmental predictors were generated for 185 West Central African Leguminosae species, each categorised according to one of five vegetation types: Afromontane, coastal, non-flooded forest, open formations, or riverine forest. The relative contribution of each environmental variable was compared between different vegetation types using a nonparametric Kruskal-Wallis analysis followed by a post-hoc Kruskal-Wallis Paired Comparison contrast. Legume species diversity patterns were explored initially using the typical method of stacking all SDMs. Subsequently, five different ensemble models were generated by partitioning SDMs according to vegetation category. Ecological modelers worked with legume specialists to improve data integrity and integrate expert opinion in the interpretation of individual species models and potential species richness predictions for different vegetation types.

RESULTS/CONCLUSIONS

Of the 14 environmental predictors used, five showed no difference in their relative contribution to the different vegetation models. Of the nine discriminating variables, the majority were related to temperature variation. The set of variables that played a major role in the Afromontane species diversity model differed significantly from the sets of variables of greatest relative important in other vegetation categories. The traditional approach of stacking all SDMs indicated overall centers of diversity in the region but the maps indicating potential species richness by vegetation type offered more detailed information on which conservation efforts can be focused.

Little ecological divergence associated with speciation in two African rain forest tree genera

BACKGROUND

The tropical rain forests (TRF) of Africa are the second largest block of this biome after the Amazon and exhibit high levels of plant endemism and diversity. Two main hypotheses have been advanced to explain speciation processes that have led to this high level of biodiversity: allopatric speciation linked to geographic isolation and ecological speciation linked to ecological gradients. Both these hypotheses rely on ecology: in the former conservation of ecological niches through time is implied, while in the latter adaptation via selection to alternative ecological niches would be a prerequisite. Here, we investigate the role of ecology in explaining present day species diversity in African TRF using a species level phylogeny and ecological niche modeling of two predominantly restricted TRF tree genera, Isolona and Monodora (Annonaceae). Both these genera, with 20 and 14 species, respectively, are widely distributed in African TRFs, with a few species occurring in slightly less humid regions such as in East Africa.

RESULTS

A total of 11 sister species pairs were identified most of them occurring in allopatry or with little geographical overlap. Our results provide a mixed answer on the role of ecology in speciation. Although no sister species have identical niches, just under half of the tests suggest that sister species do have more similar niches than expected by chance. PCA analyses also support little ecological differences between sister species. Most speciation events within both genera predate the Pleistocene, occurring during the Late Miocene and Pliocene periods.

CONCLUSIONS

Ecology is almost always involved in speciation, however, it would seem to have had a little role in species generation within Isolona and Monodora at the scale analyzed here. This is consistent with the geographical speciation model for TRF diversification. These results contrast to other studies for non-TRF plant species where ecological speciation was found to be an important factor of diversification. The Pliocene period appears to be a vital time in the generation of African TRF diversity, whereas Pleistocene climatic fluctuations have had a smaller role on speciation than previously thought.Ecological niche modeling, species level phylogeny, ecological speciation, African tropics, Isolona, Monodora, Annonaceae.