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Kearsley E, Verbeeck H, Stoffelen P, Janssens SB, Yakusu EK, Kosmala M, De Mil T, Bauters M, Kitima ER, Ndiapo JM, Chuda AL, Richardson AD, Wingate L, Ilondea BA, Beeckman H, van den Bulcke J, Boeckx P, Hufkens K. Historical tree phenology data reveal the seasonal rhythms of the Congo Basin rainforest. Plant Environ Interact 2024; 5:e10136. [PMID: 38476212 PMCID: PMC10926959 DOI: 10.1002/pei3.10136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 01/05/2024] [Accepted: 01/23/2024] [Indexed: 03/14/2024]
Abstract
Tropical forest phenology directly affects regional carbon cycles, but the relation between species-specific and whole-canopy phenology remains largely uncharacterized. We present a unique analysis of historical tropical tree phenology collected in the central Congo Basin, before large-scale impacts of human-induced climate change. Ground-based long-term (1937-1956) phenological observations of 140 tropical tree species are recovered, species-specific phenological patterns analyzed and related to historical meteorological records, and scaled to characterize stand-level canopy dynamics. High phenological variability within and across species and in climate-phenology relationships is observed. The onset of leaf phenophases in deciduous species was triggered by drought and light availability for a subset of species and showed a species-specific decoupling in time along a bi-modal seasonality. The majority of the species remain evergreen, although central African forests experience relatively low rainfall. Annually a maximum of 1.5% of the canopy is in leaf senescence or leaf turnover, with overall phenological variability dominated by a few deciduous species, while substantial variability is attributed to asynchronous events of large and/or abundant trees. Our results underscore the importance of accounting for constituent signals in canopy-wide scaling and the interpretation of remotely sensed phenology signals.
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Affiliation(s)
- Elizabeth Kearsley
- Computational and Applied Vegetation Ecology Lab, Department of Environment, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
- BlueGreen LabsMelseleBelgium
| | - Hans Verbeeck
- Computational and Applied Vegetation Ecology Lab, Department of Environment, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
| | | | - Steven B. Janssens
- Meise Botanic GardenMeiseBelgium
- Department of Biology, Leuven Plant InstituteKULeuvenLeuvenBelgium
| | - Emmanuel Kasongo Yakusu
- UGent‐Woodlab (Laboratory of Wood Technology), Department of Environment, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
- Service of Wood BiologyRoyal Museum for Central AfricaTervurenBelgium
- Faculté de gestion des ressources naturelles renouvelablesUniversité de KisanganiKisanganiDemocratic Republic of Congo
| | - Margaret Kosmala
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMassachusettsUSA
- CIBO TechnologiesCambridgeMassachusettsUSA
| | - Tom De Mil
- Forest is Life, TERRA Teaching and Research Centre, Gembloux Agro Bio‐TechUniversity of LiègeGemblouxBelgium
| | - Marijn Bauters
- Isotope Bioscience Laboratory ‐ ISOFYS, Department of Green Chemistry and TechnologyGhent UniversityGentBelgium
- Research Group of Plants and Ecosystems (PLECO), Department of BiologyUniversity of AntwerpWilrijkBelgium
| | - Elasi Ramanzani Kitima
- Institut National pour l'Etude et la Recherche Agronomiques‐INERAYangambiDemocratic Republic of Congo
| | - José Mbifo Ndiapo
- Institut National pour l'Etude et la Recherche Agronomiques‐INERAYangambiDemocratic Republic of Congo
| | - Adelard Lonema Chuda
- Institut National pour l'Etude et la Recherche Agronomiques‐INERAYangambiDemocratic Republic of Congo
| | - Andrew D. Richardson
- Center for Ecosystem Science and SocietyNorthern Arizona UniversityFlagstaffArizonaUSA
- School of Informatics, Computing and Cyber SystemsNorthern Arizona UniversityFlagstaffArizonaUSA
| | | | - Bhély Angoboy Ilondea
- UGent‐Woodlab (Laboratory of Wood Technology), Department of Environment, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
- Service of Wood BiologyRoyal Museum for Central AfricaTervurenBelgium
- Institut National pour l'Étude et la Recherche AgronomiquesKinshasaDemocratic Republic of Congo
| | - Hans Beeckman
- Service of Wood BiologyRoyal Museum for Central AfricaTervurenBelgium
| | - Jan van den Bulcke
- UGent‐Woodlab (Laboratory of Wood Technology), Department of Environment, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
| | - Pascal Boeckx
- Isotope Bioscience Laboratory ‐ ISOFYS, Department of Green Chemistry and TechnologyGhent UniversityGentBelgium
| | - Koen Hufkens
- Computational and Applied Vegetation Ecology Lab, Department of Environment, Faculty of Bioscience EngineeringGhent UniversityGentBelgium
- BlueGreen LabsMelseleBelgium
- INRAE, UMR ISPAVillenave d'OrnonFrance
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Depecker J, Verleysen L, Asimonyio JA, Hatangi Y, Kambale JL, Mwanga Mwanga I, Ebele T, Dhed'a B, Bawin Y, Staelens A, Stoffelen P, Ruttink T, Vandelook F, Honnay O. Genetic diversity and structure in wild Robusta coffee (Coffea canephora A. Froehner) populations in Yangambi (DR Congo) and their relation to forest disturbance. Heredity (Edinb) 2023; 130:145-153. [PMID: 36596880 PMCID: PMC9981769 DOI: 10.1038/s41437-022-00588-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 01/05/2023] Open
Abstract
Degradation and regeneration of tropical forests can strongly affect gene flow in understorey species, resulting in genetic erosion and changes in genetic structure. Yet, these processes remain poorly studied in tropical Africa. Coffea canephora is an economically important species, found in the understorey of tropical rainforests of Central and West Africa, and the genetic diversity harboured in its wild populations is vital for sustainable coffee production worldwide. Here, we aimed to quantify genetic diversity, genetic structure, and pedigree relations in wild C. canephora populations, and we investigated associations between these descriptors and forest disturbance and regeneration. Therefore, we sampled 256 C. canephora individuals within 24 plots across three forest categories in Yangambi (DR Congo), and used genotyping-by-sequencing to identify 18,894 SNPs. Overall, we found high genetic diversity, and no evidence of genetic erosion in C. canephora in disturbed old-growth forest, as compared to undisturbed old-growth forest. In addition, an overall heterozygosity excess was found in all populations, which was expected for a self-incompatible species. Genetic structure was mainly a result of isolation-by-distance, reflecting geographical location, with low to moderate relatedness at finer scales. Populations in regrowth forest had lower allelic richness than populations in old-growth forest and were characterised by a lower inter-individual relatedness and a lack of isolation-by-distance, suggesting that they originated from different neighbouring populations and were subject to founder effects. Wild Robusta coffee populations in the study area still harbour high levels of genetic diversity, yet careful monitoring of their response to ongoing forest degradation remains required.
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Affiliation(s)
- Jonas Depecker
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium.
- Meise Botanic Garden, Meise, Belgium.
- KU Leuven Plant Institute, Leuven, Belgium.
| | - Lauren Verleysen
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium.
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium.
| | - Justin A Asimonyio
- Centre de Surveillance de la Biodiversité et Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Yves Hatangi
- Meise Botanic Garden, Meise, Belgium
- Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Jean-Léon Kambale
- Centre de Surveillance de la Biodiversité et Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Ithe Mwanga Mwanga
- Centre de Recherche en Science Naturelles, Lwiro, Democratic Republic of the Congo
| | - Tshimi Ebele
- Institut National des Etudes et Recherches, Agronomique, Democratic Republic of the Congo
| | - Benoit Dhed'a
- Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Yves Bawin
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Ariane Staelens
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | | | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Filip Vandelook
- Meise Botanic Garden, Meise, Belgium
- KU Leuven Plant Institute, Leuven, Belgium
| | - Olivier Honnay
- Division of Ecology, Evolution and Biodiversity Conservation, KU Leuven, Leuven, Belgium
- KU Leuven Plant Institute, Leuven, Belgium
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Tournebize R, Borner L, Manel S, Meynard CN, Vigouroux Y, Crouzillat D, Fournier C, Kassam M, Descombes P, Tranchant-Dubreuil C, Parrinello H, Kiwuka C, Sumirat U, Legnate H, Kambale JL, Sonké B, Mahinga JC, Musoli P, Janssens SB, Stoffelen P, de Kochko A, Poncet V. Ecological and genomic vulnerability to climate change across native populations of Robusta coffee (Coffea canephora). Glob Chang Biol 2022; 28:4124-4142. [PMID: 35527235 DOI: 10.1111/gcb.16191] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/11/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
The assessment of population vulnerability under climate change is crucial for planning conservation as well as for ensuring food security. Coffea canephora is, in its native habitat, an understorey tree that is mainly distributed in the lowland rainforests of tropical Africa. Also known as Robusta, its commercial value constitutes a significant revenue for many human populations in tropical countries. Comparing ecological and genomic vulnerabilities within the species' native range can provide valuable insights about habitat loss and the species' adaptive potential, allowing to identify genotypes that may act as a resource for varietal improvement. By applying species distribution models, we assessed ecological vulnerability as the decrease in climatic suitability under future climatic conditions from 492 occurrences. We then quantified genomic vulnerability (or risk of maladaptation) as the allelic composition change required to keep pace with predicted climate change. Genomic vulnerability was estimated from genomic environmental correlations throughout the native range. Suitable habitat was predicted to diminish to half its size by 2050, with populations near coastlines and around the Congo River being the most vulnerable. Whole-genome sequencing revealed 165 candidate SNPs associated with climatic adaptation in C. canephora, which were located in genes involved in plant response to biotic and abiotic stressors. Genomic vulnerability was higher for populations in West Africa and in the region at the border between DRC and Uganda. Despite an overall low correlation between genomic and ecological vulnerability at broad scale, these two components of vulnerability overlap spatially in ways that may become damaging. Genomic vulnerability was estimated to be 23% higher in populations where habitat will be lost in 2050 compared to regions where habitat will remain suitable. These results highlight how ecological and genomic vulnerabilities are relevant when planning on how to cope with climate change regarding an economically important species.
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Affiliation(s)
- Rémi Tournebize
- DIADE, CIRAD, IRD, Univ. Montpellier, Montpellier, France
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Leyli Borner
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
- INRAE, Le Rheu, France
| | - Stéphanie Manel
- CEFE, CNRS, EPHE-PSL University, IRD, Univ Montpellier, Montpellier, France
| | - Christine N Meynard
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Yves Vigouroux
- DIADE, CIRAD, IRD, Univ. Montpellier, Montpellier, France
| | | | - Coralie Fournier
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, Switzerland
- School of Medicine, University of Geneva, Geneva, Switzerland
| | - Mohamed Kassam
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, Switzerland
- Danone Nutricia Research, Singapore
| | - Patrick Descombes
- Nestlé Research, Société des Produits Nestlé S.A., EPFL Innovation Park, Lausanne, Switzerland
| | | | - Hugues Parrinello
- CNRS, INSERM, Univ. Montpellier, Montpellier, France
- Montpellier GenomiX, France Génomique, Montpellier, France
| | | | | | | | - Jean-Léon Kambale
- University of Kisangani, Kisangani, Democratic Republic of the Congo
| | | | | | | | - Steven B Janssens
- Meise Botanic Garden, Meise, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | | | - Valérie Poncet
- DIADE, CIRAD, IRD, Univ. Montpellier, Montpellier, France
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Vanden Abeele S, Janssens SB, Asimonyio Anio J, Bawin Y, Depecker J, Kambale B, Mwanga Mwanga I, Ebele T, Ntore S, Stoffelen P, Vandelook F. Genetic diversity of wild and cultivated Coffea canephora in northeastern DR Congo and the implications for conservation. Am J Bot 2021; 108:2425-2434. [PMID: 34634128 PMCID: PMC9305747 DOI: 10.1002/ajb2.1769] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/02/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Many cultivated coffee varieties descend from Coffea canephora, commonly known as Robusta coffee. The Congo Basin has a century-long history of Robusta coffee cultivation and breeding, and is hypothesized to be the region of origin of many of the cultivated Robusta varieties. Since little is known about the genetic composition of C. canephora in this region, we assessed the genetic diversity of wild and cultivated C. canephora shrubs in the Democratic Republic of the Congo. METHODS Using 18 microsatellite markers, we studied the genetic composition of wild and backyard-grown C. canephora shrubs in the Tshopo and Ituri provinces and multiple accessions from the INERA Yangambi Coffee Collection. We assessed genetic clustering patterns, genetic diversity, and genetic differentiation between populations. RESULTS Genetic differentiation was relatively strong between wild and cultivated C. canephora shrubs, and both gene pools harbored multiple unique alleles. Strong genetic differentiation was also observed between wild populations. The level of genetic diversity in wild populations was similar to that of the INERA Yangambi Coffee Collection, but local wild genotypes were mostly missing from that collection. Shrubs grown in the backyards were genetically similar to the breeding material from INERA Yangambi. CONCLUSIONS Most C. canephora that is grown in local backyards originated from INERA breeding programs, while a few shrubs were obtained directly from surrounding forests. The INERA Yangambi Coffee Collection could benefit from an enrichment with local wild genotypes to increase the genetic resources available for breeding purposes and to support ex situ conservation.
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Affiliation(s)
| | - Steven B. Janssens
- Meise Botanic Garden, Nieuwelaan 38Meise1860Belgium
- Department of BiologyKU LeuvenBelgium
| | - Justin Asimonyio Anio
- Centre pour la Surveillance de la Biodiversité et Université de KisanganiKisanganiDR Congo
| | - Yves Bawin
- Meise Botanic Garden, Nieuwelaan 38Meise1860Belgium
- Department of BiologyKU LeuvenBelgium
| | - Jonas Depecker
- Meise Botanic Garden, Nieuwelaan 38Meise1860Belgium
- Department of BiologyKU LeuvenBelgium
| | - Bienfait Kambale
- Centre pour la Surveillance de la Biodiversité et Université de KisanganiKisanganiDR Congo
| | | | - Tshimi Ebele
- Institut National des Études et Recherches Agronomique, DR CongoDR Congo
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Abstract
Unlike those of coffee beans, the healthy properties of coffee leaves have been overlooked for a long time, even if they are consumed as a beverage by local communities of several African countries. Due to the presence of xanthines, diterpenes, xanthones, and several other polyphenol derivatives as main secondary metabolites, coffee leaves might be useful to prevent many daily disorders. At the same time, as for all bioactive molecules, careless use of coffee leaf infusions may be unsafe due to their adverse effects, such as the excessive stimulant effects on the central nervous system or their interactions with other concomitantly administered drugs. Moreover, the presence of some toxic diterpene derivatives requires careful analytical controls on manufactured products made with coffee leaves. Accordingly, knowledge about the properties of coffee leaves needs to be increased to know if they might be considered a good source for producing new supplements. The purpose of the present review is to highlight the biosynthesis, metabolism, and distribution of the 4 main classes of secondary metabolites present in coffee leaves, their main pharmacological and toxicological aspects, and their main roles in planta. Differences in coffee leaf chemical composition depending on the coffee species will also be carefully considered.
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Affiliation(s)
- Andrea Montis
- RD3 Department-Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Faculty of Pharmacy, Université libre de Bruxelles, Brussels, Belgium
- APFP Analytical platform of the faculty of pharmacy, Faculty of Pharmacy, Université libre de Bruxelles, Brussels, Belgium
| | - Florence Souard
- Département de Pharmacochimie Moléculaire, UMR 5063 CNRS, Université Grenoble Alpes, Saint-Martin d'Hères, France
- DPP Department - Unit of Pharmacology, Pharmacotherapy and Pharmaceutical care, Faculty of Pharmacy, Université libre de Bruxelles, Brussels, Belgium
| | - Cédric Delporte
- RD3 Department-Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Faculty of Pharmacy, Université libre de Bruxelles, Brussels, Belgium
- APFP Analytical platform of the faculty of pharmacy, Faculty of Pharmacy, Université libre de Bruxelles, Brussels, Belgium
| | - Piet Stoffelen
- Meise Botanic Garden, Domein van Bouchout, Meise, Belgium
| | - Caroline Stévigny
- RD3 Department-Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Faculty of Pharmacy, Université libre de Bruxelles, Brussels, Belgium
| | - Pierre Van Antwerpen
- RD3 Department-Unit of Pharmacognosy, Bioanalysis and Drug Discovery, Faculty of Pharmacy, Université libre de Bruxelles, Brussels, Belgium
- APFP Analytical platform of the faculty of pharmacy, Faculty of Pharmacy, Université libre de Bruxelles, Brussels, Belgium
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Vanden Abeele S, Beeckman H, De Mil T, De Troyer C, Deklerck V, Engledow H, Hubau W, Stoffelen P, Janssens SB. When xylarium and herbarium meet: linking Tervuren xylarium wood samples with their herbarium specimens at Meise Botanic Garden. Biodivers Data J 2021; 9:e62329. [PMID: 33841020 PMCID: PMC8026533 DOI: 10.3897/bdj.9.e62329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/19/2021] [Indexed: 11/12/2022] Open
Abstract
Background The current data paper aims to interlink the African plant collections of the Meise Botanic Garden Herbarium (BR) and the Royal Museum for Central Africa Xylarium (Tw). Complementing both collections strengthens the reference value of each institutional collection, as more complete metadata are made available and it enables increased quality control for the identification of wood specimens. Furthermore, the renewed connection enables the linking of available wood trait data with data on phenology, leaf morphology or even molecular information for many tree species, allowing assessments of performance of individual trees. In addition to studies at the interspecific level, comparisons at the intraspecific level become possible, which could lead to important new insights into resilience to and impact of global change, as well as biodiversity conservation or forest management of Central African forest ecosystems. New information By interlinking the Tervuren Xylarium Wood database with the recently digitised herbarium of Meise Botanic Garden, we were able to establish a link between 6,621 xylarium and 9,641 herbarium records for 6,953 plant specimens. Both institutional databases were complemented with reliable specimen metadata. The Tervuren xylarium now profits from taxonomic revisions made by botanists at Meise Botanic Garden and a list of phenotypical features for woody African species can be extended with wood anatomical descriptors. New metadata from the Tw xylarium records were used to add the country of collection to 50 linked BR herbarium specimens for which this information was missing. Furthermore, metadata available from the labels on digitised BR herbarium specimens was used to update Tw xylarium records with the date of collection (817 records), collection locality (698 records), coordinates (482 records) and altitude (817 records). In conclusion, we created a reference database with reliable botanic identities which can be used in a range of studies, such as modelling analyses, community assessments or trait analyses, all framed in a spatiotemporal context. Furthermore, the linked collections hold historical reference data and specimens that can be studied in the context of global changes.
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Affiliation(s)
- Samuel Vanden Abeele
- Meise Botanic Garden, Meise, Belgium Meise Botanic Garden Meise Belgium.,School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, United States of America School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University Ithaca United States of America
| | - Hans Beeckman
- Service of Wood Biology, Royal Museum for Central Africa, Tervuren, Belgium Service of Wood Biology, Royal Museum for Central Africa Tervuren Belgium
| | - Tom De Mil
- UGent-Woodlab, Gent, Belgium UGent-Woodlab Gent Belgium
| | - Cecile De Troyer
- Service of Wood Biology, Royal Museum for Central Africa, Tervuren, Belgium Service of Wood Biology, Royal Museum for Central Africa Tervuren Belgium
| | - Victor Deklerck
- Service of Wood Biology, Royal Museum for Central Africa, Tervuren, Belgium Service of Wood Biology, Royal Museum for Central Africa Tervuren Belgium.,Department of Chemistry, SUNY Albany, Albany, United States of America Department of Chemistry, SUNY Albany Albany United States of America
| | - Henry Engledow
- Meise Botanic Garden, Meise, Belgium Meise Botanic Garden Meise Belgium
| | - Wannes Hubau
- Service of Wood Biology, Royal Museum for Central Africa, Tervuren, Belgium Service of Wood Biology, Royal Museum for Central Africa Tervuren Belgium
| | - Piet Stoffelen
- Meise Botanic Garden, Meise, Belgium Meise Botanic Garden Meise Belgium
| | - Steven B Janssens
- Meise Botanic Garden, Meise, Belgium Meise Botanic Garden Meise Belgium
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7
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Bauters M, Meeus S, Barthel M, Stoffelen P, De Deurwaerder HPT, Meunier F, Drake TW, Ponette Q, Ebuy J, Vermeir P, Beeckman H, Wyffels F, Bodé S, Verbeeck H, Vandelook F, Boeckx P. Century-long apparent decrease in intrinsic water-use efficiency with no evidence of progressive nutrient limitation in African tropical forests. Glob Chang Biol 2020; 26:4449-4461. [PMID: 32364642 DOI: 10.1111/gcb.15145] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/27/2020] [Indexed: 06/11/2023]
Abstract
Forests exhibit leaf- and ecosystem-level responses to environmental changes. Specifically, rising carbon dioxide (CO2 ) levels over the past century are expected to have increased the intrinsic water-use efficiency (iWUE) of tropical trees while the ecosystem is gradually pushed into progressive nutrient limitation. Due to the long-term character of these changes, however, observational datasets to validate both paradigms are limited in space and time. In this study, we used a unique herbarium record to go back nearly a century and show that despite the rise in CO2 concentrations, iWUE has decreased in central African tropical trees in the Congo Basin. Although we find evidence that points to leaf-level adaptation to increasing CO2 -that is, increasing photosynthesis-related nutrients and decreasing maximum stomatal conductance, a decrease in leaf δ13 C clearly indicates a decreasing iWUE over time. Additionally, the stoichiometric carbon to nitrogen and nitrogen to phosphorus ratios in the leaves show no sign of progressive nutrient limitation as they have remained constant since 1938, which suggests that nutrients have not increasingly limited productivity in this biome. Altogether, the data suggest that other environmental factors, such as increasing temperature, might have negatively affected net photosynthesis and consequently downregulated the iWUE. Results from this study reveal that the second largest tropical forest on Earth has responded differently to recent environmental changes than expected, highlighting the need for further on-ground monitoring in the Congo Basin.
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Affiliation(s)
- Marijn Bauters
- Isotope Bioscience Laboratory - ISOFYS, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
- Computational and Applied Vegetation Ecology - CAVElab, Department of Environment, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | | | - Matti Barthel
- Sustainable Agroecosystems, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | | | - Hannes P T De Deurwaerder
- Computational and Applied Vegetation Ecology - CAVElab, Department of Environment, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Félicien Meunier
- Computational and Applied Vegetation Ecology - CAVElab, Department of Environment, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Travis W Drake
- Sustainable Agroecosystems, Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Quentin Ponette
- UCL-ELI, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Jerôme Ebuy
- UCL-ELI, Earth and Life Institute, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
- Université de Kisangani (UNIKIS/FGRNR), Kisangani, République Démocratique du Congo
| | - Pieter Vermeir
- Laboratory for Chemical Analyses - LCA, Department of Green Chemistry and Technology, Ghent University, Ghent, Belgium
| | | | - Francis Wyffels
- AIRO, Electronics and Information Systems Department, Ghent University-Imec, Ghent, Belgium
| | - Samuel Bodé
- Isotope Bioscience Laboratory - ISOFYS, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | - Hans Verbeeck
- Computational and Applied Vegetation Ecology - CAVElab, Department of Environment, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | | | - Pascal Boeckx
- Isotope Bioscience Laboratory - ISOFYS, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
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8
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Charr JC, Garavito A, Guyeux C, Crouzillat D, Descombes P, Fournier C, Ly SN, Raharimalala EN, Rakotomalala JJ, Stoffelen P, Janssens S, Hamon P, Guyot R. Complex evolutionary history of coffees revealed by full plastid genomes and 28,800 nuclear SNP analyses, with particular emphasis on Coffea canephora (Robusta coffee). Mol Phylogenet Evol 2020; 151:106906. [PMID: 32653553 DOI: 10.1016/j.ympev.2020.106906] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/17/2020] [Accepted: 07/06/2020] [Indexed: 11/16/2022]
Abstract
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 full-genome 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.
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Affiliation(s)
- Jean-Claude Charr
- Femto-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, France.
| | - Andrea Garavito
- Departamento de Ciencias biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Manizales, Colombia
| | - Christophe Guyeux
- Femto-ST Institute, UMR 6174 CNRS, Université de Bourgogne Franche-Comté, France.
| | | | | | | | - Serigne N Ly
- Institut de Recherche pour le Développement, UMR DIADE, CIRAD, Université de Montpellier, France.
| | | | | | - Piet Stoffelen
- Meise Botanic Garden, Nieuwelaan 38, BE-1860 Meise, Belgium.
| | - Steven Janssens
- Meise Botanic Garden, Nieuwelaan 38, BE-1860 Meise, Belgium.
| | - Perla Hamon
- Institut de Recherche pour le Développement, UMR DIADE, CIRAD, Université de Montpellier, France.
| | - Romain Guyot
- Institut de Recherche pour le Développement, UMR DIADE, CIRAD, Université de Montpellier, France; Department of Electronics and Automatization, Universidad Autónoma de Manizales, Manizales, Colombia.
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9
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Tosso F, Doucet J, Daïnou K, Fayolle A, Hambuckers A, Doumenge C, Agbazahou H, Stoffelen P, Hardy OJ. Highlighting convergent evolution in morphological traits in response to climatic gradient in African tropical tree species: The case of genus Guibourtia Benn. Ecol Evol 2019; 9:13114-13126. [PMID: 31871633 PMCID: PMC6912925 DOI: 10.1002/ece3.5740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/17/2019] [Accepted: 09/15/2019] [Indexed: 11/06/2022] Open
Abstract
Adaptive evolution is a major driver of organism diversification, but the links between phenotypic traits and environmental niche remain little documented in tropical trees. Moreover, trait-niche relationships are complex because a correlation between the traits and environmental niches displayed by a sample of species may result from (a) convergent evolution if different environmental conditions have selected different sets of traits, and/or (b) phylogenetic inertia if niche and morphological differences between species are simply function of their phylogenetic divergence, in which case the trait-niche correlation does not imply any direct causal link. Here, we aim to assess the respective roles of phylogenetic inertia and convergent evolution in shaping the differences of botanical traits and environmental niches among congeneric African tree species that evolved in different biomes.This issue was addressed with the tree genus Guibourtia Benn. (Leguminosae and Detarioideae), which contains 13 African species occupying various forest habitat types, from rain forest to dry woodlands, with different climate and soil conditions. To this end, we combined morphological data with ecological niche modelling and used a highly resolved plastid phylogeny of the 13 African Guibourtia species.First, we demonstrated phylogenetic signals in both morphological traits (Mantel test between phylogenetic and morphological distances between species: r = .24, p = .031) and environmental niches (Mantel test between phylogenetic and niche distances between species: r = .23, p = .025). Second, we found a significant correlation between morphology and niche, at least between some of their respective dimensions (Mantel's r = .32, p = .013), even after accounting for phylogenetic inertia (Phylogenetic Independent Contrast: r = .69, p = .018). This correlation occurred between some leaflet and flower traits and solar radiation, relative humidity, precipitations, and temperature range.Our results demonstrate the convergent evolution of some morphological traits in response to climatic factors in congeneric tree species and highlight the action of selective forces, along with neutral ones, in shaping the divergence between congeneric tropical plants.
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Affiliation(s)
- Félicien Tosso
- Forest is LifeTERRA Teaching and Research CentreGembloux Agro‐Bio TechUniversity of LiègeGemblouxBelgium
- Evolutionary Biology and Ecology UnitFaculté des SciencesUniversité Libre de BruxellesBrusselsBelgium
- Nature+ asbl, s/c Forest is LifeTERRA Teaching and Research CentreGembloux Agro-Bio TechUniversity of LiègeGemblouxBelgium
| | - Jean‐Louis Doucet
- Forest is LifeTERRA Teaching and Research CentreGembloux Agro‐Bio TechUniversity of LiègeGemblouxBelgium
| | - Kasso Daïnou
- Nature+ asbl, s/c Forest is LifeTERRA Teaching and Research CentreGembloux Agro-Bio TechUniversity of LiègeGemblouxBelgium
| | - Adeline Fayolle
- Forest is LifeTERRA Teaching and Research CentreGembloux Agro‐Bio TechUniversity of LiègeGemblouxBelgium
| | | | - Charles Doumenge
- Centre International de Recherche Agronomique pour le DéveloppementTA C‐105/D, Campus International de BaillarguetMontpellierFrance
| | - Honoré Agbazahou
- Centre International de Recherche Agronomique pour le DéveloppementTA C‐105/D, Campus International de BaillarguetMontpellierFrance
| | | | - Olivier J. Hardy
- Evolutionary Biology and Ecology UnitFaculté des SciencesUniversité Libre de BruxellesBrusselsBelgium
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Merot‐L'anthoene V, Tournebize R, Darracq O, Rattina V, Lepelley M, Bellanger L, Tranchant‐Dubreuil C, Coulée M, Pégard M, Metairon S, Fournier C, Stoffelen P, Janssens SB, Kiwuka C, Musoli P, Sumirat U, Legnaté H, Kambale J, Ferreira da Costa Neto J, Revel C, de Kochko A, Descombes P, Crouzillat D, Poncet V. Development and evaluation of a genome-wide Coffee 8.5K SNP array and its application for high-density genetic mapping and for investigating the origin of Coffea arabica L. Plant Biotechnol J 2019; 17:1418-1430. [PMID: 30582651 PMCID: PMC6576098 DOI: 10.1111/pbi.13066] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
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.
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11
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Rodríguez-Gómez R, Vanheuverzwjin J, Souard F, Delporte C, Stevigny C, Stoffelen P, De Braekeleer K, Kauffmann JM. Determination of Three Main Chlorogenic Acids in Water Extracts of Coffee Leaves by Liquid Chromatography Coupled to an Electrochemical Detector. Antioxidants (Basel) 2018; 7:E143. [PMID: 30326634 PMCID: PMC6209918 DOI: 10.3390/antiox7100143] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/05/2018] [Accepted: 10/11/2018] [Indexed: 12/19/2022] Open
Abstract
Coffee is a beverage widely consumed in the world. The coffee species most commercialized worldwide are Arabica (Coffea arabica) and Robusta (Coffea canephora). Roasted coffee beans are the most used, but coffee leaves are also consumed as infusion in several countries for traditional medicinal purposes. They contain several interesting phenolic antioxidant compounds mainly belonging to chlorogenic acids (CGAs). In the present work, a liquid chromatography-electrochemical detection (LC-EC) method was developed for the determination of three main chlorogenic acid isomers, namely 3-, 4-, and 5-caffeoylquinic acids (CQA), in coffee leaves aqueous extracts. Samples from eight coffee species, namely; Coffea arabica, Coffea canephora, Coffea liberica, Coffea humilis, Coffea mannii, Coffea charrieriana, Coffea anthonyi, and Coffea liberica var. liberica, were grown and collected in tropical greenhouses. Linearity of the calibration graphs was observed in the range from the limit of quantification to 1.0 × 10-5 M, with R² equal to 99.9% in all cases. High sensitivity was achieved with a limit of detection of 1.0 × 10-8 M for 3-CQA and 5-CQA (i.e., 3.5 µg/L) and 2.0 × 10-8 M for 4-CQA (i.e., 7.1 µg/L). The chromatographic profile of the samples harvested for each Coffea species was studied comparatively. Obtained raw data were pretreated for baseline variations and shifts in retention times between the chromatographic profiles. Principal Component Analysis (PCA) was applied to the pretreated data. According to the results, three clusters of Coffea species were found. In the water sample extracts, 5-CQA appeared to be the major isomer, and some species contained a very low amount of CQAs. Fluctuations were observed depending on the Coffea species and harvesting period. Significant differences between January and July were noticed regarding CQAs content. The species with the best CQAs/caffeine ratio was identified. The LC-EC data were validated by liquid chromatography-high resolution mass spectrometry (LC-HRMS).
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Affiliation(s)
- Rocío Rodríguez-Gómez
- Bioanalysis and Drug Discovery, RD3-Unit of Pharmacognosy, Faculty of Pharmacy, Université libre de Bruxelles, Campus Plaine CP 205/6, 1050 Brussels, Belgium.
| | - Jérôme Vanheuverzwjin
- Bioanalysis and Drug Discovery, RD3-Unit of Pharmacognosy, Faculty of Pharmacy, Université libre de Bruxelles, Campus Plaine CP 205/6, 1050 Brussels, Belgium.
| | - Florence Souard
- Bioanalysis and Drug Discovery, RD3-Unit of Pharmacognosy, Faculty of Pharmacy, Université libre de Bruxelles, Campus Plaine CP 205/6, 1050 Brussels, Belgium.
- Department of Molecular Pharmacochemistry, Université de Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France.
| | - Cédric Delporte
- Bioanalysis and Drug Discovery, RD3-Unit of Pharmacognosy, Faculty of Pharmacy, Université libre de Bruxelles, Campus Plaine CP 205/6, 1050 Brussels, Belgium.
- Analytical Platform, Faculty of Pharmacy, Université libre de Bruxelles, Campus Plaine, CP 205/05, 1050 Brussels, Belgium.
| | - Caroline Stevigny
- Bioanalysis and Drug Discovery, RD3-Unit of Pharmacognosy, Faculty of Pharmacy, Université libre de Bruxelles, Campus Plaine CP 205/6, 1050 Brussels, Belgium.
| | - Piet Stoffelen
- Botanic Garden Meise, Domein van Bouchout, Nieuwe laan 38, 1860 Meise, Belgium.
| | - Kris De Braekeleer
- Bioanalysis and Drug Discovery, RD3-Unit of Pharmacognosy, Faculty of Pharmacy, Université libre de Bruxelles, Campus Plaine CP 205/6, 1050 Brussels, Belgium.
| | - Jean-Michel Kauffmann
- Bioanalysis and Drug Discovery, RD3-Unit of Pharmacognosy, Faculty of Pharmacy, Université libre de Bruxelles, Campus Plaine CP 205/6, 1050 Brussels, Belgium.
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12
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Sosef MSM, Dauby G, Blach-Overgaard A, van der Burgt X, Catarino L, Damen T, Deblauwe V, Dessein S, Dransfield J, Droissart V, Duarte MC, Engledow H, Fadeur G, Figueira R, Gereau RE, Hardy OJ, Harris DJ, de Heij J, Janssens S, Klomberg Y, Ley AC, Mackinder BA, Meerts P, van de Poel JL, Sonké B, Stévart T, Stoffelen P, Svenning JC, Sepulchre P, Zaiss R, Wieringa JJ, Couvreur TLP. Exploring the floristic diversity of tropical Africa. BMC Biol 2017; 15:15. [PMID: 28264718 PMCID: PMC5339970 DOI: 10.1186/s12915-017-0356-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/25/2017] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Understanding the patterns of biodiversity distribution and what influences them is a fundamental pre-requisite for effective conservation and sustainable utilisation of biodiversity. Such knowledge is increasingly urgent as biodiversity responds to the ongoing effects of global climate change. Nowhere is this more acute than in species-rich tropical Africa, where so little is known about plant diversity and its distribution. In this paper, we use RAINBIO - one of the largest mega-databases of tropical African vascular plant species distributions ever compiled - to address questions about plant and growth form diversity across tropical Africa. RESULTS The filtered RAINBIO dataset contains 609,776 georeferenced records representing 22,577 species. Growth form data are recorded for 97% of all species. Records are well distributed, but heterogeneous across the continent. Overall, tropical Africa remains poorly sampled. When using sampling units (SU) of 0.5°, just 21 reach appropriate collection density and sampling completeness, and the average number of records per species per SU is only 1.84. Species richness (observed and estimated) and endemism figures per country are provided. Benin, Cameroon, Gabon, Ivory Coast and Liberia appear as the botanically best-explored countries, but none are optimally explored. Forests in the region contain 15,387 vascular plant species, of which 3013 are trees, representing 5-7% of the estimated world's tropical tree flora. The central African forests have the highest endemism rate across Africa, with approximately 30% of species being endemic. CONCLUSIONS The botanical exploration of tropical Africa is far from complete, underlining the need for intensified inventories and digitization. We propose priority target areas for future sampling efforts, mainly focused on Tanzania, Atlantic Central Africa and West Africa. The observed number of tree species for African forests is smaller than those estimated from global tree data, suggesting that a significant number of species are yet to be discovered. Our data provide a solid basis for a more sustainable management and improved conservation of tropical Africa's unique flora, and is important for achieving Objective 1 of the Global Strategy for Plant Conservation 2011-2020. In turn, RAINBIO provides a solid basis for a more sustainable management and improved conservation of tropical Africa's unique flora.
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Affiliation(s)
- Marc S M Sosef
- Botanic Garden Meise, Nieuwelaan 38, BE-1860, Meise, Belgium.
| | - Gilles Dauby
- DIADE, Université Montpellier, IRD, Montpellier, France
- Laboratoire d'Évolution biologique et Écologie, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
- CESAB/FRB, Domaine du Petit Arbois, Av. Louis Philibert, Aix-en-Provence, 13100, France
| | - Anne Blach-Overgaard
- Section for Ecoinformatics & Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
| | | | - Luís Catarino
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016, Lisbon, Portugal
| | - Theo Damen
- Wageningen University, Biosystematics Group, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Vincent Deblauwe
- DIADE, Université Montpellier, IRD, Montpellier, France
- Herbarium et Bibliothèque de Botanique Africaine, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050, Bruxelles, Belgium
- Laboratoire de Botanique systématique et d'Écologie, Département des Sciences Biologiques, École Normale Supérieure, Université de Yaoundé I, Yaoundé, Cameroon
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, Box 951496, Los Angeles, CA, 90095, USA
- International Institute of Tropical Agriculture, BP 2008 (Messa), Yaounde, Cameroon
| | - Steven Dessein
- Botanic Garden Meise, Nieuwelaan 38, BE-1860, Meise, Belgium
| | | | - Vincent Droissart
- Herbarium et Bibliothèque de Botanique Africaine, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050, Bruxelles, Belgium
- Missouri Botanical Garden, Africa & Madagascar Department, P.O. Box 299, St. Louis, Missouri, 63166-0299, USA
- AMAP, CNRS, INRA, IRD, Université Montpellier, Montpellier, France
| | - Maria Cristina Duarte
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016, Lisbon, Portugal
| | - Henry Engledow
- Botanic Garden Meise, Nieuwelaan 38, BE-1860, Meise, Belgium
| | - Geoffrey Fadeur
- Herbarium et Bibliothèque de Botanique Africaine, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050, Bruxelles, Belgium
| | - Rui Figueira
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- CEABN/InBio, Centro de Ecologia Aplicada "Professor Baeta Neves", Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisboa, Portugal
| | - Roy E Gereau
- Missouri Botanical Garden, Africa & Madagascar Department, P.O. Box 299, St. Louis, Missouri, 63166-0299, USA
| | - Olivier J Hardy
- Laboratoire d'Évolution biologique et Écologie, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
| | - David J Harris
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, UK
| | - Janneke de Heij
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
- Picturae, De Droogmakerij 12, 1851LX, Heiloo, The Netherlands
| | - Steven Janssens
- Botanic Garden Meise, Nieuwelaan 38, BE-1860, Meise, Belgium
| | - Yannick Klomberg
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
- Department of Ecology, Faculty of Science, Charles University, Vinicna 7, 128 44, Prague 2, Czech Republic
| | - Alexandra C Ley
- Institut für Geobotanik und Botanischer Garten, Im Neuwerk 21, University Halle-Wittenberg, 06108, Halle (Saale), Germany
| | - Barbara A Mackinder
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, UK
| | - Pierre Meerts
- Herbarium et Bibliothèque de Botanique Africaine, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050, Bruxelles, Belgium
- Laboratoire d'Ecologie végétale et Biogéochimie, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050, Bruxelles, Belgium
| | - Jeike L van de Poel
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
| | - Bonaventure Sonké
- Laboratoire de Botanique systématique et d'Écologie, Département des Sciences Biologiques, École Normale Supérieure, Université de Yaoundé I, Yaoundé, Cameroon
| | - Tariq Stévart
- Botanic Garden Meise, Nieuwelaan 38, BE-1860, Meise, Belgium
- Herbarium et Bibliothèque de Botanique Africaine, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050, Bruxelles, Belgium
- Missouri Botanical Garden, Africa & Madagascar Department, P.O. Box 299, St. Louis, Missouri, 63166-0299, USA
| | - Piet Stoffelen
- Botanic Garden Meise, Nieuwelaan 38, BE-1860, Meise, Belgium
| | - Jens-Christian Svenning
- Section for Ecoinformatics & Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
| | - Pierre Sepulchre
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Rainer Zaiss
- AMAP, CNRS, INRA, IRD, Université Montpellier, Montpellier, France
| | - Jan J Wieringa
- Wageningen University, Biosystematics Group, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
| | - Thomas L P Couvreur
- DIADE, Université Montpellier, IRD, Montpellier, France.
- Laboratoire de Botanique systématique et d'Écologie, Département des Sciences Biologiques, École Normale Supérieure, Université de Yaoundé I, Yaoundé, Cameroon.
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands.
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Hamon P, Grover CE, Davis AP, Rakotomalala JJ, Raharimalala NE, Albert VA, Sreenath HL, Stoffelen P, Mitchell SE, Couturon E, Hamon S, de Kochko A, Crouzillat D, Rigoreau M, Sumirat U, Akaffou S, Guyot R. Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content. Mol Phylogenet Evol 2017; 109:351-361. [PMID: 28212875 DOI: 10.1016/j.ympev.2017.02.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 12/30/2022]
Abstract
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.
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Affiliation(s)
- Perla Hamon
- UMR DIADE, IRD, BP 64501, F-34394 Montpellier cedex 5, France.
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
| | - Aaron P Davis
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom.
| | | | | | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA.
| | - Hosahalli L Sreenath
- Plant Biotechnology Division, Unit of Central Coffee Research Institute, Coffee Board, Manasagangothri, Mysore 570006, India.
| | - Piet Stoffelen
- Herbarium Plantentuin Meise, Nieuwelaan 38, 1860 Meise, Belgium.
| | - Sharon E Mitchell
- Cornell University, Institute of Biotechnology, Genomic Diversity Facility, Ithaca, NY, USA.
| | | | - Serge Hamon
- UMR DIADE, IRD, BP 64501, F-34394 Montpellier cedex 5, France.
| | | | | | - Michel Rigoreau
- Nestlé Centre R&D Tours, BP 49716, F-37097 Tours cedex 2, France.
| | - Ucu Sumirat
- Indonesian Coffee and Cocoa Research Institute Jl. PB Sudirman 90, Jember 68118, Indonesia.
| | | | - Romain Guyot
- UMR IPME, IRD, BP 64501, F-34394 Montpellier cedex 5, France.
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Dauby G, Zaiss R, Blach-Overgaard A, Catarino L, Damen T, Deblauwe V, Dessein S, Dransfield J, Droissart V, Duarte MC, Engledow H, Fadeur G, Figueira R, Gereau RE, Hardy OJ, Harris DJ, de Heij J, Janssens S, Klomberg Y, Ley AC, Mackinder BA, Meerts P, van de Poel JL, Sonké B, Sosef MSM, Stévart T, Stoffelen P, Svenning JC, Sepulchre P, van der Burgt X, Wieringa JJ, Couvreur TLP. RAINBIO: a mega-database of tropical African vascular plants distributions. PhytoKeys 2016:1-18. [PMID: 28127234 PMCID: PMC5234546 DOI: 10.3897/phytokeys.74.9723] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/04/2016] [Indexed: 05/05/2023]
Abstract
The tropical vegetation of Africa is characterized by high levels of species diversity but is undergoing important shifts in response to ongoing climate change and increasing anthropogenic pressures. Although our knowledge of plant species distribution patterns in the African tropics has been improving over the years, it remains limited. Here we present RAINBIO, a unique comprehensive mega-database of georeferenced records for vascular plants in continental tropical Africa. The geographic focus of the database is the region south of the Sahel and north of Southern Africa, and the majority of data originate from tropical forest regions. RAINBIO is a compilation of 13 datasets either publicly available or personal ones. Numerous in depth data quality checks, automatic and manual via several African flora experts, were undertaken for georeferencing, standardization of taxonomic names and identification and merging of duplicated records. The resulting RAINBIO data allows exploration and extraction of distribution data for 25,356 native tropical African vascular plant species, which represents ca. 89% of all known plant species in the area of interest. Habit information is also provided for 91% of these species.
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Affiliation(s)
- Gilles Dauby
- Institut de Recherche pour le Développement (IRD), UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France; Laboratoire d'évolution Biologique et Ecologie, Faculté des Sciences, Université Libre de Bruxelles, CP160/12, avenue F.D. Roosevelt 50, 1050 Bruxelles, Belgium; CESAB / FRB, Domaine du Petit Arbois, Av. Louis Philibert, Aix-en-Provence, 13100, France
| | - Rainer Zaiss
- Institut de Recherche pour le Développement (IRD), UMR AMAP, Boulevard de la Lironde TA A-51 / PS 2 34398 Montpellier, France
| | - Anne Blach-Overgaard
- Section for Ecoinformatics & Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark
| | - Luís Catarino
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016, Lisbon, Portugal
| | - Theo Damen
- Wageningen University, Biosystematics Group, Droevendaalsesteeg 1 6708 PB Wageningen, The Netherlands
| | - Vincent Deblauwe
- Institut de Recherche pour le Développement (IRD), UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France; Herbarium et Bibliothèque de Botanique Africaine, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050 Bruxelles, Belgium; Laboratoire de Botanique Systématique et d'Écologie, École Normale Supérieure, Université de Yaoundé I, PO Box 047, Yaoundé, Cameroon
| | - Steven Dessein
- Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium
| | | | - Vincent Droissart
- Institut de Recherche pour le Développement (IRD), UMR AMAP, Boulevard de la Lironde TA A-51 / PS 2 34398 Montpellier, France; Herbarium et Bibliothèque de Botanique Africaine, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050 Bruxelles, Belgium; Laboratoire de Botanique Systématique et d'Écologie, École Normale Supérieure, Université de Yaoundé I, PO Box 047, Yaoundé, Cameroon; Missouri Botanical Garden, Africa & Madagascar Department, St. Louis, United States of America
| | - Maria Cristina Duarte
- Centre for Ecology, Evolution and Environmental Changes (CE3C), Faculty of Sciences, University of Lisbon, Campo Grande, 1749-016, Lisbon, Portugal
| | - Henry Engledow
- Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium
| | - Geoffrey Fadeur
- Herbarium et Bibliothèque de Botanique Africaine, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050 Bruxelles, Belgium
| | - Rui Figueira
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto. Campus Agrário de Vairão, Vairão, Portugal; CEABN/InBio, Centro de Ecologia Aplicada "Professor Baeta Neves", Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Roy E Gereau
- Missouri Botanical Garden, Africa & Madagascar Department, St. Louis, United States of America
| | - Olivier J Hardy
- Laboratoire d'évolution Biologique et Ecologie, Faculté des Sciences, Université Libre de Bruxelles, CP160/12, avenue F.D. Roosevelt 50, 1050 Bruxelles, Belgium
| | - David J Harris
- Institut de Recherche pour le Développement (IRD), UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Janneke de Heij
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; Picturae, De Droogmakerij 12, 1851LX Heiloo, The Netherlands
| | | | - Yannick Klomberg
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; Department of Ecology, Faculty of Science, Charles University, Vinicna 7, CZ-12843, Prague, Czech Republic
| | - Alexandra C Ley
- Institut für Geobotanik und Botanischer Garten, University Halle-Wittenberg, Neuwerk 21, 06108 Halle, Germany
| | | | - Pierre Meerts
- Herbarium et Bibliothèque de Botanique Africaine, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050 Bruxelles, Belgium; Laboratoire d'Ecologie végétale et Biogéochimie, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050 Bruxelles, Belgium
| | | | - Bonaventure Sonké
- Laboratoire de Botanique Systématique et d'Écologie, École Normale Supérieure, Université de Yaoundé I, PO Box 047, Yaoundé, Cameroon
| | - Marc S M Sosef
- Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium
| | - Tariq Stévart
- Herbarium et Bibliothèque de Botanique Africaine, Université Libre de Bruxelles, Boulevard du Triomphe, B-1050 Bruxelles, Belgium; Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium; Missouri Botanical Garden, Africa & Madagascar Department, St. Louis, United States of America
| | - Piet Stoffelen
- Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium
| | - Jens-Christian Svenning
- Section for Ecoinformatics & Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000 Aarhus C, Denmark
| | - Pierre Sepulchre
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | | | - Jan J Wieringa
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; Wageningen University, Biosystematics Group, Droevendaalsesteeg 1 6708 PB Wageningen, The Netherlands
| | - Thomas L P Couvreur
- Institut de Recherche pour le Développement (IRD), UMR DIADE, 911 Avenue Agropolis, 34394 Montpellier, France; Laboratoire de Botanique Systématique et d'Écologie, École Normale Supérieure, Université de Yaoundé I, PO Box 047, Yaoundé, Cameroon; Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands
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Stoffelen P, Robbrecht E, Smets E. A New Species of Coffea (Rubiaceae) from Central Africa, with Notes on Tentative Other Taxa. ACTA ACUST UNITED AC 1999. [DOI: 10.2307/3668527] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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