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Freedman AH, Harrigan RJ, Zhen Y, Hamilton AM, Smith TB. Evidence for ecotone speciation across an African rainforest-savanna gradient. Mol Ecol 2023; 32:2287-2300. [PMID: 36718952 DOI: 10.1111/mec.16867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 11/07/2022] [Accepted: 01/16/2023] [Indexed: 02/01/2023]
Abstract
Accelerating climate change and habitat loss make it imperative that plans to conserve biodiversity consider species' ability to adapt to changing environments. However, in biomes where biodiversity is highest, the evolutionary mechanisms responsible for generating adaptative variation and, ultimately, new species are frequently poorly understood. African rainforests represent one such biome, as decadal debates continue concerning the mechanisms generating African rainforest biodiversity. These debates hinge on the relative importance of geographic isolation versus divergent natural selection across environmental gradients. Hindering progress is a lack of robust tests of these competing hypotheses. Because African rainforests are severely at-risk due to climate change and other anthropogenic activities, addressing this long-standing debate is critical for making informed conservation decisions. We use demographic inference and allele frequency-environment relationships to investigate mechanisms of diversification in an African rainforest skink, Trachylepis affinis, a species inhabiting the gradient between rainforest and rainforest-savanna mosaic (ecotone). We provide compelling evidence of ecotone speciation, in which gene flow has all but ceased between rainforest and ecotone populations, at a level consistent with infrequent hybridization between sister species. Parallel patterns of genomic, morphological, and physiological divergence across this environmental gradient and pronounced allele frequency-environment correlation indicate speciation is mostly probably driven by ecological divergence, supporting a central role for divergent natural selection. Our results provide strong evidence for the importance of ecological gradients in African rainforest speciation and inform conservation strategies that preserve the processes that produce and maintain biodiversity.
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Affiliation(s)
- Adam H Freedman
- Faculty of Arts and Sciences Informatics Group, Harvard University, Cambridge, Massachusetts, USA
| | - Ryan J Harrigan
- Centre for Tropical Research and Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA
| | - Ying Zhen
- Centre for Tropical Research and Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Alison M Hamilton
- Department of Biological Sciences, University of Massachusetts-Lowell, Lowell, Massachusetts, USA
| | - Thomas B Smith
- Centre for Tropical Research and Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
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Wang X, Duan F, Zhang H, Han H, Gan X. Fine-scale spatial genetic structure of the endangered plant Tetracentron sinense Oliv. (Trochodendraceae) in Leigong Mountain. Glob Ecol Conserv 2023. [DOI: 10.1016/j.gecco.2023.e02382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Origin, Persistence, and Vulnerability to Climate Changes of Podocarpus Populations in Central African Mountains. FORESTS 2022. [DOI: 10.3390/f13020208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Background and objectives—Podocarpus latifolius (synonym of P. milanjianus) is a key tree representative of Afromontane forests where it is highly threatened by climate and land-use changes. While large populations occur in East Africa, only a few isolated and usually small populations remain in western Central Africa (Cameroon to Angola). Studying the evolutionary history of such relictual populations can thus be relevant to understand their resilience under changing environments. Materials and Methods—we developed nine polymorphic nuclear microsatellites (nSSRs) to estimate genetic variability, (historical) gene flow, and demographic changes among natural populations from Central to East Africa. Results—despite the extended distribution range of P. latifolius, a strong isolation-by-distance pattern emerges at the intra-population scale, indicating low seed and pollen dispersal capacities. Central African populations display a lower genetic diversity (He = 0.34 to 0.61) and are more differentiated from each other (FST = 0.28) than are East African populations (He = 0.65 to 0.71; FST = 0.10), suggesting high genetic drift in the Central African populations. Spatial genetic structure reveals past connections between East and West Africa but also a gene flow barrier across the equator in western Central Africa. Demographic modelling anchors the history of current lineages in the Pleistocene and supports a strong demographic decline in most western populations during the last glacial period. By contrast, no signature of demographic change was detected in East African populations. Conclusions—in Cameroon, our results exclude a recent (re)colonization from one source population of all mountain ranges, but rather indicate long-term persistence of populations in each mountain with fluctuating sizes. A higher impact of genetic drift and further loss of diversity can be expected by survival through climatically unfavorable periods in such small refugial populations. Tracking the Quaternary legacy of podocarp populations is thus essential for their conservation since there is a temporal gap between environment crises and an ecological/genetic answer at the population level.
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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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Vanden Abeele S, Janssens SB, Piñeiro R, Hardy OJ. Evidence of past forest fragmentation in the Congo Basin from the phylogeography of a shade-tolerant tree with limited seed dispersal: Scorodophloeus zenkeri (Fabaceae, Detarioideae). BMC Ecol Evol 2021; 21:50. [PMID: 33784979 PMCID: PMC8011194 DOI: 10.1186/s12862-021-01781-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/15/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Comparative phylogeographic studies on rainforest species that are widespread in Central Africa often reveal genetic discontinuities within and between biogeographic regions, indicating (historical) barriers to gene flow, possibly due to repeated and/or long-lasting population fragmentation during glacial periods according to the forest refuge hypothesis. The impact of forest fragmentation seems to be modulated by the ecological amplitude and dispersal capacities of each species, resulting in different demographic histories. Moreover, while multiple studies investigated the western part of Central Africa (Lower Guinea), few have sufficiently sampled the heart of the Congo Basin (Congolia). In this study, we look for genetic discontinuities between populations of the widespread tropical tree Scorodophloeus zenkeri Harms (Fabaceae, Detarioideae) in Central Africa. Additionally, we characterize genetic diversity, selfing rate and fine-scale spatial genetic structure within populations to estimate the gene dispersal capacity of the species. RESULTS Clear intraspecific genetic discontinuities occur throughout the species' distribution range, with two genetic clusters in Congolia and four in Lower Guinea, and highest differentiation occurring between these bioregions. Genetic diversity is higher in Lower Guinea than Congolia. A spatial genetic structure characteristic of isolation by distance occurs within the genetic clusters. This allowed us to estimate gene dispersal distances (σg) for this outcrossing species with ballistic seed dispersal, which range between 100 and 250 m in areas where S. zenkeri occurs in high densities, and are in the low range of σg values compared to other tropical trees. Gene dispersal distances are larger in low density populations, probably due to extensive pollen dispersal capacity. CONCLUSIONS Fragmentation of S. zenkeri populations seems to have occurred not only in Lower Guinea but also in the Congo Basin, though not necessarily according to previously postulated forest refuge areas. The lower genetic diversity in Congolia compared to Lower Guinea parallels the known gradient of species diversity, possibly reflecting a stronger impact of past climate changes on the forest cover in Congolia. Despite its bisexual flowers, S. zenkeri appears to be mostly outcrossing. The limited dispersal observed in this species implies that genetic discontinuities resulting from past forest fragmentation can persist for a long time before being erased by gene flow.
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Affiliation(s)
- Samuel Vanden Abeele
- Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium.
- Evolutionary Biology and Ecology, Faculté Des Sciences, Université Libre de Bruxelles, Av. F.D. Roosevelt 50, 1050, Brussels, Belgium.
- School of Integrative Plant Sciences, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, 14853, USA.
| | - Steven B Janssens
- Meise Botanic Garden, Nieuwelaan 38, 1860, Meise, Belgium
- Plant Conservation and Population Biology, KU, Leuven, Belgium
| | - Rosalía Piñeiro
- Geography, College of Life and Environmental Sciences, University of Exeter, Laver Building, North Park Road, Exeter, EX4 4QE, UK
| | - Olivier J Hardy
- Evolutionary Biology and Ecology, Faculté Des Sciences, Université Libre de Bruxelles, Av. F.D. Roosevelt 50, 1050, Brussels, Belgium
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Individualistic evolutionary responses of Central African rain forest plants to Pleistocene climatic fluctuations. Proc Natl Acad Sci U S A 2020; 117:32509-32518. [PMID: 33277432 DOI: 10.1073/pnas.2001018117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Understanding the evolutionary dynamics of genetic diversity is fundamental for species conservation in the face of climate change, particularly in hyper-diverse biomes. Species in a region may respond similarly to climate change, leading to comparable evolutionary dynamics, or individualistically, resulting in dissimilar patterns. The second-largest expanse of continuous tropical rain forest (TRF) in the world is found in Central Africa. Here, present-day patterns of genetic structure are thought to be dictated by repeated expansion and contraction of TRFs into and out of refugia during Pleistocene climatic fluctuations. This refugia model implies a common response to past climate change. However, given the unrivalled diversity of TRFs, species could respond differently because of distinct environmental requirements or ecological characteristics. To test this, we generated genome-wide sequence data for >700 individuals of seven codistributed plants from Lower Guinea in Central Africa. We inferred species' evolutionary and demographic histories within a comparative phylogeographic framework. Levels of genetic structure varied among species and emerged primarily during the Pleistocene, but divergence events were rarely concordant. Demographic trends ranged from repeated contraction and expansion to continuous growth. Furthermore, patterns in genetic variation were linked to disparate environmental factors, including climate, soil, and habitat stability. Using a strict refugia model to explain past TRF dynamics is too simplistic. Instead, individualistic evolutionary responses to Pleistocene climatic fluctuations have shaped patterns in genetic diversity. Predicting the future dynamics of TRFs under climate change will be challenging, and more emphasis is needed on species ecology to better conserve TRFs worldwide.
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Lompo D, Vinceti B, Konrad H, Duminil J, Geburek T. Fine-scale spatial genetic structure, mating, and gene dispersal patterns in Parkia biglobosa populations with different levels of habitat fragmentation. AMERICAN JOURNAL OF BOTANY 2020; 107:1041-1053. [PMID: 32638366 PMCID: PMC7496244 DOI: 10.1002/ajb2.1504] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 04/07/2020] [Indexed: 05/30/2023]
Abstract
PREMISE A good understanding of genetic variation and gene dispersal in tree populations is crucial for their sustainable management, particularly in a context of rapid environmental changes. West African Sudanian savannahs are being fragmented and degraded, partly due to expansion of crop cultivation and monocultures that reduce tree density and may impact pollinators. The population dynamics of important indigenous trees could also be affected. We investigated the influence of habitat fragmentation on patterns of genetic diversity and gene dispersal of a key Sudanian agroforestry tree species, Parkia biglobosa. METHODS Using 10 highly polymorphic nuclear microsatellites, we genotyped 2475 samples from reproductive trees, seedlings, and embryos in four tree populations presenting different levels of habitat fragmentation. RESULTS Parkia biglobosa presented similar high genetic diversity across the four populations studied. Genetic diversity and inbreeding were similar between adults and embryo cohorts. In all four populations, the selfing rate was less than 1%. The effective number of pollen donors per tree was high (NEP ~ 18-22), as was the pollen immigration rate (from 34 to 74%). Pollen dispersal was characterized by a fat-tailed distribution with mean estimates exceeding 200 m. In three populations, stem diameter had a pronounced effect on male reproductive success. Here, the highest male reproductive success was observed in trees with a diameter at breast height between 60 and 75 cm. CONCLUSIONS At the scale analyzed, fragmentation does not seem to pose limitations to gene flow in any of the sites investigated, regardless of the landscape configuration associated with the different tree stands. The study provides useful insights on the reproductive biology of an important tree species in the West African savannahs.
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Affiliation(s)
- Djingdia Lompo
- Centre National de Semences Forestières01 BP 2682Ouagadougou 01Burkina Faso
- Department of Forest GeneticsAustrian Research and Training Centre for ForestsSeckendorff‐Gudent‐Weg 81131ViennaAustria
| | - Barbara Vinceti
- Bioversity InternationalViale Tre Denari 47200054MaccareseRomeItaly
| | - Heino Konrad
- Department of Forest GeneticsAustrian Research and Training Centre for ForestsSeckendorff‐Gudent‐Weg 81131ViennaAustria
| | - Jérôme Duminil
- Bioversity InternationalViale Tre Denari 47200054MaccareseRomeItaly
- UMR‐DIADEInstitut de Recherche pour le DéveloppementUniv. MontpellierMontpellierFrance
- Service Evolution Biologique et Ecologie, CP160 ⁄ 12Faculté des SciencesUniversité Libre de Bruxelles50 Av. F. Roosevelt1050BrusselsBelgium
| | - Thomas Geburek
- Department of Forest GeneticsAustrian Research and Training Centre for ForestsSeckendorff‐Gudent‐Weg 81131ViennaAustria
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Donkpegan ASL, Piñeiro R, Heuertz M, Duminil J, Daïnou K, Doucet JL, Hardy OJ. Population genomics of the widespread African savannah trees Afzelia africana and Afzelia quanzensis reveals no significant past fragmentation of their distribution ranges. AMERICAN JOURNAL OF BOTANY 2020; 107:498-509. [PMID: 32200549 DOI: 10.1002/ajb2.1449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 01/13/2020] [Indexed: 06/10/2023]
Abstract
PREMISE Few studies have addressed the evolutionary history of tree species from African savannahs. Afzelia contains economically important timber species, including two species widely distributed in African savannahs: A. africana in the Sudanian region and A. quanzensis in the Zambezian region. We aimed to infer whether these species underwent range fragmentation and/or demographic changes, possibly reflecting how savannahs responded to Quaternary climate changes. METHODS We characterized the genetic diversity and structure of these species across their distribution ranges using nuclear microsatellites (SSRs) and genotyping-by-sequencing (GBS) markers. Six SSR loci were genotyped in 241 A. africana and 113 A. quanzensis individuals, while 2800 high-quality single nucleotide polymorphisms (SNPs) were identified in 30 A. africana individuals. RESULTS Both species appeared to be mainly outcrossing. The kinship between individuals decayed with the logarithm of the distance at similar rates across species and markers, leading to relatively small Sp statistics (0.0056 for SSR and 0.0054 for SNP in A. africana, 0.0075 for SSR in A. quanzensis). The patterns were consistent with isolation by distance expectations in the absence of large-scale geographic gradients. Bayesian clustering of SSR genotypes did not detect genetic clusters within species. In contrast, SNP data resolved intraspecific genetic clusters in A. africana, illustrating the higher resolving power of GBS. However, these clusters revealed low levels of differentiation and no clear geographical entities, so that they were interpreted as resulting from the isolation by distance pattern rather than from past population fragmentation. CONCLUSIONS These results suggest that populations have remained connected throughout the large, continuous savannah landscapes. The absence of clear phylogeographic discontinuities, also found in a few other African savannah trees, indicates that their distribution ranges have not been significantly fragmented during the climatic oscillations of the Pleistocene, in contrast to patterns commonly found in African rainforest trees.
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Affiliation(s)
- Armel S L Donkpegan
- Forest is Life, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, 2 Passage des Déportés, B-5030, Gembloux, Belgium
- Evolutionary Biology and Ecology Unit, CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050, Brussels, Belgium
- Univ. Bordeaux, INRAE, BFP, 71 Avenue Edouard Bourlaux, F-33882, Villenave d'Ornon, France
| | - Rosalía Piñeiro
- University of Exeter, Geography, College of Life and Environmental Sciences, Stocker road, EX44QD, Exeter, UK
- Evolutionary Genomics, Centre for Geogenetics - Natural History Museum of Denmark, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Myriam Heuertz
- Univ. Bordeaux, INRAE, BIOGECO, 69 route d'Arcachon, F-33610, Cestas, France
| | - Jérôme Duminil
- Evolutionary Biology and Ecology Unit, CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050, Brussels, Belgium
- DIADE, IRD, University of Montpellier, 911 Avenue Agropolis, BP 64501, 34394, Montpellier, France
- Bioversity International, Forest Genetic Resources and Restoration Programme, Sub-Regional Office for Central Africa, P.O. Box 2008, Messa, Yaoundé, Cameroon
| | - Kasso Daïnou
- Forest is Life, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, 2 Passage des Déportés, B-5030, Gembloux, Belgium
- Evolutionary Biology and Ecology Unit, CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050, Brussels, Belgium
- Université d'Agriculture de Kétou, BP: 43, Kétou, Benin
| | - Jean-Louis Doucet
- Forest is Life, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, 2 Passage des Déportés, B-5030, Gembloux, Belgium
| | - Olivier J Hardy
- Evolutionary Biology and Ecology Unit, CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. D. Roosevelt, B-1050, Brussels, Belgium
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Hardy OJ, Delaide B, Hainaut H, Gillet J, Gillet P, Kaymak E, Vankerckhove N, Duminil J, Doucet J. Seed and pollen dispersal distances in two African legume timber trees and their reproductive potential under selective logging. Mol Ecol 2019; 28:3119-3134. [DOI: 10.1111/mec.15138] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/24/2019] [Accepted: 05/09/2019] [Indexed: 02/03/2023]
Affiliation(s)
- Olivier J. Hardy
- Evolutionary Biology and Ecology Unit CP 160/12 Faculté des Sciences Université Libre de Bruxelles Brussels Belgium
| | - Boris Delaide
- Evolutionary Biology and Ecology Unit CP 160/12 Faculté des Sciences Université Libre de Bruxelles Brussels Belgium
| | - Hélène Hainaut
- Evolutionary Biology and Ecology Unit CP 160/12 Faculté des Sciences Université Libre de Bruxelles Brussels Belgium
| | - Jean‐François Gillet
- TERRA Teaching and Research Centre Forest is Life Gembloux Agro‐Bio Tech Université de Liège Gembloux Belgium
- Nature Forest Environment Freelance in Tropical Forestry Porcheresse Belgium
| | - Pauline Gillet
- TERRA Teaching and Research Centre Forest is Life Gembloux Agro‐Bio Tech Université de Liège Gembloux Belgium
| | - Esra Kaymak
- Evolutionary Biology and Ecology Unit CP 160/12 Faculté des Sciences Université Libre de Bruxelles Brussels Belgium
| | - Nina Vankerckhove
- Evolutionary Biology and Ecology Unit CP 160/12 Faculté des Sciences Université Libre de Bruxelles Brussels Belgium
| | - Jérôme Duminil
- Evolutionary Biology and Ecology Unit CP 160/12 Faculté des Sciences Université Libre de Bruxelles Brussels Belgium
- DIADE, IRD Univ Montpellier Montpellier France
- Bioversity International Forest Genetic Resources and Restoration Programme Sub‐Regional Office for Central Africa Messa, Yaoundé Cameroon
| | - Jean‐Louis Doucet
- TERRA Teaching and Research Centre Forest is Life Gembloux Agro‐Bio Tech Université de Liège Gembloux Belgium
- Nature+ asbl Wavre Belgium
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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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Monthe FK, Hardy OJ, Doucet JL, Loo J, Duminil J. Extensive seed and pollen dispersal and assortative mating in the rain forest tree Entandrophragma cylindricum (Meliaceae) inferred from indirect and direct analyses. Mol Ecol 2017; 26:5279-5291. [PMID: 28734064 DOI: 10.1111/mec.14241] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 04/17/2017] [Accepted: 07/05/2017] [Indexed: 02/02/2023]
Abstract
Pollen and seed dispersal are key processes affecting the demographic and evolutionary dynamics of plant species and are also important considerations for the sustainable management of timber trees. Through direct and indirect genetic analyses, we studied the mating system and the extent of pollen and seed dispersal in an economically important timber species, Entandrophragma cylindricum (Meliaceae). We genotyped adult trees, seeds and saplings from a 400-ha study plot in a natural forest from East Cameroon using eight nuclear microsatellite markers. The species is mainly outcrossed (t = 0.92), but seeds from the same fruit are often pollinated by the same father (correlated paternity, rp = 0.77). An average of 4.76 effective pollen donors (Nep ) per seed tree contributes to the pollination. Seed dispersal was as extensive as pollen dispersal, with a mean dispersal distance in the study plot approaching 600 m, and immigration rates from outside the plot to the central part of the plot reaching 40% for both pollen and seeds. Extensive pollen- and seed-mediated gene flow is further supported by the weak, fine-scale spatial genetic structure (Sp statistic = 0.0058), corresponding to historical gene dispersal distances (σg ) reaching approximately 1,500 m. Using an original approach, we showed that the relatedness between mating individuals (Fij = 0.06) was higher than expected by chance, given the extent of pollen dispersal distances (expected Fij = 0.02 according to simulations). This remarkable pattern of assortative mating could be a phenomenon of potentially consequential evolutionary and management significance that deserves to be studied in other plant populations.
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Affiliation(s)
- Franck Kameni Monthe
- Bioversity International, c/o CIFOR Central Africa Regional Office, Yaoundé, Cameroon.,Faculté des Sciences, Service Evolution Biologique et Ecologie, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Olivier J Hardy
- Faculté des Sciences, Service Evolution Biologique et Ecologie, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Jean-Louis Doucet
- Foresterie Tropicale, Gestion des Ressources Forestières, BIOSE, Gembloux Agro-Bio Tech, Université de Liège, Gembloux, Belgium
| | - Judy Loo
- Bioversity International, Rome, Italy
| | - Jérôme Duminil
- Bioversity International, c/o CIFOR Central Africa Regional Office, Yaoundé, Cameroon.,Faculté des Sciences, Service Evolution Biologique et Ecologie, Université Libre de Bruxelles, Bruxelles, Belgium.,Institut de Recherche pour le Développement, UMR-DIADE, Montpellier, France
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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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13
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Torroba-Balmori P, Budde KB, Heer K, González-Martínez SC, Olsson S, Scotti-Saintagne C, Casalis M, Sonké B, Dick CW, Heuertz M. Altitudinal gradients, biogeographic history and microhabitat adaptation affect fine-scale spatial genetic structure in African and Neotropical populations of an ancient tropical tree species. PLoS One 2017; 12:e0182515. [PMID: 28771629 PMCID: PMC5542443 DOI: 10.1371/journal.pone.0182515] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/08/2017] [Indexed: 01/08/2023] Open
Abstract
The analysis of fine-scale spatial genetic structure (FSGS) within populations can provide insights into eco-evolutionary processes. Restricted dispersal and locally occurring genetic drift are the primary causes for FSGS at equilibrium, as described in the isolation by distance (IBD) model. Beyond IBD expectations, spatial, environmental or historical factors can affect FSGS. We examined FSGS in seven African and Neotropical populations of the late-successional rain forest tree Symphonia globulifera L. f. (Clusiaceae) to discriminate the influence of drift-dispersal vs. landscape/ecological features and historical processes on FSGS. We used spatial principal component analysis and Bayesian clustering to assess spatial genetic heterogeneity at SSRs and examined its association with plastid DNA and habitat features. African populations (from Cameroon and São Tomé) displayed a stronger FSGS than Neotropical populations at both marker types (mean Sp = 0.025 vs. Sp = 0.008 at SSRs) and had a stronger spatial genetic heterogeneity. All three African populations occurred in pronounced altitudinal gradients, possibly restricting animal-mediated seed dispersal. Cyto-nuclear disequilibria in Cameroonian populations also suggested a legacy of biogeographic history to explain these genetic patterns. Conversely, Neotropical populations exhibited a weaker FSGS, which may reflect more efficient wide-ranging seed dispersal by Neotropical bats and other dispersers. The population from French Guiana displayed an association of plastid haplotypes with two morphotypes characterized by differential habitat preferences. Our results highlight the importance of the microenvironment for eco-evolutionary processes within persistent tropical tree populations.
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Affiliation(s)
- Paloma Torroba-Balmori
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, Madrid, Spain
- Sustainable Forest Management Research Institute, University of Valladolid - INIA, Palencia, Spain
| | | | - Katrin Heer
- Institute of Experimental Ecology, University of Ulm, Ulm, Germany
- Conservation Biology and Ecology, University of Marburg, Marburg, Germany
| | - Santiago C. González-Martínez
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, Madrid, Spain
- Sustainable Forest Management Research Institute, University of Valladolid - INIA, Palencia, Spain
- UMR BIOGECO, INRA, University of Bordeaux, Cestas, France
| | - Sanna Olsson
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, Madrid, Spain
| | | | | | - Bonaventure Sonké
- Ecole Normale Supérieure, Université de Yaoundé I, Yaoundé, Cameroon
- Evolutionary Biology and Ecology, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
| | - Christopher W. Dick
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Smithsonian Tropical Research Institute, Republic of Panama
| | - Myriam Heuertz
- Department of Forest Ecology and Genetics, INIA Forest Research Centre, Madrid, Spain
- UMR BIOGECO, INRA, University of Bordeaux, Cestas, France
- Evolutionary Biology and Ecology, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
- * E-mail:
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Faye A, Deblauwe V, Mariac C, Richard D, Sonké B, Vigouroux Y, Couvreur TLP. Phylogeography of the genus Podococcus (Palmae/Arecaceae) in Central African rain forests: Climate stability predicts unique genetic diversity. Mol Phylogenet Evol 2016; 105:126-138. [PMID: 27521478 DOI: 10.1016/j.ympev.2016.08.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Revised: 08/08/2016] [Accepted: 08/09/2016] [Indexed: 11/16/2022]
Abstract
The tropical rain forests of Central Africa contain high levels of species diversity. Paleovegetation or biodiversity patterns suggested successive contraction/expansion phases on this rain forest cover during the last glacial maximum (LGM). Consequently, the hypothesis of the existence of refugia e.g. habitat stability that harbored populations during adverse climatic periods has been proposed. Understory species are tightly associated to forest cover and consequently are ideal markers of forest dynamics. Here, we used two central African rain forest understory species of the palm genus, Podococcus, to assess the role of past climate variation on their distribution and genetic diversity. Species distribution modeling in the present and at the LGM was used to estimate areas of climatic stability. Genetic diversity and phylogeography were estimated by sequencing near complete plastomes for over 120 individuals. Areas of climatic stability were mainly located in mountainous areas like the Monts de Cristal and Monts Doudou in Gabon, but also lowland coastal forests in southeast Cameroon and northeast Gabon. Genetic diversity analyses shows a clear North-South structure of genetic diversity within one species. This divide was estimated to have originated some 500,000years ago. We show that, in Central Africa, high and unique genetic diversity is strongly correlated with inferred areas of climatic stability since the LGM. Our results further highlight the importance of coastal lowland rain forests in Central Africa as harboring not only high species diversity but also important high levels of unique genetic diversity. In the context of strong human pressure on coastal land use and destruction, such unique diversity hotspots need to be considered in future conservation planning.
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Affiliation(s)
- A Faye
- Institut de Recherche pour le Développement, UMR-DIADE, BP 64501, F-34394 Montpellier cedex 5, France; Université de Yaoundé I, Ecole Normale Supérieure, Département des Sciences Biologiques, Laboratoire de Botanique systématique et d'Ecologie, B.P. 047, Yaoundé, Cameroon.
| | - V Deblauwe
- Institut de Recherche pour le Développement, UMR-DIADE, BP 64501, F-34394 Montpellier cedex 5, France; Université de Yaoundé I, Ecole Normale Supérieure, Département des Sciences Biologiques, Laboratoire de Botanique systématique et d'Ecologie, B.P. 047, Yaoundé, Cameroon
| | - C Mariac
- Institut de Recherche pour le Développement, UMR-DIADE, BP 64501, F-34394 Montpellier cedex 5, France
| | - D Richard
- Institut de Recherche pour le Développement, UMR-DIADE, BP 64501, F-34394 Montpellier cedex 5, France
| | - B Sonké
- Université de Yaoundé I, Ecole Normale Supérieure, Département des Sciences Biologiques, Laboratoire de Botanique systématique et d'Ecologie, B.P. 047, Yaoundé, Cameroon
| | - Y Vigouroux
- Institut de Recherche pour le Développement, UMR-DIADE, BP 64501, F-34394 Montpellier cedex 5, France
| | - T L P Couvreur
- Institut de Recherche pour le Développement, UMR-DIADE, BP 64501, F-34394 Montpellier cedex 5, France; Université de Yaoundé I, Ecole Normale Supérieure, Département des Sciences Biologiques, Laboratoire de Botanique systématique et d'Ecologie, B.P. 047, Yaoundé, Cameroon; Naturalis Biodiversity Centre, Botany Section, Darwinweg 2, 2333 CR Leiden, The Netherlands
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15
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Implications of spatial genetic patterns for conserving African leopards. C R Biol 2015; 338:728-37. [PMID: 26321316 DOI: 10.1016/j.crvi.2015.06.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 06/18/2015] [Accepted: 06/18/2015] [Indexed: 11/22/2022]
Abstract
The leopard (Panthera pardus) is heavily persecuted in areas where it predates livestock and threatens human well-being. Attempts to resolve human-leopard conflict typically involve translocating problem animals; however, these interventions are rarely informed by genetic studies and can unintentionally compromise the natural spatial genetic structure and diversity, and possibly the long-term persistence, of the species. No significant genetic discontinuities were definable within the southern African leopard population. Analysis of fine-scale genetic data derived from mitochondrial and nuclear DNA revealed that the primary natural process shaping the spatial genetic structure of the species is isolation-by-distance (IBD). The effective gene dispersal (σ) index can inform leopard translocations and is estimated to be 82 km for some South African leopards. The importance of adopting an evidence-based strategy is discussed for supporting the integration of genetic data, spatial planning and social learning institutions so as to promote collaboration between land managers, government agency staff and researchers.
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16
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Nistelberger HM, Coates DJ, Llorens TM, Yates CJ, Byrne M. A cryptic genetic boundary in remnant populations of a long-lived, bird-pollinated shrubBanksia sphaerocarpavar.caesia(Proteaceae). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12521] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Heidi M. Nistelberger
- Science and Conservation Division; Department of Parks and Wildlife; Bentley Delivery Centre; Locked Bag 104 Perth WA 6983 Australia
| | - David J. Coates
- Science and Conservation Division; Department of Parks and Wildlife; Bentley Delivery Centre; Locked Bag 104 Perth WA 6983 Australia
| | - Tanya M. Llorens
- Science and Conservation Division; Department of Parks and Wildlife; Bentley Delivery Centre; Locked Bag 104 Perth WA 6983 Australia
| | - Colin J. Yates
- Science and Conservation Division; Department of Parks and Wildlife; Bentley Delivery Centre; Locked Bag 104 Perth WA 6983 Australia
| | - Margaret Byrne
- Science and Conservation Division; Department of Parks and Wildlife; Bentley Delivery Centre; Locked Bag 104 Perth WA 6983 Australia
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Anthony NM, Atteke C, Bruford MW, Dallmeier F, Freedman A, Hardy O, Ibrahim B, Jeffery KJ, Johnson M, Lahm SA, Lepengue N, Lowenstein JH, Maisels F, Mboumba JF, Mickala P, Morgan K, Ntie S, Smith TB, Sullivan JP, Verheyen E, Gonder MK. Evolution and Conservation of Central African Biodiversity: Priorities for Future Research and Education in the Congo Basin and Gulf of Guinea. Biotropica 2014. [DOI: 10.1111/btp.12188] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicola M. Anthony
- Department of Biological Sciences; University of New Orleans; New Orleans Louisiana 70148 U.S.A
| | - Christiane Atteke
- Département de Biologie; Université des Sciences et Techniques de Masuku; Franceville B.P. 901 Gabon
| | - Michael W. Bruford
- Organisms and Environment Division; School of Biosciences; Cardiff University; Cardiff CF10 3TL U.K
| | - Francisco Dallmeier
- Smithsonian Conservation Biology Institute; Center for Conservation Education and Sustainability; Box 37012 MRC 705 Washington DC 20013-7012 U.S.A
| | - Adam Freedman
- Department of Ecology and Evolutionary Biology and Center for Tropical Research; Institute of Environment and Sustainability; University of California Los Angeles; Los Angeles California 90092 U.S.A
- Department of Organismic and Evolutionary Biology; Harvard University; Boston Massachusetts U.S.A
| | - Olivier Hardy
- Evolutionary Biology and Ecology; Université Libre de Bruxelles; CP 160/12 1050 Brussels Belgium
| | - Brama Ibrahim
- Département de Biologie; Université des Sciences et Techniques de Masuku; Franceville B.P. 901 Gabon
| | - Kathryn J. Jeffery
- Agence Nationale des Parcs Nationaux; Libreville BP 20379 Gabon
- School of Natural Sciences; University of Stirling; Stirling FK9 4LA U.K
- Institut de Recherche en Écologie Tropicale; BP13354 Libreville Gabon
| | - Mireille Johnson
- Gabon Biodiversity Program; Center for Conservation Education and Sustainability; Smithsonian Conservation Biology Institute; B.P. 48 Gamba Gabon
| | - Sally A. Lahm
- Department of Global Health; George Washington University; Washington DC 20037 U.S.A
| | - Nicaise Lepengue
- Département de Biologie; Université des Sciences et Techniques de Masuku; Franceville B.P. 901 Gabon
| | - Jacob H. Lowenstein
- Department of Ecology Evolution and Environmental Biology; Columbia University; New York New York 10027 U.S.A
- Division of Vertebrate Zoology; American Museum of Natural History; New York New York 10024 U.S.A
| | - Fiona Maisels
- School of Natural Sciences; University of Stirling; Stirling FK9 4LA U.K
- Wildlife Conservation Society; 2300 Southern Boulevard New York New York 10460 U.S.A
| | - Jean-François Mboumba
- Département de Biologie; Université des Sciences et Techniques de Masuku; Franceville B.P. 901 Gabon
- Equipe Biodiversité et Gestion des Territoires; UMR 7204 Muséum National d'Histoire Naturelle; Université de Rennes 1; Rennes France
| | - Patrick Mickala
- Département de Biologie; Université des Sciences et Techniques de Masuku; Franceville B.P. 901 Gabon
| | - Katy Morgan
- Department of Biological Sciences; University of New Orleans; New Orleans Louisiana 70148 U.S.A
| | - Stephan Ntie
- Département de Biologie; Université des Sciences et Techniques de Masuku; Franceville B.P. 901 Gabon
| | - Thomas B. Smith
- Department of Ecology and Evolutionary Biology and Center for Tropical Research; Institute of Environment and Sustainability; University of California Los Angeles; Los Angeles California 90092 U.S.A
| | - John P. Sullivan
- Cornell University Museum of Vertebrates; Ithaca New York 14850 U.S.A
| | - Erik Verheyen
- OD Taxonomy and Phylogeny; Vertebrates; Royal Belgian Institute of Natural Sciences; Vautierstraat 29 1000 Brussels Belgium
- Evolutionary Biology Group; Department of Biology; University of Antwerp; Groenenborgerlaan 171 2020 Antwerpen Belgium
| | - Mary K. Gonder
- Department of Biology; Drexel University; Philadelphia Pennsylvannia 19104 U.S.A
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18
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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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21
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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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Nazareno AG, Alzate-Marin AL, Pereira RAS. Dioecy, more than monoecy, affects plant spatial genetic structure: the case study of Ficus. Ecol Evol 2013; 3:3495-508. [PMID: 24223285 PMCID: PMC3797494 DOI: 10.1002/ece3.739] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 06/28/2013] [Accepted: 07/01/2013] [Indexed: 11/08/2022] Open
Abstract
In this analysis, we attempt to understand how monoecy and dioecy drive spatial genetic structure (SGS) in plant populations. For this purpose, plants of the genus Ficus were used as a comparative model due to their particular characteristics, including high species diversity, variation in life histories, and sexual systems. One of the main issues we assessed is whether dioecious fig tree populations are more spatially genetically structured than monoecious populations. Using the Sp statistic, which allows for quantitative comparisons among different studies, we compared the extent of SGS between monoecious and dioecious Ficus species. To broaden our conclusions we used published data on an additional 27 monoecious and dioecious plant species. Furthermore, genetic diversity analyses were performed for two monoecious Ficus species using 12 microsatellite markers in order to strengthen our conclusions about SGS. Our results show that dioecy, more than monoecy, significantly contributes to SGS in plant populations. On average, the estimate of Sp was six times higher for dioecious Ficus species than monoecious Ficus species and it was two times higher in dioecious than monoecious plant species. Considering these results, we emphasize that the long-distance pollen dispersal mechanism in monoecious Ficus species seems to be the dominant factor in determining weak spatial genetic structure, high levels of genetic diversity, and lack of inbreeding. Although Ficus constitute a model species to study SGS, a more general comparison encompassing a wider range of plants is required in order to better understand how sexual systems affect genetic structure.
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Affiliation(s)
- Alison G Nazareno
- Federal University of Santa Catarina, UFSC Avenida Ademar Gonzaga, 1346, 88040-000, Florianópolis, Santa Catarina, Brazil ; Programa de Pós-graduação em Biologia Comparada, FFCLRP/USP Avenida Bandeirantes, 3900, 14049-900, Ribeirão Preto, Sao Paulo, Brazil
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Forest fragmentation and edge effects on the genetic structure ofClusia sphaerocarpaandC. lechleri(Clusiaceae) in tropical montane forests. JOURNAL OF TROPICAL ECOLOGY 2013. [DOI: 10.1017/s0266467413000345] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Abstract:Fragmentation of tropical forests influences abiotic and biotic processes that affect the genetic structure of plant populations. In forest fragments, edge effects, i.e. changes of abiotic and biotic factors at forest edges, may be prevalent. In two forest fragments (c. 200 ha atc. 2450 m asl) of tropical montane forest in Bolivia, sympatric populations of the dioecious tree speciesClusia sphaerocarpaandC. lechleriwere used as case study species to compare genetic diversity and small-scale genetic structure (SGS) between edge and interior habitats. Eight microsatellite markers were employed to genotype 343 individuals including adults, juveniles and seedlings ofC. sphaerocarpaand 196 ofC. lechleri. Genetic differentiation was found between habitats in both species (ΦRT= 0.071 forC. sphaerocarpaand ΦRT= 0.028 forC. lechleri) and among ages inC. sphaerocarpa(ΦRT= 0.016). Overall, SGS was weak but significant with more pronounced SGS inC. lechleri(Sp= 0.0128) than inC. sphaerocarpa(Sp= 0.0073). However, positive spatial genetic autocorrelation extended only up to 10 m. ForC. sphaerocarpa, SGS was stronger in seedling and juvenile stages than in adults and in the forest interior than at forest edges. Our results show that edge effects can extend to the genetic level by breaking-up local genetic structures, probably due to increased gene flow and enhanced pollination and seed-dispersal interactions at forest edges.
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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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25
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Genetic diversity and the mating system in a fragmented population of Tsoongiodendron odorum. ACTA ACUST UNITED AC 2013. [DOI: 10.3724/sp.j.1003.2012.09083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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He R, Wang J, Huang H. Long-distance gene dispersal inferred from spatial genetic structure in Handeliodendron bodinieri, an endangered tree from karst forest in southwest China. BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2012.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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27
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Zheng DJ, Xie LS, Zhu JH, Zhang ZL. Low genetic diversity and local adaptive divergence of Dracaena cambodiana (Liliaceae) populations associated with historical population bottlenecks and natural selection: an endangered long-lived tree endemic to Hainan Island, China. PLANT BIOLOGY (STUTTGART, GERMANY) 2012; 14:828-838. [PMID: 22404781 DOI: 10.1111/j.1438-8677.2011.00559.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Historical population bottlenecks and natural selection have important effects on the current genetic diversity and structure of long-lived trees. Dracaena cambodiana is an endangered, long-lived tree endemic to Hainan Island, China. Our field investigations showed that only 10 populations remain on Hainan Island and that almost all have been seriously isolated and grow in distinct habitats. A considerable amount of genetic variation at the species level, but little variation at the population level, and a high level of genetic differentiation among the populations with limited gene flow in D. cambodiana were detected using inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) analyses. No significant correlation was found between genetic diversity and actual population size, as the genetic diversities were similar regardless of population size. The Mantel test revealed that there was no correlation between genetic and geographic distances among the 10 populations. The UPGMA, PCoA and Bayesian analyses showed that local adaptive divergence has occurred among the D. cambodiana populations, which was further supported by habitat-private fragments. We suggest that the current genetic diversity and population differentiation of D. cambodiana resulted from historical population bottlenecks and natural selection followed by historical isolation. However, the lack of natural regeneration of D. cambodiana indicates that former local adaptations with low genetic diversity may have been genetically weak and are unable to adapt to the current ecological environments.
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Affiliation(s)
- D-J Zheng
- Key Laboratory of Crop Genetics and Breeding of Hainan Province, Hainan Academy of Agricultural Sciences, Haikou, China Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - L-S Xie
- Key Laboratory of Crop Genetics and Breeding of Hainan Province, Hainan Academy of Agricultural Sciences, Haikou, China Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - J-H Zhu
- Key Laboratory of Crop Genetics and Breeding of Hainan Province, Hainan Academy of Agricultural Sciences, Haikou, China Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Z-L Zhang
- Key Laboratory of Crop Genetics and Breeding of Hainan Province, Hainan Academy of Agricultural Sciences, Haikou, China Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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Wang R, Compton SG, Shi YS, Chen XY. Fragmentation reduces regional-scale spatial genetic structure in a wind-pollinated tree because genetic barriers are removed. Ecol Evol 2012; 2:2250-61. [PMID: 23139883 PMCID: PMC3488675 DOI: 10.1002/ece3.344] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 06/24/2012] [Accepted: 07/02/2012] [Indexed: 11/08/2022] Open
Abstract
Gene flow strongly influences the regional genetic structuring of plant populations. Seed and pollen dispersal patterns can respond differently to the increased isolation resulting from habitat fragmentation, with unpredictable consequences for gene flow and population structuring. In a recently fragmented landscape we compared the pre- and post-fragmentation genetic structure of populations of a tree species where pollen and seed dispersal respond differentially to forest fragmentation generated by flooding. Castanopsis sclerophylla is wind-pollinated, with seeds that are dispersed by gravity and rodents. Using microsatellites, we found no significant difference in genetic diversity between pre- and post-fragmentation cohorts. Significant genetic structure was observed in pre-fragmentation cohorts, due to an unknown genetic barrier that had isolated one small population. Among post-fragmentation cohorts this genetic barrier had disappeared and genetic structure was significantly weakened. The strengths of genetic structuring were at a similar level in both cohorts, suggesting that overall gene flow of C. sclerophylla has been unchanged by fragmentation at the regional scale. Fragmentation has blocked seed dispersal among habitats, but this appears to have been compensated for by enhanced pollen dispersal, as indicated by the disappearance of a genetic barrier, probably as a result of increased wind speeds and easier pollen movement over water. Extensive pollen flow can counteract some negative effects of fragmentation and assist the long-term persistence of small remnant populations.
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Affiliation(s)
- Rong Wang
- Tiantong National Observation Station of Forest Ecosystems, Department of Environmental Sciences, East China Normal University Shanghai, 200062, China ; School of Biology, Faculty of Biological Sciences, University of Leeds Leeds, LS2 9JT, UK
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Martínez A, Ferrando A, Manunza A, Gómez M, Landi V, Jordana J, Capote J, Badaoui B, Vidal O, Delgado J, Amills M. Inferring the demographic history of a highly endangered goat breed through the analysis of nuclear and mitochondrial genetic signatures. Small Rumin Res 2012. [DOI: 10.1016/j.smallrumres.2011.11.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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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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Holstein N, Renner SS. A dated phylogeny and collection records reveal repeated biome shifts in the African genus Coccinia (Cucurbitaceae). BMC Evol Biol 2011; 11:28. [PMID: 21269492 PMCID: PMC3041684 DOI: 10.1186/1471-2148-11-28] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 01/26/2011] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Conservatism in climatic tolerance may limit geographic range expansion and should enhance the effects of habitat fragmentation on population subdivision. Here we study the effects of historical climate change, and the associated habitat fragmentation, on diversification in the mostly sub-Saharan cucurbit genus Coccinia, which has 27 species in a broad range of biota from semi-arid habitats to mist forests. Species limits were inferred from morphology, and nuclear and plastid DNA sequence data, using multiple individuals for the widespread species. Climatic tolerances were assessed from the occurrences of 1189 geo-referenced collections and WorldClim variables. RESULTS Nuclear and plastid gene trees included 35 or 65 accessions, representing up to 25 species. The data revealed four species groups, one in southern Africa, one in Central and West African rain forest, one widespread but absent from Central and West African rain forest, and one that occurs from East Africa to southern Africa. A few individuals are differently placed in the plastid and nuclear (LFY) trees or contain two ITS sequence types, indicating hybridization. A molecular clock suggests that the diversification of Coccinia began about 6.9 Ma ago, with most of the extant species diversity dating to the Pliocene. Ancestral biome reconstruction reveals six switches between semi-arid habitats, woodland, and forest, and members of several species pairs differ significantly in their tolerance of different precipitation regimes. CONCLUSIONS The most surprising findings of this study are the frequent biome shifts (in a relatively small clade) over just 6 - 7 million years and the limited diversification during and since the Pleistocene. Pleistocene climate oscillations may have been too rapid or too shallow for full reproductive barriers to develop among fragmented populations of Coccinia, which would explain the apparently still ongoing hybridization between certain species. Steeper ecological gradients in East Africa and South Africa appear to have resulted in more advanced allopatric speciation there.
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Affiliation(s)
- Norbert Holstein
- Systematic Botany and Mycology, University of Munich (LMU), Menzinger Strasse 67, Munich, Germany
| | - Susanne S Renner
- Systematic Botany and Mycology, University of Munich (LMU), Menzinger Strasse 67, Munich, Germany
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