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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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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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Lompo D, Vinceti B, Konrad H, Gaisberger H, Geburek T. Phylogeography of African Locust Bean (Parkia biglobosa) Reveals Genetic Divergence and Spatially Structured Populations in West and Central Africa. J Hered 2019; 109:811-824. [PMID: 30247720 PMCID: PMC6208456 DOI: 10.1093/jhered/esy047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 09/20/2018] [Indexed: 01/03/2023] Open
Abstract
The evolutionary history of African savannah tree species is crucial for the management of their genetic resources. In this study, we investigated the phylogeography of Parkia biglobosa and its modeled distribution under past and present climate conditions. This tree species is very valued and widespread in West Africa, providing edible and medicinal products. A large sample of 1610 individuals from 84 populations, distributed across 12 countries in Western and Central Africa, were genotyped using 8 nuclear microsatellites. Individual-based assignments clearly distinguished 3 genetic clusters, extreme West Africa (EWA), center of West Africa (CWA), and Central Africa (CA). Overall, estimates of genetic diversity were moderate to high, with lower values for populations in EWA (allelic richness after rarefaction [AR] = 6.4, expected heterozygosity [HE] = 0.78, and observed heterozygosity [HO] = 0.7) and CA (AR = 5.9, HE = 0.67, and HO = 0.61) compared with populations in CWA (AR = 7.3, HE = 0.79, and HO = 0.75). The overall population differentiation was found to be moderate (FST = 0.09). A highly significant isolation by distance pattern was detected, with a marked phylogeographic signature suggesting possible effects of past climate and geographic barriers to migration. Modeling the potential distribution of the species showed a contraction during the last glaciations followed by expansion events. The exploratory approximate Bayesian computation conducted suggests a best-supported scenario in which the cluster CWA traced back to the ancestral populations and a first split between EWA and CWA took place about 160000 years before present (BP), then a second split divided CA and CWA, about 100000 years BP. However, our genetic data do not enable us to conclusively distinguish among a few alternative possible scenarios.
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Affiliation(s)
- Djingdia Lompo
- Centre National de Semences Forestières, Ouagadougou, Burkina Faso
| | | | - Heino Konrad
- Austrian Research and Training Centre for Forests, Department of Forest Genetics, Vienna, Austria
| | | | - Thomas Geburek
- Austrian Research and Training Centre for Forests, Department of Forest Genetics, Vienna, Austria
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Rossetti DF, Gribel R, Toledo PM, Tatumi SH, Yee M, Tudela DRG, Munita CS, de Souza Coelho L. Unfolding long-term Late Pleistocene-Holocene disturbances of forest communities in the southwestern Amazonian lowlands. Ecosphere 2018. [DOI: 10.1002/ecs2.2457] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Dilce F. Rossetti
- Brazilian Institute for Space Research-INPE; Rua dos Astronautas 1758 São José dos Campos SP 12245-970 Brazil
| | - Rogério Gribel
- Coordination of Biodiversity; Brazilian National Institute of Amazonian Research-INPA; Av. André Araújo 2936 Manaus AM 69067-375 Brazil
| | - Peter M. Toledo
- Brazilian Institute for Space Research-INPE; Rua dos Astronautas 1758 São José dos Campos SP 12245-970 Brazil
| | | | - Márcio Yee
- Federal University of São Paulo; Santos SP 11070-100 Brazil
| | | | | | - Luiz de Souza Coelho
- Coordination of Biodiversity; Brazilian National Institute of Amazonian Research-INPA; Av. André Araújo 2936 Manaus AM 69067-375 Brazil
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5
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Demenou BB, Doucet JL, Hardy OJ. History of the fragmentation of the African rain forest in the Dahomey Gap: insight from the demographic history of Terminalia superba. Heredity (Edinb) 2018; 120:547-561. [PMID: 29279603 PMCID: PMC5943585 DOI: 10.1038/s41437-017-0035-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 11/02/2017] [Accepted: 11/06/2017] [Indexed: 11/08/2022] Open
Abstract
Paleo-environmental reconstructions show that the distribution of tropical African rain forests was affected by Quaternary climate changes. They suggest that the Dahomey Gap (DG)-the savanna corridor that currently separates Upper Guinean (UG, West Africa) and Lower Guinean (LG, western Central Africa) rain forest blocks-was forested during the African Humid Holocene period (from at least 9 ka till 4.5 ka), and possibly during other interglacial periods, while an open vegetation developed in the DG under drier conditions, notably during glacial maxima. Nowadays, relics of semi-deciduous forests containing UG and LG forest species are still present within the DG. We used one of these species, the pioneer tree Terminalia superba (Combretaceae), to study past forest fragmentation in the DG and its impact on infraspecific biodiversity. A Bayesian clustering analysis of 299 individuals genotyped at 14 nuclear microsatellites revealed five parapatric genetic clusters (UG, DG, and three in LG) with low to moderate genetic differentiation (Fst from 0.02 to 0.24). Approximate Bayesian Computation analyses inferred a demographic bottleneck around the penultimate glacial period in all populations. They also supported an origin of the DG population by admixture of UG and LG populations around 54,000 (27,600-161,000) years BP, thus before the Last Glacial Maximum. These results contrast with those obtained on Distemonanthus benthamianus where the DG population seems to originate from the Humid Holocene period. We discuss these differences in light of the ecology of each species. Our results challenge the simplistic view linking population fragmentation/expansion with glacial/interglacial periods in African forest species.
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Affiliation(s)
- Boris B Demenou
- Faculté des Sciences, Evolution Biologique et Ecologie, Université Libre de Bruxelles, CP160/12, Av. F. D. Roosevelt 50, B-1050, Brussels, Belgium.
| | - Jean-Louis Doucet
- TERRA Teaching and Research Centre, Central African Forests, BIOSE Department, Gembloux Agro-Bio Tech, Université de Liège, Gembloux, Belgium
| | - Olivier J Hardy
- Faculté des Sciences, Evolution Biologique et Ecologie, Université Libre de Bruxelles, CP160/12, Av. F. D. Roosevelt 50, B-1050, Brussels, Belgium
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Piñeiro R, Dauby G, Kaymak E, Hardy OJ. Pleistocene population expansions of shade-tolerant trees indicate fragmentation of the African rainforest during the Ice Ages. Proc Biol Sci 2018; 284:rspb.2017.1800. [PMID: 29093226 DOI: 10.1098/rspb.2017.1800] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/02/2017] [Indexed: 11/12/2022] Open
Abstract
The fossil record in tropical Africa suggests that dry conditions during the Ice Ages caused expansion of savannahs and contraction of the rainforest. Forest refugia have been proposed to be located in areas of Central Africa that currently harbour high rates of endemic species. However, to what extent the forest was fragmented remains unknown. Nuclear microsatellites and plastid sequences of 732 trees of two species occurring in the same habitat-mature lowland evergreen rainforests-but with remarkably different dispersal capacities-animal versus gravity-were analysed. Geographical information system tools revealed intraspecific lineages partially congruent across the two species, suggesting common past barriers to gene flow in Central Africa. According to approximate Bayesian computation, the intraspecific genetic clusters diverged during the Pleistocene (less than 2 Ma), so that intraspecific differentiation is the appropriate scale to test the aridification effect of the Ice Ages on tree populations. Demographic tests revealed clear genetic signals of population expansion in both taxa, possibly following bottleneck events after forest fragmentation, with stronger evidence of expansion after the Penultimate rather than after the Last Glacial Maximum. The differential dispersal capacity may have modulated the particular response of each species to climate change, as revealed by the stronger evidence of expansion found in the animal-dispersed species than in the gravity-dispersed one.
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Affiliation(s)
- Rosalía Piñeiro
- Université Libre de Bruxelles, Faculté des Sciences, Evolutionary Biology and Ecology, CP160/12, 50 Av. F. Roosevelt, 1050 Brussels, Belgium .,Evolutionary Genomics, Centre for Geogenetics-Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Gilles Dauby
- Université Libre de Bruxelles, Faculté des Sciences, Evolutionary Biology and Ecology, CP160/12, 50 Av. F. Roosevelt, 1050 Brussels, Belgium
| | - Esra Kaymak
- Université Libre de Bruxelles, Faculté des Sciences, Evolutionary Biology and Ecology, CP160/12, 50 Av. F. Roosevelt, 1050 Brussels, Belgium
| | - Olivier J Hardy
- Université Libre de Bruxelles, Faculté des Sciences, Evolutionary Biology and Ecology, CP160/12, 50 Av. F. Roosevelt, 1050 Brussels, Belgium
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Bennett KL, Kaddumukasa M, Shija F, Djouaka R, Misinzo G, Lutwama J, Linton YM, Walton C. Comparative phylogeography of Aedes mosquitoes and the role of past climatic change for evolution within Africa. Ecol Evol 2018; 8:3019-3036. [PMID: 29531714 PMCID: PMC5838080 DOI: 10.1002/ece3.3668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 10/26/2017] [Accepted: 10/27/2017] [Indexed: 01/01/2023] Open
Abstract
The study of demographic processes involved in species diversification and evolution ultimately provides explanations for the complex distribution of biodiversity on earth, indicates regions important for the maintenance and generation of biodiversity, and identifies biological units important for conservation or medical consequence. African and forest biota have both received relatively little attention with regard to understanding their diversification, although one possible mechanism is that this has been driven by historical climate change. To investigate this, we implemented a standard population genetics approach along with Approximate Bayesian Computation, using sequence data from two exon-primed intron-crossing (EPIC) nuclear loci and mitochondrial cytochrome oxidase subunit I, to investigate the evolutionary history of five medically important and inherently forest dependent mosquito species of the genus Aedes. By testing different demographic hypotheses, we show that Aedes bromeliae and Aedes lilii fit the same model of lineage diversification, admixture, expansion, and recent population structure previously inferred for Aedes aegypti. In addition, analyses of population structure show that Aedes africanus has undergone lineage diversification and expansion while Aedes hansfordi has been impacted by population expansion within Uganda. This congruence in evolutionary history is likely to relate to historical climate-driven habitat change within Africa during the late Pleistocene and Holocene epoch. We find differences in the population structure of mosquitoes from Tanzania and Uganda compared to Benin and Uganda which could relate to differences in the historical connectivity of forests across the continent. Our findings emphasize the importance of recent climate change in the evolution of African forest biota.
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Affiliation(s)
- Kelly Louise Bennett
- Faculty of Life SciencesComputational Evolutionary Biology GroupUniversity of ManchesterManchesterUK
| | - Martha Kaddumukasa
- Department of Arbovirology, Emerging and Re‐emerging InfectionsUganda Virus Research InstituteEntebbeUganda
- WITS Institute for Malaria ResearchSchool of Pathology Faculty of Health SciencesUniversity of WitwatersrandParktownJohannesburg
| | - Fortunate Shija
- Faculty of Life SciencesComputational Evolutionary Biology GroupUniversity of ManchesterManchesterUK
- Department of Veterinary Microbiology and ParasitologySokoine University of AgricultureMorogoroTanzania
| | - Rousseau Djouaka
- Agro‐Eco‐Health Platform for West and Central AfricaInternational Institute for Tropical AgricultureCotonouRepublic of Benin
| | - Gerald Misinzo
- Agro‐Eco‐Health Platform for West and Central AfricaInternational Institute for Tropical AgricultureCotonouRepublic of Benin
| | - Julius Lutwama
- Department of Arbovirology, Emerging and Re‐emerging InfectionsUganda Virus Research InstituteEntebbeUganda
| | - Yvonne Marie Linton
- Department of EntomologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDCUSA
- Walter Reed Biosystematics UnitSmithsonian Institution Museum Support CenterSuitlandMDUSA
- Walter Reed Army Institute of ResearchSilver SpringMDUSA
- Uniformed Services University of Health SciencesBethesdaMDUSA
| | - Catherine Walton
- Faculty of Life SciencesComputational Evolutionary Biology GroupUniversity of ManchesterManchesterUK
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8
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Ntie S, Davis AR, Hils K, Mickala P, Thomassen HA, Morgan K, Vanthomme H, Gonder MK, Anthony NM. Evaluating the role of Pleistocene refugia, rivers and environmental variation in the diversification of central African duikers (genera Cephalophus and Philantomba). BMC Evol Biol 2017; 17:212. [PMID: 28877669 PMCID: PMC5585889 DOI: 10.1186/s12862-017-1054-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/18/2017] [Indexed: 12/29/2022] Open
Abstract
Background This study aims to assess the role that Pleistocene refugia, rivers and local habitat conditions may have played in the evolutionary diversification of three central African duiker species (Cephalophus dorsalis, C. callipygus and Philantomba monticola). Genetic data from geo-referenced feces were collected from a wide range of sites across Central Africa. Historical patterns of population genetic structure were assessed using a ~ 650 bp fragment of the mitochondrial control region and contemporary patterns of genetic differentiation were evaluated using 12 polymorphic microsatellite loci. Results Mitochondrial analyses revealed that populations of C. callipygus and P. monticola in the Gulf of Guinea refugium are distinct from other populations in west central Africa. All three species exhibit signatures of past population expansion across much of the study area consistent with a history of postglacial expansion. There was no strong evidence for a riverine barrier effect in any of the three species, suggesting that duikers can readily cross major rivers. Generalized dissimilarity models (GDM) showed that environmental variation explains most of the nuclear genetic differentiation in both C. callipygus and P. monticola. The forest-savanna transition across central Cameroon and the Plateaux Batéké region in southeastern Gabon show the highest environmentally-associated turnover in genetic variability. A pattern of genetic differentiation was also evident between the coast and forest interior that may reflect differences in precipitation and/or vegetation. Conclusions Findings from this study highlight the historical impact of Pleistocene fragmentation and current influence of environmental variation on genetic structure in duikers. Conservation efforts should therefore target areas that harbor as much environmentally-associated genetic variation as possible in order to maximize species’ capacity to adapt to environmental change. Electronic supplementary material The online version of this article (10.1186/s12862-017-1054-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stephan Ntie
- Department of Biology, Université des Sciences et Techniques de Masuku, B.P.943, Franceville, Gabon.,Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA, 70148, USA
| | - Anne R Davis
- Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA, 70148, USA
| | - Katrin Hils
- Cheetah Conservation Fund, P.O. Box 1755, Otjiwarongo, Namibia.,Comparative Zoology, Institute for Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Patrick Mickala
- Department of Biology, Université des Sciences et Techniques de Masuku, B.P.943, Franceville, Gabon
| | - Henri A Thomassen
- Comparative Zoology, Institute for Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Katy Morgan
- Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA, 70148, USA
| | - Hadrien Vanthomme
- Département Ecologie et Gestion de la Biodiversité, Muséum National d'Histoire Naturelle, CNRS UMR 7179, Avenue du Petit Château, 91800, Brunoy, France
| | - Mary K Gonder
- Department of Biology, Drexel University, 3245 Chestnut St., Philadelphia, PA, 19104, USA
| | - Nicola M Anthony
- Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA, 70148, USA.
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9
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Portik DM, Leaché AD, Rivera D, Barej MF, Burger M, Hirschfeld M, Rödel M, Blackburn DC, Fujita MK. Evaluating mechanisms of diversification in a Guineo‐Congolian tropical forest frog using demographic model selection. Mol Ecol 2017; 26:5245-5263. [DOI: 10.1111/mec.14266] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/17/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Daniel M. Portik
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Adam D. Leaché
- Department of Biology University of Washington Seattle WA USA
- Burke Museum of Natural History and Culture University of Washington Seattle WA USA
| | - Danielle Rivera
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Michael F. Barej
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
| | - 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 Island
| | - Mareike Hirschfeld
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
| | - Mark‐Oliver Rödel
- 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
| | - Matthew K. Fujita
- Amphibian and Reptile Diversity Research Center The University of Texas at Arlington Arlington TX USA
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10
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Development of nuclear SNP markers for genetic tracking of Iroko, Milicia excelsa and Milicia regia. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0716-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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11
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Iloh AC, Schmidt M, Muellner-Riehl AN, Ogundipe OT, Paule J. Pleistocene refugia and genetic diversity patterns in West Africa: Insights from the liana Chasmanthera dependens (Menispermaceae). PLoS One 2017; 12:e0170511. [PMID: 28301470 PMCID: PMC5354259 DOI: 10.1371/journal.pone.0170511] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 02/19/2017] [Indexed: 11/25/2022] Open
Abstract
Processes shaping the African Guineo-Congolian rain forest, especially in the West African part, are not well understood. Recent molecular studies, based mainly on forest tree species, confirmed the previously proposed division of the western African Guineo-Congolian rain forest into Upper Guinea (UG) and Lower Guinea (LG) separated by the Dahomey Gap (DG). Here we studied nine populations in the area of the DG and the borders of LG and UG of the widespread liana species, Chasmanthera dependens (Menispermaceae) by amplified fragment length polymorphism (AFLP), a chloroplast DNA sequence marker, and modelled the distribution based on current as well as paleoclimatic data (Holocene Climate Optimum, ca. 6 kyr BP and Last Glacial Maximum, ca. 22 kyr BP). Current population genetic structure and geographical pattern of cpDNA was related to present as well as historical modelled distributions. Results from this study show that past historical factors played an important role in shaping the distribution of C. dependens across West Africa. The Cameroon Volcanic Line seems to represent a barrier for gene flow in the present as well as in the past. Distribution modelling proposed refugia in the Dahomey Gap, supported also by higher genetic diversity. This is in contrast with the phylogeographic patterns observed in several rainforest tree species and could be explained by either diverging or more relaxed ecological requirements of this liana species.
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Affiliation(s)
- Andrew Chibuzor Iloh
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, Frankfurt am Main, Germany
| | - Marco Schmidt
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, Frankfurt am Main, Germany
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, Frankfurt am Main, Germany
| | - Alexandra Nora Muellner-Riehl
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, Frankfurt am Main, Germany
- Department of Molecular Evolution and Plant Systematics & Herbarium LZ, Institute of Biology, Leipzig University, Johannisallee 21–23, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, Germany
| | | | - Juraj Paule
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, Frankfurt am Main, Germany
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12
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Barthe S, Binelli G, Hérault B, Scotti-Saintagne C, Sabatier D, Scotti I. Tropical rainforests that persisted: inferences from the Quaternary demographic history of eight tree species in the Guiana shield. Mol Ecol 2017; 26:1161-1174. [PMID: 27926985 DOI: 10.1111/mec.13949] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 11/29/2022]
Abstract
How Quaternary climatic and geological disturbances influenced the composition of Neotropical forests is hotly debated. Rainfall and temperature changes during and/or immediately after the last glacial maximum (LGM) are thought to have strongly affected the geographical distribution and local abundance of tree species. The paucity of the fossil records in Neotropical forests prevents a direct reconstruction of such processes. To describe community-level historical trends in forest composition, we turned therefore to inferential methods based on the reconstruction of past demographic changes. In particular, we modelled the history of rainforests in the eastern Guiana Shield over a timescale of several thousand generations, through the application of approximate Bayesian computation and maximum-likelihood methods to diversity data at nuclear and chloroplast loci in eight species or subspecies of rainforest trees. Depending on the species and on the method applied, we detected population contraction, expansion or stability, with a general trend in favour of stability or expansion, with changes presumably having occurred during or after the LGM. These findings suggest that Guiana Shield rainforests have globally persisted, while expanding, through the Quaternary, but that different species have experienced different demographic events, with a trend towards the increase in frequency of light-demanding, disturbance-associated species.
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Affiliation(s)
- Stéphanie Barthe
- UMR EcoFoG ("Ecologie des forêts de Guyane"), UAG, Campus Agronomique, BP 709, 97387, Kourou, French Guiana.,UMR EcoFoG ("Ecologie des forêts de Guyane"), INRA, Campus Agronomique, BP 709, 97387, Kourou, French Guiana
| | - Giorgio Binelli
- DBSV ("Dipartimento di Biotecnologie e Scienze della Vita"), Università degli Studi dell'Insubria, via J.H. Dunant 3, 21100, Varese, Italy
| | - Bruno Hérault
- UMR EcoFoG ("Ecologie des forêts de Guyane"), CIRAD, Campus Agronomique, BP 709, 97387, Kourou, French Guiana
| | - Caroline Scotti-Saintagne
- URFM ("Écologie des Forêts Méditerranéennes"), INRA, Domaine Saint_Paul, Site Agroparc, 84914, Avignon, France
| | - Daniel Sabatier
- UMR AMAP ("Botanique et modélisation de l'architecture des plantes et des végétations"), IRD, Boulevard de la Lironde, Parc Scientifique 2, 34398, Montpellier, France
| | - Ivan Scotti
- URFM ("Écologie des Forêts Méditerranéennes"), INRA, Domaine Saint_Paul, Site Agroparc, 84914, Avignon, France
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Daïnou K, Blanc-Jolivet C, Degen B, Kimani P, Ndiade-Bourobou D, Donkpegan ASL, Tosso F, Kaymak E, Bourland N, Doucet JL, Hardy OJ. Revealing hidden species diversity in closely related species using nuclear SNPs, SSRs and DNA sequences - a case study in the tree genus Milicia. BMC Evol Biol 2016; 16:259. [PMID: 27903256 PMCID: PMC5131513 DOI: 10.1186/s12862-016-0831-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 11/17/2016] [Indexed: 12/22/2022] Open
Abstract
Background Species delimitation in closely related plant taxa can be challenging because (i) reproductive barriers are not always congruent with morphological differentiation, (ii) use of plastid sequences might lead to misinterpretation, (iii) rare species might not be sampled. We revisited molecular-based species delimitation in the African genus Milicia, currently divided into M. regia (West Africa) and M. excelsa (from West to East Africa). We used 435 samples collected in West, Central and East Africa. We genotyped SNP and SSR loci to identify genetic clusters, and sequenced two plastid regions (psbA-trnH, trnC-ycf6) and a nuclear gene (At103) to confirm species’ divergence and compare species delimitation methods. We also examined whether ecological niche differentiation was congruent with sampled genetic structure. Results West African M. regia, West African and East African M. excelsa samples constituted three well distinct genetic clusters according to SNPs and SSRs. In Central Africa, two genetic clusters were consistently inferred by both types of markers, while a few scattered samples, sympatric with the preceding clusters but exhibiting leaf traits of M. regia, were grouped with the West African M. regia cluster based on SNPs or formed a distinct cluster based on SSRs. SSR results were confirmed by sequence data from the nuclear region At103 which revealed three distinct ‘Fields For Recombination’ corresponding to (i) West African M. regia, (ii) Central African samples with leaf traits of M. regia, and (iii) all M. excelsa samples. None of the plastid sequences provide indication of distinct clades of the three species-like units. Niche modelling techniques yielded a significant correlation between niche overlap and genetic distance. Conclusions Our genetic data suggest that three species of Milicia could be recognized. It is surprising that the occurrence of two species in Central Africa was not reported for this well-known timber tree. Globally, our work highlights the importance of collecting samples in a systematic way and the need for combining different nuclear markers when dealing with species complexes. Recognizing cryptic species is particularly crucial for economically exploited species because some hidden taxa might actually be endangered as they are merged with more abundant species. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0831-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kasso Daïnou
- Nature + asbl / TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, 5030, Gembloux, Belgium. .,Université d'Agriculture de Kétou, BP 43, Kétou, Benin.
| | - Céline Blanc-Jolivet
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927, Grosshansdorf, Germany
| | - Bernd Degen
- Thünen Institute of Forest Genetics, Sieker Landstrasse 2, 22927, Grosshansdorf, Germany
| | - Priscilla Kimani
- Kenya Forestry Research Institute, Biotechnology Section, P. O. Box 20412-00200, Nairobi, Kenya
| | | | - Armel S L Donkpegan
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, 5030, Gembloux, Belgium
| | - Félicien Tosso
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, 5030, Gembloux, Belgium
| | - Esra Kaymak
- Evolutionary Biology and Ecology - CP 160⁄12, Faculté des Sciences, Université Libre de Bruxelles, Av. F. Roosevelt 50, 1050, Brussels, Belgium
| | - Nils Bourland
- Service of Wood Biology, Royal Museum for Central Africa, Tervuren, Belgium
| | - Jean-Louis Doucet
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, 5030, Gembloux, Belgium
| | - Olivier J Hardy
- Evolutionary Biology and Ecology - CP 160⁄12, Faculté des Sciences, Université Libre de Bruxelles, Av. F. Roosevelt 50, 1050, Brussels, Belgium
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14
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Gaubert P, Njiokou F, Ngua G, Afiademanyo K, Dufour S, Malekani J, Bi SG, Tougard C, Olayemi A, Danquah E, Djagoun CAMS, Kaleme P, Mololo CN, Stanley W, Luo SJ, Antunes A. Phylogeography of the heavily poached African common pangolin (Pholidota, Manis tricuspis) reveals six cryptic lineages as traceable signatures of Pleistocene diversification. Mol Ecol 2016; 25:5975-5993. [PMID: 27862533 DOI: 10.1111/mec.13886] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 09/24/2016] [Accepted: 09/27/2016] [Indexed: 01/03/2023]
Abstract
Knowledge on faunal diversification in African rainforests remains scarce. We used phylogeography to assess (i) the role of Pleistocene climatic oscillations in the diversification of the African common pangolin (Manis tricuspis) and (ii) the utility of our multilocus approach for taxonomic delineation and trade tracing of this heavily poached species. We sequenced 101 individuals for two mitochondrial DNA (mtDNA), two nuclear DNA and one Y-borne gene fragments (totalizing 2602 bp). We used a time-calibrated, Bayesian inference phylogenetic framework and conducted character-based, genetic and phylogenetic delineation of species hypotheses within African common pangolins. We identified six geographic lineages partitioned into western Africa, Ghana, the Dahomey Gap, western central Africa, Gabon and central Africa, all diverging during the Middle to Late Pleistocene. MtDNA (cytochrome b + control region) was the sole locus to provide diagnostic characters for each of the six lineages. Tree-based Bayesian delimitation methods using single- and multilocus approaches gave high support for 'species' level recognition of the six African common pangolin lineages. Although the diversification of African common pangolins occurred during Pleistocene cyclical glaciations, causative correlation with traditional rainforest refugia and riverine barriers in Africa was not straightforward. We conclude on the existence of six cryptic lineages within African common pangolins, which might be of major relevance for future conservation strategies. The high discriminative power of the mtDNA markers used in this study should allow an efficient molecular tracing of the regional origin of African common pangolin seizures.
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Affiliation(s)
- Philippe Gaubert
- Institut des Sciences de l'Evolution de Montpellier (ISEM) - UM-CNRS-IRD-EPHE-CIRAD, Université de Montpellier, Place Eugène Bataillon - CC 64, 34095, Montpellier Cedex 05, France.,CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal
| | - Flobert Njiokou
- Laboratoire de Parasitologie et Ecologie, Faculté des Sciences, Université de Yaoundé I, BP 812, Yaoundé, Cameroon
| | - Gabriel Ngua
- Amigos de la Naturaleza y del Desarrollo de Guinea Ecuatorial (ANDEGE), Barrio Ukomba, S/N, Bata, Equatorial Guinea
| | - Komlan Afiademanyo
- Département de Zoologie et de Biologie Animale, Université de Lomé, BP 1515, Lomé, Togo
| | | | - Jean Malekani
- Department of Biology, University of Kinshasa, PO Box 218, Kinshasa XI, Democratic Republic of Congo
| | - Sery Gonedelé Bi
- Laboratoire de Génétique, Université Félix Houphouët Boigny d'Abidjan-Cocody, 22 BP 582, Abidjan 22, Côte d'Ivoire
| | - Christelle Tougard
- Institut des Sciences de l'Evolution de Montpellier (ISEM) - UM-CNRS-IRD-EPHE-CIRAD, Université de Montpellier, Place Eugène Bataillon - CC 64, 34095, Montpellier Cedex 05, France
| | - Ayodeji Olayemi
- Natural History Museum, Obafemi Awolowo University, HO 220005, Ile-Ife, Nigeria
| | - Emmanuel Danquah
- Department of Wildlife and Range Management, Faculty of Renewable Natural Resources, Kwame Nkrumah University of Science and Technology, University Post Office, Kumasi, Ghana
| | - Chabi A M S Djagoun
- Laboratory of Applied Ecology, Faculty of Agronomic Sciences, University of Abomey-Calavi, 01 BP 526 LEA-FSA, Cotonou, Benin
| | - Prince Kaleme
- Laboratoire de Mammalogie, Département de Biologie, Centre de Recherches en Sciences Naturelles (CRSN) - Lwiro, DS (Dépêche Spéciale) Bukavu, Democratic Republic of Congo.,Department of Zoology, University of Johannesburg, PO Box 524, Auckland Park 2006, South Africa
| | - Casimir Nebesse Mololo
- Université de Kisangani, Faculté des Sciences, B.P. 2012, Kisangani, Democratic Republic of Congo
| | - William Stanley
- Science and Education, Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL, 60605, USA
| | - Shu-Jin Luo
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Agostinho Antunes
- CIMAR/CIIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
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15
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Cazé ALR, Mäder G, Nunes TS, Queiroz LP, de Oliveira G, Diniz-Filho JAF, Bonatto SL, Freitas LB. Could refuge theory and rivers acting as barriers explain the genetic variability distribution in the Atlantic Forest? Mol Phylogenet Evol 2016; 101:242-251. [DOI: 10.1016/j.ympev.2016.05.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 05/09/2016] [Accepted: 05/10/2016] [Indexed: 11/28/2022]
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16
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Jaros U, Fischer GA, Pailler T, Comes HP. Spatial patterns of AFLP diversity in Bulbophyllum occultum (Orchidaceae) indicate long-term refugial isolation in Madagascar and long-distance colonization effects in La Réunion. Heredity (Edinb) 2016; 116:434-46. [PMID: 26883184 DOI: 10.1038/hdy.2016.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 10/21/2015] [Accepted: 12/15/2015] [Indexed: 01/30/2023] Open
Abstract
Bulbophyllum occultum, an epiphytic orchid mainly distributed in the rainforests of (north)eastern Madagascar and La Réunion, represents an interesting model case for testing the effects of anthropogenic vs historical (e.g., climate induced) habitat isolation and long-distance colonization on the genetic structure of plant species with disjunct distributions in the Madagascan region. To this aim, we surveyed amplified fragment length polymorphisms (AFLPs) across 13 populations in Madagascar and nine in La Réunion (206 individuals in total). We found overall high levels of population subdivision (Φ(PT)=0.387) and low within-population diversity (H(E), range: 0.026-0.124), indicating non-equilibrium conditions in a mainly selfing species. There was no impact of recent deforestation (Madagascar) or habitat disturbance (La Réunion) detectable on AFLP diversity. K-means clustering and BARRIER analyses identified multiple gene pools and several genetic breaks, both within and among islands. Inter-island levels of population genetic diversity and subdivision were similar, whereby inter-individual divergence in flower colour explained a significant part of gene pool divergence in La Réunion. Our results suggest that (i) B. occultum persisted across multiple isolated ('refugial') regions along the eastern rainforest corridor of Madagascar over recent climatic cycles and (ii) populations in La Réunion arose from either single or few independent introductions from Madagascar. High selfing rates and sufficient time for genetic drift likely promoted unexpectedly high population genetic and phenotypic (flower colour) differentiation in La Réunion. Overall, this study highlights a strong imprint of history on the genetic structure of a low-gene-dispersing epiphytic orchid from the Madagascan region.
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Affiliation(s)
- U Jaros
- Department of Ecology and Evolution, University of Salzburg, Salzburg, Austria
| | - G A Fischer
- Kadoorie Farm and Botanic Garden Corporation, Tai Po, N.T., Hong Kong, SAR
| | - T Pailler
- UMR CIRAD-université de La Réunion. Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Le Tampon, Réunion, France
| | - H P Comes
- Department of Ecology and Evolution, University of Salzburg, Salzburg, Austria
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17
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Vlam M, van der Sleen P, Groenendijk P, Zuidema PA. Tree Age Distributions Reveal Large-Scale Disturbance-Recovery Cycles in Three Tropical Forests. FRONTIERS IN PLANT SCIENCE 2016; 7:1984. [PMID: 28105034 PMCID: PMC5214098 DOI: 10.3389/fpls.2016.01984] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/14/2016] [Indexed: 05/06/2023]
Abstract
Over the past few decades there has been a growing realization that a large share of apparently 'virgin' or 'old-growth' tropical forests carries a legacy of past natural or anthropogenic disturbances that have a substantial effect on present-day forest composition, structure and dynamics. Yet, direct evidence of such disturbances is scarce and comparisons of disturbance dynamics across regions even more so. Here we present a tree-ring based reconstruction of disturbance histories from three tropical forest sites in Bolivia, Cameroon, and Thailand. We studied temporal patterns in tree regeneration of shade-intolerant tree species, because establishment of these trees is indicative for canopy disturbance. In three large areas (140-300 ha), stem disks and increment cores were collected for a total of 1154 trees (>5 cm diameter) from 12 tree species to estimate the age of every tree. Using these age estimates we produced population age distributions, which were analyzed for evidence of past disturbance. Our approach allowed us to reconstruct patterns of tree establishment over a period of around 250 years. In Bolivia, we found continuous regeneration rates of three species and a peaked age distribution of a long-lived pioneer species. In both Cameroon and Thailand we found irregular age distributions, indicating strongly reduced regeneration rates over a period of 10-60 years. Past fires, windthrow events or anthropogenic disturbances all provide plausible explanations for the reported variation in tree age across the three sites. Our results support the recent idea that the long-term dynamics of tropical forests are impacted by large-scale disturbance-recovery cycles, similar to those driving temperate forest dynamics.
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Affiliation(s)
- Mart Vlam
- Forest Ecology and Forest Management Group, Wageningen University and ResearchWageningen, Netherlands
- *Correspondence: Mart Vlam,
| | - Peter van der Sleen
- Forest Ecology and Forest Management Group, Wageningen University and ResearchWageningen, Netherlands
- Marine Science Institute, The University of Texas at Austin, Port AransasTX, USA
- Instituto Boliviano de Investigación ForestalSanta Cruz de la Sierra, Bolivia
| | - Peter Groenendijk
- Forest Ecology and Forest Management Group, Wageningen University and ResearchWageningen, Netherlands
- Departamento de Botánica, Escola Politécnica Superior, Universidade de Santiago de CompostelaLugo, Spain
| | - Pieter A. Zuidema
- Forest Ecology and Forest Management Group, Wageningen University and ResearchWageningen, Netherlands
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18
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Huang XC, Ci XQ, Conran JG, Li J. Application of DNA Barcodes in Asian Tropical Trees--A Case Study from Xishuangbanna Nature Reserve, Southwest China. PLoS One 2015; 10:e0129295. [PMID: 26121045 PMCID: PMC4509572 DOI: 10.1371/journal.pone.0129295] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 02/27/2015] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Within a regional floristic context, DNA barcoding is more useful to manage plant diversity inventories on a large scale and develop valuable conservation strategies. However, there are no DNA barcode studies from tropical areas of China, which represents one of the biodiversity hotspots around the world. METHODOLOGY AND PRINCIPAL FINDINGS A DNA barcoding database of an Asian tropical trees with high diversity was established at Xishuangbanna Nature Reserve, Yunnan, southwest China using rbcL and matK as standard barcodes, as well as trnH-psbA and ITS as supplementary barcodes. The performance of tree species identification success was assessed using 2,052 accessions from four plots belonging to two vegetation types in the region by three methods: Neighbor-Joining, Maximum-Likelihood and BLAST. We corrected morphological field identification errors (9.6%) for the three plots using rbcL and matK based on Neighbor-Joining tree. The best barcode region for PCR and sequencing was rbcL (97.6%, 90.8%), followed by trnH-psbA (93.6%, 85.6%), while matK and ITS obtained relative low PCR and sequencing success rates. However, ITS performed best for both species (44.6-58.1%) and genus (72.8-76.2%) identification. With trnH-psbA slightly less effective for species identification. The two standard barcode rbcL and matK gave poor results for species identification (24.7-28.5% and 31.6-35.3%). Compared with other studies from comparable tropical forests (e.g. Cameroon, the Amazon and India), the overall performance of the four barcodes for species identification was lower for the Xishuangbanna Nature Reserve, possibly because of species/genus ratios and species composition between these tropical areas. CONCLUSIONS/SIGNIFICANCE Although the core barcodes rbcL and matK were not suitable for species identification of tropical trees from Xishuangbanna Nature Reserve, they could still help with identification at the family and genus level. Considering the relative sequence recovery and the species identification performance, we recommend the use of trnH-psbA and ITS in combination as the preferred barcodes for tropical tree species identification in China.
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Affiliation(s)
- Xiao-cui Huang
- Laboratory of Plant Phylogenetics and Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Xiu-qin Ci
- Laboratory of Plant Phylogenetics and Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - John G. Conran
- Centre for Evolutionary Biology and Biodiversity & Sprigg Geobiology Centre, School of Biological Sciences, Benham Bldg DX, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Jie Li
- Laboratory of Plant Phylogenetics and Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, People’s Republic of China
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19
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Hassanin A, Khouider S, Gembu GC, M. Goodman S, Kadjo B, Nesi N, Pourrut X, Nakouné E, Bonillo C. The comparative phylogeography of fruit bats of the tribe Scotonycterini (Chiroptera, Pteropodidae) reveals cryptic species diversity related to African Pleistocene forest refugia. C R Biol 2015; 338:197-211. [DOI: 10.1016/j.crvi.2014.12.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 12/15/2014] [Accepted: 12/16/2014] [Indexed: 11/25/2022]
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20
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Ley A, Hardy O. Contrasting patterns of gene flow between sister plant species in the understorey of African moist forests – The case of sympatric and parapatric Marantaceae species. Mol Phylogenet Evol 2014; 77:264-74. [DOI: 10.1016/j.ympev.2014.04.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 02/20/2014] [Accepted: 04/17/2014] [Indexed: 11/29/2022]
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Dauby G, Duminil J, Heuertz M, Koffi GK, Stévart T, Hardy OJ. Congruent phylogeographical patterns of eight tree species in Atlantic Central Africa provide insights into the past dynamics of forest cover. Mol Ecol 2014; 23:2299-312. [DOI: 10.1111/mec.12724] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 02/18/2014] [Accepted: 03/09/2014] [Indexed: 12/01/2022]
Affiliation(s)
- G. Dauby
- Faculté des Sciences, Evolutionary Biology and Ecology; Université Libre de Bruxelles; CP160/12, 50 Av. F. Roosevelt 1050 Brussels Belgium
| | - J. Duminil
- Faculté des Sciences, Evolutionary Biology and Ecology; Université Libre de Bruxelles; CP160/12, 50 Av. F. Roosevelt 1050 Brussels Belgium
- Sub-Regional Office for Central Africa; Bioversity International, Forest Genetic Resources Programme; P.O. Box 2008 Messa Yaoundé Cameroon
| | - M. Heuertz
- Faculté des Sciences, Evolutionary Biology and Ecology; Université Libre de Bruxelles; CP160/12, 50 Av. F. Roosevelt 1050 Brussels Belgium
- Forest Ecology and Genetics; INIA Forest Research Centre; Ctra. A Coruña km 7.5 28040 Madrid Spain
- Department of Biology; Unit Ecology and Evolution; Université de Fribourg; Chemin du Musée 10 1700 Fribourg Switzerland
| | - G. K. Koffi
- Faculté des Sciences, Evolutionary Biology and Ecology; Université Libre de Bruxelles; CP160/12, 50 Av. F. Roosevelt 1050 Brussels Belgium
- UFR-Sciences de la Nature; Université Nangui Abrogoua; 02 BP 801 Abidjan Ivory Coast
| | - T. Stévart
- Africa and Madagascar Department; Missouri Botanical Garden; PO Box 299 St. Louis MO 63166-0299 USA
- Herbarium et Bibliothèque de Botanique africaine; Université Libre de Bruxelles; CP 169, 50 Av. F. Roosevelt 1050 Brussels Belgium
- National Botanic Garden of Belgium; Domein van Bouchout; Nieuwelaan 38 B-1860 Meise Belgium
| | - O. J. Hardy
- Faculté des Sciences, Evolutionary Biology and Ecology; Université Libre de Bruxelles; CP160/12, 50 Av. F. Roosevelt 1050 Brussels Belgium
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Daïnou K, Mahy G, Duminil J, Dick CW, Doucet JL, Donkpégan ASL, Pluijgers M, Sinsin B, Lejeune P, Hardy OJ. Speciation slowing down in widespread and long-living tree taxa: insights from the tropical timber tree genus Milicia (Moraceae). Heredity (Edinb) 2014; 113:74-85. [PMID: 24549110 DOI: 10.1038/hdy.2014.5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 12/18/2013] [Accepted: 12/19/2013] [Indexed: 11/09/2022] Open
Abstract
The long generation time and large effective size of widespread forest tree species can result in slow evolutionary rate and incomplete lineage sorting, complicating species delimitation. We addressed this issue with the African timber tree genus Milicia that comprises two morphologically similar and often confounded species: M. excelsa, widespread from West to East Africa, and M. regia, endemic to West Africa. We combined information from nuclear microsatellites (nSSRs), nuclear and plastid DNA sequences, and morphological systematics to identify significant evolutionary units and infer their evolutionary and biogeographical history. We detected five geographically coherent genetic clusters using nSSRs and three levels of genetic differentiation. First, one West African cluster matched perfectly with the morphospecies M. regia that formed a monophyletic clade at both DNA sequences. Second, a West African M. excelsa cluster formed a monophyletic group at plastid DNA and was more related to M. regia than to Central African M. excelsa, but shared many haplotypes with the latter at nuclear DNA. Third, three Central African clusters appeared little differentiated and shared most of their haplotypes. Although gene tree paraphyly could suggest a single species in Milicia following the phylogenetic species concept, the existence of mutual haplotypic exclusivity and nonadmixed genetic clusters in the contact area of the two taxa indicate strong reproductive isolation and, thus, two species following the biological species concept. Molecular dating of the first divergence events showed that speciation in Milicia is ancient (Tertiary), indicating that long-living tree taxa exhibiting genetic speciation may remain similar morphologically.
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Affiliation(s)
- K Daïnou
- 1] Laboratory of Tropical and Subtropical Forestry, Unit of Forest and Nature Management, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium [2] Laboratory of Applied Ecology, Faculty of Agronomic Science, University of Abomey-Calavi, Cotonou, Benin
| | - G Mahy
- Biodiversity and Landscape Unit, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
| | - J Duminil
- 1] Evolutionary Biology and Ecology, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium [2] Bioversity International, Forest Genetic Resources Programme, Sub-Regional Office for Central Africa, Yaoundé, Cameroon
| | - C W Dick
- 1] Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA [2] Smithsonian Tropical Research Institute, Gamboa, Republic of Panama
| | - J-L Doucet
- Laboratory of Tropical and Subtropical Forestry, Unit of Forest and Nature Management, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
| | - A S L Donkpégan
- Laboratory of Tropical and Subtropical Forestry, Unit of Forest and Nature Management, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
| | - M Pluijgers
- Laboratory of Tropical and Subtropical Forestry, Unit of Forest and Nature Management, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
| | - B Sinsin
- Laboratory of Applied Ecology, Faculty of Agronomic Science, University of Abomey-Calavi, Cotonou, Benin
| | - P Lejeune
- Unit of Forest and Nature Management, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
| | - O J Hardy
- Evolutionary Biology and Ecology, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
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Heuertz M, Duminil J, Dauby G, Savolainen V, Hardy OJ. Comparative phylogeography in rainforest trees from Lower Guinea, Africa. PLoS One 2014; 9:e84307. [PMID: 24416215 PMCID: PMC3885573 DOI: 10.1371/journal.pone.0084307] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 11/13/2013] [Indexed: 11/18/2022] Open
Abstract
Comparative phylogeography is an effective approach to assess the evolutionary history of biological communities. We used comparative phylogeography in fourteen tree taxa from Lower Guinea (Atlantic Equatorial Africa) to test for congruence with two simple evolutionary scenarios based on physio-climatic features 1) the W-E environmental gradient and 2) the N-S seasonal inversion, which determine climatic and seasonality differences in the region. We sequenced the trnC-ycf6 plastid DNA region using a dual sampling strategy: fourteen taxa with small sample sizes (dataset 1, mean n = 16/taxon), to assess whether a strong general pattern of allele endemism and genetic differentiation emerged; and four taxonomically well-studied species with larger sample sizes (dataset 2, mean n = 109/species) to detect the presence of particular shared phylogeographic patterns. When grouping the samples into two alternative sets of two populations, W and E, vs. N and S, neither dataset exhibited a strong pattern of allelic endemism, suggesting that none of the considered regions consistently harboured older populations. Differentiation in dataset 1 was similarly strong between W and E as between N and S, with 3-5 significant F ST tests out of 14 tests in each scenario. Coalescent simulations indicated that, given the power of the data, this result probably reflects idiosyncratic histories of the taxa, or a weak common differentiation pattern (possibly with population substructure) undetectable across taxa in dataset 1. Dataset 2 identified a common genetic break separating the northern and southern populations of Greenwayodendron suaveolens subsp. suaveolens var. suaveolens, Milicia excelsa, Symphonia globulifera and Trichoscypha acuminata in Lower Guinea, in agreement with differentiation across the N-S seasonal inversion. Our work suggests that currently recognized tree taxa or suspected species complexes can contain strongly differentiated genetic lineages, which could lead to misinterpretation of phylogeographic patterns. Therefore the evolutionary processes of such taxa require further study in African tropical rainforests.
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Affiliation(s)
- Myriam Heuertz
- Université Libre de Bruxelles, Faculté des Sciences, Evolutionary Biology and Ecology, Brussels, Belgium
- INIA, Forest Research Centre, Forest Ecology and Genetics, Madrid, Spain
- * E-mail:
| | - Jérôme Duminil
- Université Libre de Bruxelles, Faculté des Sciences, Evolutionary Biology and Ecology, Brussels, Belgium
- Bioversity International, Forest Genetic Resources Programme, Sub-Regional Office for Central Africa, Yaoundé, Cameroon
| | - Gilles Dauby
- Université Libre de Bruxelles, Faculté des Sciences, Evolutionary Biology and Ecology, Brussels, Belgium
| | - Vincent Savolainen
- Imperial College London, South Kensington Campus, London, United Kingdom
- Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, London, United Kingdom
| | - Olivier J. Hardy
- Université Libre de Bruxelles, Faculté des Sciences, Evolutionary Biology and Ecology, Brussels, Belgium
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Duminil J, Brown RP, Ewédjè EEBK, Mardulyn P, Doucet JL, Hardy OJ. Large-scale pattern of genetic differentiation within African rainforest trees: insights on the roles of ecological gradients and past climate changes on the evolution of Erythrophleum spp (Fabaceae). BMC Evol Biol 2013; 13:195. [PMID: 24028582 PMCID: PMC3848707 DOI: 10.1186/1471-2148-13-195] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 08/20/2013] [Indexed: 11/28/2022] Open
Abstract
Background The evolutionary events that have shaped biodiversity patterns in the African rainforests are still poorly documented. Past forest fragmentation and ecological gradients have been advocated as important drivers of genetic differentiation but their respective roles remain unclear. Using nuclear microsatellites (nSSRs) and chloroplast non-coding sequences (pDNA), we characterised the spatial genetic structure of Erythrophleum (Fabaceae) forest trees in West and Central Africa (Guinea Region, GR). This widespread genus displays a wide ecological amplitude and taxonomists recognize two forest tree species, E. ivorense and E. suaveolens, which are difficult to distinguish in the field and often confused. Results Bayesian-clustering applied on nSSRs of a blind sample of 648 specimens identified three major gene pools showing no or very limited introgression. They present parapatric distributions correlated to rainfall gradients and forest types. One gene pool is restricted to coastal evergreen forests and corresponds to E. ivorense; a second one is found in gallery forests from the dry forest zone of West Africa and North-West Cameroon and corresponds to West-African E. suaveolens; the third gene pool occurs in semi-evergreen forests and corresponds to Central African E. suaveolens. These gene pools have mostly unique pDNA haplotypes but they do not form reciprocally monophyletic clades. Nevertheless, pDNA molecular dating indicates that the divergence between E. ivorense and Central African E. suaveolens predates the Pleistocene. Further Bayesian-clustering applied within each major gene pool identified diffuse genetic discontinuities (minor gene pools displaying substantial introgression) at a latitude between 0 and 2°N in Central Africa for both species, and at a longitude between 5° and 8°E for E. ivorense. Moreover, we detected evidence of past population declines which are consistent with historical habitat fragmentation induced by Pleistocene climate changes. Conclusions Overall, deep genetic differentiation (major gene pools) follows ecological gradients that may be at the origin of speciation, while diffuse differentiation (minor gene pools) are tentatively interpreted as the signature of past forest fragmentation induced by past climate changes.
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Affiliation(s)
- Jerome Duminil
- Service Evolution Biologique et Ecologie, CP160⁄12, Faculté des Sciences, Université Libre de Bruxelles, 50 Av, F, Roosevelt, 1050 Brussels, Belgium.
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Budde KB, González-Martínez SC, Hardy OJ, Heuertz M. The ancient tropical rainforest tree Symphonia globulifera L. f. (Clusiaceae) was not restricted to postulated Pleistocene refugia in Atlantic Equatorial Africa. Heredity (Edinb) 2013; 111:66-76. [PMID: 23572126 DOI: 10.1038/hdy.2013.21] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Understanding the history of forests and their species' demographic responses to past disturbances is important for predicting impacts of future environmental changes. Tropical rainforests of the Guineo-Congolian region in Central Africa are believed to have survived the Pleistocene glacial periods in a few major refugia, essentially centred on mountainous regions close to the Atlantic Ocean. We tested this hypothesis by investigating the phylogeographic structure of a widespread, ancient rainforest tree species, Symphonia globulifera L. f. (Clusiaceae), using plastid DNA sequences (chloroplast DNA [cpDNA], psbA-trnH intergenic spacer) and nuclear microsatellites (simple sequence repeats, SSRs). SSRs identified four gene pools located in Benin, West Cameroon, South Cameroon and Gabon, and São Tomé. This structure was also apparent at cpDNA. Approximate Bayesian Computation detected recent bottlenecks approximately dated to the last glacial maximum in Benin, West Cameroon and São Tomé, and an older bottleneck in South Cameroon and Gabon, suggesting a genetic effect of Pleistocene cycles of forest contraction. CpDNA haplotype distribution indicated wide-ranging long-term persistence of S. globulifera both inside and outside of postulated forest refugia. Pollen flow was four times greater than that of seed in South Cameroon and Gabon, which probably enabled rapid population recovery after bottlenecks. Furthermore, our study suggested ecotypic differentiation-coastal or swamp vs terra firme-in S. globulifera. Comparison with other tree phylogeographic studies in Central Africa highlighted the relevance of species-specific responses to environmental change in forest trees.
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Affiliation(s)
- K B Budde
- INIA, Forest Research Centre, Department of Forest Ecology and Genetics, Carretera A Coruña km 7.5, Madrid, Spain.
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Parmentier I, Duminil J, Kuzmina M, Philippe M, Thomas DW, Kenfack D, Chuyong GB, Cruaud C, Hardy OJ. How effective are DNA barcodes in the identification of African rainforest trees? PLoS One 2013; 8:e54921. [PMID: 23565134 PMCID: PMC3615068 DOI: 10.1371/journal.pone.0054921] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 12/20/2012] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND DNA barcoding of rain forest trees could potentially help biologists identify species and discover new ones. However, DNA barcodes cannot always distinguish between closely related species, and the size and completeness of barcode databases are key parameters for their successful application. We test the ability of rbcL, matK and trnH-psbA plastid DNA markers to identify rain forest trees at two sites in Atlantic central Africa under the assumption that a database is exhaustive in terms of species content, but not necessarily in terms of haplotype diversity within species. METHODOLOGY/PRINCIPAL FINDINGS We assess the accuracy of identification to species or genus using a genetic distance matrix between samples either based on a global multiple sequence alignment (GD) or on a basic local alignment search tool (BLAST). Where a local database is available (within a 50 ha plot), barcoding was generally reliable for genus identification (95-100% success), but less for species identification (71-88%). Using a single marker, best results for species identification were obtained with trnH-psbA. There was a significant decrease of barcoding success in species-rich clades. When the local database was used to identify the genus of trees from another region and did include all genera from the query individuals but not all species, genus identification success decreased to 84-90%. The GD method performed best but a global multiple sequence alignment is not applicable on trnH-psbA. CONCLUSIONS/SIGNIFICANCE Barcoding is a useful tool to assign unidentified African rain forest trees to a genus, but identification to a species is less reliable, especially in species-rich clades, even using an exhaustive local database. Combining two markers improves the accuracy of species identification but it would only marginally improve genus identification. Finally, we highlight some limitations of the BLAST algorithm as currently implemented and suggest possible improvements for barcoding applications.
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Affiliation(s)
- Ingrid Parmentier
- Evolutionary Biology and Ecology – Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
| | - Jérôme Duminil
- Evolutionary Biology and Ecology – Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
- Sub-regional Office for Central Africa, Bioversity International, Yaoundé, Cameroon
| | - Maria Kuzmina
- Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario, University of Guelph, Guelph, Ontario, Canada
| | - Morgane Philippe
- Evolutionary Biology and Ecology – Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
| | - Duncan W. Thomas
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - David Kenfack
- Department of Botany, Smithsonian Institution, Washington, D.C., United States of America
| | - George B. Chuyong
- Department of Plant and Animal Sciences, University of Buea, Buea, Cameroon
| | - Corinne Cruaud
- Institut de Génomique – Génoscope, Commissariat à l′énergie atomique et aux énergies alternatives (CEA), Evry, France
| | - Olivier J. Hardy
- Evolutionary Biology and Ecology – Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
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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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Ossa G, Kramer-Schadt S, Peel AJ, Scharf AK, Voigt CC. The movement ecology of the straw-colored fruit bat, Eidolon helvum, in sub-Saharan Africa assessed by stable isotope ratios. PLoS One 2012; 7:e45729. [PMID: 23029206 PMCID: PMC3448674 DOI: 10.1371/journal.pone.0045729] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 08/20/2012] [Indexed: 11/18/2022] Open
Abstract
Flying foxes (Pteropodidae) are key seed dispersers on the African continent, yet their migratory behavior is largely unknown. Here, we studied the movement ecology of the straw-colored fruit bat, Eidolon helvum, and other fruit bats by analyzing stable isotope ratios in fur collected from museum specimens. In a triple-isotope approach based on samples of two ecologically similar non-migratory pteropodids, we first confirmed that a stable isotope approach is capable of delineating between geographically distinct locations in Sub-Saharan Africa. A discriminant function analysis assigned 84% of individuals correctly to their capture site. Further, we assessed how well hydrogen stable isotope ratios (δ(2)H) of fur keratin collected from non-migratory species (n = 191 individuals) records variation in δ(2)H of precipitation water in sub-Saharan Africa. Overall, we found positive, negative and no correlations within the six studied species. We then developed a reduced major axis regression equation based on individual data of non-migratory species to predict where potentially migratory E. helvum (n = 88) would come from based on their keratin δ(2)H. Across non-migratory species, δ(2)H of keratin and local water correlated positively. Based on the isoscape origin model, 22% of E. helvum were migratory, i.e. individuals had migrated over at least 250 km prior to their capture. Migratory individuals came from locations at a median distance of about 860 km from the collection site, four even from distances of at least 2,000 km. Ground-truthing of our isoscape origin model based on keratin δ(2)H of extant E. helvum (n = 76) supported a high predictive power of assigning the provenance of African flying foxes. Our study highlights that stable isotope ratios can be used to explain the migratory behavior of flying foxes, even on the isotopically relatively homogenous African continent, and with material collected by museums many decades or more than a century ago.
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Affiliation(s)
- Gonzalo Ossa
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | | | - Alison J. Peel
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- Institute of Zoology, Zoological Society of London, Regent’s Park, London, United Kingdom
| | - Anne K. Scharf
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Christian C. Voigt
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
- Behavioral Biology, Freie Universität Berlin, Germany
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Daïnou K, Laurenty E, Mahy G, Hardy OJ, Brostaux Y, Tagg N, Doucet JL. Phenological patterns in a natural population of a tropical timber tree species, Milicia excelsa (Moraceae): Evidence of isolation by time and its interaction with feeding strategies of dispersers. AMERICAN JOURNAL OF BOTANY 2012; 99:1453-1463. [PMID: 22912370 DOI: 10.3732/ajb.1200147] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
PREMISE OF THE STUDY Population genetic structuring over limited timescales is commonly viewed as a consequence of spatial constraints. Indirect approaches have recently revealed reproductive isolation resulting from flowering time (so-called isolation by time, IBT). Since phenological processes can be subject to selection, the persistence of flowering asynchrony may be due to opposing selective pressures during mating, dispersal, and regeneration phases. Our study aimed to investigate phenology, fruit handling by animals, and their interaction in a timber tree species, Milicia excelsa. METHODS We analyzed phenological data collected over 6 years on 69 genotyped trees in a Cameroonian natural rainforest complemented by data from germination trials and field observations of dispersers. KEY RESULTS Initiation of flowering was correlated with variation in temperature and relative humidity, but was also affected by genetic factors: pairwise differences in flowering time between nearby individuals correlated with kinship coefficient, and earliness of flowering remained stable over time. A decrease in mean seed production per fruit with increasing flowering time suggests selection against late bloomers. However, germination rate was not affected by seed collection date, and the main seed disperser, the bat Eidolon helvum, seemed to increase in abundance at the end of the reproductive season and preferred trees in open habitats where early and late bloomers are expected. CONCLUSIONS The pairwise approach performs well in detecting IBT. The persistence of different mating pools in such a case may result from a trade off between selective forces during the mating and seed dispersal processes.
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Affiliation(s)
- Kasso Daïnou
- Laboratory of Tropical and Subtropical Forestry, Unit of Forest and Nature Management, GxABT, University of Liege, 2 Passage des déportés, 5030 Gembloux, Belgium.
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Odee DW, Telford A, Wilson J, Gaye A, Cavers S. Plio-Pleistocene history and phylogeography of Acacia senegal in dry woodlands and savannahs of sub-Saharan tropical Africa: evidence of early colonisation and recent range expansion. Heredity (Edinb) 2012; 109:372-82. [PMID: 22929152 DOI: 10.1038/hdy.2012.52] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Drylands are extensive across sub-Saharan Africa, socio-economically and ecologically important yet highly sensitive to environmental changes. Evolutionary history, as revealed by contemporary intraspecific genetic variation, can provide valuable insight into how species have responded to past environmental and population changes and guide strategies to promote resilience to future changes. The gum arabic tree (Acacia senegal) is an arid-adapted, morphologically diverse species native to the sub-Saharan drylands. We used variation in nuclear sequences (internal transcribed spacer (ITS)) and two types of chloroplast DNA (cpDNA) markers (PCR-RFLP, cpSSR) to study the phylogeography of the species with 293 individuals from 66 populations sampled across its natural range. cpDNA data showed high regional and rangewide haplotypic diversity (h(T(cpSSR))=0.903-0.948) and population differentiation (G(ST(RFLP))=0.700-0.782) with a phylogeographic pattern that indicated extensive historical gene flow via seed dispersal. Haplotypes were not restricted to any of the four varieties, but showed significant geographic structure (G(ST(cpSSR))=0.392; R(ST)=0.673; R(ST)>R(ST) (permuted)), with the major division separating East and Southern Africa populations from those in West and Central Africa. Phylogenetic analysis of ITS data indicated a more recent origin for the clade including West and Central African haplotypes, suggesting range expansion in this region, possibly during the Holocene humid period. In conjunction with paleobotanical evidence, our data suggest dispersal to West Africa, and across to the Arabian Peninsula and Indian subcontinent, from source populations located in the East African region during climate oscillations of the Plio-Pleistocene.
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Affiliation(s)
- D W Odee
- Centre for Ecology & Hydrology, Bush Estate, Penicuik, Midlothian, Scotland, UK.
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Couvreur TLP, Porter-Morgan H, Wieringa JJ, Chatrou LW. Little ecological divergence associated with speciation in two African rain forest tree genera. BMC Evol Biol 2011; 11:296. [PMID: 21985574 PMCID: PMC3203876 DOI: 10.1186/1471-2148-11-296] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Accepted: 10/11/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The tropical rain forests (TRF) of Africa are the second largest block of this biome after the Amazon and exhibit high levels of plant endemism and diversity. Two main hypotheses have been advanced to explain speciation processes that have led to this high level of biodiversity: allopatric speciation linked to geographic isolation and ecological speciation linked to ecological gradients. Both these hypotheses rely on ecology: in the former conservation of ecological niches through time is implied, while in the latter adaptation via selection to alternative ecological niches would be a prerequisite. Here, we investigate the role of ecology in explaining present day species diversity in African TRF using a species level phylogeny and ecological niche modeling of two predominantly restricted TRF tree genera, Isolona and Monodora (Annonaceae). Both these genera, with 20 and 14 species, respectively, are widely distributed in African TRFs, with a few species occurring in slightly less humid regions such as in East Africa. RESULTS A total of 11 sister species pairs were identified most of them occurring in allopatry or with little geographical overlap. Our results provide a mixed answer on the role of ecology in speciation. Although no sister species have identical niches, just under half of the tests suggest that sister species do have more similar niches than expected by chance. PCA analyses also support little ecological differences between sister species. Most speciation events within both genera predate the Pleistocene, occurring during the Late Miocene and Pliocene periods. CONCLUSIONS Ecology is almost always involved in speciation, however, it would seem to have had a little role in species generation within Isolona and Monodora at the scale analyzed here. This is consistent with the geographical speciation model for TRF diversification. These results contrast to other studies for non-TRF plant species where ecological speciation was found to be an important factor of diversification. The Pliocene period appears to be a vital time in the generation of African TRF diversity, whereas Pleistocene climatic fluctuations have had a smaller role on speciation than previously thought.Ecological niche modeling, species level phylogeny, ecological speciation, African tropics, Isolona, Monodora, Annonaceae.
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Affiliation(s)
- Thomas L P Couvreur
- Institut de Recherche pour le Développement (IRD), UMR DIA-DE, DYNADIV researche group, 911, avenue Agropolis, BP 64501, F-34394 Montpellier cedex 5, France.
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Logossa ZA, Camus-Kulandaivelu L, Allal F, Vaillant A, Sanou H, Kokou K, Bouvet JM. Molecular data reveal isolation by distance and past population expansion for the shea tree (Vitellaria paradoxa C.F. Gaertn) in West Africa. Mol Ecol 2011; 20:4009-27. [PMID: 21914014 DOI: 10.1111/j.1365-294x.2011.05249.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While the genetic structure of many tree species in temperate, American and Asian regions is largely explained by climatic oscillations and subsequent habitat contractions and expansions, little is known about Africa. We investigated the genetic diversity and structure of shea tree (Vitellaria paradoxa,) in Western Africa, an economically important tree species in the Sudano-Sahelian zone. Eleven nuclear microsatellites (nuc) were used to genotype 673 trees selected in 38 populations. They revealed moderate to high within-population diversity: allelic richness ranged from R(nuc) = 3.99 to 5.63. This diversity was evenly distributed across West Africa. Populations were weakly differentiated (F(STnuc) = 0.085; P < 0.0001) and a pattern of isolation by distance was noted. No phylogeographic signal could be detected across the studied sample. Additionally, two chloroplast microsatellite loci, leading to 11 chlorotypes, were used to analyse a sub-set of 370 individuals. Some variation in chloroplast allelic richness among populations could be detected (R(cp) = 0.00 to 4.36), but these differences were not significant. No trend with latitude and longitude were observed. Differentiation was marked (G(STcp) = 0.553; P < 0.0001), but without a significant phylogeographical signal. Population expansion was detected considering the total population using approximate Bayesian computation (nuclear microsatellites) and mismatch distribution (chloroplast microsatellites) methods. This expansion signal and the isolation by distance pattern could be linked to the past climatic conditions in West Africa during the Pleistocene and Holocene which should have been favourable to shea tree development. In addition, human activities through agroforestry and domestication (started 10,000 bp) have probably enhanced gene flow and population expansion.
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Koffi KG, Hardy OJ, Doumenge C, Cruaud C, Heuertz M. Diversity gradients and phylogeographic patterns in Santiria trimera (Burseraceae), a widespread African tree typical of mature rainforests. AMERICAN JOURNAL OF BOTANY 2011; 98:254-264. [PMID: 21613114 DOI: 10.3732/ajb.1000220] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
PREMISE OF THE STUDY New insights into the history of the African rainforest can be gathered from the phylogeographic structures of their constituent species, but few studies have been performed in this ecosystem. We studied the phylogeographic structure of Santiria trimera, a primate- and bird-dispersed, dioecious tree typical of mature African rainforests. METHODS We sequenced three chloroplast DNA (cpDNA) regions (trnL-F, rbcL, and rpl36-infA-rps8) in 377 individuals from 42 populations. RESULTS Sequence chromatograms regularly displayed double peaks of unequal heights. Cloning of PCR products and sequencing of outgroup taxa led to assigning the taller peak in ambiguous sequence positions to cpDNA. A total of 14 polymorphic cpDNA sites and 12 haplotypes were detected. Populations from three distinct biogeographic regions, namely, Upper Guinea, Lower Guinea, and the volcanic island of São Tomé, did not share any haplotype, indicating allopatric divergence. In Lower Guinea, Gabonese forests had high diversity mainly from the sympatry of two genetically divergent morphotypes, whereas forests of eastern Cameroon were less diversified. The two haplotypes of the morphotype without stilt roots were distributed north and south of the Ogooué River, suggesting refuges on both sides of the river bed. CONCLUSIONS The divergence between Upper and Lower Guinean rainforests is explained by the discontinuity of forest between those regions throughout most of the Quaternary. The distribution of rare endemic haplotypes concurred with proposed Pleistocene rainforest refuges in west and southwest Cameroon. Overall, phylogeographic structure is consistent with the biogeographic hypotheses largely based on patterns of species diversity.
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Affiliation(s)
- K Guillaume Koffi
- Université Libre de Bruxelles, Evolutionary Biology and Ecology cp 160/12, Av. F.D. Roosevelt 50; B-1050 Brussels, Belgium.
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