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Cuni-Sanchez A, Martin EH, Uzabaho E, Ngute ASK, Bitariho R, Kayijamahe C, Marshall AR, Mohamed NA, Mseja GA, Nkwasibwe A, Rovero F, Sheil D, Tinkasimire R, Tumugabirwe L, Feeley KJ, Sullivan MJP. Evidence of thermophilization in Afromontane forests. Nat Commun 2024; 15:5554. [PMID: 38987543 PMCID: PMC11236992 DOI: 10.1038/s41467-024-48520-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 05/03/2024] [Indexed: 07/12/2024] Open
Abstract
Thermophilization is the directional change in species community composition towards greater relative abundances of species associated with warmer environments. This process is well-documented in temperate and Neotropical plant communities, but it is uncertain whether this phenomenon occurs elsewhere in the tropics. Here we extend the search for thermophilization to equatorial Africa, where lower tree diversity compared to other tropical forest regions and different biogeographic history could affect community responses to climate change. Using re-census data from 17 forest plots in three mountain regions of Africa, we find a consistent pattern of thermophilization in tree communities. Mean rates of thermophilization were +0.0086 °C·y-1 in the Kigezi Highlands (Uganda), +0.0032 °C·y-1 in the Virunga Mountains (Rwanda-Uganda-Democratic Republic of the Congo) and +0.0023 °C·y-1 in the Udzungwa Mountains (Tanzania). Distinct from other forests, both recruitment and mortality were important drivers of thermophilzation in the African plots. The forests studied currently act as a carbon sink, but the consequences of further thermophilization are unclear.
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Affiliation(s)
- Aida Cuni-Sanchez
- Department of International Environmental and Development Studies (NORAGRIC), Norwegian University of Life Sciences, Ås, Norway.
- Department of Environment and Geography, University of York, York, UK.
| | | | | | - Alain S K Ngute
- Forest Research Institute, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Robert Bitariho
- Institute of Tropical Forest Conservation, Mbarara University of Science and Technology, Mbarara, Uganda
| | | | - Andrew R Marshall
- Forest Research Institute, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- Flamingo Land Ltd, Malton, UK
| | | | | | - Aventino Nkwasibwe
- Institute of Tropical Forest Conservation, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Francesco Rovero
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- MUSE-Museo delle Scienze, Trento, Italy
| | - Douglas Sheil
- Forest Ecology and Forest Management Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Rogers Tinkasimire
- Institute of Tropical Forest Conservation, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Lawrence Tumugabirwe
- Institute of Tropical Forest Conservation, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Kenneth J Feeley
- Department of Biology, University of Miami, Coral Gables, FL, USA
- Fairchild Tropical Botanic Garden, Coral Gables, FL, USA
| | - Martin J P Sullivan
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK.
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2
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Din Dipita A, Missoup AD, Aguillon S, Lecompte E, Momboua BR, Chaber AL, Abernethy K, Njiokou F, Tindo M, Ntie S, Gaubert P. Genetic tracing of the illegal trade of the white-bellied pangolin (Phataginus tricuspis) in western Central Africa. Sci Rep 2024; 14:13131. [PMID: 38849460 PMCID: PMC11161582 DOI: 10.1038/s41598-024-63666-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/30/2024] [Indexed: 06/09/2024] Open
Abstract
The white-bellied pangolin is subject to intense trafficking, feeding both local and international trade networks. In order to assess its population genetics and trace its domestic trade, we genotyped 562 pangolins from local to large bushmeat markets in western central Africa. We show that the two lineages described from the study region (WCA and Gab) were overlapping in ranges, with limited introgression in southern Cameroon. There was a lack of genetic differentiation across WCA and a significant signature of isolation-by-distance possibly due to unsuspected dispersal capacities involving a Wahlund effect. We detected a c. 74.1-82.5% decline in the effective population size of WCA during the Middle Holocene. Private allele frequency tracing approach indicated up to 600 km sourcing distance by large urban markets from Cameroon, including Equatorial Guinea. The 20 species-specific microsatellite loci provided individual-level genotyping resolution and should be considered as valuable resources for future forensic applications. Because admixture was detected between lineages, we recommend a multi-locus approach for tracing the pangolin trade. The Yaoundé market was the main hub of the trade in the region, and thus should receive specific monitoring to mitigate pangolins' domestic trafficking. Our study also highlighted the weak implementation of CITES regulations at European borders.
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Affiliation(s)
- Alain Din Dipita
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of Science, University of Douala, 24157, Douala, Cameroon.
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UT3), Toulouse, Bâtiment 4R1, 118 route de Narbonne, 31062 Toulouse Cedex 9, France.
| | - Alain Didier Missoup
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of Science, University of Douala, 24157, Douala, Cameroon.
| | - Samantha Aguillon
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UT3), Toulouse, Bâtiment 4R1, 118 route de Narbonne, 31062 Toulouse Cedex 9, France
| | - Emilie Lecompte
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UT3), Toulouse, Bâtiment 4R1, 118 route de Narbonne, 31062 Toulouse Cedex 9, France
| | - Brice Roxan Momboua
- Agence Nationale des Parcs Nationaux, Libreville, Gabon
- Département de Biologie, Faculté des Sciences, Université des Sciences et Techniques de Masuku, Franceville, Gabon
| | - Anne-Lise Chaber
- School of Animal and Veterinary Sciences, University of Adelaide, Adelaide SA, Australia
| | - Katharine Abernethy
- African Forest Ecology Group, Biological and Environmental Sciences, University of Stirling, Stirling, UK
- Institut de Recherche en Ecologie Tropicale, Libreville, Gabon
| | - Flobert Njiokou
- Laboratoire de Parasitologie et Ecologie, Faculté des Sciences, Universite de Yaoundé I, Yaoundé, 812, Cameroon
| | - Maurice Tindo
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of Science, University of Douala, 24157, Douala, Cameroon
| | - Stephan Ntie
- Laboratoire de Biologie Moléculaire et Cellulaire (LABMC), Département de Biologie, Université des Sciences et Techniques de Masuku, Franceville, Gabon
| | - Philippe Gaubert
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UT3), Toulouse, Bâtiment 4R1, 118 route de Narbonne, 31062 Toulouse Cedex 9, France.
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR), Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal.
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3
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Núñez CL, Clark JS, Poulsen JR. Disturbance sensitivity shapes patterns of tree species distribution in Afrotropical lowland rainforests more than climate or soil. Ecol Evol 2024; 14:e11329. [PMID: 38698930 PMCID: PMC11063613 DOI: 10.1002/ece3.11329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 02/20/2024] [Accepted: 04/07/2024] [Indexed: 05/05/2024] Open
Abstract
Understanding how tropical forests respond to abiotic environmental changes is critical for preserving biodiversity, mitigating climate change, and maintaining ecosystem services in the coming century. To evaluate the relative roles of the abiotic environment and human disturbance on Central African tree community composition, we employ tree inventory data, remotely sensed climatic data, and soil nutrient data collected from 30 1-ha plots distributed across a large-scale observational experiment in forests that had been differently impacted by logging and hunting in northern Republic of Congo. We show that the composition of Afrotropical plant communities at this scale responds to human disturbance more than to climate, with particular sensitivities to hunting and distance to the nearest village (a proxy for other human activities, including tree-cutting and gathering). These findings contrast neotropical predictions, highlighting the unique ecological, evolutionary, and anthropogenic history of Afrotropical forests.
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Affiliation(s)
- Chase L. Núñez
- Department for the Ecology of Animal SocietiesMax Planck Institute of Animal BehaviorKonstanzGermany
- Centre for the Advanced Study of Collective BehaviourUniversity of KonstanzKonstanzGermany
- Department of BiologyUniversity of KonstanzKonstanzGermany
- University Program in EcologyDuke UniversityDurhamNorth CarolinaUSA
- Nicholas School of the EnvironmentDuke UniversityDurhamNorth CarolinaUSA
| | - James S. Clark
- University Program in EcologyDuke UniversityDurhamNorth CarolinaUSA
- Nicholas School of the EnvironmentDuke UniversityDurhamNorth CarolinaUSA
| | - John R. Poulsen
- University Program in EcologyDuke UniversityDurhamNorth CarolinaUSA
- Nicholas School of the EnvironmentDuke UniversityDurhamNorth CarolinaUSA
- The Nature ConservancyBoulderColoradoUSA
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4
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Tapondjou Nkonmeneck WP, Allen KE, Hime PM, Knipp KN, Kameni MM, Tchassem AM, Gonwouo LN, Brown RM. Diversification and historical demography of Rhampholeon spectrum in West-Central Africa. PLoS One 2022; 17:e0277107. [PMID: 36525408 PMCID: PMC9757597 DOI: 10.1371/journal.pone.0277107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 10/19/2022] [Indexed: 12/23/2022] Open
Abstract
Pygmy Chameleons of the genus Rhampholeon represent a moderately diverse, geographically circumscribed radiation, with most species (18 out of 19 extant taxa) limited to East Africa. The one exception is Rhampholeon spectrum, a species restricted to West-Central African rainforests. We set out to characterize the geographic basis of genetic variation in this disjunctly distributed Rhampholeon species using a combination of multilocus Sanger data and genomic sequences to explore population structure and range-wide phylogeographic patterns. We also employed demographic analyses and niche modeling to distinguish between alternate explanations to contextualize the impact of past geological and climatic events on the present-day distribution of intraspecific genetic variation. Phylogenetic analyses suggest that R. spectrum is a complex of five geographically delimited populations grouped into two major clades (montane vs. lowland). We found pronounced population structure suggesting that divergence and, potentially, speciation began between the late Miocene and the Pleistocene. Sea level changes during the Pleistocene climatic oscillations resulted in allopatric divergence associated with dispersal over an ocean channel barrier and colonization of Bioko Island. Demographic inferences and range stability mapping each support diversification models with secondary contact due to population contraction in lowland and montane refugia during the interglacial period. Allopatric divergence, congruent with isolation caused by geologic uplift of the East African rift system, the "descent into the Icehouse," and aridification of sub-Saharan Africa during the Eocene-Oligocene are identified as the key events explaining the population divergence between R. spectrum and its closely related sister clade from the Eastern Arc Mountains. Our results unveil cryptic genetic diversity in R. spectrum, suggesting the possibility of a species complex distributed across the Lower Guinean Forest and the Island of Bioko. We highlight the major element of species diversification that modelled today's diversity and distributions in most West-Central African vertebrates.
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Affiliation(s)
- Walter Paulin Tapondjou Nkonmeneck
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - Kaitlin E. Allen
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - Paul M. Hime
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - Kristen N. Knipp
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - Marina M. Kameni
- Laboratory of Zoology, Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
| | - Arnaud M. Tchassem
- Laboratory of Zoology, Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
| | - LeGrand N. Gonwouo
- Laboratory of Zoology, Faculty of Science, University of Yaoundé I, Yaoundé, Cameroon
| | - Rafe M. Brown
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
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5
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Marshall CAM, Dabo J, Mensah M, Ekpe P, Kpadehyea JT, Haba OO, Bilivogui D, Hawthorne WD. Predictors of plant endemism in two west African forest hotspots. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.980660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Centres of endemism have been much studied by biogeographers, ecologists, and evolutionary theorists, and are considered conservation priorities. It is therefore important to understand the ecological traits of restricted range taxa, and the landscape-scale drivers of high endemism. Here, we investigate correlates of floristic endemism within two of west Africa’s forest biodiversity hotspots at local scale. We assembled distribution data for 1,042 vascular plant taxa from 114 sample locations within forest reserves of south west Ghana, and for 1,735 vascular plant taxa from 454 sample locations within the Nimba Mountains (Liberia and Guinea). A quantitative index of global endemism called the Genetic Heat Index was modelled linearly. We tested the significance of modern climate, altitude and disturbance as factors predicting endemism rates in these two forest reserves. Annual rainfall was significantly and positively related to endemism rates in both south west Ghana and the Nimba Mountains. Altitude was a significant predictor of endemism rates in the Nimba Mountains, with a quadratic relationship highlighting particularly high endemism over 1,000 m. Local topography rather than altitude was a significant predictor or endemism in SW Ghana, where altitude varies less. Areas of high rainfall and high altitude are geographically restricted across the western African forests, acting as edaphic islands driving spatial isolation. Disturbed vegetation samples had lower endemism rates than undisturbed samples in both Nimba and SW Ghana, and overall pioneer species had wider areas of occupancy than shade-bearing species. Endemism rates increased slightly with each year following clearance. Disturbance thus creates and maintains vegetation types which support a lower proportion of globally rare species in the two biodiversity hotspots surveyed. From the point of view of the conservation of globally rare plants, it is important to keep additional disturbance in the south west Ghana hotspot, particularly Ankasa, to a minimum, as is the current practice, and in the Nimba mountains to establish community forests which may be left relatively undisturbed amid farming and mining activities.
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6
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Veron G, Daniel C, Pagani P, Do Linh San E, Kitchener AC, Hassanin A. A tale of two African mongooses (Carnivora: Herpestidae): differing genetic diversity and geographical structure across a continent. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00321-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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7
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Adjossou K, Kokou K, Deconchat M. Floristic composition and turnover analysis in Dahomey Gap and the surrounding sub-humid Togolese mountain minor forest refuges: Importance for biogeography and biodiversity conservation in sub-Saharan Africa. Ecol Evol 2022; 12:e9304. [PMID: 36225837 PMCID: PMC9532220 DOI: 10.1002/ece3.9304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 07/28/2022] [Accepted: 08/26/2022] [Indexed: 11/07/2022] Open
Abstract
The origin of Dahomey Gap (DG) flora is one of the central biogeographical questions in sub-Saharan, which has been addressed in several studies. However, floristic evidence based on representative samples from the DG seems to be lacking in the scientific debate. The present study was conducted to fill this gap. Specifically, we assessed Togolese mountain riparian forests as minor forest refugia, examined their contribution to larger sub-Saharan forest refugia, and discussed the significance of these findings for biogeography and biodiversity conservation. Southwest Togo, West Africa, and sub-Saharan Upper Guinea Region Floristic data were collected in riparian forests through an intensive botanical inventory (n = 198; 50 × 10 m2). A comparative analysis was performed based on the floristic evidence related to forest refuges. The results showed significantly high species richness (868 species) and a high gamma and beta diversity associated with spatial turnover patterns. They also showed a high affinity between the study forests and large sub-Saharan forest refugia. Riparian forests share about 60% of their current species richness with large sub-Saharan forest refugia and contained refuge bio-indicator species. The floristic evidence, consistent with those of other studies, suggests that Togolese mountains would have very ancient origins and have experienced paleoclimatic events. The studied riparian would have served as refuges during recurrent climatic episodes. Our results support the minimal forest fragmentation hypothesis (network of refugia along rivers). However, they seem to be incompatible with the idea that the DG flora may be essentially a relic of the early Holocene. In sub-Saharan Africa, where maintaining a vast area of natural forest is difficult due to human pressure, efforts to preserve maximum species diversity should include a focus on the conservation of minor forest refuges, particularly in sub-humid mountain riparian zone.
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Affiliation(s)
- Kossi Adjossou
- Département de Botanique, Laboratoire de la Recherche Forestière, Faculté des SciencesUniversité de LoméLoméTogo
| | - Kouami Kokou
- Département de Botanique, Laboratoire de la Recherche Forestière, Faculté des SciencesUniversité de LoméLoméTogo
| | - Marc Deconchat
- Dynafor, INRAEUniversité de ToulouseCastanet‐TolosanFrance
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8
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van Noort S, Shaw SR, Copeland RS. Revision of the endemic African genus Dinapsis (Dinapsini, Megalyridae, Hymenoptera) with description of seven new species. Zookeys 2022; 1112:27-122. [PMID: 36760621 PMCID: PMC9848780 DOI: 10.3897/zookeys.1112.82307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/16/2022] [Indexed: 11/12/2022] Open
Abstract
The endemic Afrotropical genus Dinapsis is revised, and seven new species are described and illustrated: D.bicolor van Noort & Shaw, sp. nov., D.gamka van Noort & Shaw, sp. nov., D.igneus van Noort & Shaw, sp. nov., D.spinitibia van Noort & Shaw, sp. nov., D.taita van Noort & Shaw, sp. nov., D.tricolor Shaw & van Noort, sp. nov., D.zulu Shaw & van Noort, sp. nov. The distribution of the Central African Republican species D.centralis Shaw & van Noort, 2009 is extended to include Cameroon, Kenya and Uganda. Dinapsisturneri Waterston, 1922, previously only known from the poorly preserved holotype female, is redescribed based on newly collected specimens. The distribution of this Western Cape species is extended to include the Eastern and Northern Cape provinces of South Africa. Four distinct species groups within the genus are proposed and diagnosed. An illustrated identification key to all described species of Dinapsis is provided. Online interactive Lucid keys to Afrotropical megalyrid genera and Dinapsis species are available at http://www.waspweb.org.
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Affiliation(s)
- Simon van Noort
- Research and Exhibitions Department, South African Museum, Iziko Museums of South Africa, PO Box 61, Cape Town 8000 South AfricaSouth African Museum, Iziko Museums of South AfricaCape TownSouth Africa,Department of Biological Sciences, University of Cape Town, Private Bag, Rondebosch, 7701, South AfricaUniversity of Cape TownCape TownSouth Africa
| | - Scott Richard Shaw
- U.W. Insect Museum, Department of Ecosystem Science and Management (3354), University of Wyoming, 1000 East University Avenue, Laramie, Wyoming 82071-3354, USAUniversity of WyomingLaramieUnited States of America
| | - Robert S. Copeland
- International Centre of Insect Physiology and Ecology (ICIPE), P.O. Box 30772 Nairobi, KenyaInternational Centre of Insect Physiology and Ecology (ICIPE)NairobiKenya,Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington DC, USANational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
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9
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Rocha JL, Vaz Pinto P, Siegismund HR, Meyer M, Jansen van Vuuren B, Veríssimo L, Ferrand N, Godinho R. African climate and geomorphology drive evolution and ghost introgression in sable antelope. Mol Ecol 2022; 31:2968-2984. [PMID: 35305042 DOI: 10.1111/mec.16427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 02/13/2022] [Accepted: 03/04/2022] [Indexed: 11/27/2022]
Abstract
The evolutionary history of African ungulates has been largely explained in the light of Pleistocene climatic oscillations and the way these influenced the distribution of vegetation types, leading to range expansions and/or isolation in refugia. In contrast, comparatively fewer studies have addressed the continent's environmental heterogeneity and the role played by its geomorphological barriers. In this study, we performed a range-wide analysis of complete mitogenomes of sable antelope (Hippotragus niger) to explore how these different factors may have contributed as drivers of evolution in South-Central Africa. Our results supported two sympatric and deeply divergent mitochondrial lineages in west Tanzanian sables, which can be explained as the result of introgressive hybridization of a mitochondrial ghost lineage from an archaic, as-yet-undefined, congener. Phylogeographic subdivisions into three main lineages suggest that sable diversification may not have been solely driven by climatic events affecting populations differently across a continental scale. Often in interplay with climate, geomorphological features have also clearly shaped the species' patterns of vicariance, where the East Africa Rift System and the Eastern Arc Mountains acted as geological barriers. Subsequent splits among southern populations may be linked to rearrangements in the Zambezi system, possibly framing the most recent time when the river attained its current drainage profile. This work underscores how the use of comprehensive mitogenomic datasets on a model species with a wide geographic distribution can contribute to a much-enhanced understanding of environmental, geomorphological, and evolutionary patterns in Africa throughout the Quaternary.
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Affiliation(s)
- Joana L Rocha
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal
| | - Pedro Vaz Pinto
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,TwinLab CIBIO/ISCED, Instituto Superior de Ciências da Educação da Huíla, Lubango, Angola.,Fundação Kissama, Rua Joaquim Capango 49, Luanda, Angola
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Bettine Jansen van Vuuren
- Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Luís Veríssimo
- Fundação Kissama, Rua Joaquim Capango 49, Luanda, Angola
| | - Nuno Ferrand
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,TwinLab CIBIO/ISCED, Instituto Superior de Ciências da Educação da Huíla, Lubango, Angola.,Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park, 2006, South Africa
| | - Raquel Godinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal.,TwinLab CIBIO/ISCED, Instituto Superior de Ciências da Educação da Huíla, Lubango, Angola.,Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park, 2006, South Africa
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10
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Cooper JC, Crouch NMA, Ferguson AW, Bates JM. Climatic refugia and reduced extinction correlate with underdispersion in mammals and birds in Africa. Ecol Evol 2022; 12:e8752. [PMID: 35356571 PMCID: PMC8941498 DOI: 10.1002/ece3.8752] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/18/2022] [Accepted: 03/03/2022] [Indexed: 11/16/2022] Open
Abstract
Macroevolutionary patterns, often inferred from metrics of community relatedness, are often used to ascertain major evolutionary processes shaping communities. These patterns have been shown to be informative of biogeographic barriers, of habitat suitability and invasibility (especially with regard to environmental filtering), and of regions that function as evolutionary cradles (i.e., sources of diversification) or museums (i.e., regions of reduced extinction). Here, we analyzed continental datasets of mammal and bird distributions to identify primary drivers of community evolution on the African continent for mostly endothermic vertebrates. We find that underdispersion (i.e., relatively low phylogenetic diversity compared to species richness) closely correlates with specific ecoregions that have been identified as climatic refugia in the literature, regardless of whether these specific regions have been touted as cradles or museums. Using theoretical models of identical communities that differ only with respect to extinction rates, we find that even small suppressions of extinction rates can result in underdispersed communities, supporting the hypothesis that climatic stability can lead to underdispersion. We posit that large‐scale patterns of under‐ and overdispersion between regions of similar species richness are more reflective of a particular region’s extinction potential, and that the very nature of refugia can lead to underdispersion via the steady accumulation of species richness through diversification within the same ecoregion during climatic cycles. Thus, patterns of environmental filtering can be obfuscated by environments that coincide with biogeographic refugia, and considerations of regional biogeographic history are paramount for inferring macroevolutionary processes.
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Affiliation(s)
- Jacob C Cooper
- Committee on Evolutionary Biology University of Chicago Chicago Illinois USA.,Negaunee Integrative Research Center Field Museum Chicago Illinois USA.,Present address: University of Kansas Biodiversity Institute Lawrence Kansas USA
| | - Nicholas M A Crouch
- Department of Geophysical Sciences University of Chicago Chicago Illinois USA
| | - Adam W Ferguson
- Gantz Family Collections Center Field Museum Chicago Illinois USA
| | - John M Bates
- Negaunee Integrative Research Center Field Museum Chicago Illinois USA
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11
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Núñez CL, Poulsen JR, White LJT, Medjibe V, Clark JS. Distinct Community-Wide Responses to Forecasted Climate Change in Afrotropical Forests. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2021.742626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
More refined knowledge of how tropical forests respond to changes in the abiotic environment is necessary to mitigate climate change, maintain biodiversity, and preserve ecosystem services. To evaluate the unique response of diverse Afrotropical forest communities to disturbances in the abiotic environment, we employ country-wide tree species inventories, remotely sensed climate data, and future climate predictions collected from 104 1-ha plots in the central African country of Gabon. We predict a 3–8% decrease in Afrotropical forest species richness by the end of the century, in contrast to the 30–50% loss of plant diversity predicted to occur with equivalent warming in the Neotropics. This work reveals that forecasts of community species composition are not generalizable across regions, and more representative studies are needed in understudied diverse biomes. This study serves as an important counterpoint to work done in the Neotropics by providing contrasting predictions for Afrotropical forests with substantially different ecological, evolutionary, and anthropogenic histories.
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12
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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. AMERICAN JOURNAL OF BOTANY 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] [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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13
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Pradhan N, Norris RW, Decher J, Peterhans JK, Gray CR, Bauer G, Carleton MD, Kilpatrick CW. Phylogenetic relationships and biogeography of the Hybomys division (Muridae: Murinae: Arvicanthini), rodents endemic to Africa's rainforests. JOURNAL OF VERTEBRATE BIOLOGY 2021. [DOI: 10.25225/jvb.21034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Nelish Pradhan
- Department of Biology, University of Vermont, Burlington, USA; e-mail: ,
| | - Ryan W. Norris
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University at Lima, Lima, USA; e-mail: ,
| | - Jan Decher
- Mammal Section, Zoological Research Museum Alexander Koenig, Bonn, Germany; e-mail:
| | | | | | - George Bauer
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University at Lima, Lima, USA; e-mail: ,
| | - Michael D. Carleton
- Department of Vertebrate Zoology, Mammal Division, National Museum of Natural History, Washington, USA; e-mail:
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14
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Jaynes KE, Myers EA, Gvoždík V, Blackburn DC, Portik DM, Greenbaum E, Jongsma GFM, Rödel MO, Badjedjea G, Bamba-Kaya A, Baptista NL, Akuboy JB, Ernst R, Kouete MT, Kusamba C, Masudi FM, McLaughlin PJ, Nneji LM, Onadeko AB, Penner J, Vaz Pinto P, Stuart BL, Tobi E, Zassi-Boulou AG, Leaché AD, Fujita MK, Bell RC. Giant Tree Frog diversification in West and Central Africa: Isolation by physical barriers, climate, and reproductive traits. Mol Ecol 2021; 31:3979-3998. [PMID: 34516675 DOI: 10.1111/mec.16169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/18/2021] [Accepted: 09/02/2021] [Indexed: 01/25/2023]
Abstract
Secondary sympatry amongst sister lineages is strongly associated with genetic and ecological divergence. This pattern suggests that for closely related species to coexist in secondary sympatry, they must accumulate differences in traits that mediate ecological and/or reproductive isolation. Here, we characterized inter- and intraspecific divergence in three giant tree frog species whose distributions stretch across West and Central Africa. Using genome-wide single-nucleotide polymorphism data, we demonstrated that species-level divergence coincides temporally and geographically with a period of large-scale forest fragmentation during the late Pliocene. Our environmental niche models further supported a dynamic history of climatic suitability and stability, and indicated that all three species occupy distinct environmental niches. We found modest morphological differentiation amongst the species with significant divergence in tympanum diameter and male advertisement call. In addition, we confirmed that two species occur in secondary sympatry in Central Africa but found no evidence of hybridization. These patterns support the hypothesis that cycles of genetic exchange and isolation across West and Central Africa have contributed to globally significant biodiversity. Furthermore, divergence in both ecology and reproductive traits appear to have played important roles in maintaining distinct lineages. At the intraspecific level, we found that climatic refugia, precipitation gradients, marine incursions, and potentially riverine barriers generated phylogeographic structure throughout the Pleistocene and into the Holocene. Further studies examining phenotypic divergence and secondary contact amongst these geographically structured populations may demonstrate how smaller scale and more recent biogeographic barriers contribute to regional diversification.
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Affiliation(s)
- Kyle E Jaynes
- Department of Biology, Adrian College, Michigan, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Integrative Biology, W.K. Kellogg Biological Station, Michigan State University, Michigan, USA.,Ecology, Evolution, and Behavior Program, Michigan State University, Michigan, USA
| | - Edward A Myers
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Václav Gvoždík
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.,Department of Zoology, National Museum, Prague, Czech Republic
| | - David C Blackburn
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
| | - Daniel M Portik
- Herpetology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, California, USA
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | - Gregory F M Jongsma
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA.,Department of Biology, University of Florida, Florida, USA
| | - Mark-Oliver Rödel
- Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
| | - Gabriel Badjedjea
- Département d'Ecologie et Biodiversité des Ressources Aquatiques, Centre de Surveillance de la Biodiversité, Université de Kisangani, Kisangani, République Démocratique du Congo
| | | | - Ninda L Baptista
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal.,Faculdade de Ciências da, Universidade do Porto, Porto, Portugal.,Instituto Superior de Ciências da Educação da Huíla (ISCED-Huíla), Rua Sarmento Rodrigues, Lubango, Angola
| | - Jeannot B Akuboy
- Département d'Ecologie et Biodiversité des Ressources Terrestres, Centre de Surveillance de la Biodiversité, Université de Kisangani, République Démocratique du Congo, Kisangani
| | - Raffael Ernst
- Museum of Zoology, Senckenberg Natural History Collections Dresden, Dresden, Germany
| | - Marcel T Kouete
- Department of Natural History, Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA.,School of Natural Resources and Environment, University of Florida, Florida, USA
| | - Chifundera Kusamba
- Laboratoire d'Herpétologie, Département de Biologie, Centre de Recherche en Sciences Naturelles, République Démocratique du Congo, Lwiro
| | - Franck M Masudi
- Département d'Ecologie et Biodiversité des Ressources Terrestres, Centre de Surveillance de la Biodiversité, Université de Kisangani, République Démocratique du Congo, Kisangani
| | - Patrick J McLaughlin
- Bioko Biodiversity Protection Project, Drexel University, Philadelphia, Pennsylvania, USA.,Institute of Conservation Science and Learning, Bristol Zoological Society, Bristol, UK
| | - Lotanna M Nneji
- Department of Ecology and Evolutionary Biology, Princeton University, New Jersey, USA
| | - Abiodun B Onadeko
- Department of Zoology, Faculty of Science, University of Lagos, Lagos, Nigeria
| | - Johannes Penner
- Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany.,Chair of Wildlife Ecology and Wildlife Management, University of Freiburg, Freiburg, Germany
| | - Pedro Vaz Pinto
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, Vairão, Portugal.,Fundação Kissama, Luanda, Angola
| | - Bryan L Stuart
- Section of Research & Collections, North Carolina Museum of Natural Sciences, North Carolina, USA
| | - Elie Tobi
- Gabon Biodiversity Program, Smithsonian Conservation Biology Institute, Gamba, Gabon
| | | | - Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, USA
| | - Matthew K Fujita
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - Rayna C Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Herpetology Department, Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, California, USA
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15
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Barratt CD, Lester JD, Gratton P, Onstein RE, Kalan AK, McCarthy MS, Bocksberger G, White LC, Vigilant L, Dieguez P, Abdulai B, Aebischer T, Agbor A, Assumang AK, Bailey E, Bessone M, Buys B, Carvalho JS, Chancellor R, Cohen H, Danquah E, Deschner T, Dongmo ZN, Doumbé OA, Dupain J, Duvall CS, Eno-Nku M, Etoga G, Galat-Luong A, Garriga R, Gatti S, Ghiurghi A, Goedmakers A, Granjon AC, Hakizimana D, Head J, Hedwig D, Herbinger I, Hermans V, Jones S, Junker J, Kadam P, Kambi M, Kienast I, Kouakou CY, N Goran KP, Langergraber KE, Lapuente J, Laudisoit A, Lee KC, Maisels F, Mirghani N, Moore D, Morgan B, Morgan D, Neil E, Nicholl S, Nkembi L, Ntongho A, Orbell C, Ormsby LJ, Pacheco L, Piel AK, Pintea L, Plumptre AJ, Rundus A, Sanz C, Sommer V, Sop T, Stewart FA, Sunderland-Groves J, Tagg N, Todd A, Ton E, van Schijndel J, VanLeeuwe H, Vendras E, Welsh A, Wenceslau JFC, Wessling EG, Willie J, Wittig RM, Yoshihiro N, Yuh YG, Yurkiw K, Boesch C, Arandjelovic M, Kühl H. Quantitative estimates of glacial refugia for chimpanzees (Pan troglodytes) since the Last Interglacial (120,000 BP). Am J Primatol 2021; 83:e23320. [PMID: 34402081 DOI: 10.1002/ajp.23320] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 07/06/2021] [Accepted: 07/28/2021] [Indexed: 11/12/2022]
Abstract
Paleoclimate reconstructions have enhanced our understanding of how past climates have shaped present-day biodiversity. We hypothesize that the geographic extent of Pleistocene forest refugia and suitable habitat fluctuated significantly in time during the late Quaternary for chimpanzees (Pan troglodytes). Using bioclimatic variables representing monthly temperature and precipitation estimates, past human population density data, and an extensive database of georeferenced presence points, we built a model of changing habitat suitability for chimpanzees at fine spatio-temporal scales dating back to the Last Interglacial (120,000 BP). Our models cover a spatial resolution of 0.0467° (approximately 5.19 km2 grid cells) and a temporal resolution of between 1000 and 4000 years. Using our model, we mapped habitat stability over time using three approaches, comparing our modeled stability estimates to existing knowledge of Afrotropical refugia, as well as contemporary patterns of major keystone tropical food resources used by chimpanzees, figs (Moraceae), and palms (Arecacae). Results show habitat stability congruent with known glacial refugia across Africa, suggesting their extents may have been underestimated for chimpanzees, with potentially up to approximately 60,000 km2 of previously unrecognized glacial refugia. The refugia we highlight coincide with higher species richness for figs and palms. Our results provide spatio-temporally explicit insights into the role of refugia across the chimpanzee range, forming the empirical foundation for developing and testing hypotheses about behavioral, ecological, and genetic diversity with additional data. This methodology can be applied to other species and geographic areas when sufficient data are available.
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Affiliation(s)
- Christopher D Barratt
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany.,Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jack D Lester
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Paolo Gratton
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Biology, University of Rome "Tor Vergata", Roma, Italy
| | - Renske E Onstein
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - Ammie K Kalan
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Maureen S McCarthy
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Gaëlle Bocksberger
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Lauren C White
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Linda Vigilant
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Paula Dieguez
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Barrie Abdulai
- Research for Evidence-based and Achievable Decisions Sierra Leone (READ-SL), Sierra Leone
| | - Thierry Aebischer
- Conservation et Plan d'aménagement de l'Aire de Conservation de Chinko, African Parks Network, Chinko Project, Kocho, RCA and active collaborator of the University of Fribourg, WegmannLab, Fribourg, Switzerland
| | - Anthony Agbor
- African Parks Centurion Building, Lonehill, South Africa
| | - Alfred K Assumang
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Emma Bailey
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mattia Bessone
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Joana S Carvalho
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Rebecca Chancellor
- Departments of Anthropology & Sociology and Psychology, West Chester University, West Chester, Pennsylvania, USA
| | - Heather Cohen
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Emmanuel Danquah
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Tobias Deschner
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | | | - Jef Dupain
- Antwerp Zoo Foundation, Antwerp Zoo Society, Antwerpen, Belgium
| | - Chris S Duvall
- Department of Geography and Environmental Studies, University of New Mexico, Albuquerque, New Mexico, USA
| | - Manasseh Eno-Nku
- World Wide Fund for Nature, Panda House Bastos, Yaounde, Cameroon
| | - Gilles Etoga
- World Wide Fund for Nature, Panda House Bastos, Yaounde, Cameroon
| | - Anh Galat-Luong
- IRD (The French National Research Institute for Development), France
| | - Rosa Garriga
- Tacugama Chimpanzee Sanctuary, Freetown, Sierra Leone
| | - Sylvain Gatti
- West African Primate Conservation Action (WAPCA), Accra, Ghana
| | | | | | - Anne-Céline Granjon
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Josephine Head
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Daniela Hedwig
- Elephant Listening Project, Center for Conservation Bioacoustics, Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA
| | | | - Veerle Hermans
- Taï Chimpanzee Project, CSRS, Abidjan, Ivory Coast.,Centre for Research and Conservation, Antwerp Zoo Society, Antwerpen, Belgium
| | - Sorrel Jones
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jessica Junker
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - Parag Kadam
- Department of Archaeology and Anthropology, University of Cambridge, Cambridge, UK
| | - Mohamed Kambi
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Ivonne Kienast
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Kouamé P N Goran
- World Wide Fund for Nature, Panda House Bastos, Yaounde, Cameroon
| | - Kevin E Langergraber
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA.,Institute of Human Origins, Arizona State University, Tempe, Arizona, USA
| | - Juan Lapuente
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Comoé Chimpanzee Conservation Project, Comoé National Park, Kakpin, Ivory Coast
| | - Anne Laudisoit
- Ecohealth Alliance, New York City, New York, USA.,Department of Biology, Evolutionary Ecology Group, University of Antwerp, Antwerpen, Belgium
| | - Kevin C Lee
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Fiona Maisels
- Wildlife Conservation Society (WCS), Bronx, New York, USA.,Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, UK
| | - Nadia Mirghani
- Jane Goodall Institute Spain and Senegal, Dindefelo Biological Station, Dindefelo, Kedougou, Senegal
| | - Deborah Moore
- Department of Anthropology, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Bethan Morgan
- Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, UK.,San Diego Zoo Global, Escondido, California, USA.,Ebo Forest Research Project, Yaounde, Cameroon
| | - David Morgan
- Lester E Fisher Center for the Study and Conservation of Apes, Lincoln Park Zoo, Chicago, Illinois, USA
| | - Emily Neil
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sonia Nicholl
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Louis Nkembi
- Environment and Rural Development Foundation, Buea, Cameroon
| | - Anne Ntongho
- World Wide Fund for Nature, Panda House Bastos, Yaounde, Cameroon
| | | | - Lucy Jayne Ormsby
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Alex K Piel
- Department of Anthropology, University College London, London, UK
| | | | - Andrew J Plumptre
- Key Biodiversity Area Secretariat, c/o BirdLife International, Cambridge, UK
| | - Aaron Rundus
- Department of Psychology, West Chester University, West Chester, Pennsylvania, USA
| | - Crickette Sanz
- Department of Anthropology, Washington University in St. Louis, Saint Louis, Missouri, USA.,Wildlife Conservation Society, Congo Program, Brazzaville, Republic of Congo
| | - Volker Sommer
- Department of Anthropology, University College London, London, UK.,Gashaka Primate Project, Serti, Taraba State, Nigeria
| | - Tenekwetche Sop
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany.,Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Fiona A Stewart
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK.,Wildlife Conservation Society, Congo Program, Brazzaville, Republic of Congo
| | | | - Nikki Tagg
- Centre for Research and Conservation, Antwerp Zoo Society, Antwerpen, Belgium
| | | | - Els Ton
- Chimbo Foundation, Oudemirdum, Netherlands
| | | | | | - Elleni Vendras
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Adam Welsh
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Erin G Wessling
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Jacob Willie
- Centre for Research and Conservation, Antwerp Zoo Society, Antwerpen, Belgium
| | - Roman M Wittig
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Taï Chimpanzee Project, CSRS, Abidjan, Ivory Coast
| | | | - Yisa Ginath Yuh
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Geography, Planning and Environmental Studies, University of Concordia, Montréal, Quebec, Canada
| | - Kyle Yurkiw
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Pan Verus Project, Outamba-Kilimi National Park, Sierra Leone
| | - Christophe Boesch
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mimi Arandjelovic
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Hjalmar Kühl
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany.,Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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16
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Imani G, Kalume J, Marchant R, Calders K, Batumike R, Bulonvu F, Cuni‐Sanchez A. Tree diversity and carbon stocks in the Itombwe Mountains of eastern DR Congo. Biotropica 2021. [DOI: 10.1111/btp.13008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gérard Imani
- Biology Department Faculty of Sciences Université Officielle de Bukavu Bukavu Democratic Republic of the Congo
| | - John Kalume
- Biology Department Faculty of Sciences Université Officielle de Bukavu Bukavu Democratic Republic of the Congo
| | - Rob Marchant
- Department of Environment and Geography University of York York UK
| | - Kim Calders
- Computational & Applied Vegetation Ecology (CAVElab) Department of Environment Ghent University Ghent Belgium
| | - Rodrigue Batumike
- Environment Department Faculty of Sciences Université du Cinquantenaire de Lwiro Kabare Democratic Republic of the Congo
| | - Franklin Bulonvu
- Water and forest Department Institut Supérieur d’Agroforesterie et de Gestion de l’Environnement de Kahuzi‐Biega (ISAGE‐KB Kalehe Democratic Republic of the Congo
| | - Aida Cuni‐Sanchez
- Department of Environment and Geography University of York York UK
- Department of International Environmental and Development Studies (NORAGRIC) Norwegian University of Life Sciences As Norway
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17
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Texier N, Dauby G, Bidault E, Lowry PP, Ikabanga DU, Stévart T. An efficient method for defining plant species under High Conservation Value (HCV) criterion 1 based on the IUCN Red List criteria: A case study using species endemic to Gabon. J Nat Conserv 2021. [DOI: 10.1016/j.jnc.2021.126027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Piñeiro R, Hardy OJ, Tovar C, Gopalakrishnan S, Garrett Vieira F, Gilbert MTP. Contrasting genetic signal of recolonization after rainforest fragmentation in African trees with different dispersal abilities. Proc Natl Acad Sci U S A 2021; 118:e2013979118. [PMID: 34210795 PMCID: PMC8271564 DOI: 10.1073/pnas.2013979118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although today the forest cover is continuous in Central Africa, this may have not always been the case, as the scarce fossil record in this region suggests that arid conditions might have significantly reduced tree density during the ice ages. Our aim was to investigate whether the dry ice age periods left a genetic signature on tree species that can be used to infer the date of the past fragmentation of the rainforest. We sequenced reduced representation libraries of 182 samples representing five widespread legume trees and seven outgroups. Phylogenetic analyses identified an early divergent lineage for all species in West Africa (Upper Guinea) and two clades in Central Africa: Lower Guinea-North and Lower Guinea-South. As the structure separating the Northern and Southern clades-congruent across species-cannot be explained by geographic barriers, we tested other hypotheses with demographic model testing using δαδι. The best estimates indicate that the two clades split between the Upper Pliocene and the Pleistocene, a date compatible with forest fragmentation driven by ice age climatic oscillations. Furthermore, we found remarkably older split dates for the shade-tolerant tree species with nonassisted seed dispersal than for light-demanding species with long-distance wind-dispersed seeds. Different recolonization abilities after recurrent cycles of forest fragmentation seem to explain why species with long-distance dispersal show more recent genetic admixture between the two clades than species with limited seed dispersal. Despite their old history, our results depict the African rainforests as a dynamic biome where tree species have expanded relatively recently after the last glaciation.
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Affiliation(s)
- Rosalía Piñeiro
- The GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark;
- Unit of Evolutionary Biology and Ecology, Faculté des Sciences, Université Libre de Bruxelles, B-1050 Brussels, Belgium
- Geography, College of Life and Environmental Sciences, CLES, University of Exeter, Exeter EX4 4RJ, United Kingdom
| | - Olivier J Hardy
- Unit of Evolutionary Biology and Ecology, Faculté des Sciences, Université Libre de Bruxelles, B-1050 Brussels, Belgium
| | - Carolina Tovar
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond TW9 3AB, United Kingdom
| | | | | | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
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19
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Allen KE, Greenbaum E, Hime PM, Tapondjou N. WP, Sterkhova VV, Kusamba C, Rödel M, Penner J, Peterson AT, Brown RM. Rivers, not refugia, drove diversification in arboreal, sub-Saharan African snakes. Ecol Evol 2021; 11:6133-6152. [PMID: 34141208 PMCID: PMC8207163 DOI: 10.1002/ece3.7429] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/12/2021] [Accepted: 02/18/2021] [Indexed: 12/26/2022] Open
Abstract
The relative roles of rivers versus refugia in shaping the high levels of species diversity in tropical rainforests have been widely debated for decades. Only recently has it become possible to take an integrative approach to test predictions derived from these hypotheses using genomic sequencing and paleo-species distribution modeling. Herein, we tested the predictions of the classic river, refuge, and river-refuge hypotheses on diversification in the arboreal sub-Saharan African snake genus Toxicodryas. We used dated phylogeographic inferences, population clustering analyses, demographic model selection, and paleo-distribution modeling to conduct a phylogenomic and historical demographic analysis of this genus. Our results revealed significant population genetic structure within both Toxicodryas species, corresponding geographically to river barriers and divergence times from the mid-Miocene to Pliocene. Our demographic analyses supported the interpretation that rivers are indications of strong barriers to gene flow among populations since their divergence. Additionally, we found no support for a major contraction of suitable habitat during the last glacial maximum, allowing us to reject both the refuge and river-refuge hypotheses in favor of the river-barrier hypothesis. Based on conservative interpretations of our species delimitation analyses with the Sanger and ddRAD data sets, two new cryptic species are identified from east-central Africa. This study highlights the complexity of diversification dynamics in the African tropics and the advantages of integrative approaches to studying speciation in tropical regions.
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Affiliation(s)
- Kaitlin E. Allen
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Eli Greenbaum
- Department of Biological SciencesUniversity of Texas at El PasoEl PasoTXUSA
| | - Paul M. Hime
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Walter P. Tapondjou N.
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Viktoria V. Sterkhova
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Chifundera Kusamba
- Laboratoire d’Hérpétologie, Département de BiologieCentre de Recherche en Sciences NaturellesLwiroDemocratic Republic of Congo
| | - Mark‐Oliver Rödel
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
| | - Johannes Penner
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity ScienceBerlinGermany
- Chair of Wildlife Ecology and ManagementUniversity of FreiburgFreiburgGermany
| | - A. Townsend Peterson
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
| | - Rafe M. Brown
- Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceKSUSA
- Biodiversity InstituteUniversity of KansasLawrenceKSUSA
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20
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Vanden Abeele S, Janssens SB, Piñeiro R, Hardy OJ. Evidence of past forest fragmentation in the Congo Basin from the phylogeography of a shade-tolerant tree with limited seed dispersal: Scorodophloeus zenkeri (Fabaceae, Detarioideae). BMC Ecol Evol 2021; 21:50. [PMID: 33784979 PMCID: PMC8011194 DOI: 10.1186/s12862-021-01781-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/15/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Comparative phylogeographic studies on rainforest species that are widespread in Central Africa often reveal genetic discontinuities within and between biogeographic regions, indicating (historical) barriers to gene flow, possibly due to repeated and/or long-lasting population fragmentation during glacial periods according to the forest refuge hypothesis. The impact of forest fragmentation seems to be modulated by the ecological amplitude and dispersal capacities of each species, resulting in different demographic histories. Moreover, while multiple studies investigated the western part of Central Africa (Lower Guinea), few have sufficiently sampled the heart of the Congo Basin (Congolia). In this study, we look for genetic discontinuities between populations of the widespread tropical tree Scorodophloeus zenkeri Harms (Fabaceae, Detarioideae) in Central Africa. Additionally, we characterize genetic diversity, selfing rate and fine-scale spatial genetic structure within populations to estimate the gene dispersal capacity of the species. RESULTS Clear intraspecific genetic discontinuities occur throughout the species' distribution range, with two genetic clusters in Congolia and four in Lower Guinea, and highest differentiation occurring between these bioregions. Genetic diversity is higher in Lower Guinea than Congolia. A spatial genetic structure characteristic of isolation by distance occurs within the genetic clusters. This allowed us to estimate gene dispersal distances (σg) for this outcrossing species with ballistic seed dispersal, which range between 100 and 250 m in areas where S. zenkeri occurs in high densities, and are in the low range of σg values compared to other tropical trees. Gene dispersal distances are larger in low density populations, probably due to extensive pollen dispersal capacity. CONCLUSIONS Fragmentation of S. zenkeri populations seems to have occurred not only in Lower Guinea but also in the Congo Basin, though not necessarily according to previously postulated forest refuge areas. The lower genetic diversity in Congolia compared to Lower Guinea parallels the known gradient of species diversity, possibly reflecting a stronger impact of past climate changes on the forest cover in Congolia. Despite its bisexual flowers, S. zenkeri appears to be mostly outcrossing. The limited dispersal observed in this species implies that genetic discontinuities resulting from past forest fragmentation can persist for a long time before being erased by gene flow.
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Affiliation(s)
- Samuel Vanden Abeele
- Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium.
- Evolutionary Biology and Ecology, Faculté Des Sciences, Université Libre de Bruxelles, Av. F.D. Roosevelt 50, 1050, Brussels, Belgium.
- School of Integrative Plant Sciences, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, 14853, USA.
| | - Steven B Janssens
- Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium
- Plant Conservation and Population Biology, KU, Leuven, Belgium
| | - Rosalía Piñeiro
- Geography, College of Life and Environmental Sciences, University of Exeter, Laver Building, North Park Road, Exeter, EX4 4QE, UK
| | - Olivier J Hardy
- Evolutionary Biology and Ecology, Faculté Des Sciences, Université Libre de Bruxelles, Av. F.D. Roosevelt 50, 1050, Brussels, Belgium
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21
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Voelker G, Huntley JW, Bryja J, Denys C, Šumbera R, Demos TC, Lavrenchenko L, Nicolas V, Gnoske TP, Kerbis Peterhans JC. Molecular systematics and biogeographic history of the African climbing-mouse complex (Dendromus). Mol Phylogenet Evol 2021; 161:107166. [PMID: 33798668 DOI: 10.1016/j.ympev.2021.107166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/08/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
Climbing mice in the genus Dendromus (sensu lato) are widely distributed in Africa, south of the Saharan Desert. The 17 currently recognized species in the genus range from widespread taxa to single-mountain endemics, and there is considerable variation across species with respect to habitats occupied. These habitats range from arid grasslands and savannahs to sub-alpine and alpine vegetation. Using the most comprehensive geographic and genetic survey to date and after reviewing many type specimens, we assess the systematics and biogeography of Dendromus. Given the structure of our molecular phylogenetic hypotheses, in which we recover six major clades, we propose the recognition of three genera within the Dendromus group (sensu lato): in addition to Dendromus (26 lineages), we suggest the retention of Megadendromus (monotypic) and the resurrection of the genus Poemys (six lineages). From our model-based molecular phylogenetic results and morphological comparisons, we suggest that six formerly synonymized taxa should be resurrected, and we highlight 14 previously undescribed lineages. We also constructed time-calibrations on our phylogeny, and performed ancestral area reconstructions using BioGeoBEARS. Based on fossil evidence, Dendromus appears to have had a widespread African distribution dating back to the Late Miocene (8-10 Ma), and our basal ancestral area reconstruction (Ethiopians Highlands + Eastern African Mountains + Zambezian region) supports this. Divergence of the six major clades we recover (Poemys, Megadendromus and four within Dendromus) occurred prior to or at the Miocene-Pliocene boundary 5.3 Ma. Biogeographically, Megadendromus is restricted to the Ethiopian Highlands. The ancestral area for Poemys is reconstructed as the Zambezian region, with species distributions ranging from South Africa to Western Africa. The ancestral area for Dendromus is reconstructed as the Ethiopian Highlands, with the ancestral areas of the four major clades being reconstructed as Ethiopian Highlands, Albertine Rift, South Africa or Western Africa. None of the four Dendromus clades are reciprocally monophyletic with respect to distributional area.
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Affiliation(s)
- G Voelker
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, United States.
| | - J W Huntley
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, United States
| | - J Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic; Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - C Denys
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - R Šumbera
- Department of Zoology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - T C Demos
- Science and Education, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, United States
| | - L Lavrenchenko
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia
| | - V Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP51, 75005 Paris, France
| | - T P Gnoske
- Science and Education, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, United States
| | - J C Kerbis Peterhans
- Science and Education, Field Museum of Natural History, 1400 S. Lake Shore Drive, Chicago, IL 60605, United States; College of Arts & Sciences, Roosevelt University, 430 S. Michigan Avenue, Chicago, IL 60605, United States
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22
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Individualistic evolutionary responses of Central African rain forest plants to Pleistocene climatic fluctuations. Proc Natl Acad Sci U S A 2020; 117:32509-32518. [PMID: 33277432 DOI: 10.1073/pnas.2001018117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Understanding the evolutionary dynamics of genetic diversity is fundamental for species conservation in the face of climate change, particularly in hyper-diverse biomes. Species in a region may respond similarly to climate change, leading to comparable evolutionary dynamics, or individualistically, resulting in dissimilar patterns. The second-largest expanse of continuous tropical rain forest (TRF) in the world is found in Central Africa. Here, present-day patterns of genetic structure are thought to be dictated by repeated expansion and contraction of TRFs into and out of refugia during Pleistocene climatic fluctuations. This refugia model implies a common response to past climate change. However, given the unrivalled diversity of TRFs, species could respond differently because of distinct environmental requirements or ecological characteristics. To test this, we generated genome-wide sequence data for >700 individuals of seven codistributed plants from Lower Guinea in Central Africa. We inferred species' evolutionary and demographic histories within a comparative phylogeographic framework. Levels of genetic structure varied among species and emerged primarily during the Pleistocene, but divergence events were rarely concordant. Demographic trends ranged from repeated contraction and expansion to continuous growth. Furthermore, patterns in genetic variation were linked to disparate environmental factors, including climate, soil, and habitat stability. Using a strict refugia model to explain past TRF dynamics is too simplistic. Instead, individualistic evolutionary responses to Pleistocene climatic fluctuations have shaped patterns in genetic diversity. Predicting the future dynamics of TRFs under climate change will be challenging, and more emphasis is needed on species ecology to better conserve TRFs worldwide.
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23
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Helmstetter AJ, Amoussou BEN, Bethune K, Kamdem NG, Glèlè Kakaï R, Sonké B, Couvreur TLP. Phylogenomic approaches reveal how climate shapes patterns of genetic diversity in an African rain forest tree species. Mol Ecol 2020; 29:3560-3573. [PMID: 32743910 DOI: 10.1111/mec.15572] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 07/08/2020] [Accepted: 07/13/2020] [Indexed: 12/23/2022]
Abstract
The world's second largest expanse of tropical rainforest is in Central Africa, and it harbours enormous species diversity. Population genetic studies have consistently revealed significant structure across Central African rainforest plants. In particular, previous studies have repeatedly demonstrated a north-south genetic discontinuity around the equatorial line, in a continuous expanse of rainforest where a climatic inversion is documented. Here, we took a phylogeographic approach by sequencing 351 nuclear markers in 112 individuals across the distribution of the African rainforest tree species Annickia affinis (Annonaceae). We showed for the first time that the north-south divide is the result of a single, major colonization event across the climatic inversion from an ancestral population located in Gabon. We suggested that differences in ecological niche of populations located on either side of this inversion may have contributed to this phylogenetic discontinuity. We found evidence for inland dispersal, predominantly in northern areas, and variable demographic histories among genetic clusters, indicating that populations responded differently to past climate change. We show how newly developed genomic tools can provide invaluable insights into our understanding of tropical rainforest evolutionary dynamics.
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Affiliation(s)
| | - Biowa E N Amoussou
- IRD, UMR DIADE, Université de Montpellier, Montpellier, France.,Faculté des Sciences Agronomiques, Université d'Abomey-Calavi, Cotonou, Benin
| | - Kevin Bethune
- IRD, UMR DIADE, Université de Montpellier, Montpellier, France
| | - Narcisse G Kamdem
- Laboratoire de Botanique Systématique et d'Ecologie, Département des Sciences Biologiques, Ecole Normale Supérieure, Université de Yaoundé I, Yaoundé, Cameroon
| | - Romain Glèlè Kakaï
- Laboratoire de Biomathématiques et d'Estimations Forestières, Université d'Abomey-Calavi, Cotonou, Bénin
| | - Bonaventure Sonké
- Laboratoire de Botanique Systématique et d'Ecologie, Département des Sciences Biologiques, Ecole Normale Supérieure, Université de Yaoundé I, Yaoundé, Cameroon
| | - Thomas L P Couvreur
- IRD, UMR DIADE, Université de Montpellier, Montpellier, France.,Laboratoire de Botanique Systématique et d'Ecologie, Département des Sciences Biologiques, Ecole Normale Supérieure, Université de Yaoundé I, Yaoundé, Cameroon
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24
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Massa B. Revision of the Afrotropical genus Leiodontocercus (Orthoptera, Tettigoniidae, Phaneropterinae) with a description of four new species. Zookeys 2020; 951:47-65. [PMID: 32774105 PMCID: PMC7390807 DOI: 10.3897/zookeys.951.53814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/09/2020] [Indexed: 11/12/2022] Open
Abstract
Specimens belonging to the genus Leiodontocercus are rare or even absent in natural history museum collections; this is likely due to at least two reasons, notably, their relatively small size, and, the sheer difficulty in finding them in dense Afrotropical forests. Until recently, three species from less than fifteen specimens were known from this genus, whose identification relied on a singular diagnostic character, that is, the shape of the male cerci. The present contribution is based on the examination of thirty specimens collected from various countries, ranging from central to west Africa; apart from the male cerci, a second diagnostic character – the stridulatory file – is used to distinguish species, even though it is difficult to examine in mounted specimens. As a result, four new species were detected, namely, L.viciisp. nov., L.spinicercatussp. nov. (from the Central African Republic), L.muticussp. nov. (from Gabon and Cameroon) and L.philipporumsp. nov. (from Côte d’Ivoire). Moreover, L.condylus is recorded from the Central African Republic, the only country where three species of this genus co-occur. It is suggested that population isolation during fluctuating humid and dry periods, consequent to the influence of Ice Age impact during the Pleistocene in tropical central Africa, is the best explanation for the adaptive radiation of the group.
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25
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Abstract
The relationship of evolution with diet and environment can provide insights into modern disease. Fossil evidence shows apes, and early human ancestors were fruit eaters living in environments with strongly seasonal climates. Rapid cooling at the end of the Middle Miocene (15-12 Ma: millions of years ago) increased seasonality in Africa and Europe, and ape survival may be linked with a mutation in uric acid metabolism. Climate stabilized in the later Miocene and Pliocene (12-5 Ma), and fossil apes and early hominins were both adapted for life on ground and in trees. Around 2.5 Ma, early species of Homo introduced more animal products into their diet, and this coincided with developing bipedalism, stone tool technology and increase in brain size. Early species of Homo such as Homo habilis still lived in woodland habitats, and the major habitat shift in human evolution occurred at 1.8 Ma with the origin of Homo erectus. Homo erectus had increased body size, greater hunting skills, a diet rich in meat, control of fire and understanding about cooking food, and moved from woodland to savannah. Group size may also have increased at the same time, facilitating the transmission of knowledge from one generation to the next. The earliest fossils of Homo sapiens appeared about 300 kyr, but they had separated from Neanderthals by 480 kyr or earlier. Their diet shifted towards grain-based foods about 100 kyr ago, and settled agriculture developed about 10 kyr ago. This pattern remains for many populations to this day and provides important insights into current burden of lifestyle diseases.
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Affiliation(s)
- P Andrews
- From the, Natural History Museum, London University College, London, UK
| | - R J Johnson
- University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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26
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Dagallier LMJ, Janssens SB, Dauby G, Blach‐Overgaard A, Mackinder BA, Droissart V, Svenning J, Sosef MSM, Stévart T, Harris DJ, Sonké B, Wieringa JJ, Hardy OJ, Couvreur TLP. Cradles and museums of generic plant diversity across tropical Africa. THE NEW PHYTOLOGIST 2020; 225:2196-2213. [PMID: 31665816 PMCID: PMC7027791 DOI: 10.1111/nph.16293] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/20/2019] [Indexed: 05/27/2023]
Abstract
Determining where species diversify (cradles) and persist (museums) over evolutionary time is fundamental to understanding the distribution of biodiversity and for conservation prioritization. Here, we identify cradles and museums of angiosperm generic diversity across tropical Africa, one of the most biodiverse regions on Earth. Regions containing nonrandom concentrations of young (neo-) and old (paleo-) endemic taxa were identified using distribution data of 1719 genera combined with a newly generated time-calibrated mega-phylogenetic tree. We then compared the identified regions with the current network of African protected areas (PAs). At the generic level, phylogenetic diversity and endemism are mainly concentrated in the biogeographically complex region of Eastern Africa. We show that mountainous areas are centres of both neo- and paleo-endemism. By contrast, the Guineo-Congolian lowland rain forest region is characterized by widespread and old lineages. We found that the overlap between centres of phylogenetic endemism and PAs is high (> 85%). We show the vital role played by mountains acting simultaneously as cradles and museums of tropical African plant biodiversity. By contrast, lowland rainforests act mainly as museums for generic diversity. Our study shows that incorporating large-scale taxonomically verified distribution datasets and mega-phylogenies lead to an improved understanding of tropical plant biodiversity evolution.
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Affiliation(s)
| | | | - Gilles Dauby
- AMAP, IRD, CIRAD, CNRS, INRAUniversity of MontpellierBd de la Lironde34398MontpellierFrance
| | - Anne Blach‐Overgaard
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE)Department of BioscienceAarhus UniversityNy Munkegade 114DK‐8000Aarhus CDenmark
- Section for Ecoinformatics and BiodiversityDepartment of BioscienceAarhus UniversityNy Munkegade 114DK‐8000Aarhus CDenmark
| | | | - Vincent Droissart
- AMAP, IRD, CIRAD, CNRS, INRAUniversity of MontpellierBd de la Lironde34398MontpellierFrance
| | - Jens‐Christian Svenning
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE)Department of BioscienceAarhus UniversityNy Munkegade 114DK‐8000Aarhus CDenmark
- Section for Ecoinformatics and BiodiversityDepartment of BioscienceAarhus UniversityNy Munkegade 114DK‐8000Aarhus CDenmark
| | | | - Tariq Stévart
- Meise Botanic GardenNieuwelaan 38BE‐1860MeiseBelgium
- Herbarium et Bibliothèque de Botanique AfricaineUniversité Libre de BruxellesBoulevard du TriompheB‐1050BruxellesBelgium
- Africa & Madagascar DepartmentMissouri Botanical GardenSt LouisMO631109USA
| | - David J. Harris
- Royal Botanic Garden Edinburgh20A Inverleith RowEdinburghEH3 5LRUK
| | - Bonaventure Sonké
- Laboratoire de Botanique systématique et d'ÉcologieDépartement des Sciences BiologiquesÉcole Normale SupérieureUniversité de Yaoundé IBP 047YaoundéCameroon
| | - Jan J. Wieringa
- Naturalis Biodiversity CenterDarwinweg 22333 CRLeidenthe Netherlands
| | - Olivier J. Hardy
- Evolutionary Biology and EcologyFaculté des SciencesUniversité Libre de BruxellesAv. F.D. Roosevelt 501050BrusselsBelgium
| | - Thomas L. P. Couvreur
- DIADE, IRDUniversity of Montpellier911 Avenue Agropolis34394MontpellierFrance
- Naturalis Biodiversity CenterDarwinweg 22333 CRLeidenthe Netherlands
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27
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Van de Perre F, Willig MR, Presley SJ, Mukinzi IJC, Gambalemoke MS, Leirs H, Verheyen E. Functional volumes, niche packing and species richness: biogeographic legacies in the Congo Basin. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191582. [PMID: 32269793 PMCID: PMC7137932 DOI: 10.1098/rsos.191582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 01/22/2020] [Indexed: 06/11/2023]
Abstract
Understanding the determinants of species coexistence in complex and species-rich communities is a fundamental goal of ecology. Patterns of species coexistence depend on how biotic interactions and environmental filtering act over ecological and evolutionary time scales. Climatic fluctuations in lowland rainforests of the Congo Basin led to the number of vertebrate species being significantly lower in central compared with northern ecoregions of the Basin. We used null models to assess whether climatic variations affected the community assembly of shrews. A consistent limit to functional similarity of species was not related to species richness. Rather, species richness is constrained by environmental factors, and these constraints are stronger in the central lowland forests of the Congo Basin. By constraining species geographic distributions, historical effects of rainforest refugia arising from climatic fluctuations may affect contemporary species composition of local shrew communities. The Congo River represents a vicariance event that led to allopatric speciation of shrews and continues to represent a barrier to dispersal. Ultimately, the historical effects of this barrier have led to differences in the functional volume of shrew communities in northern and central ecoregions. We suggest that the analyses of community assembly can be used to identify Holocene refugia in the Congo Basin.
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Affiliation(s)
| | - Michael R. Willig
- Department of Ecology & Evolutionary Biology, Center for Environmental Sciences & Engineering, and Institute of the Environment, University of Connecticut, Storrs, CT 06269-4210, USA
| | - Steven J. Presley
- Department of Ecology & Evolutionary Biology, Center for Environmental Sciences & Engineering, and Institute of the Environment, University of Connecticut, Storrs, CT 06269-4210, USA
| | - Itoka Jean-Claude Mukinzi
- Centre de Surveillance de la Biodiversité, University of Kisangani, Kisangani, Democratic Republic of the Congo
| | | | - Herwig Leirs
- Evolutionary Ecology Group, University of Antwerp, 2610 Antwerp, Belgium
| | - Erik Verheyen
- Evolutionary Ecology Group, University of Antwerp, 2610 Antwerp, Belgium
- OD Taxonomy and Phylogeny, Royal Belgian Institute for Natural Sciences, 1000 Brussels, Belgium
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28
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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] [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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Garot E, Joët T, Combes MC, Severac D, Lashermes P. Plant population dynamics on oceanic islands during the Late Quaternary climate changes: genetic evidence from a tree species (Coffea mauritiana) in Reunion Island. THE NEW PHYTOLOGIST 2019; 224:974-986. [PMID: 31291469 DOI: 10.1111/nph.16052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/04/2019] [Indexed: 06/09/2023]
Abstract
Past climatic fluctuations have played a major role in shaping the current plant biodiversity. Although harbouring an exceptional biota, oceanic islands have received little attention in studies on species demographic history and past vegetation patterns. We investigated the impact of past climatic changes on the effective population size of a tree (Coffea mauritiana) that is endemic to Reunion Island, located in the south-western Indian Ocean (SWIO). Demographic changes were inferred using summary statistics calculated from genomic data. Using ecological niche modelling and the current distribution of genetic diversity, the paleodistribution of the species was also assessed. A reduction in the effective population size of C. mauritiana during the last glaciation maximum was inferred. The distribution of the species was reduced on the western side of the island, due to low rainfall. It appeared that a major reduction in rainfall and a slight temperature decrease prevailed in the SWIO. Our findings indicated that analyses on the current patterns of intraspecific genetic variations can efficiently contribute to past climatic changes characterisation in remote islands. Identifying area with higher resilience in oceanic islands could provide guidance in forest management and conservation faced to the global climate change.
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Affiliation(s)
- Edith Garot
- IRD, University of Montpellier, DIADE, 34394, Montpellier, France
| | - Thierry Joët
- IRD, University of Montpellier, DIADE, 34394, Montpellier, France
| | | | - Dany Severac
- MGX, University of Montpellier, CNRS, INSERM, 34095, Montpellier, France
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30
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Roos C, Kothe M, Alba DM, Delson E, Zinner D. The radiation of macaques out of Africa: Evidence from mitogenome divergence times and the fossil record. J Hum Evol 2019; 133:114-132. [DOI: 10.1016/j.jhevol.2019.05.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 04/14/2019] [Accepted: 05/31/2019] [Indexed: 01/30/2023]
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31
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Multigene fossil-calibrated analysis of the African lampeyes (Cyprinodontoidei: Procatopodidae) reveals an early Oligocene origin and Neogene diversification driven by palaeogeographic and palaeoclimatic events. ORG DIVERS EVOL 2019. [DOI: 10.1007/s13127-019-00396-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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32
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Ley AC, Herzog P, Lachmuth S, Abwe AE, Christian MF, Sesink Clee PR, Abwe EE, Morgan BJ, Gonder MK. Phenotypic variability along a climatic gradient in a perennial afrotropical rainforest understorey herb. Basic Appl Ecol 2018. [DOI: 10.1016/j.baae.2018.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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33
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Tosso F, Hardy OJ, Doucet JL, Daïnou K, Kaymak E, Migliore J. Evolution in the Amphi-Atlantic tropical genus Guibourtia (Fabaceae, Detarioideae), combining NGS phylogeny and morphology. Mol Phylogenet Evol 2017; 120:83-93. [PMID: 29222064 DOI: 10.1016/j.ympev.2017.11.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 11/22/2017] [Accepted: 11/30/2017] [Indexed: 11/16/2022]
Abstract
Tropical rain forests support a remarkable diversity of tree species, questioning how and when this diversity arose. The genus Guibourtia (Fabaceae, Detarioideae), characterized by two South American and 13 African tree species growing in various tropical biomes, is an interesting model to address the role of biogeographic processes and adaptation to contrasted environments on species diversification. Combining whole plastid genome sequencing and morphological characters analysis, we studied the timing of speciation and diversification processes in Guibourtia through molecular dating and ancestral habitats reconstruction. All species except G. demeusei and G. copallifera appear monophyletic. Dispersal from Africa to America across the Atlantic Ocean is the most plausible hypothesis to explain the occurrence of Neotropical Guibourtia species, which diverged ca. 11.8 Ma from their closest African relatives. The diversification of the three main clades of African Guibourtia is concomitant to Miocene global climate changes, highlighting pre-Quaternary speciation events. These clades differ by their reproductive characters, which validates the three subgenera previously described: Pseudocopaiva, Guibourtia and Gorskia. Within most monophyletic species, plastid lineages start diverging from each other during the Pliocene or early Pleistocene, suggesting that these species already arose during this period. The multiple transitions between rain forests and dry forests/savannahs inferred here through the plastid phylogeny in each Guibourtia subgenus address thus new questions about the role of phylogenetic relationships in shaping ecological niche and morphological similarity among taxa.
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Affiliation(s)
- Félicien Tosso
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, B-5030 Gembloux, Belgium; Evolutionary Biology and Ecology Unit CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. Roosevelt, B-1050 Brussels, Belgium.
| | - Olivier J Hardy
- Evolutionary Biology and Ecology Unit CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. Roosevelt, B-1050 Brussels, Belgium.
| | - Jean-Louis Doucet
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, B-5030 Gembloux, Belgium.
| | - Kasso Daïnou
- Nature + asbl / TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, 5030 Gembloux, Belgium; BIOSE Department, Management of Forest Resources, Gembloux Agro-Bio Tech, Université de Liège, Passage des Déportés 2, B-5030 Gembloux, Belgium; Université Nationale d'Agriculture, BP 43 Kétou, Benin.
| | - Esra Kaymak
- Evolutionary Biology and Ecology Unit CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. Roosevelt, B-1050 Brussels, Belgium.
| | - Jérémy Migliore
- Evolutionary Biology and Ecology Unit CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. Roosevelt, B-1050 Brussels, Belgium.
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Bell RC, Parra JL, Badjedjea G, Barej MF, Blackburn DC, Burger M, Channing A, Dehling JM, Greenbaum E, Gvoždík V, Kielgast J, Kusamba C, Lötters S, McLaughlin PJ, Nagy ZT, Rödel M, Portik DM, Stuart BL, VanDerWal J, Zassi‐Boulou AG, Zamudio KR. Idiosyncratic responses to climate‐driven forest fragmentation and marine incursions in reed frogs from Central Africa and the Gulf of Guinea Islands. Mol Ecol 2017; 26:5223-5244. [DOI: 10.1111/mec.14260] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 07/03/2017] [Accepted: 07/12/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Rayna C. Bell
- Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington DC USA
- Museum of Vertebrate Zoology University of California, Berkeley CA USA
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
| | - Juan L. Parra
- Grupo de Ecología y Evolución de Vertebrados Instituto de Biología Universidad de Antioquia Medellín Colombia
| | - Gabriel Badjedjea
- Département d'Ecologie et Biodiversité des ressources Aquatiques Centre de Surveillance de la Biodiversité Kisangani Democratic Republic of the Congo
| | - Michael F. Barej
- Museum für Naturkunde ‐ Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
| | - David C. Blackburn
- Florida Museum of Natural History University of Florida Gainesville FL USA
- Department of Herpetology California Academy of Sciences San Francisco CA USA
| | - Marius Burger
- African Amphibian Conservation Research Group Unit for Environmental Sciences and Management North‐West University Potchefstroom South Africa
- Flora Fauna & Man, Ecological Services Ltd. Tortola British Virgin Islands
| | - Alan Channing
- Biodiversity and Conservation Biology Department University of the Western Cape Bellville South Africa
| | - Jonas Maximilian Dehling
- Abteilung Biologie Institut für Integrierte Naturwissenschaften Universität Koblenz‐Landau Koblenz Germany
| | - Eli Greenbaum
- Department of Biological Sciences University of Texas at El Paso El Paso TX USA
| | - Václav Gvoždík
- Institute of Vertebrate Biology Czech Academy of Sciences Brno Czech Republic
- Department of Zoology National Museum Prague Czech Republic
| | - Jos Kielgast
- Section of Freshwater Biology Department of Biology University of Copenhagen Copenhagen Denmark
- Center for Macroecology, Evolution and Climate Natural History Museum of Denmark Copenhagen Denmark
| | - Chifundera Kusamba
- Laboratoire d'Herpétologie Département de Biologie Centre de Recherche en Sciences Naturelles Lwiro Democratic Republic of the Congo
| | | | | | - Zoltán T. Nagy
- Museum für Naturkunde ‐ Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
- Royal Belgian Institute of Natural Sciences Brussels Belgium
| | - Mark‐Oliver Rödel
- Museum für Naturkunde ‐ Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
| | - Daniel M. Portik
- Museum of Vertebrate Zoology University of California, Berkeley CA USA
- Department of Biology University of Texas Arlington TX USA
| | | | - Jeremy VanDerWal
- Centre for Tropical Biodiveristy & Climate Change College of Science and Engineering James Cook University Townsville Qld Australia
- Division of Research and Innovation eResearch Centre James Cook University Townsville Qld Australia
| | | | - Kelly R. Zamudio
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
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Torroba-Balmori P, Budde KB, Heer K, González-Martínez SC, Olsson S, Scotti-Saintagne C, Casalis M, Sonké B, Dick CW, Heuertz M. Altitudinal gradients, biogeographic history and microhabitat adaptation affect fine-scale spatial genetic structure in African and Neotropical populations of an ancient tropical tree species. PLoS One 2017; 12:e0182515. [PMID: 28771629 PMCID: PMC5542443 DOI: 10.1371/journal.pone.0182515] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/08/2017] [Indexed: 01/08/2023] Open
Abstract
The analysis of fine-scale spatial genetic structure (FSGS) within populations can provide insights into eco-evolutionary processes. Restricted dispersal and locally occurring genetic drift are the primary causes for FSGS at equilibrium, as described in the isolation by distance (IBD) model. Beyond IBD expectations, spatial, environmental or historical factors can affect FSGS. We examined FSGS in seven African and Neotropical populations of the late-successional rain forest tree Symphonia globulifera L. f. (Clusiaceae) to discriminate the influence of drift-dispersal vs. landscape/ecological features and historical processes on FSGS. We used spatial principal component analysis and Bayesian clustering to assess spatial genetic heterogeneity at SSRs and examined its association with plastid DNA and habitat features. African populations (from Cameroon and São Tomé) displayed a stronger FSGS than Neotropical populations at both marker types (mean Sp = 0.025 vs. Sp = 0.008 at SSRs) and had a stronger spatial genetic heterogeneity. All three African populations occurred in pronounced altitudinal gradients, possibly restricting animal-mediated seed dispersal. Cyto-nuclear disequilibria in Cameroonian populations also suggested a legacy of biogeographic history to explain these genetic patterns. Conversely, Neotropical populations exhibited a weaker FSGS, which may reflect more efficient wide-ranging seed dispersal by Neotropical bats and other dispersers. The population from French Guiana displayed an association of plastid haplotypes with two morphotypes characterized by differential habitat preferences. Our results highlight the importance of the microenvironment for eco-evolutionary processes within persistent tropical tree populations.
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Affiliation(s)
- Paloma Torroba-Balmori
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, Madrid, Spain
- Sustainable Forest Management Research Institute, University of Valladolid - INIA, Palencia, Spain
| | | | - Katrin Heer
- Institute of Experimental Ecology, University of Ulm, Ulm, Germany
- Conservation Biology and Ecology, University of Marburg, Marburg, Germany
| | - Santiago C. González-Martínez
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, Madrid, Spain
- Sustainable Forest Management Research Institute, University of Valladolid - INIA, Palencia, Spain
- UMR BIOGECO, INRA, University of Bordeaux, Cestas, France
| | - Sanna Olsson
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, Madrid, Spain
| | | | | | - Bonaventure Sonké
- Ecole Normale Supérieure, Université de Yaoundé I, Yaoundé, Cameroon
- Evolutionary Biology and Ecology, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
| | - Christopher W. Dick
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Smithsonian Tropical Research Institute, Republic of Panama
| | - Myriam Heuertz
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, Madrid, Spain
- UMR BIOGECO, INRA, University of Bordeaux, Cestas, France
- Evolutionary Biology and Ecology, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
- * E-mail:
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36
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de la Estrella M, Forest F, Wieringa JJ, Fougère-Danezan M, Bruneau A. Insights on the evolutionary origin of Detarioideae, a clade of ecologically dominant tropical African trees. THE NEW PHYTOLOGIST 2017; 214:1722-1735. [PMID: 28323330 DOI: 10.1111/nph.14523] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 02/13/2017] [Indexed: 06/06/2023]
Abstract
African tropical forests are generally considered less diverse than their Neotropical and Asian counterparts. By contrast, the Detarioideae is much more diverse in Africa than in South America and Asia. To better understand the evolution of this contrasting diversity pattern, we investigated the biogeographical and ecological origin of this subfamily, testing whether they originated in dry biomes surrounding the Tethys Seaway as currently hypothesized for many groups of Leguminosae. We constructed the largest time-calibrated phylogeny for the subfamily to date, reconstructed ancestral states for geography and biome/habitat, estimated diversification and extinction rates, and evaluated biome/habitat and geographic shifts in Detarioideae. The ancestral habitat of Detarioideae is postulated to be a primary forest (terra firme) originated in Africa-South America, in the early Palaeocene, after which several biome/habitat and geographic shifts occurred. The origin of Detarioideae is older than previous estimates, which postulated a dry (succulent) biome origin according to the Tethys Seaway hypothesis, and instead we reveal a post Gondwana and terra firme origin for this early branching clade of legumes. Detarioideae include some of the most dominant trees in evergreen forests and have likely played a pivotal role in shaping continental African forest diversity.
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Affiliation(s)
- Manuel de la Estrella
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK
- Institut de recherche en biologie végétale and Département de Sciences biologiques, Université de Montréal, 4101 Sherbrooke est, Montréal, QC, H1X 2B2, Canada
| | - Félix Forest
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK
| | - Jan J Wieringa
- Naturalis Biodiversity Centre, National Herbarium of the Netherlands, Darwinweg 2, 2333, CR Leiden, the Netherlands
| | - Marie Fougère-Danezan
- Institut de recherche en biologie végétale and Département de Sciences biologiques, Université de Montréal, 4101 Sherbrooke est, Montréal, QC, H1X 2B2, Canada
- Université de Toulouse, EDB (Laboratoire Evolution et Diversité Biologique), UMR5174, F-31062, Toulouse, France
- CNRS, UPS, EDB (Laboratoire Evolution et Diversité Biologique), UMR5174, 118 route de Narbonne, F-31062, Toulouse, France
| | - Anne Bruneau
- Institut de recherche en biologie végétale and Département de Sciences biologiques, Université de Montréal, 4101 Sherbrooke est, Montréal, QC, H1X 2B2, Canada
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37
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Eberle J, Rödder D, Beckett M, Ahrens D. Landscape genetics indicate recently increased habitat fragmentation in African forest-associated chafers. GLOBAL CHANGE BIOLOGY 2017; 23:1988-2004. [PMID: 28063178 DOI: 10.1111/gcb.13616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 11/22/2016] [Accepted: 12/14/2016] [Indexed: 06/06/2023]
Abstract
Today, indigenous forests cover less than 0.6% of South Africa's land surface and are highly fragmented. Most forest relicts are very small and typically occur in fire-protected gorges along the eastern Great Escarpment. Yet, they hold a unique and valuable fauna with high endemism and ancient phylogenetic lineages, fostered by long-term climatic stability and complex microclimates. Despite numerous studies on southern African vegetation cover, the current state of knowledge about the natural extension of indigenous forests is rather fragmentary. We use an integrated approach of population-level phylogeography and climatic niche modeling of forest-associated chafer species to assess connectivity and extent of forest habitats since the last glacial maximum. Current and past species distribution models ascertained potential fluctuations of forest distribution and supported a much wider potential current extension of forests based on climatic data. Considerable genetic admixture of mitochondrial and nuclear DNA among many populations and an increase in mean population mutation rate in Extended Bayesian Skyline Plots of all species indicated more extended or better connected forests in the recent past (<5 kya). Genetic isolation of certain populations, as revealed by population differentiation statistics (GST'), as well as landscape connectivity statistics and habitat succession scenarios suggests considerable loss of habitat connectivity. As major anthropogenic influence is likely, conservational actions need to be considered.
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Affiliation(s)
- Jonas Eberle
- Zoologisches Forschungsmuseum A. Koenig, Centre of Taxonomy and Evolutionary Research, Adenauerallee 160, 53113, Bonn, Germany
| | - Dennis Rödder
- Zoologisches Forschungsmuseum A. Koenig, Centre of Taxonomy and Evolutionary Research, Adenauerallee 160, 53113, Bonn, Germany
| | - Marc Beckett
- Zoologisches Forschungsmuseum A. Koenig, Centre of Taxonomy and Evolutionary Research, Adenauerallee 160, 53113, Bonn, Germany
| | - Dirk Ahrens
- Zoologisches Forschungsmuseum A. Koenig, Centre of Taxonomy and Evolutionary Research, Adenauerallee 160, 53113, Bonn, Germany
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38
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Donkpegan ASL, Doucet JL, Migliore J, Duminil J, Dainou K, Piñeiro R, Wieringa JJ, Champluvier D, Hardy OJ. Evolution in African tropical trees displaying ploidy-habitat association: The genus Afzelia (Leguminosae). Mol Phylogenet Evol 2016; 107:270-281. [PMID: 27825871 DOI: 10.1016/j.ympev.2016.11.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 10/26/2016] [Accepted: 11/04/2016] [Indexed: 11/30/2022]
Abstract
Polyploidy has rarely been documented in rain forest trees but it has recently been found in African species of the genus Afzelia (Leguminosae), which is composed of four tetraploid rain forest species and two diploid dry forest species. The genus Afzelia thus provides an opportunity to examine how and when polyploidy and habitat shift occurred in Africa, and whether they are associated. In this study, we combined three plastid markers (psbA, trnL, ndhF), two nuclear markers (ribosomal ITS and the single-copy PEPC E7 gene), plastomes (obtained by High Throughput Sequencing) and morphological traits, with an extensive taxonomic and geographic sampling to explore the evolutionary history of Afzelia. Both nuclear DNA and morphological vegetative characters separated diploid from tetraploid lineages. Although the two African diploid species were well differentiated genetically and morphologically, the relationships among the tetraploid species were not resolved. In contrast to the nuclear markers, plastid markers revealed that one of the diploid species forms a well-supported clade with the tetraploids, suggesting historical hybridisation, possibly in relation with genome duplication (polyploidization) and habitat shift from dry to rain forests. Molecular dating based on fossil-anchored gene phylogenies indicates that extant Afzelia started diverging c. 14.5 or 20Ma while extant tetraploid species started diverging c. 7.0 or 9.4Ma according to plastid and nuclear DNA, respectively. Additional studies of tropical polyploid plants are needed to assess whether the ploidy-habitat association observed in African Afzelia would reflect a role of polyploidization in niche divergence in the tropics.
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Affiliation(s)
- Armel S L Donkpegan
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liège, 2 Passage des Déportés, B-5030 Gembloux, Belgium; Evolutionary Biology and Ecology Unit CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050 Brussels, Belgium.
| | - Jean-Louis Doucet
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liège, 2 Passage des Déportés, B-5030 Gembloux, Belgium; BIOSE, Management of Forest Resources, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, B-5030, Belgium.
| | - Jérémy Migliore
- Evolutionary Biology and Ecology Unit CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050 Brussels, Belgium.
| | - Jérôme Duminil
- Evolutionary Biology and Ecology Unit CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050 Brussels, Belgium; Bioversity International, c/o CIFOR Central Africa Regional Office P.O. Box 2008 Messa, Yaoundé, Cameroon; Institut de Recherche pour le Développement, UMR-DIADE, BP 64501, 34394 Montpellier, France.
| | - Kasso Dainou
- BIOSE, Management of Forest Resources, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, B-5030, Belgium; Nature+ asbl, Winstar Park, Rue Provinciale 62, 1301, Wavre, Belgium; Université d'Agriculture de Kétou, BP: 43, Kétou, Benin.
| | - Rosalía Piñeiro
- Conservation, Jodrell Laboratory, Royal Botanic Gardens, Kew, TW9 3DS, Richmond, Surrey, UK.
| | - Jan J Wieringa
- Naturalis Biodiversity Centre, National Herbarium of The Netherlands, Darwinweg 2, 2333 CR Leiden, The Netherlands.
| | | | - Olivier J Hardy
- Evolutionary Biology and Ecology Unit CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050 Brussels, Belgium.
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Faye A, Deblauwe V, Mariac C, Richard D, Sonké B, Vigouroux Y, Couvreur TLP. Phylogeography of the genus Podococcus (Palmae/Arecaceae) in Central African rain forests: Climate stability predicts unique genetic diversity. Mol Phylogenet Evol 2016; 105:126-138. [PMID: 27521478 DOI: 10.1016/j.ympev.2016.08.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 08/08/2016] [Accepted: 08/09/2016] [Indexed: 11/16/2022]
Abstract
The tropical rain forests of Central Africa contain high levels of species diversity. Paleovegetation or biodiversity patterns suggested successive contraction/expansion phases on this rain forest cover during the last glacial maximum (LGM). Consequently, the hypothesis of the existence of refugia e.g. habitat stability that harbored populations during adverse climatic periods has been proposed. Understory species are tightly associated to forest cover and consequently are ideal markers of forest dynamics. Here, we used two central African rain forest understory species of the palm genus, Podococcus, to assess the role of past climate variation on their distribution and genetic diversity. Species distribution modeling in the present and at the LGM was used to estimate areas of climatic stability. Genetic diversity and phylogeography were estimated by sequencing near complete plastomes for over 120 individuals. Areas of climatic stability were mainly located in mountainous areas like the Monts de Cristal and Monts Doudou in Gabon, but also lowland coastal forests in southeast Cameroon and northeast Gabon. Genetic diversity analyses shows a clear North-South structure of genetic diversity within one species. This divide was estimated to have originated some 500,000years ago. We show that, in Central Africa, high and unique genetic diversity is strongly correlated with inferred areas of climatic stability since the LGM. Our results further highlight the importance of coastal lowland rain forests in Central Africa as harboring not only high species diversity but also important high levels of unique genetic diversity. In the context of strong human pressure on coastal land use and destruction, such unique diversity hotspots need to be considered in future conservation planning.
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Affiliation(s)
- A Faye
- Institut de Recherche pour le Développement, UMR-DIADE, BP 64501, F-34394 Montpellier cedex 5, France; Université de Yaoundé I, Ecole Normale Supérieure, Département des Sciences Biologiques, Laboratoire de Botanique systématique et d'Ecologie, B.P. 047, Yaoundé, Cameroon.
| | - V Deblauwe
- Institut de Recherche pour le Développement, UMR-DIADE, BP 64501, F-34394 Montpellier cedex 5, France; Université de Yaoundé I, Ecole Normale Supérieure, Département des Sciences Biologiques, Laboratoire de Botanique systématique et d'Ecologie, B.P. 047, Yaoundé, Cameroon
| | - C Mariac
- Institut de Recherche pour le Développement, UMR-DIADE, BP 64501, F-34394 Montpellier cedex 5, France
| | - D Richard
- Institut de Recherche pour le Développement, UMR-DIADE, BP 64501, F-34394 Montpellier cedex 5, France
| | - B Sonké
- Université de Yaoundé I, Ecole Normale Supérieure, Département des Sciences Biologiques, Laboratoire de Botanique systématique et d'Ecologie, B.P. 047, Yaoundé, Cameroon
| | - Y Vigouroux
- Institut de Recherche pour le Développement, UMR-DIADE, BP 64501, F-34394 Montpellier cedex 5, France
| | - T L P Couvreur
- Institut de Recherche pour le Développement, UMR-DIADE, BP 64501, F-34394 Montpellier cedex 5, France; Université de Yaoundé I, Ecole Normale Supérieure, Département des Sciences Biologiques, Laboratoire de Botanique systématique et d'Ecologie, B.P. 047, Yaoundé, Cameroon; Naturalis Biodiversity Centre, Botany Section, Darwinweg 2, 2333 CR Leiden, The Netherlands
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Dowell SA, Portik DM, de Buffrénil V, Ineich I, Greenbaum E, Kolokotronis SO, Hekkala ER. Molecular data from contemporary and historical collections reveal a complex story of cryptic diversification in the Varanus (Polydaedalus) niloticus Species Group. Mol Phylogenet Evol 2016; 94:591-604. [DOI: 10.1016/j.ympev.2015.10.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 09/09/2015] [Accepted: 10/06/2015] [Indexed: 11/16/2022]
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Kindler C, Moosig M, Branch WR, Harvey J, Kehlmaier C, Nagy ZT, Prokop H, Široký P, Fritz U. Comparative phylogeographies of six species of hinged terrapins (Pelusiosspp.) reveal discordant patterns and unexpected differentiation in theP. castaneus/P. chapinicomplex andP. rhodesianus. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12647] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Carolin Kindler
- Museum of Zoology; Senckenberg Dresden; A. B. Meyer Building Dresden 01109 Germany
| | - Maggie Moosig
- Museum of Zoology; Senckenberg Dresden; A. B. Meyer Building Dresden 01109 Germany
| | - William R. Branch
- Department of Herpetology; Port Elizabeth Museum; P.O. Box 13147 Humewood 6013 South Africa
- Department of Zoology; Nelson Mandela Metropolitan University; P.O. Box 77000 Port Elizabeth 6031 South Africa
| | - James Harvey
- 35 Carbis Road Pietermaritzburg 3201 South Africa
| | - Christian Kehlmaier
- Museum of Zoology; Senckenberg Dresden; A. B. Meyer Building Dresden 01109 Germany
| | - Zoltán T. Nagy
- Royal Belgian Institute of Natural Sciences; JEMU; Rue Vautier 29 Brussels 1000 Belgium
| | | | - Pavel Široký
- Department of Biology and Wildlife Diseases; Faculty of Veterinary Hygiene and Ecology; University of Veterinary and Pharmaceutical Sciences Brno; Palackého tř. 1/3 Brno 612 42 Czech Republic
| | - Uwe Fritz
- Museum of Zoology; Senckenberg Dresden; A. B. Meyer Building Dresden 01109 Germany
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Bostoen K, Clist B, Doumenge C, Grollemund R, Hombert JM, Muluwa JK, Maley J. Middle to Late Holocene Paleoclimatic Change and the Early Bantu Expansion in the Rain Forests of Western Central Africa. CURRENT ANTHROPOLOGY 2015. [DOI: 10.1086/681436] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Mairal M, Pokorny L, Aldasoro JJ, Alarcón M, Sanmartín I. Ancient vicariance and climate-driven extinction explain continental-wide disjunctions in Africa: the case of the Rand Flora genusCanarina(Campanulaceae). Mol Ecol 2015; 24:1335-54. [DOI: 10.1111/mec.13114] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 02/10/2015] [Accepted: 02/11/2015] [Indexed: 01/17/2023]
Affiliation(s)
- M. Mairal
- Real Jardín Botánico (RJB-CSIC); 28014 Madrid Spain
| | - L. Pokorny
- Real Jardín Botánico (RJB-CSIC); 28014 Madrid Spain
| | - J. J. Aldasoro
- Institut Botànic de Barcelona (IBB-CSIC); 08038 Barcelona Spain
| | - M. Alarcón
- Institut Botànic de Barcelona (IBB-CSIC); 08038 Barcelona Spain
| | - I. Sanmartín
- Real Jardín Botánico (RJB-CSIC); 28014 Madrid Spain
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Mitchell MW, Locatelli S, Sesink Clee PR, Thomassen HA, Gonder MK. Environmental variation and rivers govern the structure of chimpanzee genetic diversity in a biodiversity hotspot. BMC Evol Biol 2015; 15:1. [PMID: 25608511 PMCID: PMC4314796 DOI: 10.1186/s12862-014-0274-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 12/15/2014] [Indexed: 11/13/2022] Open
Abstract
Background The mechanisms that underlie the diversification of tropical animals remain poorly understood, but new approaches that combine geo-spatial modeling with spatially explicit genetic data are providing fresh insights on this topic. Data about the diversification of tropical mammals remain particularly sparse, and vanishingly few opportunities exist to study endangered large mammals that increasingly exist only in isolated pockets. The chimpanzees of Cameroon represent a unique opportunity to examine the mechanisms that promote genetic differentiation in tropical mammals because the region is home to two chimpanzee subspecies: Pan troglodytes ellioti and P. t. trogolodytes. Their ranges converge in central Cameroon, which is a geographically, climatically and environmentally complex region that presents an unparalleled opportunity to examine the roles of rivers and/or environmental variation in influencing the evolution of chimpanzee populations. Results We analyzed microsatellite genotypes and mtDNA HVRI sequencing data from wild chimpanzees sampled at a fine geographic scale across Cameroon and eastern Nigeria using a spatially explicit approach based upon Generalized Dissimilarity Modeling. Both the Sanaga River and environmental variation were found to contribute to driving separation of the subspecies. The importance of environmental variation differed among subspecies. Gene-environment associations were weak in P. t. troglodytes, whereas environmental variation was found to play a much larger role in shaping patterns of genetic differentiation in P. t. ellioti. Conclusions We found that both the Sanaga River and environmental variation likely play a role in shaping patterns of chimpanzee genetic diversity. Future studies using single nucleotide polymorphism (SNP) data are necessary to further understand how rivers and environmental variation contribute to shaping patterns of genetic variation in chimpanzees. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0274-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew W Mitchell
- Department of Biology, Drexel University, Philadelphia 19104, Pennsylvania, USA.
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The population genetics of wild chimpanzees in Cameroon and Nigeria suggests a positive role for selection in the evolution of chimpanzee subspecies. BMC Evol Biol 2015; 15:3. [PMID: 25608610 PMCID: PMC4314757 DOI: 10.1186/s12862-014-0276-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 12/15/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chimpanzees (Pan troglodytes) can be divided into four subspecies. Substantial phylogenetic evidence suggests that these subspecies can be grouped into two distinct lineages: a western African group that includes P. t. verus and P. t. ellioti and a central/eastern African group that includes P. t. troglodytes and P. t. schweinfurthii. The geographic division of these two lineages occurs in Cameroon, where the rages of P. t. ellioti and P. t. troglodytes appear to converge at the Sanaga River. Remarkably, few population genetic studies have included wild chimpanzees from this region. RESULTS We analyzed microsatellite genotypes of 187 wild, unrelated chimpanzees, and mitochondrial control region sequencing data from 604 chimpanzees. We found that chimpanzees in Cameroon and eastern Nigeria comprise at least two, and likely three populations. Both the mtDNA and microsatellite data suggest that there is a primary separation of P. t. troglodytes in southern Cameroon from P. t. ellioti north and west of the Sanaga River. These two populations split ~200-250 thousand years ago (kya), but have exchanged one migrant per generation since separating. In addition, P. t. ellioti consists of two populations that split from one another ~4 kya. One population is located in the rainforests of western Cameroon and eastern Nigeria, whereas the second population appears to be confined to a savannah-woodland mosaic in central Cameroon. CONCLUSIONS Our findings suggest that there are as many as three genetically distinct populations of chimpanzees in Cameroon and eastern Nigeria. P. t. troglodytes in southern Cameroon comprises one population that is separated from two populations of P. t. ellioti in western and central Cameroon, respectively. P. t. ellioti and P. t. troglodytes appear to be characterized by a pattern of isolation-with-migration, and thus, we propose that neutral processes alone can not explain the differentiation of P. t. ellioti and P. t. troglodytes.
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Kadu CAC, Konrad H, Schueler S, Muluvi GM, Eyog-Matig O, Muchugi A, Williams VL, Ramamonjisoa L, Kapinga C, Foahom B, Katsvanga C, Hafashimana D, Obama C, Geburek T. Divergent pattern of nuclear genetic diversity across the range of the Afromontane Prunus africana mirrors variable climate of African highlands. ANNALS OF BOTANY 2013; 111:47-60. [PMID: 23250908 PMCID: PMC3523648 DOI: 10.1093/aob/mcs235] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 10/01/2012] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Afromontane forest ecosystems share a high similarity of plant and animal biodiversity, although they occur mainly on isolated mountain massifs throughout the continent. This resemblance has long provoked questions on former wider distribution of Afromontane forests. In this study Prunus africana (one of the character trees of Afromontane forests) is used as a model for understanding the biogeography of this vegetation zone. METHODS Thirty natural populations from nine African countries covering a large part of Afromontane regions were analysed using six nuclear microsatellites. Standard population genetic analysis as well as Bayesian and maximum likelihood models were used to infer genetic diversity, population differentiation, barriers to gene flow, and recent and all migration among populations. KEY RESULTS Prunus africana exhibits strong divergence among five main Afromontane regions: West Africa, East Africa west of the Eastern Rift Valley (ERV), East Africa east of the ERV, southern Africa and Madagascar. The strongest divergence was evident between Madagascar and continental Africa. Populations from West Africa showed high similarity with East African populations west of the ERV, whereas populations east of the ERV are closely related to populations of southern Africa, respectively. CONCLUSIONS The observed patterns indicate divergent population history across the continent most likely associated to Pleistocene changes in climatic conditions. The high genetic similarity between populations of West Africa with population of East Africa west of the ERV is in agreement with faunistic and floristic patterns and provides further evidence for a historical migration route. Contrasting estimates of recent and historical gene flow indicate a shift of the main barrier to gene flow from the Lake Victoria basin to the ERV, highlighting the dynamic environmental and evolutionary history of the region.
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Affiliation(s)
- Caroline A. C. Kadu
- Federal Research and Training Centre for Forests, Natural Hazards and Landscape (BFW), Department of Forest Genetics, Hauptstraße 7, A-1140 Vienna, Austria
- Kenyatta University, PO Box 43844, Nairobi, Kenya
| | - Heino Konrad
- Federal Research and Training Centre for Forests, Natural Hazards and Landscape (BFW), Department of Forest Genetics, Hauptstraße 7, A-1140 Vienna, Austria
| | - Silvio Schueler
- Federal Research and Training Centre for Forests, Natural Hazards and Landscape (BFW), Department of Forest Genetics, Hauptstraße 7, A-1140 Vienna, Austria
| | | | - Oscar Eyog-Matig
- Bioversity International SSA, c/o CIFOR Regional Office, PO Box 2008, Messa, Yaounde, Cameroon
| | | | - Vivienne L. Williams
- School of Animal, Plant & Environmental Sciences, University of the Witwatersrand, Private Bag 3, Wits 2050, Johannesburg, South Africa
| | - Lolona Ramamonjisoa
- Silo National des Graines Forestieres (SNGF), PO Box 5091, Antananarivo-101, Madagascar
| | - Consolatha Kapinga
- Tanzania Forestry Research Institute (TAFORI), PO Box 1854, Morogoro, Tanzania
| | - Bernard Foahom
- Institute of Agricultural Research for Development (IRAD), PO Box 2123 or 2067, Yaounde, Cameroon
| | - Cuthbert Katsvanga
- Faculty of Agriculture and Environmental Science (Forestry Unit), Bindura University of Science Education, P. Bag 1020, Bindura, Zimbabwe
| | - David Hafashimana
- National Forestry Resources Research Institute (NaFORRI), PO Box 1752, Kampala, Uganda
| | - Crisantos Obama
- Coordinador Nacional de la COMIFAC Ministerio de Agricultura y Bosques BP 207, Bata, Equatorial Guinea
| | - Thomas Geburek
- Federal Research and Training Centre for Forests, Natural Hazards and Landscape (BFW), Department of Forest Genetics, Hauptstraße 7, A-1140 Vienna, Austria
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Zinner D, Wertheimer J, Liedigk R, Groeneveld LF, Roos C. Baboon phylogeny as inferred from complete mitochondrial genomes. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012. [PMID: 23180628 PMCID: PMC3572579 DOI: 10.1002/ajpa.22185] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Baboons (genus Papio) are an interesting phylogeographical primate model for the evolution of savanna species during the Pleistocene. Earlier studies, based on partial mitochondrial sequence information, revealed seven major haplogroups indicating multiple para- and polyphylies among the six baboon species. The most basal splits among baboon lineages remained unresolved and the credibility intervals for divergence time estimates were rather large. Assuming that genetic variation within the two studied mitochondrial loci so far was insufficient to infer the apparently rapid early radiation of baboons we used complete mitochondrial sequence information of ten specimens, representing all major baboon lineages, to reconstruct a baboon phylogeny and to re-estimate divergence times. Our data confirmed the earlier tree topology including the para- and polyphyletic relationships of most baboon species; divergence time estimates are slightly younger and credibility intervals narrowed substantially, thus making the estimates more precise. However, the most basal relationships could not be resolved and it remains open whether (1) the most southern population of baboons diverged first or (2) a major split occurred between southern and northern clades. Our study shows that complete mitochondrial genome sequences are more effective to reconstruct robust phylogenies and to narrow down estimated divergence time intervals than only short portions of the mitochondrial genome, although there are also limitations in resolving phylogenetic relationships. Am J Phys Anthropol, 2013. © 2012 Wiley Periodicals, Inc.
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Affiliation(s)
- Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Göttingen, Germany.
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BEN FALEH ABDERRAOUF, GRANJON LAURENT, TATARD CAROLINE, BORATYŃSKI ZBYSZEK, COSSON JEANFRANCOIS, SAID KHALED. Phylogeography of two cryptic species of African desert jerboas (Dipodidae: Jaculus). Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01920.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Nicolas V, Missoup AD, Colyn M, Cruaud C, Denys C. West-Central African Pleistocene Lowland Forest Evolution Revealed by the Phylogeography of Misonne's Soft-Furred Mouse. AFRICAN ZOOLOGY 2012. [DOI: 10.3377/004.047.0119] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Junker K, Lhermitte-Vallarino N, Barbuto M, Ineich I, Wanji S, Bain O. New species of Rhabdias (Nematoda: Rhabdiasidae) from Afrotropical anurans, including molecular evidence and notes on biology. Folia Parasitol (Praha) 2010; 57:47-61. [DOI: 10.14411/fp.2010.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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