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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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Tack W, Engledow H, Veríssimo Pereira N, Amani C, Bachman SP, Barberá P, Beentje HJ, Bouka GUD, Cheek M, Cosiaux A, Dauby G, De Block P, Ewango CEN, Fischer E, Gereau RE, Hargreaves S, Harvey-Brown Y, Ikabanga DU, Ilunga wa Ilunga E, Kalema J, Kamau P, Lachenaud O, Luke Q, Mwanga Mwanga I, Ndolo Ebika ST, Nkengurutse J, Nsanzurwimo A, Ntore S, Richards SL, Shutsha Ehata R, Simo-Droissart M, Stévart T, Sosef MSM. The ECAT dataset: expert-validated distribution data of endemic and sub-endemic trees of Central Africa (Dem. Rep. Congo, Rwanda, Burundi). PhytoKeys 2022; 206:137-151. [PMID: 36761267 PMCID: PMC9849015 DOI: 10.3897/phytokeys.206.77379] [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] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 08/15/2022] [Indexed: 06/18/2023]
Abstract
In this data paper, we present a specimen-based occurrence dataset compiled in the framework of the Conservation of Endemic Central African Trees (ECAT) project with the aim of producing global conservation assessments for the IUCN Red List. The project targets all tree species endemic or sub-endemic to the Central African region comprising the Democratic Republic of the Congo (DR Congo), Rwanda, and Burundi. The dataset contains 6361 plant collection records with occurrences of 8910 specimens from 337 taxa belonging to 153 genera in 52 families. Many of these tree taxa have restricted geographic ranges and are only known from a small number of herbarium specimens. As assessments for such taxa can be compromised by inadequate data, we transcribed and geo-referenced specimen label information to obtain a more accurate and complete locality dataset. All specimen data were manually cleaned and verified by botanical experts, resulting in improved data quality and consistency.
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Affiliation(s)
- Wesley Tack
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
| | - Henry Engledow
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
| | - Nuno Veríssimo Pereira
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
| | - Christian Amani
- Université Officielle de Bukavu, Bukavu, Democratic Republic of the CongoIUCN SSC Eastern African Plant Red List Authority (EAPRLA)GlandSwitzerland
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
| | - Steven P. Bachman
- Royal Botanic Gardens, Kew, Richmond, Surrey, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Patricia Barberá
- Missouri Botanical Garden, Africa & Madagascar Department, St. Louis, MO 63110, USAMissouri Botanical Garden, Africa & Madagascar DepartmentSt. LouisUnited States of America
| | - Henk J. Beentje
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
- Royal Botanic Gardens, Kew, Richmond, Surrey, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Gaël U. D. Bouka
- Laboratoire de Biodiversité, de Gestion des Ecosystèmes et de l’Environnement, Faculté des Sciences et Techniques, Université Marien Ngouabi, BP 69, Brazzaville, Democratic Republic of the CongoUniversité Marien NgouabiBrazzavilleDemocratic Republic of the Congo
| | - Martin Cheek
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
- Royal Botanic Gardens, Kew, Richmond, Surrey, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Ariane Cosiaux
- Plant Systematics and Ecology Laboratory, University of Yaoundé I, P.O. Box 047, Yaoundé, CameroonUniversity of Yaoundé IYaoundéCameroon
- Institut de Recherche pour le Développement, Université de Montpellier, Montpellier, FranceUniversité de MontpellierMontpellierFrance
| | - Gilles Dauby
- Institut de Recherche pour le Développement, Université de Montpellier, Montpellier, FranceUniversité de MontpellierMontpellierFrance
| | - Petra De Block
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
| | - Corneille E. N. Ewango
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
- AMAP, Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, FranceUniversité de KisanganiKisanganiDemocratic Republic of the Congo
| | - Eberhard Fischer
- Centre de Surveillance de la Biodiversité, Université de Kisangani, Kisangani, Democratic Republic of the CongoUniversity of Koblenz and LandauKoblenzGermany
- University of Koblenz-Landau, Universitätsstraße 1, Koblenz, 56070, GermanyIUCN SSC Central Africa Plant Red List Authority (CARLA)GlandSwitzerland
| | - Roy E. Gereau
- Missouri Botanical Garden, Africa & Madagascar Department, St. Louis, MO 63110, USAMissouri Botanical Garden, Africa & Madagascar DepartmentSt. LouisUnited States of America
- University of Koblenz-Landau, Universitätsstraße 1, Koblenz, 56070, GermanyIUCN SSC Central Africa Plant Red List Authority (CARLA)GlandSwitzerland
| | - Serene Hargreaves
- Royal Botanic Gardens, Kew, Richmond, Surrey, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Yvette Harvey-Brown
- IUCN SSC Central Africa Plant Red List Authority (CARLA), Gland, SwitzerlandBotanic Gardens Conservation InternationalRichmondUnited Kingdom
| | - Davy U. Ikabanga
- Botanic Gardens Conservation International, Richmond, Surrey, UKUniversity of Sciences and Techniques of MasukuFrancevilleGabon
| | - Edouard Ilunga wa Ilunga
- Department of Biology, Faculty of Sciences, University of Sciences and Techniques of Masuku, BP: 941, Franceville, GabonUniversité de LubumbashiLubumbashiDemocratic Republic of the Congo
| | - James Kalema
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
- Herbarium de Lubumbashi, Université de Lubumbashi, 1825, Route Kasapa, Lubumbashi, Democratic Republic of the CongoMakerere University Herbarium, Department of Plant Sciences Microbiology and BiotechnologyKampalaUganda
| | - Peris Kamau
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
- Makerere University Herbarium, Department of Plant Sciences Microbiology and Biotechnology, P.O. Box 7062, Kampala, UgandaEast African Herbarium, National Museums of KenyaNairobiKenya
| | - Olivier Lachenaud
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
- East African Herbarium, National Museums of Kenya, P.O. Box 45166-00100, Nairobi, KenyaUniversité Libre de BruxellesBrusselsBelgium
| | - Quentin Luke
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
- Makerere University Herbarium, Department of Plant Sciences Microbiology and Biotechnology, P.O. Box 7062, Kampala, UgandaEast African Herbarium, National Museums of KenyaNairobiKenya
| | - Ithe Mwanga Mwanga
- Herbarium et Bibliothèque de Botanique africaine, C.P. 265, Université Libre de Bruxelles, Campus de la Plaine, Boulevard du Triomphe 1050, Brussels, BelgiumCentre de Recherche en Sciences Naturelles CRSN/Lwiro, Laboratoire de Systématiquement et Taxonomie végétaleBukavuDemocratic Republic of the Congo
| | - Sydney T. Ndolo Ebika
- Laboratoire de Biodiversité, de Gestion des Ecosystèmes et de l’Environnement, Faculté des Sciences et Techniques, Université Marien Ngouabi, BP 69, Brazzaville, Democratic Republic of the CongoUniversité Marien NgouabiBrazzavilleDemocratic Republic of the Congo
| | - Jacques Nkengurutse
- Centre de Recherche en Sciences Naturelles CRSN/Lwiro, Laboratoire de Systématiquement et Taxonomie végétale, D.S. Bukavu, Democratic Republic of the CongoUniversity of BurundiBujumburaBurundi
| | - Aimable Nsanzurwimo
- Department of Biology, Faculty of Science, University of Burundi, P.O. Box 2700, Bujumbura, BurundiDepartment of Biotechnologies, Faculty of Applied Sciences, INES-RuhengeriRuhengeriRwanda
| | - Salvator Ntore
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
- IUCN SSC Eastern African Plant Red List Authority (EAPRLA), Gland, SwitzerlandUniversité Officielle de BukavuBukavuDemocratic Republic of the Congo
- University of Koblenz-Landau, Universitätsstraße 1, Koblenz, 56070, GermanyIUCN SSC Central Africa Plant Red List Authority (CARLA)GlandSwitzerland
| | - Sophie L. Richards
- Royal Botanic Gardens, Kew, Richmond, Surrey, UKRoyal Botanic GardensRichmondUnited Kingdom
| | - Reddy Shutsha Ehata
- AMAP, Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, FranceUniversité de KisanganiKisanganiDemocratic Republic of the Congo
| | - Murielle Simo-Droissart
- Plant Systematics and Ecology Laboratory, University of Yaoundé I, P.O. Box 047, Yaoundé, CameroonUniversity of Yaoundé IYaoundéCameroon
- Department of Biotechnologies, Faculty of Applied Sciences, INES-Ruhengeri, B.P.155 Ruhengeri, RwandaUCN SSC Central Africa Plant Red List Authority (CARLA)GlandSwaziland
| | - Tariq Stévart
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
- Missouri Botanical Garden, Africa & Madagascar Department, St. Louis, MO 63110, USAMissouri Botanical Garden, Africa & Madagascar DepartmentSt. LouisUnited States of America
- University of Koblenz-Landau, Universitätsstraße 1, Koblenz, 56070, GermanyIUCN SSC Central Africa Plant Red List Authority (CARLA)GlandSwitzerland
- East African Herbarium, National Museums of Kenya, P.O. Box 45166-00100, Nairobi, KenyaUniversité Libre de BruxellesBrusselsBelgium
| | - Marc S. M. Sosef
- Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, BelgiumMeise Botanic GardenMeiseBelgium
- University of Koblenz-Landau, Universitätsstraße 1, Koblenz, 56070, GermanyIUCN SSC Central Africa Plant Red List Authority (CARLA)GlandSwitzerland
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