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.).

RésuméLa tribu des Monodoreae (Annonaceae) est composée de 11 genres et 90 espèces des forêts tropicales humides d'Afrique. Tout les genres sont taxonomiquement bien résolus, à part les genres Uvariodendron et Uvariopsis qui manquent d'une révision taxonomique récente. Ici, nous avons utilisé une approche phylogénomique robuste pour estimer l'arbre phylogénétique des Monodoreae, et tester les limites de genres et d'espèces. Pour cela, nous avons inclut les 90 espèces acceptées, et avons séquencé plus de 300 gènes. Tous les genres sont retrouvés monophylétiques, à part le genre Uvariopsis pour lequel l'espèce Uvariopsistripetala se retrouve exclue. Nous rétablissons donc le genre monotypique Dennettia et son unique espèce Dennettiatripetala. Nous érigeons une nouvelle tribu, les Ophrypetaleae trib. nov., pour accueillir les genres Ophrypetalum et Sanrafaelia, car nous les retrouvons exclus de la tribu des Monodoreae avec un bon support. Au niveau infra-générique, les genres Isolona, Monodora, Uvariastrum, Uvariodendron et Uvariopsis montrent de faibles supports de noeuds et des conflits phylogénétiques, ce qui suggère que des processus d'évolution se déroulent au niveau des populations. Nos résultats soutiennent également, sur un plan moléculaire, la description de plusieurs nouvelles espèces d'Uvariodendron et d'Uvariopsis, de même que plusieurs synonymies. Enfin, nous présentons une révision taxonomique des genres Dennettia, Uvariodendron et Uvariopsis, qui contiennent respectivement un, 18 et 17 espèces. Nous fournissons une clé des 11 genres de Monodoreae, et décrivons quatre nouvelles espèces pour la science: Uvariodendronkimbozaense Dagallier & Couvreur, sp. nov., Uvariodendronmossambicense Robson ex Dagallier & Couvreur, sp. nov., Uvariodendronpilosicarpum Dagallier & Couvreur, sp. nov. et Uvariopsisoligocarpa Dagallier & Couvreur, sp. nov., et fournissons une description provisoire de trois autres potentielles. Nous effectuons des lectotypifications et des changements nomenclaturaux tels que des synonymies et des nouvelles combinaisons (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. stat. nov., et Uvariopsissolheidiivar.letestui (Pellegr.) Dagallier & Couvreur, comb. stat. nov.).

A Taxonomically-verified and Vouchered Checklist of the Vascular Plants of the Republic of Guinea.

The Checklist of the Vascular Plants of the Republic of Guinea (CVPRG) is a specimen-based, expert-validated knowledge product, which provides a concise synthesis and overview of current knowledge on 3901 vascular plant species documented from Guinea (Conakry), West Africa, including their accepted names and synonyms, as well as their distribution and status within Guinea (indigenous or introduced, endemic or not). The CVPRG is generated automatically from the Guinea Collections Database and the Guinea Names Backbone Database, both developed and maintained at the Royal Botanic Gardens, Kew, in collaboration with the staff of the National Herbarium of Guinea. A total of 3505 indigenous vascular plant species are reported of which 3328 are flowering plants (angiosperms); this represents a 26% increase in known indigenous angiosperms since the last floristic overview. Intended as a reference for scientists documenting the diversity and distribution of the Guinea flora, the CVPRG will also inform those seeking to safeguard the rich plant diversity of Guinea and the societal, ecological and economic benefits accruing from these biological resources.

The phylogeny and global biogeography of Primulaceae based on high-throughput DNA sequence data.

The angiosperm family Primulaceae is morphologically diverse and distributed nearly worldwide. However, phylogenetic uncertainty has obstructed the identification of major morphological and biogeographic transitions within the clade. We used target capture sequencing with the Angiosperms353 probes, taxon-sampling encompassing nearly all genera of the family, tree-based sequence curation, and multiple phylogenetic approaches to investigate the major clades of Primulaceae and their relationship to other Ericales. We generated dated phylogenetic trees and conducted broad-scale biogeographic analyses as well as stochastic character mapping of growth habit. We show that Ardisia, a pantropical genus and the largest in the family, is not monophyletic, with at least 19 smaller genera nested within it. Neotropical members of Ardisia and several smaller genera form a clade, an ancestor of which arrived in the Neotropics and began diversifying about 20 Ma. This Neotropical clade is most closely related to Elingamita and Tapeinosperma, which are most diverse on islands of the Pacific. Both Androsace and Primula are non-monophyletic by the inclusion of smaller genera. Ancestral state reconstructions revealed that there have either been parallel transitions to an herbaceous habit in Primuloideae, Samolus, and at least three lineages of Myrsinoideae, or a common ancestor of nearly all Primulaceae was herbaceous. Our results provide a robust estimate of phylogenetic relationships across Primulaceae and show that a revised classification of Myrsinoideae and several other clades within the family is necessary to render all genera monophyletic.

Biogeographic history and environmental niche evolution in the palearctic genus Helianthemum (Cistaceae).

The biogeographic history and the degree of environmental niche conservatism provide essential clues to decipher the underlying macroevolutionary processes of species diversification and to understand contemporary patterns of biodiversity. The genus Helianthemum constitutes an excellent case study to investigate the impact of the geo-climatic changes and the environmental niche shifts on the origins of plant species diversity in the Mediterranean hotspot. It is a palearctic species-rich lineage with c. 140 species and subspecies mostly belonging to three distinct evolutionary radiations, almost confined to the Mediterranean region and occurring across varied environmental conditions. In this work, we studied the ample and rapid diversification of the genus Helianthemum across its whole distribution range by performing phylogenetic reconstructions of ancestral ranges and environmental niche evolution. We observed a striking synchrony of biogeographic movements with niche shifts between the three major clades of the genus Helianthemum, likely related to the geo-climatic events occurred in the Mediterranean Basin since the Upper Miocene. In particular, Late Miocene and Early Pliocene were dominated by episodes of range expansions, the Late Pliocene by range contraction and vicariance events, and Pleistocene by most intense environmental niche shifts and in-situ diversification. Our study also provides evidence for four main environmental niches in Helianthemum (i.e., Mediterranean, subdesert, humid-montane and subtropical-insular) and a tendency toward environmental niche conservatism within different subclades, with few niche shifts mostly occurring from Mediterranean ancestors. The relative longer time spent in Mediterranean areas by the ancestors of Helianthemum suggests that the larger species diversity observed in the Mediterranean (i.e. Northern Africa and Southern Europe) may have been generated by a time-for-speciation effect reinforced by environmental niche conservatism. Overall, our work highlights the role of the Mediterranean Basin as a 'cradle of diversity' and an 'evolutionary hub', facilitating the environmental transitions and determining the building up of a global plant biodiversity hotspot.

Factors Affecting Targeted Sequencing of 353 Nuclear Genes From Herbarium Specimens Spanning the Diversity of Angiosperms.

The world's herbaria collectively house millions of diverse plant specimens, including endangered or extinct species and type specimens. Unlocking genetic data from the typically highly degraded DNA obtained from herbarium specimens was difficult until the arrival of high-throughput sequencing approaches, which can be applied to low quantities of severely fragmented DNA. Target enrichment involves using short molecular probes that hybridise and capture genomic regions of interest for high-throughput sequencing. In this study on herbariomics, we used this targeted sequencing approach and the Angiosperms353 universal probe set to recover up to 351 nuclear genes from 435 herbarium specimens that are up to 204 years old and span the breadth of angiosperm diversity. We show that on average 207 genes were successfully retrieved from herbarium specimens, although the mean number of genes retrieved and target enrichment efficiency is significantly higher for silica gel-dried specimens. Forty-seven target nuclear genes were recovered from a herbarium specimen of the critically endangered St Helena boxwood, Mellissia begoniifolia, collected in 1815. Herbarium specimens yield significantly less high-molecular-weight DNA than silica gel-dried specimens, and genomic DNA quality declines with sample age, which is negatively correlated with target enrichment efficiency. Climate, taxon-specific traits, and collection strategies additionally impact target sequence recovery. We also detected taxonomic bias in targeted sequencing outcomes for the 10 most numerous angiosperm families that were investigated in depth. We recommend that (1) for species distributed in wet tropical climates, silica gel-dried specimens should be used preferentially; (2) for species distributed in seasonally dry tropical climates, herbarium and silica gel-dried specimens yield similar results, and either collection can be used; (3) taxon-specific traits should be explored and established for effective optimisation of taxon-specific studies using herbarium specimens; (4) all herbarium sheets should, in future, be annotated with details of the preservation method used; (5) long-term storage of herbarium specimens should be in stable, low-humidity, and low-temperature environments; and (6) targeted sequencing with universal probes, such as Angiosperms353, should be investigated closely as a new approach for DNA barcoding that will ensure better exploitation of herbarium specimens than traditional Sanger sequencing approaches.

Kupeantha (Coffeeae, Rubiaceae), a new genus from Cameroon and Equatorial Guinea.

Two new coffee relatives (tribe Coffeeae, Rubiaceae), discovered during botanical expeditions to Cameroon, are examined for generic placement, and the placement of three previously known species (Argocoffeopsis fosimondi, A. spathulata and Calycosiphonia pentamera) is reinvestigated using plastid sequence (accD-psa1, rpl16, trnL-F) and morphological data. Seed biochemistry of the new species and pollen micromorphology (only one of the two species) are also studied. Based on the plastid sequence data, the new taxa are nested in a well-supported monophyletic group that includes Argocoffeopsis and Calycosiphonia. Within this clade, three well-supported subclades are recovered that are morphologically easy to diagnose: (1) Calycosiphonia (excluding C. pentamera), (2) Argocoffeopsis (excluding A. fosimondi and A. spathulata), and (3) a clade including the above excluded species, in addition to the new species. Based on the results, Kupeantha, a new genus of five species, is described, including two new Critically Endangered taxa from the Highlands of Cameroon: Kupeantha ebo and K. kupensis. Phytochemical analysis of Kupeantha seeds reveals compounds assigned as hydroxycinnamic acid derivatives, amino acids and ent-kaurane diterpenoids; caffeine was not detected. Kupeantha is the first new genus described in tribe Coffeeae in 40 years.

Origin and diversification of winged bean (Psophocarpus tetragonolobus (L.) DC.), a multipurpose underutilized legume.

PREMISE OF THE STUDY: For many crops, research into the origin and partitioning of genetic variation is limited and this can slow or prevent crop improvement programs. Many of these underutilized crops have traits that could be of benefit in a changing climate due to stress tolerance or nutritional properties. Winged bean (Psophocarpus tetragonolobus (L.) DC.) is one such crop. All parts of the plant can be eaten, from the roots to the seeds, and is high in protein as well as other micronutrients. The goal of our study was to identify the wild progenitor and analyze the partitioning of genetic variation in the crop. METHODS: We used molecular phylogenetic analyses (cpDNA and nuclear ITS sequencing) to resolve relationships between all species in the genus, and population genetics (utilizing microsatellites) to identify genetic clusters of winged bean accessions and compare this to geography. KEY RESULTS: We find that winged bean is genetically distinct from all other members of the genus. We also provide support for four groups of species in the genus, largely, but not completely, corresponding to the results of previous morphological analyses. Within winged bean, population genetic analysis using 10 polymorphic microsatellite markers suggests four genetic groups; however, there is little correspondence between the genetic variation and the geography of the accessions. CONCLUSIONS: The true wild progenitor of winged bean remains unknown (or is extinct). There has likely been large-scale cross-breeding, trade, and transport of winged bean and/or multiple origins of the crop.

Kindia (Pavetteae, Rubiaceae), a new cliff-dwelling genus with chemically profiled colleter exudate from Mt Gangan, Republic of Guinea.

A new genus Kindia (Pavetteae, Rubiaceae) is described with a single species, Kindia gangan, based on collections made in 2016 during botanical exploration of Mt Gangan, Kindia, Republic of Guinea in West Africa. The Mt Gangan area is known for its many endemic species including the only native non-neotropical Bromeliaceae Pitcairnia feliciana. Kindia is the fourth endemic vascular plant genus to be described from Guinea. Based on chloroplast sequence data, the genus is part of Clade II of tribe Pavetteae. In this clade, it is sister to Leptactina sensu lato (including Coleactina and Dictyandra). K. gangan is distinguished from Leptactina s.l. by the combination of the following characters: its epilithic habit; several-flowered axillary inflorescences; distinct calyx tube as long as the lobes; a infundibular-campanulate corolla tube with narrow proximal section widening abruptly to the broad distal section; presence of a dense hair band near base of the corolla tube; anthers and style deeply included, reaching about mid-height of the corolla tube; anthers lacking connective appendages and with sub-basal insertion; pollen type 1; pollen presenter (style head) winged and glabrous (smooth and usually hairy in Leptactina); orange colleters producing a vivid red exudate, which encircle the hypanthium, and occur inside the calyx and stipules. Kindia is a subshrub that appears restricted to bare, vertical rock faces of sandstone. Fruit dispersal and pollination by bats is postulated. Here, it is assessed as Endangered EN D1 using the 2012 IUCN standard. High resolution LC-MS/MS analysis revealed over 40 triterpenoid compounds in the colleter exudate, including those assigned to the cycloartane class. Triterpenoids are of interest for their diverse chemical structures, varied biological activities, and potential therapeutic value.