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Of the 130 known coffee (Coffea) species, very few have been properly evaluated for their beverage quality. The diversity of wild coffee species is considered critical to the long-term sustainability of the coffee sector, particularly under climate change. The challenge is finding coffee crops that satisfy agronomic criteria, now and under the altered climatic conditions of the future, as well as consumer requirements for flavour. We evaluated the sensory characteristics of three wild coffee species with four independent sensory panels, and the key environmental/agronomic requirements of these wild species based on a literature review.Coffea congensis and C. stenophylla have a lower unroasted seed weight compared to C. arabica and C. canephora, while C. brevipes has the largest. Sensory analysis showed that the main differences between species was for the fruitiness attribute. Coffea stenophylla was the fruitiest wild species, and was considered an Arabica-like coffee. The flavour profile range of C. stenophylla covers herb-like, vegetal, floral and fruit; C. brevipes resembles C. stenophylla in some respects. Opinions concerning C. congensis were contradictory and several judges considered the industry-standard coffee flavour wheel not suitable for the beverage produced from this species.The three wild species have the required sensory qualities for commercialization. According to published data, C. stenophylla has agronomic potential, especially in warmer climates than Arabica areas. Coffea brevipes and C. congensis have the potential to be easily crossed with C. canephora to form interspecific hybrids capable of adapting to different climatic and agronomic conditions. © 2022 The Authors. Journal of The Science of Food and Agriculture published by John WileySons Ltd on behalf of Society of Chemical Industry.

SummarySix new species of Coffea are described as new to science: Coffea callmanderi, C. darainensis, C. kalobinonensis, C. microdubardii, C. pustulata and C. rupicola. All six species are endemic to northern Madagascar; four species are narrowly endemic to specific forest areas. Associated information, including distribution maps, conservation assessments, phenology and taxonomic notes are provided, and two species are illustrated with line drawings.

PREMISE Comprising five families that vastly differ in species richness-ranging from Gelsemiaceae with 13 species to the Rubiaceae with 13,775 species-members of the Gentianales are often among the most species-rich and abundant plants in tropical forests. Despite considerable phylogenetic work within particular families and genera, several alternative topologies for family-level relationships within Gentianales have been presented in previous studies. METHODS Here we present a phylogenomic analysis based on nuclear genes targeted by the Angiosperms353 probe set for approximately 150 species, representing all families and approximately 85% of the formally recognized tribes. We were able to retrieve partial plastomes from off-target reads for most taxa and infer phylogenetic trees for comparison with the nuclear-derived trees. RESULTS We recovered high support for over 80% of all nodes. The plastid and nuclear data are largely in agreement, except for some weakly to moderately supported relationships. We discuss the implications of our results for the order's classification, highlighting points of increased support for previously uncertain relationships. Rubiaceae is sister to a clade comprising (Gentianaceae + Gelsemiaceae) + (Apocynaceae + Loganiaceae). CONCLUSIONS The higher-level phylogenetic relationships within Gentianales are confidently resolved. In contrast to recent studies, our results support the division of Rubiaceae into two subfamilies: Cinchonoideae and Rubioideae. We do not formally recognize Coptosapelteae and Luculieae within any particular subfamily but treat them as incertae sedis. Our framework paves the way for further work on the phylogenetics, biogeography, morphological evolution, and macroecology of this important group of flowering plants.

Cultivated Arabica coffee outside Ethiopia is plagued by low genetic diversity, compromising disease resistance, climate resiliency and sensory potential. Access to the wider genetic diversity of this species may circumvent some of these problems. In addition to Ethiopia, South Sudan has been postulated as a center of origin for Arabica coffee, but this has never been genetically confirmed. We used simple sequence repeat (SSR) markers to assess the genetic diversity of wild and cultivated populations of Arabica coffee from the Boma Plateau in South Sudan, against farmed accessions (of wild origin) from Ethiopia, Yemen, and global cultivars. Our results not only validate Boma Plateau as part of the natural distribution and as a center of origin for Arabica coffee but also indicate that wild populations in South Sudan are genetically distinct from Ethiopian Arabica. This newly identified genetic diversity within Arabica could have the potential for crop improvement through selection and use in breeding programs. Observations and analyses show that the extent and health of the wild population of Arabica in South Sudan have declined. Urgent action should be taken to conserve (in situ and ex situ) the unique, remaining genetic diversity of wild Arabica populations in South Sudan.

Climate change poses a considerable challenge for coffee farming, due to increasing temperatures, worsening weather perturbations, and shifts in the quantity and timing of precipitation. Of the actions required for ensuring climate resilience for coffee, changing the crop itself is paramount, and this may have to include using alternative coffee crop species. In this study we use a multidisciplinary approach to elucidate the identity, distribution, and attributes, of two minor coffee crop species from East Africa: Coffea racemosa and C. zanguebariae. Using DNA sequencing and morphology, we elucidate their phylogenetic relationships and confirm that they represent two distinct but closely related species. Climate profiling is used to understand their basic climatic requirements, which are compared to those of Arabica (C. arabica) and robusta (C. canephora) coffee. Basic agronomic data (including yield) and sensory information are provided and evaluated. Coffea racemosa and C. zanguebariae possess useful traits for coffee crop plant development, particularly heat tolerance, low precipitation requirement, high precipitation seasonality (dry season tolerance) and rapid fruit development (c. 4 months flowering to mature fruit). These attributes would be best accessed via breeding programs, although these species also have niche-market potential, particularly after further pre-farm selection and post-harvest optimization.

BACKGROUND: Enset (Ensete ventricosum, Musaceae) is an African crop that currently provides the staple food for approx. 20 million Ethiopians. Whilst wild enset grows over much of East and Southern Africa and the genus extends across Asia to China, it has only ever been domesticated in the Ethiopian Highlands. Here, smallholder farmers cultivate hundreds of landraces across diverse climatic and agroecological systems. SCOPE: Enset has several important food security traits. It grows over a relatively wide range of conditions, is somewhat drought-tolerant, and can be harvested at any time of the year, over several years. It provides an important dietary starch source, as well as fibres, medicines, animal fodder, roofing and packaging. It stabilizes soils and microclimates and has significant cultural importance. In contrast to the other cultivated species in the family Musaceae (banana), enset has received relatively little research attention. Here, we review and critically evaluate existing research, outline available genomic and germplasm resources, aspects of pathology, and explore avenues for crop development. CONCLUSION: Enset is an underexploited starch crop with significant potential in Ethiopia and beyond. Research is lacking in several key areas: empirical studies on the efficacy of current agronomic practices, the genetic diversity of landraces, approaches to systematic breeding, characterization of existing and emerging diseases, adaptability to new ranges and land-use change, the projected impact of climate change, conservation of crop wild relatives, by-products or co-products or non-starch uses, and the enset microbiome. We also highlight the limited availability of enset germplasm in living collections and seedbanks, and the lack of knowledge of reproductive and germination biology needed to underpin future breeding. By reviewing the current state of the art in enset research and identifying gaps and opportunities, we hope to catalyse the development and sustainable exploitation of this neglected starch crop. ispartof: ANNALS OF BOTANY vol:123 issue:5 pages:747-766 ispartof: location:England status: published

There are numerous factors to consider when developing climate-resilient coffee crops, including the ability to tolerate altered climatic conditions, meet agronomic and value chain criteria, and satisfy consumer preferences for flavour (aroma and taste). We evaluated the sensory characteristics and key environmental requirements for the enigmatic narrow-leaved coffee (Coffea stenophylla), a wild species from Upper West Africa1. We confirm historical reports of a superior flavour1–3 and uniquely, and remarkably, reveal a sensory profile analogous to high-quality Arabica coffee. We demonstrate that this species grows and crops under the same range of key climatic conditions as (sensorially inferior) robusta and Liberica coffee4–9 and at a mean annual temperature 6.2–6.8 °C higher than Arabica coffee, even under equivalent rainfall conditions. This species substantially broadens the climate envelope for high-quality coffee and could provide an important resource for the development of climate-resilient coffee crop plants. Coffea stenophylla is a recently rediscovered, narrow-leaved wild coffee from Upper West Africa. Rigorous sensory evaluation (tasting) rates its flavour profile as analogous to high-quality Arabica coffee, but it can grow at much higher temperatures.

Background – This contribution is part of an ongoing study on the taxonomy and the phylogenetic relationships of the Malagasy representatives of the tribe Pavetteae (Rubiaceae).Material and methods – Taxonomic methods follow normal practice of herbarium taxonomy. A molecular study using the plastid markers rps16, trnT-F, petD, and accD-psa1, the nuclear ribosomal marker ITS and the nuclear MADS-box gene marker PI was executed.Key results – Five new species are described from littoral, lowland, or mid-elevation humid forests in eastern Madagascar. They are characterized by compact inflorescences with small, sessile flowers, a densely pubescent style, large placentas with 2–3 immersed ovules, seeds with a small, superficial hilum not surrounded by a thickened annulus, and pollen grains with supratectal elements. The phylogenetic tree, which included three of the five new species, showed an unresolved backbone but high support for distal nodes grouping species. The new species form a distinct monophyletic clade among the other Malagasy Pavetteae genera and are recognised at genus level under the name Tarennella. Provisional IUCN Red List assessments show that Tarennella homolleana is Vulnerable, T. cordatifolia and T. sanguinea are Endangered, T. puberula is Critically Endangered, and T. coronata is Critically Endangered (Possibly Extinct).

Coffea arabica (Arabica) and C. canephora (robusta) almost entirely dominate global coffee production. Various challenges at the production (farm) level, including the increasing prevalence and severity of disease and pests and climate change, indicate that the coffee crop portfolio needs to be substantially diversified in order to ensure resilience and sustainability. In this study, we use a multidisciplinary approach (herbarium and literature review, fieldwork and DNA sequencing) to elucidate the identity, whereabouts, and potential attributes, of two poorly known coffee crop species: C. affinis and C. stenophylla. We show that despite widespread (albeit small-scale) use as a coffee crop species across Upper West Africa and further afield more than 100 years ago, these species are now extremely rare in the wild and are not being farmed. Fieldwork enabled us to rediscover C. stenophylla in Sierra Leone, which previously had not been recorded in the wild there since 1954. We confirm that C. stenophylla is an indigenous species in Guinea, Sierra Leone, and Ivory Coast. Coffea affinis was discovered in the wild in Sierra Leone for the first time, having previously been found only in Guinea and Ivory Coast. Prior to our rediscovery, C. affinis was last seen in the wild in 1941, although sampling of an unidentified herbarium specimen reveals that it was collected in Guinea-Conakry in 2015. DNA sequencing using plastid and ITS markers was used to: (1) confirm the identity of museum and field collected samples of C. stenophylla; (2) identify new accessions of C. affinis; (3) refute hybrid status for C. affinis; (4) identify accessions confused with C. affinis; (5) show that C. affinis and C. stenophylla are closely related, and possibly a single species; (6) substantiate the hybrid C. stenophylla × C. liberica; (7) demonstrate the use of plastid and nuclear markers as a simple means of identifying F1 and early-generation interspecific hybrids in Coffea; (8) infer that C. liberica is not monophyletic; and (9) show that hybridization is possible across all the major groups of key Africa Coffea species (Coffee Crop Wild Relative Priority Groups I and II). Coffea affinis and C. stenophylla may possess useful traits for coffee crop plant development, including taste differentiation, disease resistance, and climate resilience. These attributes would be best accessed via breeding programs, although the species may have niche-market potential via minimal domestication.

Highlights • Lipophilic extracts of ground roast Arabica coffees were authenticated by benchtop NMR. • Small amounts of esterified 16-O-methylcafestol were found in Arabica coffees. • The compound identity was confirmed by NMR and MS experiments. • 16-OMC remains a useful marker for non-Arabicas as these contain much higher amounts. • 6 out of 60 retail Arabicas contained significant amounts of non-Arabica species., High-field and low-field proton NMR spectroscopy were used to analyse lipophilic extracts from ground roast coffees. Using a sample preparation method that produced concentrated extracts, a small marker peak at 3.16 ppm was observed in 30 Arabica coffees of assured origin. This signal has previously been believed absent from Arabicas, and has been used as a marker for detecting adulteration with robusta. Via 2D 600 MHz NMR and LC-MS, 16-O-methylcafestol and 16-O-methylkahweol were detected for the first time in Arabica roast coffee and shown to be responsible for the marker peak. Using low-field NMR, robusta in Arabica could be detected at levels of the order of 1–2% w/w. A surveillance study of retail purchased “100% Arabica” coffees found that 6 out of 60 samples displayed the 3.16 ppm marker signal to a degree commensurate with adulteration at levels of 3–30% w/w.

International audience; A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus(Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been lim-ited by low levels of sequence divergence, leading to insufficient topological resolution and statisticalsupport in phylogenetic trees, particularly for the major lineages and for the numerous species occurringin Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesisfor coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed,lab-based workflow to integrate short read next-generation sequencing for low numbers of additionalsamples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) asthe most likely ancestral locality for the origin of the coffee genus, with independent radiations acrossAfrica, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolutionof caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. Highand consistent caffeine content is found only in species from the equatorial, fully humid environmentsof West and Central Africa, possibly as an adaptive response to increased levels of pest predation.Moderate caffeine production, however, evolved at least one additional time recently (between 2 and4 Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already inplace during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subjectto convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate

Coffea arabica (Arabica) and C. canephora (robusta) almost entirely dominate global coffee production. Various challenges at the production (farm) level, including the increasing prevalence and severity of disease and pests and climate change, indicate that the coffee crop portfolio needs to be substantially diversified in order to ensure resilience and sustainability. In this study, we use a multidisciplinary approach (herbarium and literature review, fieldwork and DNA sequencing) to elucidate the identity, whereabouts, and potential attributes, of two poorly known coffee crop species: C. affinis and C. stenophylla. We show that despite widespread (albeit small-scale) use as a coffee crop species across Upper West Africa and further afield more than 100 years ago, these species are now extremely rare in the wild and are not being farmed. Fieldwork enabled us to rediscover C. stenophylla in Sierra Leone, which previously had not been recorded in the wild there since 1954. We confirm that C. stenophylla is an indigenous species in Guinea, Sierra Leone, and Ivory Coast. Coffea affinis was discovered in the wild in Sierra Leone for the first time, having previously been found only in Guinea and Ivory Coast. Prior to our rediscovery, C. affinis was last seen in the wild in 1941, although sampling of an unidentified herbarium specimen reveals that it was collected in Guinea-Conakry in 2015. DNA sequencing using plastid and ITS markers was used to: (1) confirm the identity of museum and field collected samples of C. stenophylla; (2) identify new accessions of C. affinis; (3) refute hybrid status for C. affinis; (4) identify accessions confused with C. affinis; (5) show that C. affinis and C. stenophylla are closely related, and possibly a single species; (6) substantiate the hybrid C. stenophylla × C. liberica; (7) demonstrate the use of plastid and nuclear markers as a simple means of identifying F1 and early-generation interspecific hybrids in Coffea; (8) infer that C. liberica is not monophyletic; and (9) show that hybridization is possible across all the major groups of key Africa Coffea species (Coffee Crop Wild Relative Priority Groups I and II). Coffea affinis and C. stenophylla may possess useful traits for coffee crop plant development, including taste differentiation, disease resistance, and climate resilience. These attributes would be best accessed via breeding programs, although the species may have niche-market potential via minimal domestication.

Galanthus bursanus (Amaryllidaceae), a new snowdrop species endemic to the Marmara Sea region (Bursa Province, NW Turkey), is described and illustrated. Morphological differences between the new species and other possibly related Galanthus taxa (G. plicatus subsp. byzantinus, G. ×valentinei nothosubsp. subplicatus, and G. reginae-olgae subsp. reginae-olgae) are discussed. Photographs (habitat and morphology), a distribution map and a preliminary conservation assessment are provided.

Extinction threatens at least 60% of wild coffee species, including those that are key to the future of the global coffee sector., Wild coffee species are critical for coffee crop development and, thus, for sustainability of global coffee production. Despite this fact, the extinction risk and conservation priority status of the world’s coffee species are poorly known. Applying IUCN Red List of Threatened Species criteria to all (124) wild coffee species, we undertook a gap analysis for germplasm collections and protected areas and devised a crop wild relative (CWR) priority system. We found that at least 60% of all coffee species are threatened with extinction, 45% are not held in any germplasm collection, and 28% are not known to occur in any protected area. Existing conservation measures, including those for key coffee CWRs, are inadequate. We propose that wild coffee species are extinction sensitive, especially in an era of accelerated climatic change.

The specialty coffee sector represents opportunities for coffee farmers and other actors due to increased value within the supply chain, driven by elevated consumer purchase prices. We investigated these relationships up to the export stage, as well as the potential for specialty coffee to improve stakeholder participation in biodiversity conservation. Household data was collected from a sample of 272 coffee farmers belonging to five primary cooperatives, in the heavily forested area of Yayu, in the Illubabor administrative zone of Oromia regional state in south-western Ethiopia, for the 2017/2018 harvest season. Qualitative and quantitative data, gathered between 2015 and 2019, from focus group discussions, was used to supplement the survey and to explain the empirical findings. We show that the income from coffee (and thus household income) can be increased, in some cases substantially, via participation in the specialty coffee market. The unit price for coffee was much higher than standard market prices and those including certification premiums. Whilst quality is a key factor for specialty coffee, income increases via the specialty market are caveat bound. In particular, there is a critical requirement for efficient and effective cooperative management, and we provide suggestions for improvements. In the long-term, more focus is needed to increase the financial and human capacities of Ethiopian coffee cooperatives, to make them more effective partners in the specialty coffee value chain. The high conversion rates from harvested to clean exportable specialty coffee (8:1, or higher) is identified as a major constraint on profitability. We show that specialty coffee can bring about positive environmental benefits. Elevating coffee prices and farm profitability to bring household income levels to around or above the global poverty line may ensure the continuation of forest coffee production, and thus the retention of forest. The increases in income via specialty coffee production, reported in the study, were achieved without increasing land use or the application of environmentally costly inputs. Moreover, analysis of satellite data shows that a large proportion of the coffee farms surveyed retain a level of forest cover and quality approaching primary (undisturbed) forest, and that the coffee production area at Yayu has not experienced any significant deforestation (since 2000). We recommend that coffee premiums linked to environmental benefit should demonstrate clearly defined and appropriate metrics, as we have demonstrated here for forest (canopy) quality and coverage (area).

Coffee genetic resources are being lost at a rapid pace, leading to loss of genetic diversity. Various threats contribute to the erosion of coffee genetic diversity such as human population pressures leading to conversion of land to agriculture, deforestation and land degradation; low coffee prices leading to abandoning of coffee trees in forests and gardens and shifting cultivation to other more remunerative crops; and climate change. Additionally, the cultivated species of coffee (Coffea arabica L.) has a very narrow genetic base. Increased incidence of pests and diseases associated with climate change is leading to significant crop losses, threatening livelihoods in many coffee growing countries. A comprehensive conservation strategy for coffee should take into account complementary methods of in situ and ex situ conservation. The development of molecular techniques has expanded the possibilities and tools for genetic analysis for efficient conservation and use of coffee genetic resources. Before it is too late, a thorough evaluation of existing germplasm should be performed based upon which a comprehensive conservation strategy could be developed. A case study using four different Coffea species in Madagascar is discussed.

Arabica coffee (Coffea arabica) is a key crop in many tropical countries and globally provides an export value of over US$13 billion per year. Wild Arabica coffee is of fundamental importance for the global coffee sector and of direct importance within Ethiopia, as a source of harvestable income and planting stock. Published studies show that climate change is projected to have a substantial negative influence on the current suitable growing areas for indigenous Arabica in Ethiopia and South Sudan. Here we use all available future projections for the species based on multiple general circulation models (GCMs), emission scenarios, and migration scenarios, to predict changes in Extent of Occurrence (EOO), Area of Occupancy (AOO), and population numbers for wild Arabica coffee. Under climate change our results show that population numbers could reduce by 50% or more (with a few models showing over 80%) by 2088. EOO and AOO are projected to decline by around 30% in many cases. Furthermore, present‐day models compared to the near future (2038), show a reduction for EOO of over 40% (with a few cases over 50%), although EOO should be treated with caution due to its sensitivity to outlying occurrences. When applying these metrics to extinction risk, we show that the determination of generation length is critical. When applying the International Union for Conservation of Nature's Red list of Threatened Species (IUCN Red List) criteria, even with a very conservative generation length of 21 years, wild Arabica coffee is assessed as Threatened with extinction (placed in the Endangered category) under a broad range of climate change projections, if no interventions are made. Importantly, if we do not include climate change in our assessment, Arabica coffee is assessed as Least Concern (not threatened) when applying the IUCN Red List criteria., Arabica coffee (Coffea arabica) is a key crop in many tropical countries and globally provides an export value of over US$13 billion per year. Wild Arabica coffee is of fundamental importance for the global coffee sector and of direct importance within Ethiopia, as a source of harvestable income and planting stock. In this paper we show that under climate change alone, population numbers could reduce by 50% or more (with a few models showing over 80%) by 2088. When applying the International Union for Conservation of Nature’s Red list of Threatened Species (IUCN Red List) criteria, even with a very conservative generation length of 21 years, wild Arabica coffee is assessed as Threatened with extinction (placed in the Endangered category) under a broad range of climate change projections, if no interventions are made. Importantly, if we do not include climate change in our assessment, Arabica coffee is assessed as Least Concern (not threatened) when applying the IUCN Red List criteria.

Coffee farming provides livelihoods for around 15 million farmers in Ethiopia and generates a quarter of the country's export earnings. Against a backdrop of rapidly increasing temperatures and decreasing rainfall, there is an urgent need to understand the influence of climate change on coffee production. Using a modelling approach in combination with remote sensing, supported by rigorous ground-truthing, we project changes in suitability for coffee farming under various climate change scenarios, specifically by assessing the exposure of coffee farming to future climatic shifts. We show that 39-59% of the current growing area could experience climatic changes that are large enough to render them unsuitable for coffee farming, in the absence of significant interventions or major influencing factors. Conversely, relocation of coffee areas, in combination with forest conservation or re-establishment, could see at least a fourfold (400%) increase in suitable coffee farming area. We identify key coffee-growing areas that are susceptible to climate change, as well as those that are climatically resilient.

Livestock numbers are increasing to supply the growing demand for meat-rich diets. The sustainability of this trend has been questioned, and future environmental changes, such as climate change, may cause some regions to become less suitable for livestock. Livestock and wild herbivores are strongly dependent on the nutritional chemistry of forage plants. Nutrition is positively linked to weight gains, milk production and reproductive success, and nutrition is also a key determinant of enteric methane production. In this meta-analysis, we assessed the effects of growing conditions on forage quality by compiling published measurements of grass nutritive value and combining these data with climatic, edaphic and management information. We found that forage nutritive value was reduced at higher temperatures and increased by nitrogen fertiliser addition, likely driven by a combination of changes to species identity and changes to physiology and phenology. These relationships were combined with multiple published empirical models to estimate forage- and temperature-driven changes to cattle enteric methane production. This suggested a previously undescribed positive climate change feedback, where elevated temperatures reduce grass nutritive value and correspondingly may increase methane production by 0.9 % with a 1 °C temperature rise and 4.5 % with a 5 °C rise (model average), thus creating an additional climate forcing effect. Future methane production increases are expected to be largest in parts of North America, central and eastern Europe and Asia, with the geographical extent of hotspots increasing under a high emissions scenario. These estimates require refinement and a greater knowledge of the abundance, size, feeding regime and location of cattle, and the representation of heat stress should be included in future modelling work. However, our results indicate that the cultivation of more nutritious forage plants and reduced livestock farming in warming regions may reduce this additional source of pastoral greenhouse gas emissions.

International audience; In this study we investigate the large and diverse Rubiaceae-Gardenieae and closely related tribes Bertiereae, Coffeeae, Cremasporeae, Octotropideae, and Pavetteae. Some of the tribes or groups have been shown to be monophyletic and strongly supported, but the phylogeny of this large complex is still far from being satisfactorily elucidated particularly for Gardenieae, both in terms of intertribal relationships as well as tribal delimitations. We reconstruct the phylogeny of the complex using an extensive sampling of 108 genera and five plastid DNA regions. Phylogenetic relationships demonstrate that Gardenieae sensu Andreasen & Bremer is polyphyletic, as Burchellia, Didymosalpinx, Monosalpinx, and Mantalania are closer to Octotropideae-Cremasporeae. In addition, Pavetteae and the investigated members of Aulacocalyceae are nested in a supported but partially unresolved Gardenieae-Pavetteae clade. Within this clade, several strongly supported groups are resolved: an Aidia group, an Alibertia group, a Gardenia group, Pavetteae including Pelagodendron, a Porterandia group, a Randia group, a Rothmannia group (including Aulacocalyx and Heinsenia), a Sherbournia group, and the two isolated genera Massularia and Schumanniophyton. The latter genus presented a high rate of genetic substitutions, which resulted in perturbations of the phylogenetic reconstruction. A revised tribal circumscription is given for Gardenieae, the Alibertia group is recognized at tribal level as an emended Cordiereae, and a new tribe, Sherbournieae, is described to accommodate the members of the Sherbournia group.

Chapelieria is a genus endemic to Madagascar, currently comprising a single species: C. madagascariensis. In this contribution two new species of Chapelieria are described as new to science: C. septentrionalis and C. multiflora. An emended circumscription, description and line drawing are provided for C. madagascariensis. A full description, notes (distribution, habitat and ecology, phenology), a distribution map and conservation assessment are provided for each of the three species. An updated generic description and a species identification key are also given.

A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) as the most likely ancestral locality for the origin of the coffee genus, with independent radiations across Africa, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolution of caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. High and consistent caffeine content is found only in species from the equatorial, fully humid environments of West and Central Africa, possibly as an adaptive response to increased levels of pest predation. Moderate caffeine production, however, evolved at least one additional time recently (between 2 and 4Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already in place during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subject to convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate.

International audience; The completion of the genome assembly for the economically important coffee plant Coffea canephora (Rubiaceae) has allowed the use of bioinformatic tools to identify and characterize a diverse array of transposable elements (TEs), which can be used in evolutionary studies of the genus. An overview of the copy number and location within the C. canephora genome of four TEs is presented. These are tested for their use as molecular markers to unravel the evolutionary history of the Millotii Complex, a group of six wild coffee (Coffea) species native to Madagascar. Two TEs from the Gypsy superfamily successfully recovered some species boundaries and geographic structure among samples, whereas a TE from the Copia superfamily did not. Notably, species occurring in evergreen moist forests of eastern and southeastern Madagascawere divergent with respect to species in other habitats and regions. Our results suggest that the peak of transpositional activity of the Gypsy and Copia TEs occurred, respectively, before and after the speciation events of the tested Madagascan species. We conclude that the utilization of active TEs has considerable potential to unravel the evolutionary history and delimitation of closely related Coffea species. However, the selection of TE needs to be experimentally tested, since each element has its own evolutionary history. Different TEs with similar copy number in a given species can render different dendrograms; thus copy number is not a good selection criterion to attain phylogenetic resolution.

† Background and Aims The coffee genus (Coffea) comprises 124 species, and is indigenous to the Old World Tropics. Due to its immense economic importance, Coffea has been the focus of numerous genetic diversity studies, but despite this effort it remains insufficiently studied. In this study the genetic diversity and genetic structure of Coffea across Africa and the Indian Ocean islands is investigated. † Methods Genetic data were produced using 13 polymorphic nuclear microsatellite markers (simple sequence repeats, SSRs), including seven expressed sequence tag-SSRs, and the data were analysed using model- and non-model-based methods. The study includes a total of 728 individuals from 60 species. † Key Results Across Africa and the Indian Ocean islands Coffea comprises a closely related group of species with an overall pattern of genotypes running from west to east. Genetic structure was identified in accordance with pre-determined geographical regions and phylogenetic groups. There is a good relationship between morpho-taxonomic species delimitations and genetic units. Genetic diversity in African and Indian Ocean Coffea is high in terms of number of alleles detected, and Madagascar appears to represent a place of significant diversification in terms of allelic richness and species diversity. † Conclusions Cross-species SSR transferability in African and Indian Ocean islands Coffea was very efficient. On the basis of the number of private alleles, diversification in East Africa and the Indian Ocean islands appears to be more recent than in West and West-Central Africa, although this general trend is complicated in Africa by the position of species belonging to lineages connecting the main geographical regions. The general pattern of phylogeography is not in agreement with an overall east to west (Mascarene, Madagascar, East Africa, West Africa) increase in genome size, the high proportion of shared alleles between the four regions or the high numbers of exclusive shared alleles between pairs or triplets of regions.

— Resolving phylogenetic relationships within the economically important genus Coffea (Rubiaceae) has proven to be difficult due to low levels of plastid and nuclear ITS sequence divergence. The recent identification of a large number of conserved, single-copy, putatively orthologous genes (COSII) provides a unique opportunity to apply regions of the nuclear genome to phylogenetic studies of Euasterid species. We expand a previously published plastid data set of Coffea with the addition of three new plastid regions and a single COSII nuclear locus. Significant phylogenetic incongruence is identified between the plastid and nuclear COSII data sets, and a combined analysis is performed after removal of incongruent taxa. Phylogenetic results from plastid, nuclear, and combined plastid/nuclear data sets allow the novel identification of early diverging lineages in Coffea. Specifically, the data show that a group of predominately Lower-Guinea/Congolian Coffea species form a clade that is sister to the ...

International audience; In the past, the circumscription of the large genus Psychotria (Rubiaceae) was difficult, until molecular phylogenetic studies revealed its considerable paraphyly, enabling the delimitation of its major lineages and the grouping of related genera, and most notably the separation of Psychotria and its relatives (former Psychotrieae) into two tribes: Psychotrieae and Palicoureeae. The genus Margaritopsis, which is included in Palicoureeae, encompasses 27 Neotropical species, and in previous studies these have been shown to be close relatives of a group of eight Psychotria species that occur over a large region extending from South-East Asia to tropical South Pacific through Malesia (= the AMP region, defined as including South-East Asia, Malesia, tropical Australia, Melanesia, Micronesia, New Caledonia and Polynesia). A molecular phylogenetic study, using one nuclear DNA region (ITS) and four plastid DNA regions (ndhF, rps16, trnH-psbA, trnT-F), is undertaken in order to test the placement of 17 AMP Psychotria species within Palicoureeae. The phylogenetic results show that they form a monophyletic clade (= clade G), which also includes the monotypic Fijian genus Readea and Hodgkinsonia frutescens from Australia. Clade G is embedded in a well-supported grade with five Neotropical representatives of Margaritopsis. A morphological survey based on twenty characters, with the potential to circumscribe generic entities, shows that the monophyly of clade G is supported by a character combination that is similar to species of Neotropical Margaritopsis, confirming their inclusion in this genus. Taxonomic and nomenclatural work on these species is required to formalize nomenclatural implications. Based on the same set of morphological characters, but in absence of molecular data, 28 other Psychotria species from the AMP region were detected as likely candidates for inclusion in Margaritopsis, allowing the estimation of species richness of clade G to be a minimum of 47 species. Within clade G, five well-supported subclades and a Readea lineage are delimited and each of these is generally supported by unique morphological features. Phylogenetic topologies reveal biogeographical patterns, including a main route of dispersal from western to eastern parts of the AMP region, with subsequent dispersals between archipelagos in the region.

A taxonomic revision of Madagascan Gardenia is presented, to include four species and two subspecies. Three species, Gardenia sambiranensis Rakoton. & A. P. Davis, G. manongarivenis Rakoton. & A. P. Davis, G. brevicalyx Rakoton. & A. P. Davis and one subspecies, G. rutenbergiana subsp. australis Rakoton. & A. P. Davis, are described as new to science. Identification keys, descriptions, distribution maps, illustrations, species notes (distribution, habitat and ecology, phenology), and conservation assessments are provided. Madagascan Gardenia species are restricted to western Madagascar, in seasonally dry and sub-humid vegetation types. At least two species demonstrate broad ecological and anthropogenic tolerance, which may make them suitable for vegetation restoration projects in western Madagascar.

Madagascar has 59 species of Coffea, of which 42 are listed as Critically Endangered, Endangered, or Vulnerable by criteria of the Red List Category system of the World Conservation Union. In an attempt to assess the conservation value of ex situ collections of Malagasy coffee species, a study was undertaken using the field genebank collections maintained at the Kianjavato Coffee Research Station. Three species were selected for this purpose, C. kianjavatensis, C. montis-sacri, and C. vatovavyensis, and for comparative purposes extant, in situ populations of the same species were studied. Parentage analyses of ex situ propagated offspring of C. kianjavatensis and C. montis-sacri were performed to assess if crossing with other Coffea species maintained in the field genebank is compromising the genetic integrity of the collection. For these three species, higher genetic diversity was observed in the ex situ populations compared to the in situ populations, highlighting the importance of preserving the plants currently in ex situ collections. Parentage analyses of seed-propagated offspring of C. kianjavatensis and C. montis-sacri revealed that cross contamination with pollen from other Coffea species in the ex situ field genebank is occurring. These results have significant implications for the conservation management of wild Coffea species and for the management of ex situ genebanks.

Madagascar has 59 described species of Coffea, of which 42 are listed as critically endangered, endangered, or vulnerable by the criteria of the Red List Category system of the World Conservation Union (IUCN). The littoral forest of Madagascar is a distinctive type of humid evergreen forest restricted to unconsolidated sand located within a few kilometers of the Indian Ocean, now persisting only as small fragments with ca. 10 % of its original range remaining. In an attempt to understand the genetic diversity of Madagascan coffee species, we studied ex situ and in situ populations of Coffea commersoniana, an endemic species of the littoral forests of southeastern Madagascar and soon to be impacted by mining activities in that region. The in situ populations studied showed higher genetic diversity than the ex situ population. The genetic partitioning among the two in situ populations of C. commersoniana was high enough to necessitate keeping the two populations separate for restoration purposes. Based on these findings, recommendations for conservation management (in situ and ex situ) are made.

The coffee berry borer, Hypothenemus hampei (Coleoptera: Curculionidae: Scolytinae), is the most devastating insect pest of coffee throughout the world. The insect is endemic to Africa but can now be found throughout nearly all coffee-producing countries. One area of basic biology of the insect that remains unresolved is that of its alternative host plants, i.e. which fruits of plants, other than coffee, can the insect survive and reproduce in. An in-depth survey of the literature revealed an article by Schedl listing 21 genera in 13 families in which the insect was collected, mainly in the Democratic Republic of Congo. This overlooked reference, together with information provided in other early articles, suggests that H. hampei is polyphagous, and could provide, if confirmed in the field, critical information on the evolution of this insect’s diet, ecology and host range. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107, 86‐94.

Morphological and molecular phylogenetic studies show that there is a close relationship between Coffea and Psilanthus. In this study we reassess species relationships based on improved species sampling for Psilanthus, including P. melanocarpus, a species that shares morpho-taxonomic characters of both genera. Analyses are performed using parsimony and Bayesian inference, on sequence data from four plastid regions [trnL–F intron, trnL–F IGS, rpl16 intron and accD–psa1 intergenic spacer (IGS)] and the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (ITS 1/5.8S/ITS 2). Several major lineages with geographical coherence, as identified in previous studies based on smaller and larger data sets, are supported. Our results also confirm previous studies showing that the level of sequence divergence between Coffea and Psilanthus species is negligible, particularly given the much longer branch lengths separating other genera of tribe Coffeeae. There are strong indications that neither Psilanthus nor Coffea is monophyletic. Psilanthus melanocarpus is nested with the Coffea–Psilanthus clade, which means that there is only one critical difference between Coffea and Psilanthus; the former has a long-emergent style and the latter a short, included style. Based on these new data, in addition to other systematically informative evidence from a broad range of studies, and especially morphology, Psilanthus is subsumed into Coffea. This decision increases the number of species in Coffea from 104 to 124, extends the distribution to tropical Asia and Australasia and broadens the morphological characterization of the genus. The implications for understanding the evolutionary history of Coffea are discussed. A group of closely related species is informally named the ‘Coffea liberica alliance’. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 167, 357–377.

Phialiphora Groeninckx is described as a new herbaceous genus of Rubiaceae, endemic to NW Madagascar. The genus belongs to the predominantly herbaceous tribe Spermacoceae, and comprises two species: P. bevazahensis Groeninckx and P. capitulata Groeninckx. Phialiphora is unique within Spermacoceae in having heart-shaped placentas distally attached to the septum with a stalk. The generic name refers to the involucrate head-like inflorescences. Molecular data, based on atpB-rbcL, petD, rps16, and trnL-trnF sequences, demonstrate that Phialiphora belongs to the Hedyotis-Oldenlandia complex of the tribe Spermacoceae. The genus shares a common ancestor with the Madagascan endemics Astiella Jovet, Thamnoldenlandia Groeninckx and Amphistemon Groeninckx. Our study supports the hypothesis that the current diversity of Spermacoceae on Madagascar is the result of several independent colonisation events since the Eocene, most likely by long-distance dispersal from the African continent. A key to the genera of Spermacoceae on Madagascar is provided.

We present phylogenetic analyses of 32 taxa of Amaryllidaceae tribe Galantheae, 6 taxa of other Eurasian genera of Amaryllidaceae and Phaedranassa dubia as outgroup in order to provide a phylogenetic framework for selection of candidate plants for lead discovery in relation to Alzheimer’s disease. We used DNA sequences from the nuclear ribosomal internal transcribed spacer (ITS) and the plastid matK and trnL-F regions. Phylogenetic analyses using maximum parsimony and Bayesian inference strongly support a monophyletic tribe Galantheae in a narrow sense, including only Acis, Galanthus and Leucojum. Infrageneric relationships of Galanthus only partly support previous classifications. Alkaloid profiles and inhibition of acetylcholinesterase (AChE) were investigated for 18 taxa using gas chromatography–mass spectrometry (GC–MS) and an assay measuring inhibition of AChE activity. AChE inhibitory activity was found in all investigated clades and was correlated with alkaloid profiles of the plants. Lowest IC50 values were expressed by extracts containing either galanthamine or lycorine type compounds. Evaluation of available chemistry and activity data in a phylogenetic framework could be used to select target species for further investigation.

Recent studies on the circumscription of the tribe Coffeeae (Rubiaceae) revealed a weakly supported clade containing Tricalysia A. Rich. and the allied genera Argocoffeopsis Lebrun, Calycosiphonia Pierre ex Robbr., Belonophora Hook. f., Diplospora DC., Discospermum Dalzell, Nostolachma T. Durand, and Xantonnea Pierre ex Pit. The phylogenetic relationships of Tricalysia and these allied taxa are investigated further using sequence data from four plastid regions (trnL-F intron and intergenic spacer, rpL16 intron, accD-psa1 intergenic spacer, and PetD). Our results demonstrate that Tricalysia sensu Robbrecht is not monophyletic. The genus name Tricalysia should be restricted to taxa from subgenus Tricalysia; subgenus Empogona (Hook. f.) Robbr. is sister to the genus Diplospora and is recognized at the generic level. The 34 necessary new combinations for Empogona Hook. f. are provided: E. acidophylla (Robbr.) J. Tosh & Robbr., E. aequatoria (Robbr.) J. Tosh & Robbr., E. africana (Sim) J. Tosh & Robbr...

Analyses of distribution, diversity, endemism, and taxonomic effort for Rubiaceae are reported, based on queries from a World Rubiaceae Checklist database. Rubiaceae are widespread and occur in all major regions of the world except the Antarctic Continent, but are predominantly a group in the tropics with greatest diversity in low- to mid-altitude humid forests. A count of Rubiaceae species and genera is given (13,143 spp./611 genera), which confirms that this is the fourth largest angiosperm family. Psychotria L. is the largest genus in the Rubiaceae (1834 spp.) and the third largest angiosperm genus. Most genera (72%) have fewer than 10 species and 211 are monotypic. Calculation of relative species diversity and percentage endemism enables areas of high diversity and endemism to be enumerated, and identifies areas where further field collecting and taxonomic research are required. Endemism is generally high in Rubiaceae, which supports data from recent studies showing that many species have restricted distributions. Given the assumed ecologic sensitivity of Rubiaceae, in combination with a range of other factors including restricted distribution, we suggest that species in this family are particularly vulnerable to extinction. The rate at which new species are being described is inadequate; more resources are required before the diversity of Rubiaceae is satisfactorily enumerated.

A new species of Argocoffeopsis, A. spathulata, is described as new to science. A description, line drawing, distribution map and conservation assessment are provided.

A first phylogenetic placement of Petitiocodon based on molecular sequence data from three plastid regions (accD-psa1, rpl16 and trnL-F) is presented, in conjunction with a reassessment of morphology for the genus. Our results do not support an evolutionary affinity between Petitiocodon and Tricalysia (Coffeeae) as suggested by previous studies, but they confirm other research that Petitiocodon and Didymosalpinx are distinct genera. Placement of Petitiocodon in tribe Octotropideae is well-supported on the basis of molecular data and floral and carpological characters. © 2008 Nationaal Herbarium Nederland, Leiden University branch. ispartof: Blumea vol:53 issue:3 pages:549-565 status: published