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Background and Aims Condensed tannins, responsible for berry and wine astringency, may have been selected during grapevine domestication. This work examines the phylogenetic distribution of condensed tannins throughout the Vitaceae phylogenetic tree. Methods Green berries and mature leaves of representative true-to-type members of the Vitaceae were collected before ‘véraison’, freeze-dried and pulverized, and condensed tannins were measured following depolymerization by nucleophilic addition of 2-mercaptoethanol to the C4 of the flavan-3-ol units in an organic acidic medium. Reaction products were separated and quantified by ultrahigh pressure liquid chromatography/diode array detection/mass spectrometry. Key Results and Conclusions The original ability to incorporate epigallocatechin (EGC) into grapevine condensed tannins was lost independently in both the American and Eurasian/Asian branches of the Vitaceae, with exceptional cases of reversion to the ancestral EGC phenotype. This is particularly true in the genus Vitis, where we now find two radically distinct groups differing with respect to EGC content. While Vitis species from Asia are void of EGC, 50 % of the New World Vitis harbour EGC. Interestingly, the presence of EGC is tightly coupled with the degree of leaf margin serration. Noticeably, the rare Asian EGC-forming species are phylogenetically close to Vitis vinifera, the only remnant representative of Vitis in Eurasia. Both the wild ancestral V. vinifera subsp. sylvestris as well as the domesticated V. vinifera subsp. sativa can accumulate EGC and activate galloylation biosynthesis that compete for photoassimilates and reductive power.

Background and aims – The genus Carapichea (Rubiaceae), recently resurrected and separated from Psychotria, currently includes 24 Neotropical species and is morphologically heterogeneous. A revision of the genus in the Guianas is presented here, as part of the authors’ work on the Rubiaceae treatment in the Flora of the Guianas series. Material and methods – This paper is based on a study of herbarium specimens from BBS, BM, BR, BRB, CAY, INPA, K, P, P-JJR, and U; type specimens from other herbaria were consulted online. Some of the species were also studied in the field by the authors. Normal practices of herbarium taxonomy have been applied. Results – Three species previously included in Carapichea (C. altsonii, C. nivea, and C. sandwithiana) show aberrant characters for the genus and are transferred to Notopleura; new combinations are published for the former two (N. altsonii and N. nivea). Eight species of Carapichea, one of them still imperfectly known, are recorded from the Guianas; a ninth species, C. araguariensis, is included in this revision as it is expected to occur in the region. New combinations are published for two species: Carapichea galbaoensis and C. squamelligera, based on Psychotria galbaoensis and P. squamelligera, respectively; the former species was previously included in synonymy of C. guianensis, which is here redefined in a narrower sense. The delimitation of C. ligularis is expanded to include C. pacimonica as a synonym. The first records of C. adinantha in French Guiana – and the Guiana Shield – are documented. The taxonomy of the two remaining species, C. tillettii and C. urniformis, is left unchanged. For every species a complete description is presented, as well as data on distribution, ecology, phenology, local names (when known), and a list of collections studied.

Background and aims – Sustainable management of the medicinal plant resources provided by tropical forests is of utmost importance to human populations in developing countries. Trees and shrubs of the genus Vitex (Lamiaceae) are of great medicinal importance in Haut-Katanga (SE D.R. Congo), frequently used to treat tropical diseases. However, the security of supply is threatened, particularly by urban sprawl and mining. A conservation strategy for medicinal plants is urgently needed. In this context, we try to better understand the ecological factors (mostly soil) explaining the distribution of three medicinal species of Vitex (Lamiaceae) (V. fischeri, V. madiensis, and V. mombassae) that co-occur in the tropical dry woodlands in the region of Lubumbashi. Material and methods – In 114 plots (10 m radius), comprising at least one species of Vitex, all woody species with a DBH ≥ 10 cm were inventoried and soil samples were collected. Multivariate Regression Trees (MRT) combined with indicator species index IndVal and Redundancy analysis (RDA) were used to characterise habitats and woody plant communities associated to each Vitex species and to explain the variability of plant community composition. Key results – Four habitats were identified, and the three Vitex species differ significantly in ecological range. Vitex fischeri is a specialist of a most distinctive community on high Mg and low Al soil (termite mounds). Vitex mombassae is indicative of one habitat, corresponding to low altitude (< 1230 m) plots. Vitex madiensis has a broader range, being a generalist of all habitats except termite mounds. Conclusion – These results emphasise the importance of a detailed knowledge of species ecology to design species-specific conservation strategies, even for congeneric species occurring in sympatry in the same landscape.

Assisted gene flow interventions such as plant translocations are valuable complementary techniques to habitat restoration. Bringing new genetic variants can contribute to increasing genetic diversity and evolutionary resilience, counteract inbreeding depression and improve plant fitness through heterosis. Large, highly genetically variable populations are usually recommended as sources for translocation. Unfortunately, many critically endangered species only occur as small populations, which are expected to show low genetic variation, high inbreeding level, paucity of compatible mates in self-incompatible species, and increased genetic divergence. Therefore, assessment of population genetic status is required for an appropriate choice of the source populations. In this paper, we exemplify the different analyses relevant for genetic evaluation of populations combining both molecular (plastid and nuclear) markers and fitness-related quantitative traits. We assessed the genetic status of the adult generation and their seed progeny (the potential translocation founders) of small populations of Campanula glomerata (Campanulaceae), a self-incompatible insect-pollinated herbaceous species critically endangered in Belgium. Only a few small populations remain, so that the species has been part of a restoration project of calcareous grasslands implementing plant translocations. In particular, we estimated genetic diversity, inbreeding levels, genetic structure in adults and their seed progeny, recent bottlenecks, clonal extent in adults, contemporary gene flow, effective population size (Ne), and parentage, sibship and seed progeny fitness variation. Small populations of C. glomerata presented high genetic diversity, and extensive contemporary pollen flow within populations, with multiple parentage among seed progenies, and so could be good seed source candidates for translocations. As populations are differentiated from each other, mixing the sources will not only optimize the number of variants and of compatible mates in translocated populations, but also representativeness of species regional genetic diversity. Genetic diversity is no immediate threat to population persistence, but small Ne, restricted among-population gene flow, and evidence of processes leading to genetic erosion, inbreeding and inbreeding depression in the seed progeny require management measures to counteract these trends and stochastic vulnerability. Habitat restoration facilitating recruitment, flowering and pollination, reconnecting populations by biological corridors or stepping stones, and creating new populations through translocations in protected areas are particularly recommended.

International audience; Sixteen new Asteraceae are added to the non-indigenous flora of Tunisia. Six of them (Dimorphotheca ecklonis, Gaillardia pulchella, Gazania linearis var. linearis, Guizotia abyssinica, Rudbeckia triloba and Tithonia diversifolia) are also new for the flora of North Africa. Chrysanthemum morifolium is here first reported for the Mediterranean Basin. Seven genera (Argyranthemum, Bidens, Dimorphotheca, Gaillardia, Guizotia, Rudbeckia and Tithonia) are recorded for the first time for the vascular flora of Tunisia. Most of these species escaped from gardens and pots and became casual along roadsides and/or disturbed areas after cypsela dispersion (except for Chrysanthemum morifolium). Some species, even though appearing to be well established locally and are potentially invasive at a worldwide level, still do not behave so in Tunisia. In addition to the floristic notes, the typification of the names Dimorphotheca ecklonis, Gorteria linearis and Mirasolia diversifolia are discussed.

International audience; In this data paper, we present a specimen-based occurrence dataset compiled in the framework of the Conservation of Endemic Central African Trees (ECAT) project with the aim of producing global conservation assessments for the IUCN Red List. The project targets all tree species endemic or sub-endemic to the Central African region comprising the Democratic Republic of the Congo (DR Congo), Rwanda, and Burundi. The dataset contains 6361 plant collection records with occurrences of 8910 specimens from 337 taxa belonging to 153 genera in 52 families. Many of these tree taxa have restricted geographic ranges and are only known from a small number of herbarium specimens. As assessments for such taxa can be compromised by inadequate data, we transcribed and geo-referenced specimen label information to obtain a more accurate and complete locality dataset. All specimen data were manually cleaned and verified by botanical experts, resulting in improved data quality and consistency.

Tens of millions of images from biological collections have become available online in the last two decades. In parallel, there has been a dramatic increase in the capabilities of image analysis technologies, especially those involving machine learning and computer vision. Whilst image analysis has become mainstream in consumer applications, it is still only used on an artisanal basis in the biological collections community, largely because the image corpora are dispersed. Yet, there is massive untapped potential for novel applications and research if the images of collection objects could be made accessible as a single corpus. In this paper, we make the case for building infrastructure that could support image analysis of collection objects. We show that such an infrastructure is entirely feasible and well worth the investment.

Despite a long history of botanical collecting in the three oceanic islands of the Gulf of Guinea, no recent studies have documented floristic patterns. This chapter summarizes information on the vascular plants of the islands, including inventories conducted on Príncipe and São Tomé since 2017, as well as two recent expeditions to Annobón. An updated database of the vascular flora was compiled, which includes 14,376 records representing 1285 species and infraspecific taxa (1028 native). Príncipe has 445 species and infraspecific taxa (394 native), São Tomé has 1044 (842 native), and Annobón has 344 (274 native). Recent inventory work has generated collections of more than 90% of the endemic woody species. Several very rare taxa were rediscovered, includingBalthasaria mannii(Oliv.) Verdc., 1969 (Pentaphylacaceae) andPsychotria exelliiR. Alves, Figueiredo and A.P. Davis, 2005 (Rubiaceae), neither of which had been seen for more than 50 years. At least 17 species new to science were also discovered on Príncipe and São Tomé. Of the 1028 indigenous taxa, 164 (16%) are currently considered endemic to the islands. Of the 285 species evaluated according to the IUCN Red List criteria, 2 (0.7%) were Data Deficient, 226 (79.3%) Least Concern or Near Threatened, 55 (19.3%) threatened (including 3 Critically Endangered, 21 Endangered, and 31 Vulnerable), and 2 (0.7%) Extinct. On São Tomé and Príncipe, 325 plant species are used in traditional medicine, 37 of which are endemic. These results should be used to identify new priority sites for conservation, including on Annobón, where priority sites are less well defined.

Background and aims – A recent taxonomic and molecular study of the genus Cyrtorchis revealed three new species. Here, we describe one of these new species, endemic to the Cameroon Volcanic Line (CVL), and compare it to its closest relatives. Its conservation status is provided along with detailed information on its ecology and reproductive biology.Material and methods – A detailed examination of 21 herbarium specimens was performed using standard practices of herbarium taxonomy. The conservation status of the new species was assessed using the IUCN Red List Categories and Criteria. Furthermore, we investigated the reproductive biology of the new species in an easily accessible subpopulation in Cameroon and tested the hypothesis of hawkmoth pollination in the genus Cyrtorchis. Key results – The newly discovered species, here named C. okuensis, is restricted to the montane forest (1600 to 2500 m elevation) of the CVL and is currently assessed as Near Threatened (NT). Among angraecoid orchids in which hawkmoth pollination is recorded (~16 species), C. okuensis has the shortest nectar spur (19–40 mm). In situ observations revealed hawkmoths with short proboscis of the genus Hippotion (H. celerio, H. eson, and H. osiris) as the main pollinators. The rate of pollination and fruiting under natural conditions was low and among the 448 surveyed flowers only 38.8% (174/448 flowers) had their pollinia removed, 19% produced fruits (87/448 flowers), and 16% (70/448 flowers) set mature fruits. Conclusion – Cyrtorchis okuensis is clearly differentiated from C. submontana by its longer and wider floral bracts, longer anther caps, and wider triangular dorsal sepal.

The study of population genetic structure congruence between hosts and pathogens gives important insights into their shared phylogeographic and coevolutionary histories. We studied the population genetic structure of castrating anther-smut fungi (Microbotryumgenus) and of their host plants, theSilene nutansspecies complex, and the morphologically and genetically closeS. italica,which can be found in sympatry. Phylogeographic population genetic structure related to persistence in separate glacial refugia has been recently revealed in theS. nutansplant species complex across Western Europe, identifying several distinct lineages. We genotyped 171 associated plant-pathogen pairs of anther-smut fungi and their host plant individuals using microsatellite markers and plant chloroplastic SNPs. We found clear differentiation between fungal populations parasitizingS. nutansandS. italicaplants. The population genetic structure of fungal strains parasitizing theS. nutansplant species complex mirrored the host plant genetic structure, suggesting that the pathogen was isolated in glacial refugia together with its host and/or that it has specialized on the plant genetic lineages. Using random forest approximate Bayesian computation (ABC-RF), we found that the divergence history of the fungal lineages onS. nutanswas congruent with the one previously inferred for the host plant and likely occurred with ancient but no recent gene flow. Genome sequences confirmed the genetic structure and the absence of recent gene flow between fungal genetic lineages. Our analyses of host-pathogen individual pairs contribute to a better understanding of co-evolutionary histories between hosts and pathogens in natural ecosystems, in which such studies are still scarce.

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., SCOPUS: ar.j, info:eu-repo/semantics/published

International audience; Since natural habitats are disappearing fast, there is an urgent need to collect, characterize, and phenotype banana (Musa spp.) crop wild relatives to identify unique genotypes with specific traits that fill the gaps in our gene banks. We report on a collection mission in Papua New Guinea carried out in 2019. Seed containing bunches were collected from Musa peekelii ssp. angustigemma (N.W.Simmonds) Argent (3), M. schizocarpa N. W. Simmonds (4), M. balbisiana Colla (3), M. acuminata ssp. banksii (F. Muell.) Simmonds (14), M. boman Argent (3), M. ingens Simmonds (2), M. maclayi ssp. maclayi F.Muell. ex Mikl.-Maclay (1), and M. lolodensis Cheesman (1). This material, together with the seeds collected during a previous mission in 2017, form the basis for the development of a wild banana seed bank. For characterization and phenotyping, we focused on the most ubiquitous indigenous species of Papua New Guinea: M. acuminata ssp. banksii, the ancestor of most edible bananas. We calculated that the median genomic dissimilarity of the M. acuminata ssp. banksii accessions was 4% and that they differed at least 5% from accessions present in the International Transit Centre, the world's largest banana gene bank. High-throughput phenotyping revealed drought avoidance strategies with significant differences in root/shoot ratio, soil water content sensitivity, and response towards vapor pressure deficit (VPD). We deliver a proof of principle that the wild diversity is not yet fully covered in the gene banks and that wild M. acuminata ssp. banksii populations contain individuals with unique traits, useful for drought tolerance breeding programs.

The genus Thelopsis was classified in the family Stictidaceae but its systematic position has never been investigated by molecular methods. In order to determine its family placement and to test its monophyly, fungal DNA of recent collections of Thelopsis specimens was sequenced. Phylogenetic analyses using nuLSU, RPB2 and mtSSU sequences reveal that members of Thelopsis form a monophyletic group within the genus Gyalecta as currently accepted. The placement of Thelopsis, including the generic type T. rubella, within the genus Gyalecta challenges the generic circumscription of this group because Thelopsis is well recognized by the combination of morphological characters: perithecioid ascomata, well-developed periphysoids, polysporous asci and small, few-septate ellipsoid-oblong ascospores. The sterile sorediate Opegrapha corticola is also placed in the Gyalectaceae as sister species to Thelopsis byssoidea + T. rubella. Ascomata of O. corticola are illustrated for the first time and support its placement in the genus Thelopsis. The hypothesis that O. corticola might represent the sorediate fertile morph of T. rubella is not confirmed because the species is phylogenetically and morphologically distinct. Thelopsis is recovered as polyphyletic, with T. melathelia being placed as sister species to Ramonia. The new combinations Thelopsis corticola (Coppins & P. James) Sanderson & Ertz comb. nov. and Ramonia melathelia (Nyl.) Ertz comb. nov. are introduced and a new species of Gyalecta, G. amsterdamensis Ertz, is described from Amsterdam and Saint-Paul Islands, characterized by a sterile thallus with discrete soralia. Petractis luetkemuelleri and P. nodispora are accommodated in the new genus Neopetractis, differing from the generic type (P. clausa) by having a different phylogenetic position and a different photobiont. Francisrosea bicolor Ertz & Sanderson gen. & sp. nov. is described for a sterile sorediate lichen somewhat similar to Opegrapha corticola but having an isolated phylogenetic position as sister to a clade including Gyalidea praetermissa and the genera Neopetractis and Ramonia. Gyalecta farlowii, G. nidarosiensis and G. carneola are placed in a molecular phylogeny for the first time. The taxonomic significance of morphological characters in Gyalectaceae is discussed.

International audience; Background and aims - Despite the ongoing taxonomical revision of the entire (sub)-Antarctic diatom flora, our knowledge on the ecology and community associations of moss-inhabiting diatoms is still rather limited. In the present study, our research aim was to survey the diversity together with the environmental factors structuring the epiphytic moss diatom communities on Ile Amsterdam (TAAF), a small volcanic island in the southern Indian Ocean. Material and methods - A morphology-based dataset and (physico)chemical measurements were used for the ecological and biogeographical analysis of moss-inhabiting diatom flora from Ile Amsterdam. In total, 148 moss samples were examined using light microscopy. Key results - The analysis revealed the presence of 125 diatom taxa belonging to 38 genera. The uniqueness of the Ile Amsterdam diatom flora is mainly reflected by the species composition of the dominant genera Pinnularia, Nitzschia, Humidophila, and Luticola, with a large number of unknown and often new species. This highly specific diatom flora, together with differences in the habitats sampled and the isolated position of the island, resulted in very low similarity values between Ile Amsterdam and the other islands of the Southern Ocean. From a biogeographical point of view, 40% of the taxa have a typical cosmopolitan distribution, whereas 22% of all observed species can be considered endemic to Ile Amsterdam, with another 17% species showing a restricted sub-Antarctic distribution. The NMDS analysis, based on a cluster dendrogram, divides the samples into six main groups. For each group, indicator species were determined. Both environmental data and diatom distributions indicate that apart from elevation, specific conductance, pH, and moisture are the major factors determining the structure of moss-inhabiting diatom communities on Ile Amsterdam. Conclusion - The isolated geographic position and unique climatological and geological features of the island shaped the presence of a unique diatom flora, characterised by many endemic species. The results of the study are of prime importance for further (palaeo-)ecological and biogeographical research.

DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstream molecular species identification. This document (1) specifies the data and metadata required to ensure the relevance, the accessibility and traceability of DNA barcodes and (2) specifies the recommendations for DNA harvesting and for the storage of both voucher specimens/samples and barcode data, (undefined)

International audience; There is a growing interest in elucidating the biogeographical processes underlying biodiversity patterns of seaweeds, with recent studies largely focusing on red and brown macroalgae. This study focuses on the siphonous green algal family Udoteaceae, which is diverse and globally distributed in tropical to warm-temperate seas, and includes species that form important components of tropical reefs. We explored the historical processes that have shaped current biodiversity patterns in the family by analyzing a comprehensive dataset of 568 specimens sampled across its geographical range, and including 45 species, corresponding to 59% of the known diversity. Historical biogeographical analysis was based on a three-locus time-calibrated phylogeny, and probabilistic modeling of geographical range evolution. Many species were found to have restricted ranges, indicative of low dispersal capacity. Our analysis points toward a Western Tethys origin and early diversification of the Udoteaceae in the Triassic period. Three centers of diversity were identified, which are, in order of highest species richness, the Central Indo-Pacific, the Western Indian Ocean, and the Greater Caribbean. Different drivers have likely played a role in shaping these diversity centres. Species richness in the Central Indo-Pacific likely resulted from speciation within the region, as well as recolonization from neighbouring regions, and overlap of some wider ranged species, corroborating the "biodiversity feedback" model. Species richness in the Western Indian Ocean can be explained by ancient and more recent diversification within the region, and dispersal from the 2 Central Indo-Pacific. The Greater Caribbean region was colonized more recently, followed by diversification within the region.

Early stages of speciation in plants might involve genetic incompatibilities between plastid and nuclear genomes, leading to inter-lineage hybrid breakdown due to the disruption between co-adapted plastid and nuclear genes encoding subunits of the same plastid protein complexes. We tested this hypothesis in Silene nutans, a gynodioecious Caryophyllaceae, where four distinct genetic lineages exhibited strong reproductive isolation among each other, resulting in chlorotic or variegated hybrids. By sequencing the whole gene content of the four plastomes through gene capture, and a large part of the nuclear genes encoding plastid subunits from RNAseq data, we searched for non-synonymous substitutions fixed in each lineage on both genomes. Lineages of S. nutans exhibited a high level of dN/dS ratios for plastid and nuclear genes encoding most plastid complexes, with a strong pattern of coevolution for genes encoding the subunits of ribosome and cytochrome b6/f that could explain the chlorosis of hybrids. Overall, relaxation of selection due to past bottlenecks and positive selection have driven the diversity pattern observed in S. nutans plastid complexes, leading to plastid-nuclear incompatibilities. We discuss the possible role of gynodioecy in the evolutionary dynamics of the plastomes through linked selection.

International audience; Leaves of the wild yam species Dioscorea sansibarensis display prominent forerunner or “drip” tips filled with extracellular bacteria of the species Orrella dioscoreae.1 This species of yam is native to Madagascar and tropical Africa and reproduces mainly asexually through aerial bulbils and underground tubers, which also contain a small population of O. dioscoreae.2,3 Despite apparent vertical transmission, the genome of O. dioscoreae does not show any of the hallmarks of genome erosion often found in hereditary symbionts (e.g., small genome size and accumulation of pseudogenes).4, 5, 6 We investigated here the range and distribution of leaf symbiosis between D. sansibarensis and O. dioscoreae using preserved leaf samples from herbarium collections that were originally collected from various locations in Africa. We recovered DNA from the extracellular symbiont in all samples, showing that the symbiosis is widespread throughout continental Africa and Madagascar. Despite the degraded nature of this DNA, we constructed 17 symbiont genomes using de novo methods without relying on a reference. Phylogenetic and genomic analyses revealed that horizontal transmission of symbionts and horizontal gene transfer have shaped the evolution of the symbiont. These mechanisms could help explain lack of signs of reductive genome evolution despite an obligate host-associated lifestyle. Furthermore, phylogenetic analysis of D. sansibarensis based on plastid genomes revealed a strong geographical clustering of samples and provided evidence that the symbiosis originated at least 13 mya, earlier than previously estimated.3

International audience; For decades coffees were associated with the genus Coffea. In 2011, the closely related genus Psilanthus was subsumed into Coffea. However, results obtained in 2017-based on 28,800 nuclear SNPs-indicated that there is not substantial phylogenetic support for this incorporation. In addition, a recent study of 16 plastid fullgenome sequences highlighted an incongruous placement of Coffea canephora (Robusta coffee) between maternal and nuclear trees. In this study, similar global features of the plastid genomes of Psilanthus and Coffea are observed. In agreement with morphological and physiological traits, the nuclear phylogenetic tree clearly separates Psilanthus from Coffea (with exception to C. rhamnifolia, closer to Psilanthus than to Coffea). In contrast, the maternal molecular tree was incongruent with both morphological and nuclear differentiation, with four main clades observed, two of which include both Psilanthus and Coffea species, and two with either Psilanthus or Coffea species. Interestingly, Coffea and Psilanthus taxa sampled in West and Central Africa are members of the same group. Several mechanisms such as the retention of ancestral polymorphisms due to incomplete lineage sorting, hybridization leading to homoploidy (without chromosome doubling) and alloploidy (for C. arabica) are involved in the evolutionary history of the coffee species. While sharing similar morphological characteristics, the genetic relationships within C. canephora have shown that some populations are well differentiated and genetically isolated. Given the position of its closely-related species, we may also consider C. canephora to be undergoing a long process of speciation with an intermediate step of (sub-)speciation.

International audience; Determining where species diversify (cradles) and persist (museums) over evolutionary time is fundamental to understanding the distribution of biodiversity and for conservation prioriti-zation. 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.

BGPI : Equipe 5 : Biologie Evolutive des Champignons Phytopathogènes (BECphy); International audience; Study of the congruence of population genetic structure between hosts and pathogens gives important insights into their shared phylogeographical and coevolutionary histories. We studied the population genetic structure of castrating anther-smut fungi (genus Microbotryum) and of their host plants, the Silene nutans species complex, and the morphologically and genetically closely related Silene italica, which can be found in sympatry. Phylogeographical population genetic structure related to persistence in separate glacial refugia has been recently revealed in the S. nutans plant species complex across Western Europe, identifying several distinct lineages. We genotyped 171 associated plant-pathogen pairs of anther-smut fungi and their host plant individuals using microsatellite markers and plant chloroplastic single nucleotide polymorphisms. We found clear differentiation between fungal populations parasitizing S. nutans and S. italica plants. The population genetic structure of fungal strains parasitizing the S. nutans plant species complex mirrored the host plant genetic structure, suggesting that the pathogen was isolated in glacial refugia together with its host and/or that it has specialized on the plant genetic lineages. Using random forest approximate Bayesian computation (ABC-RF), we found that the divergence history of the fungal lineages on S. nutans was congruent with that previously inferred for the host plant and probably occurred with ancient but no recent gene flow. Genome sequences confirmed the genetic structure and the absence of recent gene flow between fungal genetic lineages. Our analyses of individual host-pathogen pairs contribute to a better understanding of co-evolutionary histories between hosts and pathogens in natural ecosystems, in which such studies remain scarce.

Phylogenies are a central and indispensable tool for evolutionary and ecological research. Even though most angiosperm families are well investigated from a phylogenetic point of view, there are far less possibilities to carry out large-scale meta-analyses at order level or higher. Here, we reconstructed a large-scale dated phylogeny including nearly 1/8th of all angiosperm species, based on two plastid barcoding genes, matK (incl. trnK) and rbcL. Novel sequences were generated for several species, while the rest of the data were mined from GenBank. The resulting tree was dated using 56 angiosperm fossils as calibration points. The resulting megaphylogeny is one of the largest dated phylogenetic tree of angiosperms yet, consisting of 36,101 sampled species, representing 8,399 genera, 426 families and all orders. This novel framework will be useful for investigating different broad scale research questions in ecological and evolutionary biology., info:eu-repo/semantics/published

International audience; This is the eleventh of a series of miscellaneous contributions, by various authors, where hitherto unpublished data relevant to both the Med-Checklist and the Euro+Med (or Sisyphus) projects are presented. This instalment deals with the families Anacardiaceae, Asparagaceae (incl. Hyacinthaceae), Bignoniaceae, Cactaceae, Compositae, Cruciferae, Cyperaceae, Ericaceae, Gramineae, Labiatae, Leguminosae, Orobanchaceae, Polygonaceae, Rosaceae, Solanaceae and Staphyleaceae. It includes new country and area records and taxonomic and distributional considerations for taxa in Bidens, Campsis, Centaurea, Cyperus, Drymocallis, Engem, Hoffmannseggia, Hypopitys, Lavandula, Lithraea, Melilotus, Nicotiana, Olimarabidopsis, Opuntia, Orobanche, Phelipanche, Phragmites, Rumex, Salvia, Schinus, Staphylea, and a new combination in Drimia.

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN. Publisher’s Note A first version of this text was prepared by the first eight authors and the last one, given here. The other listed co-authors in the article PDF support the content, and their actual contributions varied from only support to additions that substantially improved the content. The full details of all co-authors, with their affiliations, are included in Supplementary Table 1 after p.175 of the article for reasons of clarity and space. Slavomír Adamčík Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23 Bratislava, Slovakia Teuvo Ahti Finnish Museum of Natural History, P.O. Box 7, 00014 University of Helsinki, Finland M. Catherine Aime Purdue University, 915 W. State St., West Lafayette, Indiana 47907, U.S.A. A. Martyn Ainsworth Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom László Albert Hungarian Mycological Society, 1087 Könyves Kálmán krt. 40, Budapest, Hungary Edgardo Albertó Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús, Universidad Nacional de San Martin-Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina Alberto Altés García Facultad de Biología, Ciencias Ambientales y Química, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain Dmitry Ageev SIGNATEC Ltd., 630090, Novosibirsk, Akademgorodok (Novosibirsk Scientific Center), Inzhenernaya str., 22, Russia Reinhard Agerer Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80638 München, Germany Begona Aguirre-Hudson Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom Joe Ammirati University of Washington, Seattle, Washington 98195-1800, U.S.A. Harry Andersson Eichhahnweg 29a, 38108 Braunschweig, Germany Claudio Angelini Jardín Botánico Nacional Dr. Rafael Ma. Moscoso, Apartado 21-9, Santo Domingo, Dominican Republic Vladimír Antonín Moravian Museum, Zeny trh 6, 659 37 Brno, Czech Republic Takayuki Aoki Genetic Resources Center, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan André Aptroot ABL Herbarium, G.v.d.Veenstraat 107, 3762 XK Soest, The Netherlands Didier Argaud 40 rue du Justemont, 57290 Fameck, France Blanca Imelda Arguello Sosa Instituto Tecnológico de Ciudad Victoria, Tecnológico Nacional de México, Ciudad Victoria, Tamaulipas, Mexico Arne Aronsen Torødveien 54, 3135 Torød, Norway Ulf Arup Biological Museum, Lund University, Box 117, 221 00 Lund, Sweden Bita Asgari Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization, Tehran, Iran Boris Assyov Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 2 Gagarin Str., 1113 Sofia, Bulgaria Violeta Atienza Facultad de Ciencias Biológicas, Universitat de València, C/Dr Moliner 50, 46100, Burjasot, Valencia, Spain Ditte Bandini Panoramastr 47, 69257 Wiesenbach, Germany João Luís Baptista-Ferreira Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências da Universidade de Lisboa, 1749-016 Lisboa, Portugal Hans-Otto Baral Blaihofstr. 42, 72074 Tübingen, Germany Tim Baroni The State University of New York, 340 Bowers Hall, P.O. Box 2000, Cortland, New York 13045, U.S.A. Robert Weingart Barreto Universidade Federal de Viçosa, 36570-000, Viçosa, Minas Gerais, Brazil Henry Beker (1) Royal Holloway, University of London, United Kingdom; (2) Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium Ann Bell 45 Gurney Road, Lower Hutt, New Zealand Jean-Michel Bellanger CEFE UMR5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, INSERM, 1919 Route de Mende, 34293 Montpellier Cédex 5, France Francesco Bellù Naturmusem of Bolzano, CP 104, 39100, Bolzano, Italy Martin Bemmann Kleingemünderstraße 111, 69118 Heidelberg, Germany Mika Bendiksby NTNU, University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway Egil Bendiksen Norwegian Institute for Nature Research, Gaustadalleen 21, 0349 Oslo, Norway Katriina Bendiksen Natural History Museum, University of Oslo, P.O. 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Box 85167, 3508 AD, Utrecht, The Netherlands; (2) Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands David Boertmann Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark Tanja Böhning AG Geobotanik Schleswig-Holstein & Hamburg, c/o University of Kiel, Olshausenstraße 75, 24098 Kiel, Germany Florent Boittin Ascomycete.org, 36 rue de la Garde, 69005 Lyon, France Carlos G. Boluda Conservatoire et Jardin botaniques de la Ville de Genève, 1292 Genève, Switzerland Menno W. 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Bart Buyck Muséum National d’Histoire Naturelle, CP 39, ISYEB, UMR 7205 CNRS MNHN UPMC EPHE, 12 rue Buffon, 75005 Paris, France Ana Rosa Burgaz Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain Vicent Calatayud Fundación CEAM, c/ Charles R. Darwin, 14, Parque Tecnológico, 46980 Paterna, Valencia, Spain Philippe Callac INRA, MycSA, CS 20032, 33882 Villenave d’Ornon, France Emanuele Campo Associazione Micologica Bresadola, Via Alessandro Volta 46, 38123 Trento, Italy Massimo Candusso Via Ottone Primo 90, 17021, Alassio, Savona, Italy Brigitte Capoen Queffioec, rue de Saint Gonval, 22710 Penvenan, France Joaquim Carbó Roser, 60, 17257 Torroella de Montgrí, Girona, Spain Matteo Carbone Via Don Luigi Sturzo 173 16148 Genova, Italy Rafael F. Castañeda-Ruiz Instituto de Investigaciones Fundamentales en Agricultura, Tropical ‘Alejandro de Humboldt’, OSDE, Grupo Agrícola, Calle 1 Esq. 2, Santiago de Las Vegas, C. Habana 17200, Cuba Michael A. 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Matthias Lutz Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076 Tübingen, Germany Dan Mahoney Callaghan Innovation, 69 Gracefield Road, Lower Hutt 5010, New Zealand Ekaterina Malysheva Komarov Botanical Institute of the Russian Academy of Sciences, 2 Prof. Popov Street, St. Petersburg, 197376, Russia Vera Malysheva Komarov Botanical Institute of the Russian Academy of Sciences, 2 Prof. Popov Street, St. Petersburg, 197376, Russia Patinjareveettil Manimohan University of Calicut, Kerala, 673 635, India Yasmina Marin-Felix Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD, Utrecht, The Netherlands Guilhermina Marques Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Tras-os-Montes and Alto Douro, Laboratory of Mycology and Soil Microbiology, 5000-801 Vila Real, Portugal Rubén Martínez-Gil Ascomycete.org, 36 rue de la Garde, 69005 Lyon, France Guy Marson Musée national d’histoire naturelle, 25 rue Münster, 2160 Luxembourg, Luxembourg Gerardo Mata Instituto de Ecología, A.C., Carretera antigua a Coatepec 351, El Haya, Xalapa 91070, Veracruz, Mexico P. Brandon Matheny University of Tennessee, Knoxville, Tennessee 37996, U.S.A. Geir Harald Mathiassen Tromsø University Museum, University of Tromsø — The Arctic University of Norway, 9037 Tromsø, Norway Neven Matočec Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia Helmut Mayrhofer Institute of Biology, University of Graz, Holteiasse 6, 8010 Graz, Austria Mehdi Mehrabi Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization, Tehran, Iran Ireneia Melo Botanical Garden, National Museum of Natural History and Science, University of Lisbon, Portugal Armin Mešić Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia Andrew S. Methven Savannah State University, Savannah, Georgia 31404, U.S.A Otto Miettinen Finnish Museum of Natural History, P.O. Box 7, 00014 University of Helsinki, Finland Ana M. Millanes Romero Universidad Rey Juan Carlos, 28933 Móstoles, Madrid, Spain Andrew N. Miller Illinois Natural History Survey, University of Illinois Urbana-Champaign, 1816 South Oak Street, Champaign, Illinois 61820-6970, U.S.A. James K. Mitchell Harvard University, 22 Divinity Avenue, Cambridge, Massachusetts 02138, U.S.A. Roland Moberg Museum of Evolution, Uppsala University, Norbyvägen 16, 75236 Uppsala, Sweden Pierre-Arthur Moreau Université Lille, Fac. Pharma. Lille, EA4483 IMPECS, 59000 Lille, France Gabriel Moreno Facultad de Biología, Ciencias Ambientales y Química, Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain Olga Morozova Komarov Botanical Institute of the Russian Academy of Sciences, 2 Prof. Popov Street, St. Petersburg, 197376, Russia Asunción Morte Facultad de Biología, Universidad de Murcia, Campus de Espinardo, 30100 Murcia, Spain Lucia Muggia University of Trieste, via L. Giorgieri 10, 34127 Trieste, Italy Guillermo Muñoz González Avda Valvanera N.32, 5D, 26500 Calahorra, La Rioja, Spain Leena Myllys Finnish Museum of Natural History, P.O. Box 7, 00014 University of Helsinki, Finland István Nagy Institute of Biology, Eötvös Loránd University, Pázmány Péter sétány 1/c, 1117 Budapest, Hungary László G. Nagy Institute of Biochemistry, BRC-HAS, 6726 Szeged, Temesvari krt. 62, 6726 Szeged, Hungary Maria Alice Neves Universidade Federal de Santa Catarina, Campus Universitário Reitor João David Ferreira Lima, Trindade, Florianópolis, Santa Catarina CEP 88040-900, Brazil Tuomo Niemelä Finnish Museum of Natural History, P.O. Box 7, 00014 University of Helsinki, Finland Pier Luigi Nimis University of Trieste, via L. Giorgieri 10, 34127 Trieste, Italy Nicolas Niveiro Instituto de Botánica del Nordeste, Universidad Nacional de Nordeste-Consejo Nacional de Investigaciones Científicas y Técnicas, Sargento Cabral 2131, CC 209, Corrientes Capital, Argentina Machiel E. Noordeloos Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands Anders Nordin Museum of Evolution, Uppsala University, Norbyvägen 16, 75236 Uppsala, Sweden Sara Raouia Noumeur Faculty of Natural and Life Sciences, University of Batna 2, 05000 Batna, Algeria Yuri Novozhilov Komarov Botanical Institute of the Russian Academy of Sciences, 2 Prof. Popov Street, St. Petersburg, 197376, Russia Jorinde Nuytinck Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands Esteri Ohenoja Botanical Museum, University of Oulu, Finland Patricia Oliveira Fiuza Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Bairro Novo Horizonte, CEP:44036-900, Feira de Santana, Bahia, Brazil Alan Orange National Museum of Wales, Cardiff CF10 3NP, United Kingdom Alexander Ordynets University of Kassel, Heinrich-Plett-Strasse 40, 34132 Kassel, Germany Beatriz Ortiz-Santana USDA Forest Service, Northern Research Station, One Gifford Pinchot Dr, Madison, Wisconsin 53726, U.S.A. Leticia Pacheco Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina, 09340 México, D. F., Mexico Ferenc Pál-Fám Faculty of Agricultural and Environmental Sciences, Kaposvar University, 7400 Kaposvar, Hungary Melissa Palacio Universidade Federal do Rio Grande do Sul, Brazil Zdeněk Palice Faculty of Science, Charles University, Benátská 2, 128 01 Praha 2, Czech Republic Viktor Papp Szent Istvan University, 1118 Budapest, Menesi st. 44, Hungary Kadri Pärtelv Institute of Ecology and Earth Sciences, 40 Lai Street, Tartu 51005, Estonia Julia Pawlowska Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland Aurelia Paz Urb. La Llosa, 219, 39509 Villanueva de la Peña, Mazcuerras, Cantabria, Spain Ursula Peintner Institut für Mikrobiologie, Universität Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria Shaun Pennycook Manaaki Whenua Landcare Research, Private Bag 92170, Auckland 1072, New Zealand Olinto Liparini Pereira Universidade Federal de Viçosa, 36570-000, Viçosa, Minas Gerais, Brazil Pablo Pérez Daniëls University of Córdoba, 14071, Córdoba, Spain Miquel À. Pérez-De-Gregorio Capella C/ Pau Casals, 6, 1º, 1ª, 17001, Girona, Spain Carlos Manuel Pérez del Amo C/ Luis de Ulloa, 1, 7º I, 26004 Logroño, Navarra, Spain Sergio Pérez Gorjón Universidad de Salamanca, Avda. Licenciado Mendez Nieto s/n, 37007 Salamanca, Spain Sergio Pérez-Ortega Real Jardín Botánico-CSIC, Plaza de Murillo 2, 28014, Madrid, Spain Israel Pérez-Vargas Facultad de Farmacia, Universidad de La Laguna, c/ Astrofísico Sánchez s/n 38071 La Laguna, Tenerife, Canary Islands, Spain Brian A. Perry California State University East Bay, Hayward, California 94542, U.S.A. Jens H. Petersen Nøruplundvej 2, 8400 Ebeltoft, Denmark Ronald H. Petersen University of Tennessee, Knoxville, Tennessee 37996, U.S.A. Donald H. Pfister Harvard University, 22 Divinity Avenue, Cambridge MA 02138, U.S.A. Chayanard Phukhamsakda Mae Fah Luang University, Chang Wat Chiang Rai 57100, Thailand Marcin Piątek W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Krakow, Poland Meike Piepenbring Faculty of Biosciences, Goethe University Frankfurt am Main, Germany Raquel Pino-Bodas Real Jardín Botánico-CSIC, Plaza de Murillo 2, 28014, Madrid, Spain Juan Pablo Pinzón Esquivel Universidad Autónoma de Yucatán, Carretera Mérida-Xmatkuil Km. 15.5, Apdo. Postal: 4-116 Itzimná,C.P: 97100, Merida, Yucatan, Mexico Paul Pirot Rue des Peupliers 10, 6840 Neufchâteau, Belgium Eugene S. Popov Komarov Botanical Institute of the Russian Academy of Sciences, 2 Prof. Popov Street, St. Petersburg, 197376, Russia Orlando Popoff Instituto de Botánica del Nordeste, Universidad Nacional de Nordeste-Consejo Nacional de Investigaciones Científicas y Técnicas, Sargento Cabral 2131, CC 209, Corrientes Capital, Argentina María Prieto Álvaro Universidad Rey Juan Carlos, 28933 Móstoles, Madrid, Spain Christian Printzen Senckenberg Forschungsinstitut und Naturmuseum Frankfurt, Abteilung Botanik und Molekulare Evolutionsforschung, Herbarium Senckenbergianum (FR), Senckenberganlage 25, 60325 Frankfurt am Main, Germany Nadezhda Psurtseva Komarov Botanical Institute of the Russian Academy of Sciences, 2 Prof. Popov Street, St. Petersburg, 197376, Russia Witoon Purahong Helmholtz Centre for Environmental Research GmbH — UFZ, Theodor-Lieser-Straße 4, 06120 Halle, Germany Luis Quijada Harvard University, 22 Divinity Avenue, Cambridge, Massachusetts 02138, U.S.A. Gerhard Rambold University of Bayreuth, Universitätsstrasse 30, 95447 Bayreuth, Germany Natalia A. Ramírez Instituto de Botánica del Nordeste, Universidad Nacional de Nordeste-Consejo Nacional de Investigaciones Científicas y Técnicas, Sargento Cabral 2131, CC 209, Corrientes Capital, Argentina Huzefa Raja University of North Carolina at Greensboro, 435 Sullivan Science Building, PO Box 26170, Greensboro North Carolina 27402-6170, U.S.A. Olivier Raspé Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium Tania Raymundo Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Miguel Hidalgo, Santo Tomás, 11340 Ciudad de México, Mexico Martina Réblová Institute of Botany, Czech Academy of Sciences, Pruhonice, Czech Republic Yury A. Rebriev Southern Scientific Center, Russian Academy of Sciences, 41 Chehova str., Rostov-on-Don, 344006, Russia Juan de Dios Reyes García Paseo Virgen de Linarejos 6 2 D, Linares, Jaen, Spain Miguel Ángel Ribes Ripoll Avda. Pablo Neruda 120 F, 2°D, 28018 Madrid, Spain Franck Richard CEFE UMR5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, INSERM, 1919 Route de Mende, 34293 Montpellier Cédex 5, France Mike J. Richardson Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, United Kingdom Víctor J. Rico Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain Gerardo Lucio Robledo Instituto Multidisciplinario de Biología Vegetal, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Córdoba, Casilla de Correo 495, 5000 Córdoba, Argentina Flavia Rodrigues Barbosa Universidade Federal de Mato Grosso, Av. Alexandre Ferronato, 1200, Setor Industrial, Sinop, Mato Grosso, Brazil Cristina Rodriguez-Caycedo UT Southwestern Medical Center, Dallas, Texas 75390, U.S.A. Pamela Rodriguez-Flakus W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Krakow, Poland Anna Ronikier W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Krakow, Poland Luis Rubio Casas Ul. Andrieja Sacharowa 1/1, 30-806 Kraków, Poland Katerina Rusevska Institute of Biology, Faculty of Natural Science and Mathematics, Ss. Cyril and Methodius University, Arhimedova 5, 1000 Skopje, Republic of Macedonia Günter Saar Dammenmühle 7, 77933 Lahr-Sulz, Germany Irja Saar Institute of Ecology and Earth Sciences, 40 Lai Street, Tartu 51005, Estonia Isabel Salcedo University of the Basque Country (UPV/EHU), Apdo 644, 48080 Bilbao, Spain Sergio M. Salcedo Martínez Facultad de Ciencias Biológicas, UANL. Ave. Pedro de Alba s/n esq. Manuel Barragán Cd. Universitaria, San Nicolás de los Garza Nuevo León, CP. 66451, Mexico Carlos A. Salvador Montoya Instituto de Botánica del Nordeste, Universidad Nacional de Nordeste-Consejo Nacional de Investigaciones Científicas y Técnicas, Sargento Cabral 2131, CC 209, Corrientes Capital, Argentina Santiago Sánchez-Ramírez University of Toronto, 100 Queen’s Park, Toronto, Ontario M5S 2C6, Canada J. Vladimir Sandoval-Sierra Health Science Centre, University of Tennessee, U.S.A. Sergi Santamaria Facultat de Biociències, Edifici C, Despatx C1/331, Campus de la UAB, 08193 Bellaterra, (Cerdanyola del Vallès), Barcelona, Spain Josiane Santana Monteiro Botany Coordination, Museu Paraense Emílio Goeldi, 66077-830, Belém, Pará, Brazil Hans Josef Schroers Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000 Ljubljana, Slovenia Barbara Schulz Institute of Microbiology, Technische Universität Braunschweig, Germany Geert Schmidt-Stohn Burgstr. 25, 29553 Bienenbüttel, Germany Trond Schumacher University of Oslo, P.O.Box 1066, Blindern, 0316 Oslo, Norway Beatrice Senn-Irlet RU Biodiversity and Conservation Biology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstr. 111, 8903 Birmensdorf, Switzerland Hana Ševčíková Moravian Museum, Zeny trh 6, 659 37 Brno, Czech Republic Oleg Shchepin Komarov Botanical Institute of the Russian Academy of Sciences, 2 Prof. Popov Street, St. Petersburg, 197376, Russia Takashi Shirouzu Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan Anton Shiryaev Institute of Plant & Animal Ecology Ural Branch of the Russian Academy of Sciences, 620144 Ekaterinburg, 8 March str., 202/3, Russia Klaus Siepe Geeste 133, 46342 Velen, Germany Esteban B. Sir Fundación Miguel Lillo, Consejo Nacional de Investigaciones Científicas y Técnicas, Miguel Lillo 251, San Miguel de Tucumán 4000, Tucumán, Argentina Mohammad Sohrabi Iranian Research Organization for Science and Technology, P.O. Box 33535111, Tehran, Iran Karl Soop Swedish Museum of Natural History, P.O. Box 50007, 104 05 Stockholm, Sweden Viacheslav Spirin Finnish Museum of Natural History, P.O. Box 7, 00014 University of Helsinki, Finland Toby Spribille University of Alberta, Edmonton, Alberta T6G 2R3, Canada Marc Stadler Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany Joost Stalpers Torenlaan 43, 3742CR Baarn, The Netherlands Soili Stenroos Finnish Museum of Natural History, P.O. Box 7, 00014 University of Helsinki, Finland Ave Suija Institute of Ecology and Earth Sciences, 40 Lai Street, Tartu 51005, Estonia Stellan Sunhede Hökaskog Sandbacken 1, 533 92 Lundsbrunn, Sweden Sten Svantesson University of Gothenburg, Box 461, 40530 Göteborg, Sweden Sigvard Svensson Biological Museum, Lund University, Box 117, 221 00 Lund, Sweden Tatyana Yu. Svetasheva (1) Komarov Botanical Institute of the Russian Academy of Sciences, 2 Prof. Popov Street, St. Petersburg, 197376, Russia; (2) Department of Technologies of Living Systems, Tula State Lev Tolstoy Pedagogical University, Lenin ave. 125, Tula, 300026, Russia Krzysztof Świerkosz Museum of Natural History, Wrocław University, ul. H. Sienkiewicza 5, 50-335 Wrocław, Poland Heidi Tamm Institute of Ecology and Earth Sciences, 40 Lai Street, Tartu 51005, Estonia Hatira Taskin Faculty of Agriculture, University of Çukurova, 01330 Adana, Turkey Adrien Taudière CEFE UMR5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, INSERM, 1919 Route de Mende, 34293 Montpellier Cédex 5, France Jan-Olof Tedebrand Sundsvall Mycological Society, Medelpad, Sweden Raúl Tena Lahoz C/Arreñales del Portillo B 21 1°D, 44003 Teruel, Spain Marina Temina Institute of Evolution, University of Haifa, Aba Khoushi Ave. 199, Mt. Carmel, Haifa 3498838, Israel Arne Thell Biological Museum, Lund University, Box 117, 221 00 Lund, Sweden Marco Thines Faculty of Biosciences, Goethe University Frankfurt am Main, Germany Göran Thor Swedish University of Agricultural Sciences, P. O. Box 7044, 750 07 Uppsala, Sweden Holger Thüs State Museum of Natural History Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany Leif Tibell Evolutionary Biology Centre, Norbyvägen 18D, 75236 Uppsala, Sweden Sanja Tibell Evolutionary Biology Centre, Norbyvägen 18D, 75236 Uppsala, Sweden Einar Timdal Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318 Oslo, Norway Zdenko Tkalčec Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia Tor Tønsberg University of Bergen, Allégaten 41, P.O. Box 7800, 5020 Bergen, Norway Gérard Trichies 5, impasse des Écoles S7700 Neufchef, France Dagmar Triebel Botanische Staatssammlung München, Menzinger Straße 67, 80638 München, Germany Andrei Tsurykau (1) F. Skorina Gomel State University, Sovetskaja Str. 104, 246019 Gomel, Belarus; (2) Institute of Natural Sciences, Samara National Research University, Moskovskoye shosse 34, 443086 Samara, Russia Rodham E. Tulloss Herbarium Amanitarum Rooseveltensis, P. O. Box 57, Roosevelt, New Jersey 08555-0057, U.S.A. Veera Tuovinen University of Alberta, Edmonton, Alberta T6G 2R3, Canada Miguel Ulloa Sosa Universidad Nacional Autónoma de México, Tercer Circuito/Sin Número, Ciudad Universitaria, Ciudad de México, C. P. 04510, Mexico Carlos Urcelay Instituto Multidisciplinario de Biología Vegetal, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Córdoba, Casilla de Correo 495, 5000 Córdoba, Argentina François Valade 11 rue haras, le boqueteau, 91240 Saint-Michel-sur-Orge, France Ricardo Valenzuela Garza Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Miguel Hidalgo, Santo Tomás, 11340 Ciudad de México, Mexico Pieter van den Boom Arafura 16, 5691 JA Son, The Netherlands Nicolas Van Vooren Ascomycete.org, 36 rue de la Garde, 69005 Lyon, France Aida M. 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Mattioli 25, 10125, Torino, Italy Hermann Voglmayr University of Vienna, Rennweg 14, 1030 Vienna, Austria Sergey Volobuev Komarov Botanical Institute of the Russian Academy of Sciences, 2 Prof. Popov Street, St. Petersburg, 197376, Russia Wolfgang von Brackel Kirchenweg 2, 91341 Röttenbach, Germany Elena Voronina Lomonosov Moscow State University, Biology Faculty, Moscow, Russia Grit Walther Arvid-Harnack-Str. 4, 07743 Jena, Germany Roy Watling Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, United Kingdom Evi Weber Blaihofstr. 42, 72074 Tübingen, Germany Mats Wedin Swedish Museum of Natural History, P.O. Box 50007, 104 05 Stockholm, Sweden Øyvind Weholt Nord University, Nesna, 8700 Nesna, Norway Martin Westberg Museum of Evolution, Uppsala University, Norbyvägen 16, 75236 Uppsala, Sweden Eugene Yurchenko Polessky State University, Dnyaprouskai flatylii str. 23, 225710, Pinsk, Belarus Petr Zehnálek Faculty of Science, Charles University, Benátská 2, 128 01 Praha 2, Czech Republic Huang Zhang Kunming University of Science & Technology, Kunming, China Mikhail P. Zhurbenko Komarov Botanical Institute of the Russian Academy of Sciences, 2 Prof. Popov Street, St. Petersburg, 197376, Russia The following institutions are also supporting the present text (institutional support means that committees from the mentioned) Asociación Micológica Carlos Spegazzini (Argentina) Austrian Mycological Society (Austria) Croatian Mycological Society (Croatia) Committee of the Czech Scientific Society for Mycology (Czech Republic) The Netherlands Mycological Society (The Netherlands) Sociedad Española de Liquenología (Portugal/Spain) Iberian Mycological Society (which is under constitution, Portugal/Spain) Federación de Asociaciones Micológicas Andaluzas (FAMA) (Spain) Asociación Botánica y Micológica de Jaén (Spain) Asociación Micológica Hispalense Muscaria (Spain) Societat Micològica Valenciana (Spain)

International audience; Craterispermum capitatum and C. gabonicum, two new species of Rubiaceae, are described from the Lower Guinea and Congolian Domains. Detailed descriptions and distribution maps are provided for each species, their conservation status is assessed and their taxonomic affinities are discussed. Craterispermum gabonicum is unique within the genus because of the strong dimorphism in brevistylous and longistylous flowers and inflorescences. We hypothesize that this species shows some form of dioecy. The distribution of C. capitatum shows a wide disjunction: the species is present in the Lower Guinean and Congolian Domains but absent from Gabon and South Cameroon. An identification key for the Craterispermum species present in the Lower Guinean and Congolian Domains is given.; Craterispermum capitatum et C. gabonicum, deux nouvelles espèces de la famille des Rubiaceae, des Domaines Bas Guinéen et Congolais sont décrites. Des descriptions détaillées et des cartes de distribution sont données pour chacune des espèces, leur statut de conservation est évalué et leurs affinités taxonomiques discutée. Craterispermum gabonicum est unique dans le genre en raison d’un dimorphisme avéré entre les fleurs, mais aussi les inflorescences brévistyles et longistyles. L’hypothèse de l’existence d’une tendance vers la dioécie chez cette espèce est émise. La distribution C. capitatum présente une importante disjonction: l’espèce est présente dans les Domaines Bas Guinéen et Congolais, mais absente au Gabon et au sud du Cameroun. Une clé d’identification pour les espèces de Craterispermum présentes dans les Domaines Bas Guinéen et Congolais est donnée.

International audience; The tropical to warm-temperate marine brown macroalgal genus Lobophora (Dictyotales, Phaeophyceae) recently drew attention because of its striking regional diversity. In this study we reassess Lobophora global species diversity, and species distributions, and explore how historical factors have shaped current diversity patterns. We applied a series of algorithmic species delineation techniques on a global mitochondrial cox3 dataset of 598 specimens, resulting in an estimation of 98–121 species. This diversity by far exceeds traditional diversity estimates based on morphological data. A multi-locus time-calibrated species phylogeny using a relaxed molecular clock, along with DNA-confirmed species distribution data was used to analyse ancestral area distributions, dispersal-vicariance-founder events, and temporal patterns of diversification under different biogeographical models. The origin of Lobophora was estimated in the Upper Cretaceous (−75 to −60 MY), followed by gradual diversification until present. While most speciation events were inferred within marine realms, founder events also played a non-negligible role in Lobophora diversification. The Central Indo-Pacific showed the highest species diversity as a result of higher speciation events in this region. Most Lobophora species have small ranges limited to marine realms. Lobophora probably originated in the Tethys Sea and dispersed repeatedly in the Atlantic (including the Gulf of Mexico) and Pacific Oceans. The formation of the major historical marine barriers (Terminal Tethyan event, Isthmus of Panama, Benguela upwelling) did not act as important vicariance events. Long-distance dispersal presumably represented an important mode of speciation over evolutionary time-scales. The limited geographical ranges of most Lobophora species, however, vouch for the rarity of such events.

Study of the congruence of population genetic structure between hosts and pathogens gives important insights into their shared phylogeographical and coevolutionary histories. We studied the population genetic structure of castrating anther-smut fungi (genus Microbotryum) and of their host plants, the Silene nutans species complex, and the morphologically and genetically closely related Silene italica, which can be found in sympatry. Phylogeographical population genetic structure related to persistence in separate glacial refugia has been recently revealed in the S. nutans plant species complex across Western Europe, identifying several distinct lineages. We genotyped 171 associated plant-pathogen pairs of anther-smut fungi and their host plant individuals using microsatellite markers and plant chloroplastic single nucleotide polymorphisms. We found clear differentiation between fungal populations parasitizing S. nutans and S. italica plants. The population genetic structure of fungal strains parasitizing the S. nutans plant species complex mirrored the host plant genetic structure, suggesting that the pathogen was isolated in glacial refugia together with its host and/or that it has specialized on the plant genetic lineages. Using random forest approximate Bayesian computation (ABC-RF), we found that the divergence history of the fungal lineages on S. nutans was congruent with that previously inferred for the host plant and probably occurred with ancient but no recent gene flow. Genome sequences confirmed the genetic structure and the absence of recent gene flow between fungal genetic lineages. Our analyses of individual host-pathogen pairs contribute to a better understanding of co-evolutionary histories between hosts and pathogens in natural ecosystems, in which such studies remain scarce.

International audience; Coffee species such as Coffea canephora P. (Robusta) and C. arabica L. (Arabica) are important cash crops in tropical regions around the world. C. arabica is an allotetraploid (2n = 4x = 44) originating from a hybridization event of the two diploid species C. canephora and C. eugenioides (2n = 2x = 22). Interestingly, these progenitor species harbour a greater level of genetic variability and are an important source of genes to broaden the narrow Arabica genetic base. Here, we describe the development, evaluation and use of a single-nucleotide polymorphism (SNP) array for coffee trees. A total of 8580 unique and informative SNPs were selected from C. canephora and C. arabica sequencing data, with 40% of the SNP located in annotated genes. In particular, this array contains 227 markers associated to 149 genes and traits of agronomic importance. Among these, 7065 SNPs (~82.3%) were scorable and evenly distributed over the genome with a mean distance of 54.4 Kb between markers. With this array, we improved the Robusta high-density genetic map by adding 1307 SNP markers, whereas 945 SNPs were found segregating in the Arabica mapping progeny. A panel of C. canephora accessions was successfully discriminated and over 70% of the SNP markers were transferable across the three species. Furthermore, the canephora-derived subgenome of C. arabica was shown to be more closely related to C. canephora accessions from northern Uganda than to other current populations. These validated SNP markers and high-density genetic maps will be useful to molecular genetics and for innovative approaches in coffee breeding.

International audience; Background and aims – The rapid expansion of human activities in South Cameroon, particularly mining in mountainous areas, threatens this region’s exceptional biodiversity. To comprehend the effects of land-use change on plant diversity and identify conservation priorities, we aim at providing a first comprehensive plant checklist of the Ngovayang Massif, focusing on the two richest plant families, Orchidaceae and Rubiaceae.Location – The Ngovayang Massif Area (NMA) is located in the South Region of Cameroon. It is covered by lowland and submontane rainforest (100 to 1110 m elevation).Methods – We compiled a dataset of 6116 georeferenced herbarium specimens, of which 2787 belong to Rubiaceae and Orchidaceae. We used rarefaction methods to explore sampling and diversity patterns, and investigated the altitudinal distribution of rare and/or threatened taxa.Key results – The NMA, which houses about 1500 vascular plant taxa, is the richest documented area for Rubiaceae in Atlantic Central Africa (ACA) and the fifth for Orchidaceae, with respectively 281 and 111 taxa. Among these taxa, 178 (45%) are endemic to ACA and 67 (17%) are considered globally threatened according to IUCN categories and criteria. We show that higher elevation areas (> 750 m), which are also the main areas targeted for mining, are the richest in endangered and/or rare species. Three new records for Cameroon are reported here.Conclusion – The NMA represents an Important Plant Area of Cameroon as confirmed by its exceptional plant diversity (> 20% of the total Flora of Cameroon), by the concentration of many threatened and/or restricted range species (10 taxa are strict endemics of the massif) as well as by the threat on rare habitats (i.e. the submontane vegetation above ~750 m elevation). A management plan involving in situ and ex situ conservation actions is urgently needed to reduce the potential threats of future mining activities.

Despite the specialization of floral traits towards particular floral visitors (pollination syndrome), insect-pollinated plants can display generalist rather than specialist interactions with their pollinators. This is the case of several Silene species that were viewed as nocturnally pollinated but are factually visited, and then potentially pollinated, by both nocturnal and diurnal insects. This opens the question of the consistency of pollination syndromes and the impact of different pollinator assemblages on plant reproductive success. In this work, we measured diurnal and nocturnal pollinators’ contributions to pollination success (fruit and seed production) and offspring quality (seed mass and germination rate) of hermaphrodite plants in an artificial population of Silene nutans, by experimentally restricting pollinator access and controlling for floral and resource traits. We found that fruit and seed production was higher for nocturnal pollination, and that only very few seeds were produced by diurnal visitors. In our experimental system, plants did not benefit from being open during daytime, as they showed no fruit or seed production advantage in the open pollination treatment compared to the nocturnal one. Seeds generated from diurnal pollination were heavier but did not germinate better, so that the plant fitness proxy remained higher for nocturnal pollination than diurnal one, without any obvious evidence of a pollination mixed strategy. These data are in accordance with the nocturnal pollination syndrome of S. nutans, contrasting with several other studies carried out on other Silene species.

International audience; Coffee bean extracts are consumed all over the world as beverage and there is a growing interest in coffee leaf extracts as food supplements. The wild diversity in Coffea (Rubiaceae) genus is large and could offer new opportunities and challenges. In the present work, a metabolomics approach was implemented to examine leaf chemical composition of 9 Coffea species grown in the same environmental conditions. Leaves were analyzed by LC-HRMS and a comprehensive statistical workflow was designed. It served for univariate hypothesis testing and multivariate modeling by PCA and partial PLS-DA on the Workflow4Metabolomics infrastructure. The first two axes of PCA and PLS-DA describes more than 40% of variances with good values of explained variances. This strategy permitted to investigate the metabolomics data and their relation with botanic and genetic informations. Finally, the identification of several key metabolites for the discrimination between species was further characterized.

International audience; Lichen-gastropod interactions generally focus on the potential deterrent or toxic role of secondary metabolites. To better understand lichen-gastropod interactions, a controlled feeding experiment was designed to identify the parts of the lichen Argopsis friesiana consumed by the Subantarctic land snail Notodiscus hookeri. Besides profiling secondary metabolites in various lichen parts (apothecia, cephalodia, phyllocladia and fungal axis of the pseudopodetium), we investigated potentially beneficial resources that snails can utilize from the lichen (carbohydrates, amino acids, fatty acids, polysaccharides and total nitrogen). Notodiscus hookeri preferred cephalodia and algal layers, which had high contents of carbohydrates, nitrogen, or both. Apothecia were avoided, perhaps due to their low contents of sugars and polyols. Although pseudopodetia were characterized by high content of arabitol, they were also rich in medullary secondary compounds, which may explain why they were not consumed. Thus, the balance between nutrients (particularly nitrogen and polyols) and secondary metabolites appears to play a key role in the feeding preferences of this snail.

International audience; We here explore the diversity and ecology, and update the taxonomy of the fern family Hymenophyllaceae, which forms one of the most diverse and emblematic fern assemblages in rainforests of the Mascarene archipelago in western Indian Ocean. Since 1999, we extracted data from floras, literature, and field investigations conducted, and from an exhaustive examination of the collections at P, REU, and MAU. Our checklist recognizes 26 taxa involving 23 species, 2 local varieties and 1 new forma. We reconsider area of distribution in Mascarene Hymenophyllaceae and at least 3 species appear to be restricted to the archipelago. We discuss the updated taxonomy and discrimination of each taxon (including a new nomenclatural proposition for Hymenophyllum tenellum here renamed as H. fumarioides) and provide a dichotomous key. We present and discuss the ecology and elevational distribution of each species, in addition to the local endemicity. Finally, we emphasize the importance of threatened lowland rainforests and of wet ravines in semi-dry forests, which host a high level of diversity in the context of local conservation of habitats.

Aquatic biomonitoring has become an essential task in Europe and many other regions as a consequence of strong anthropogenic pressures affecting the health of lakes, rivers, oceans and groundwater. A typical assessment of the environmental quality status, such as it is required by European but also North American and other legislation, relies on matching the composition of assemblages of organisms identified using morphological criteria present in aquatic ecosystems to those expected in the absence of anthropogenic pressures. Through decade-long and difficult intercalibration exercises among networks of regulators and scientists in European countries, a pragmatic biomonitoring approach was developed and adopted, which now produces invaluable information. Nonetheless, this approach is based on several hundred different protocols, making it susceptible to issues with comparability, scale and resolution. Furthermore, data acquisition is often slow due to a lack of taxonomic experts for many taxa and regions and time-consuming morphological identification of organisms. High-throughput genetic screening methods such as (e)DNA metabarcoding have been proposed as a possible solution to these shortcomings. Such "next-generation biomonitoring", also termed "biomonitoring 2.0", has many advantages over the traditional approach in terms of speed, comparability and costs. It also creates the potential to include new bioindicators and thereby further improves the assessment of aquatic ecosystem health. However, several major conceptual and technological challenges still hinder its implementation into legal and regulatory frameworks. Academic scientists sometimes tend to overlook legal or socioeconomic constraints, which regulators have to consider on a regular basis. Moreover, quantification of species abundance or biomass remains a significant bottleneck to releasing the full potential of these approaches. Here, we highlight the main challenges for next-generation aquatic biomonitoring and outline principles and good practic, COST - European Cooperation in Science and Technology(CA15219). COST Action DNAqua-Net (CA15219), supported by the COST (European Cooperation in Science and Technology) programme

International audience; Genetic structure in broadly distributed herbs may be shaped by past climate events, leading to distinct genetic lineages, and possibly to different Evolutionary Significant Units (ESUs). We identified the potential glacial refugia, postglacial (re)colonization routes, contact zones and ESUs in the widespread but locally rare Silene nutans to propose appropriate conservation strategies related to migration history-related genetic structure. We sequenced four plastid DNA markers from 136 populations covering S. nutans European distribution range. We built a network on concatenated sequences using statistical parsimony and performed Bayesian and Maximum Likelihood analyses to build a phylogenetic tree. Haplotype genetic diversity and between-population differentiation (G(ST), N-ST) were calculated. Based on 23 plastid haplotypes, populations were ascribed to seven strongly differentiated genetic lineages. Potential refugia were identified: in the Iberian and Italian Peninsulas, expanding to south-western France and the Alps, respectively; in south-central France, reaching England and Belgium; an eastern refugium, following a north-westward expansion; in the Balkans, expanding to north-eastern Italy, and in the Carpathians. Several contact zones were identified. Silene nutans consists of a cryptic assemblage of genetically distinct taxa, with at least seven ESUs. Evaluating the distribution range, the abundance, and the conservation status of each ESU is necessary for the preservation of the S. nutans species complex at European and regional levels. Ex situ conservation and genetic restoration involving plant translocations must consider the phylogeographic history and the distinct genetic lineages to avoid the introduction of poorly adapted plants and outbreeding depression leading to non-viable hybrid progeny, especially in contact zones.

International audience; Five species of the terrestrial diatom genus Luticola D. G. Mann were found during a taxonomic survey of two small volcanic islands, Ile Amsterdam and Ile Saint-Paul (Southern Indian Ocean). Apart from the two already known Luticola species L. beyensii Van de Vijver et al. and L. subcrozetensis Van de Vijver et al., two new species are described: L. ivetana Chattova and Van de Vijver sp. nov. and L. vancampiana Chattova and Van de Vijver sp. nov. Finally, one, up to now unknown, Luticola species is briefly discussed and illustrated. Detailed morphological descriptions of these taxa are provided based on both light and scanning electron microscopy observations. Morphological features of the new species are compared to morphologically similar taxa, and notes on their ecology and biogeography are added.

The Red List Categories and the accompanying five criteria developed by the International Union for Conservation of Nature (IUCN) provide an authoritative and comprehensive methodology to assess the conservation status of organisms. Red List criterion B, which principally uses distribution data, is the most widely used to assess conservation status, particularly of plant species. No software package has previously been available to perform large-scale multispecies calculations of the three main criterion B parameters [extent of occurrence (EOO), area of occupancy (AOO) and an estimate of the number of locations] and provide preliminary conservation assessments using an automated batch process. We developed ConR, a dedicated R package, as a rapid and efficient tool to conduct large numbers of preliminary assessments, thereby facilitating complete Red List assessment. ConR (1) calculates key geographic range parameters (AOO and EOO) and estimates the number of locations sensu IUCN needed for an assessment under criterion B; (2) uses this information in a batch process to generate preliminary assessments of multiple species; (3) summarize the parameters and preliminary assessments in a spreadsheet; and (4) provides a visualization of the results by generating maps suitable for the submission of full assessments to the IUCN Red List. ConR can be used for any living organism for which reliable georeferenced distribution data are available. As distributional data for taxa become increasingly available via large open access datasets, ConR provides a novel, timely tool to guide and accelerate the work of the conservation and taxonomic communities by enabling practitioners to conduct preliminary assessments simultaneously for hundreds or even thousands of species in an efficient and time-saving way., SCOPUS: ar.j, info:eu-repo/semantics/published

The new genus and speciesDucatina umbilicatais described from Îles Crozet and Îles Kerguelen. This lichen is characterized by an umbilicate thallus with a black verrucose lower surface and a greyish to dark olivaceous smooth upper surface having large verrucae, large semi-immersed cephalodia, semi-immersed apothecia with a prominent thalline margin, simple, mainly ellipsoid ascospores of 23–42×12–25 µm and the presence of unknown chemical compounds. Phylogenetic analyses using nuLSU and mtSSU sequences placeDucatinain theTrapeliaceae(Baeomycetales). The new taxon is closely related toOrceolina antarcticaandO.kerguelensis, two other lichens endemic to these subantarctic islands, differing by its morphology and the lack of chemical compounds.Ducatinais the only genus in theTrapeliaceaeto develop a large umbilicate thallus.

International audience

The lichenized genus Steinera is revised for the archipelagos of Crozet and of Kerguelen, with a high level of endemism revealed. It is shown to represent a good example of convergent evolution between two different orders. Phylogenetic analyses using nuLSU, RPB1 and mtSSU sequences show that two different species groups can be recognized: Steinera s. str. belongs to the Arctomiaceae (Arctomiales) and is characterized notably by species having pluriseptate ascospores, and a second species group belongs to the Koerberiaceae (Peltigerales) and is characterized notably by simple ascospores sometimes having a plasma-bridge. The genus Henssenia is newly described to accommodate this latter group. The type species of Steinera is shown to have been erroneously treated in the past, with Steinera molybdoplaca being the type of Steinera and “ S .” glaucella belonging to the genus Henssenia . A sorediate morph is recorded for S. molybdoplaca and the results confirmed using a 4-gene phylogeny, including nuITS sequences. Some species previously described in the genera Arctomia and Massalongia from the Southern Hemisphere are shown to belong to Steinera s. str. Five new species are described: Steinera isidiata Ertz & R.S. Poulsen, S. membranacea Ertz & R.S. Poulsen, S. lebouvieri Ertz, S. pannarioides Ertz & R.S. Poulsen and Henssenia subglaucella Ertz & R.S. Poulsen along with seven new combinations: Steinera intricata (Ovstedal) Ertz, S . latispora (Ovstedal) Ertz, S. olechiana (Alstrup & Sochting) Ertz & Sochting, S . subantarctica (Ovstedal) Ertz, Henssenia glaucella (Tuck.) Ertz, R.S. Poulsen & Sochting, H. radiata (P. James & Henssen) Ertz and H. werthii (Zahlbr.) Ertz, R.S. Poulsen & Sochting. An epitype is chosen for Henssenia glaucella and a neotype for H. werthii . “ Steinera” symptychia has an isolated phylogenetic position in the Koerberiaceae and might represent a distinct, new genus. World-wide identification keys to the species of Henssenia and Steinera are provided.

As a result of recent or past evolutionary processes, a single species might consist of distinct Evolutionary Significant Units (ESUs), even corresponding to cryptic species. Determining the underlying mechanisms of range shifts and the processes at work in the build-up of divergent ESUs requires elucidating the factors that contribute to population genetic divergence across a species' range. We investigated the large-scale patterns of genetic structure in the perennial herbaceous plant species Silene nutans (Caryophyllaceae) in Western Europe. We sampled and genotyped 111 populations using 13 nuclear microsatellite loci and 6 plastid single-nucleotide polymorphisms. Broad-scale spatial population genetic structure was examined using Bayesian clustering, spatial multivariate analyses and measures of hierarchical genetic differentiation. The genotypic structure of S. nutans was typical of a predominantly allogamous mating system. We also identified plastid lineages with no intra-population polymorphism, mirroring two genetically differentiated nuclear lineages. No evidence of admixture was found. Spatial trends in genetic diversity further suggested independent leading-edge expansion associated with founding events and subsequent genetic erosion. Overall, our findings suggested speciation processes in S. nutans and highlighted striking patterns of distinct stepwise recolonisation of Western Europe shaped by Quaternary climate oscillations. Two main potential ESUs can be defined in Western Europe, corresponding to Eastern and Western nuclear-plastid lineages. In situ preservation of populations and genetic rescue implying ex situ conservation techniques should take the lineage identity into account. This is particularly true in Great Britain, northern France and Belgium, where S. nutans is rare and where distinct lineages co-occur in close contact.

F.T. Kützing introduced Cocconeis molesta with only an uninformative description and a poor illustration: C. molesta has small, oblong valves and is an epiphyte. Another species, Cocconeis diaphana, described by William Smith, is said to have larger valves than C. molesta, with frustules that are relatively oblong. Smith described two forms: one with a distinct fascia on its raphe valve (var. β), the other without this feature. A third species, Cocconeis dirupta was described by Gregory, who expressed doubts that it differed from C. diaphana. Finally, Cocconeis molesta var. crucifera Grunow was first introduced in Van Heurck’s Atlas but was subsequently treated by Van Heurck as a synonym of C. molesta. No previous account has examined the type material of these species. In this paper, we undertake that task and examine type slides and raw material in order to discriminate these different taxa. We conclude by recognizing three species: Cocconeis molesta Kütz., C. diaphana W.Sm. and C. dirupta W.Greg. Cocconeis diaphana var. β is considered to be a synonym of C. dirupta and C. molesta var. crucifera is considered to be a synonym of C. molesta. Lectotypes are designated for C. diaphana and C. dirupta.

International audience; Notodiscus hookeri is the only native land snail of the sub-Antarctic present in Crozet Archipelago. Two shell ecophenotypes co-exist on Possession Island and feed exclusively on lichens [1] that are symbiotic organisms widely distributed in sub-Antarctic islands. To improve our understanding of lichen-snail trophic interactions, the endemic tripartite lichen Argopsis friesiana was selected. The snail belonging to the organic ecophenotype occurs sympatrically with A. friesiana. Profiling and quantification of the major secondary metabolites in the whole lichen were carried out by LC-DAD-MS. Two main compounds were identified, the depside atranorin (8.2 mg g-1 DM) and the depsidone argopsin. Besides, a screening of primary metabolites was carried out to determine which compounds could be useful for the snail energetic demands. Glutamate, glutamine, gamma-aminobutyric acid and alpha-alanine were the main amino acids found in the lichen in low concentrations (0.4 mg·g-1 DM). Carbohydrates, including arabitol (10.2 mg g-1), mannitol (4.0.10-4 mg g-1) and sucrose (3.0.10-4 mg g-1), were also identified. In cultivation, N. hookeri snails were fed with fructified thalli of A. friesiana. Snails (n = 20) ate the podetia cortex and phyllocladia but they clearly avoided apothecia, the reproductive organs. This sectorial damage of the lichen by the snail suggested a differential distribution of the metabolites. Therefore, a profiling of secondary compounds was performed by Direct Analysis in Real Time – Mass Spectroscopy (DART-MS) [2] on each morphological part of the lichen (phyllocladia, apothecia, podetia and cephalodia). The identification and distribution of secondary metabolites, fatty acids, amino acids and carbohydrates should help us to determine whether metabolites affect snail feeding choice and which of them could be involved.

We used allozymes to investigate the structure of genetic variation in populations of the perennial herb Silene nutans at local (Denmark), regional (Nordic area) and wide (over a 19° latitudinal gradient) geographic scales in north-western Europe. New data from Denmark were combined with data from previously studied Fennoscandian and western populations. We related patterns of nuclear variation for 26 Fennoscandian and western populations to the phylogeographic patterns revealed by four plastid (chloroplast) DNA markers. Levels of genetic diversity were similar within Denmark and Sweden/N Finland. Compared to Sweden/N Finland, the Danish populations show lower and nonsignificant FIS values. The genetic structure reveals no grouping of the Danish populations according to their geographic origin (Jutland-Zealand). Within Nordic populations (from Denmark, Sweden and N Finland), there is a weak geographic pattern of allozyme differentiation. The high latitude populations are genetically depauperate compared with populations from Western Europe. At the whole north-western European scale, the structure of allozyme variation within S. nutans shows geographic differentiation (Nordic versus western populations), and some congruence with plastid phylogeographic patterns. A high level of allozyme genetic differentiation is found between Nordic and western populations (8.0 %), but also between populations within haplotype categories (19.4 %). The overall geographic structure of allozyme variation of S. nutans appears to be primarily a reflection of past (postglacial) migration history, whereas more recent adaptive and stochastic processes have occurred at more local scales.

International audience; As first observed on a group of taxa related to Cocconeis peltoides Hustedt, several other Cocconeis eHRenbeRG (Bacillariophyta) taxa possess a row of minute marginal pores on the external side of their sternum valve (SV) connected to small and simple internal portules, or processes. These processes are often located in continuity with the striae, but can also be slightly shifted or distant from the distal areola of the striae. The row of pores is often, but not always, externally separated from the stria by a crista marginalis. Within Cocconeis, and possibly all raphid diatoms, these processes seem unique and restricted to a few taxa. A list is presented of the taxa pertaining (or close) to Cocconeis that are actually known to share these micro–structures. In addition, the morphological variability of the processes is described in detail and a morphological comparison of the taxa is provided. The characteristic features of taxa showing a row of SV processes permit the tentative definition of several morphological groups. It is difficult to prove the taxonomic affiliation of these taxa and demonstrate or refute that these processes are ancestral characters. Some of these taxa are rare and restricted to low latitudes (e.g., tropical taxa) while others are frequent and ubiquitous. Abbreviations: (LM) light microscope, (SEM) scanning electron microscope, (RV) raphe valve, (SV) sternum valve, (RVVC) raphe valve valvocopula, (SVVC) sternum valve valvocopula

International audience; Ochrolechia kerguelensis Ertz & Kukwa is described as new to science from the subantarctic islands of Kerguelen. It is characterized by pruinose ascomata, usually 4-spored asci, large ascospores of 50-90 × 32-56 µm, the production of gyrophoric acid only in the apothecia and the lack of variolaric acid. A photobiont with cells containing orange guttules such as in trentepohlioid algae is recorded for the first time in the genus Ochrolechia, being present in O. austroamericana and O. kerguelensis. Ochrolechia antarctica is reinstated from the synonymy of O. parella and treated as a distinct species. Chemical and morphological differences between these taxa are discussed. Ochrolechia chilensis and O. deceptionis are treated as synonyms of O. antarctica. The phylogenetic placement of O. antarctica, O. austroamericana and O. kerguelensis is investigated using mtSSU rDNA sequences and a Bayesian analysis. A key to all fertile, saxicolous Ochrolechia species with a C+ red epihymenium occurring in the Southern Hemisphere is presented. © 2016 Magnolia Press.

Background In the past few years, functional genomics information has been rapidly accumulating on Rubiaceae species and especially on those belonging to the Coffea genus (coffee trees). An increasing number of expressed sequence tag (EST) data and EST- or genomic-derived microsatellite markers have been generated, together with Conserved Ortholog Set (COS) markers. This considerably facilitates comparative genomics or map-based genetic studies through the common use of orthologous loci across different species. Similar genomic information is available for e.g. tomato or potato, members of the Solanaceae family. Since both Rubiaceae and Solanaceae belong to the Euasterids I (lamiids) integration of information on genetic markers would be possible and lead to more efficient analyses and discovery of key loci involved in important traits such as fruit development, quality, and maturation, or adaptation. Our goal was to develop a comprehensive web data source for integrated information on validated orthologous markers in Rubiaceae. Description MoccaDB is an online MySQL-PHP driven relational database that houses annotated and/or mapped microsatellite markers in Rubiaceae. In its current release, the database stores 638 markers that have been defined on 259 ESTs and 379 genomic sequences. Marker information was retrieved from 11 published works, and completed with original data on 132 microsatellite markers validated in our laboratory. DNA sequences were derived from three Coffea species/hybrids. Microsatellite markers were checked for similarity, in vitro tested for cross-amplification and diversity/polymorphism status in up to 38 Rubiaceae species belonging to the Cinchonoideae and Rubioideae subfamilies. Functional annotation was provided and some markers associated with described metabolic pathways were also integrated. Users can search the database for marker, sequence, map or diversity information through multi-option query forms. The retrieved data can be browsed and downloaded, along with protocols used, using a standard web browser. MoccaDB also integrates bioinformatics tools (CMap viewer and local BLAST) and hyperlinks to related external data sources (NCBI GenBank and PubMed, SOL Genomic Network database). Conclusion We believe that MoccaDB will be extremely useful for all researchers working in the areas of comparative and functional genomics and molecular evolution, in general, and population analysis and association mapping of Rubiaceae and Solanaceae species, in particular.