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Cuni-Sanchez A, Martin EH, Uzabaho E, Ngute ASK, Bitariho R, Kayijamahe C, Marshall AR, Mohamed NA, Mseja GA, Nkwasibwe A, Rovero F, Sheil D, Tinkasimire R, Tumugabirwe L, Feeley KJ, Sullivan MJP. Evidence of thermophilization in Afromontane forests. Nat Commun 2024; 15:5554. [PMID: 38987543 PMCID: PMC11236992 DOI: 10.1038/s41467-024-48520-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 05/03/2024] [Indexed: 07/12/2024] Open
Abstract
Thermophilization is the directional change in species community composition towards greater relative abundances of species associated with warmer environments. This process is well-documented in temperate and Neotropical plant communities, but it is uncertain whether this phenomenon occurs elsewhere in the tropics. Here we extend the search for thermophilization to equatorial Africa, where lower tree diversity compared to other tropical forest regions and different biogeographic history could affect community responses to climate change. Using re-census data from 17 forest plots in three mountain regions of Africa, we find a consistent pattern of thermophilization in tree communities. Mean rates of thermophilization were +0.0086 °C·y-1 in the Kigezi Highlands (Uganda), +0.0032 °C·y-1 in the Virunga Mountains (Rwanda-Uganda-Democratic Republic of the Congo) and +0.0023 °C·y-1 in the Udzungwa Mountains (Tanzania). Distinct from other forests, both recruitment and mortality were important drivers of thermophilzation in the African plots. The forests studied currently act as a carbon sink, but the consequences of further thermophilization are unclear.
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Affiliation(s)
- Aida Cuni-Sanchez
- Department of International Environmental and Development Studies (NORAGRIC), Norwegian University of Life Sciences, Ås, Norway.
- Department of Environment and Geography, University of York, York, UK.
| | | | | | - Alain S K Ngute
- Forest Research Institute, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Robert Bitariho
- Institute of Tropical Forest Conservation, Mbarara University of Science and Technology, Mbarara, Uganda
| | | | - Andrew R Marshall
- Forest Research Institute, University of the Sunshine Coast, Sippy Downs, QLD, Australia
- Flamingo Land Ltd, Malton, UK
| | | | | | - Aventino Nkwasibwe
- Institute of Tropical Forest Conservation, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Francesco Rovero
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- MUSE-Museo delle Scienze, Trento, Italy
| | - Douglas Sheil
- Forest Ecology and Forest Management Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Rogers Tinkasimire
- Institute of Tropical Forest Conservation, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Lawrence Tumugabirwe
- Institute of Tropical Forest Conservation, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Kenneth J Feeley
- Department of Biology, University of Miami, Coral Gables, FL, USA
- Fairchild Tropical Botanic Garden, Coral Gables, FL, USA
| | - Martin J P Sullivan
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK.
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Swart RC, Geerts S, Geldenhuys CJ, Pauw J, Coetzee A. Weak latitudinal trends in reproductive traits of Afromontane forest trees. ANNALS OF BOTANY 2024; 133:711-724. [PMID: 37407025 PMCID: PMC11082511 DOI: 10.1093/aob/mcad080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 07/05/2023] [Indexed: 07/07/2023]
Abstract
BACKGROUND AND AIMS Is the increase in species diversity patterns towards lower latitudes linked to reproductive traits? Plant reproductive organs influence reproductive isolation and hence species divergence. Abiotic differences between temperate and tropical regions can also directly impact on plant reproductive traits. Here we provide a novel overview of southern hemisphere, Afromontane forest tree taxonomical patterns and ask whether reproductive traits relate to latitude, while accounting for environmental (tree height) and evolutionary (biogeographical affinity) selective forces. METHODS We compiled a novel dataset with (1) flower colour, size and pollination syndrome and (2) fruit colour, size and dispersal syndrome for 331 tree species found in six Afromontane forest regions. We categorized each species into latitudinal distribution using these six regions, spanning the southern Cape (34º S) to Mount Kenya (0º S). Additionally, we gathered maximum tree height (m) for each species and determined the global distribution of all 196 tree genera (Afrotropical, Palaeotropical or Pantropical). KEY RESULTS Species, genera and families showed a general decrease in richness away from tropical and subtropical forests towards warm temperate forests. Southern Afrotemperate forests (the furthest south) had the highest tree endemism. There was no relationship between latitude and the reproductive traits tested here. Biogeographical affinity related to fruit colour and dispersal syndrome, with palaeotropical genera showing relative increases in black-purple fruit colour compared with pantropical genera, and palaeotropical genera showing relative increases in biotic seed dispersal compared with Afrotropical genera, which showed higher relative abiotic seed dispersal. Taller trees had a higher chance to be wind or insect pollinated (compared with bird pollinated) and had larger fruits. CONCLUSIONS Latitude explained patterns in Afromontane tree taxonomic diversity; however, tree reproductive traits did not relate to latitude. We suggest that phylogenetic conservatism or convergence, or both, explain the reported patterns.
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Affiliation(s)
- R C Swart
- Department of Conservation Management, Faculty of Science, George Campus, Nelson Mandela University, George 6530, South Africa
| | - S Geerts
- Department of Conservation and Marine Sciences, Cape Peninsula University of Technology, PO Box 652, Cape Town, 8000, South Africa
| | - C J Geldenhuys
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria 0184, South Africa
| | - J Pauw
- Department of Conservation Management, Faculty of Science, George Campus, Nelson Mandela University, George 6530, South Africa
| | - A Coetzee
- Department of Conservation Management, Faculty of Science, George Campus, Nelson Mandela University, George 6530, South Africa
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Three spatially separate records confirm the presence of and provide a range extension for the giant pangolin Smutsia gigantea in Kenya. ORYX 2022. [DOI: 10.1017/s0030605322000126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Abstract
Pangolins are some of the most overexploited but least studied mammals. The giant pangolin Smutsia gigantea is the largest of the eight pangolin species, measuring up to 180 cm in length and weighing up to 40 kg. It is a nocturnal, solitary species that occurs at low densities and little is known regarding its biology and ecology. It is distributed widely across the rainforests and forest savannah mosaics of equatorial Africa but its exact range extent is unknown. Apart from a single record in Kenya predating 1971, the eastern limit of its range was thought only to extend to central Uganda and western Tanzania. Here we present three spatially separate records confirming the presence of this species in Kenyan Afromontane forests. The three records are c. 120 km apart and c. 500 km east of the nearest confirmed giant pangolin population in Uganda. These records represent a significant range extension for the species and highlight the biodiversity and conservation importance of the Afromontane forests of western Kenya.
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Lyam PT, Duque-Lazo J, Hauenschild F, Schnitzler J, Muellner-Riehl AN, Greve M, Ndangalasi H, Myburgh A, Durka W. Climate change will disproportionally affect the most genetically diverse lineages of a widespread African tree species. Sci Rep 2022; 12:7035. [PMID: 35488120 PMCID: PMC9054768 DOI: 10.1038/s41598-022-11182-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/19/2022] [Indexed: 12/05/2022] Open
Abstract
Global climate change is proceeding at an alarming rate with major ecological and genetic consequences for biodiversity, particularly in drylands. The response of species to climate change may differ between intraspecific genetic groups, with major implications for conservation. We used molecular data from 10 nuclear and two chloroplast genomes to identify phylogeographic groups within 746 individuals from 29 populations of Senegalia senegal, a savannah tree species in sub-Saharan Africa. Three phylogroups are identified corresponding to Sudano-Sahelian, Zambezian and Southern African biogeographic regions in West, East and Southern Africa. Genetic diversity was highest in Southern and Zambesian and lowest in the Sudano-Sahelian phylogroups. Using species distribution modeling, we infer highly divergent future distributions of the phylogroups under three climate change scenarios. Climate change will lead to severe reductions of distribution area of the genetically diverse Zambezian (- 41-- 54%) and Southern (- 63-- 82%) phylogroups, but to an increase for the genetically depauperate Sudano-Sahelian (+ 7- + 26%) phylogroups. This study improves our understanding of the impact of climate change on the future distribution of this species. This knowledge is particularly useful for biodiversity management as the conservation of genetic resources needs to be considered in complementary strategies of in-situ conservation and assisted migration.
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Affiliation(s)
- Paul T Lyam
- Department of Molecular Evolution and Plant Systematics and Herbarium (LZ), Institute of Biology, Leipzig University, Johannisallee 21-23, 04103, Leipzig, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany.
- National Centre for Genetic Resources and Biotechnology, NCRI complex, Moor Plantation, P.M.B 5282, Ibadan, Nigeria.
| | | | - Frank Hauenschild
- Department of Molecular Evolution and Plant Systematics and Herbarium (LZ), Institute of Biology, Leipzig University, Johannisallee 21-23, 04103, Leipzig, Germany
| | - Jan Schnitzler
- Department of Molecular Evolution and Plant Systematics and Herbarium (LZ), Institute of Biology, Leipzig University, Johannisallee 21-23, 04103, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
| | - Alexandra N Muellner-Riehl
- Department of Molecular Evolution and Plant Systematics and Herbarium (LZ), Institute of Biology, Leipzig University, Johannisallee 21-23, 04103, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
| | - Michelle Greve
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, 0002, South Africa
| | - Henry Ndangalasi
- Department of Botany, University of Dar Es Salaam, P.O. Box 35060, Dar es Salaam, Tanzania
| | - Annerine Myburgh
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, 0002, South Africa
| | - Walter Durka
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany
- Department of Community Ecology (BZF), Helmholtz Centre for Environmental Research-UFZ, Theodor-Lieser-Str. 4, 06120, Halle, Germany
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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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Saina JK, Gichira AW, Ngarega BK, Li ZZ, Gituru RW, Hu GW, Liao K. Development and utilization of microsatellite markers to assess genetic variation coupled with modelling range shifts of Dodonaea viscosa (L.) Jacq. in isolated Taita Hills and Mount Kenya forests. Mol Biol Rep 2021; 49:917-929. [PMID: 34741709 DOI: 10.1007/s11033-021-06911-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Understanding genetic variation is critical for the protection and maintenance of fragmented and highly disturbed habitats. The Taita Hills of Kenya are the northernmost part of the Eastern Arc Mountains and have been identified as one of the world's top ten biodiversity hotspots. Over the past century the current forests in the Taita Hills have become highly fragmented. In order to appraise the influence of anthropological disturbance and fragmentation on plant species in these mountains, we studied the genetic variation and population structure of Dodonaea viscosa (L.) Jacq. (Sapindaceae), using newly developed microsatellite (SSR) markers, combined with ecological niche modelling analyses (ENMs). METHODS AND RESULTS We utilized the Illumina paired-end technology to sequence D. viscosa's genome and developed its microsatellite markers. In total, 646,428 sequences were analyzed, and 49,836 SSRs were identified from 42,638 sequences. A total of 18 out of 25 randomly selected primer pairs were designed to test polymorphism among 92 individuals across eight populations. The average observed heterozygosity and expected heterozygosity ranged from 0.119 to 0.982 and from 0.227 to 0.691, respectively. Analysis of molecular variance (AMOVA) revealed 78% variance within populations and only 20% among the eight populations. According to ENM results, D. viscosa's suitable habitats have been gradually reducing since the last glacial maximum (LGM), and the situation will worsen under the extreme pessimist scenario of (representative concentration pathway) RCP 8.5. Moreover, genetic diversity was significantly greater in larger fragments. CONCLUSIONS In the present study, we successfully developed and tested SSR markers for D. viscosa. Study results indicate that fragmentation would constitute a severe threat to plant forest species. Therefore, urgent conservation management of smaller fragmented patches is necessary to protect this disturbed region and maintain the genetic resources.
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Affiliation(s)
- Josphat K Saina
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Andrew W Gichira
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Boniface K Ngarega
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Zhi-Zhong Li
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Robert W Gituru
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.,Department of Botany, Jomo Kenyatta University of Agriculture and Technology, Nairobi, 62000-00200, Kenya
| | - Guang-Wan Hu
- University of Chinese Academy of Sciences, Beijing, 100049, China.,Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Kuo Liao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
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7
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Pérez‐Pérez MA, Yu W. Pleistocene origin and colonization history of Lobelia columnaris Hook. f. (Campanulaceae: Lobelioideae) across sky islands of West Central Africa. Ecol Evol 2021; 11:15860-15873. [PMID: 34824795 PMCID: PMC8601881 DOI: 10.1002/ece3.8256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/27/2021] [Accepted: 08/02/2021] [Indexed: 11/08/2022] Open
Abstract
We aimed to infer ancestral area and historical colonization of Lobelia columnaris in the sky islands of Bioko and Cameroon through dated phylogeny using chloroplast genomes. Specifically, we aim to answer the following questions: (1) What are the phylogenetic relationships among Bioko Island and Cameroon populations? (2) Are the older populations found in the older sky islands? We assembled novel plastomes from 20 individuals of L. columnaris from 5 mountain systems. The plastome data were explored with phylogenetic analyses using Maximum Likelihood and Bayesian Inference. The populations of L. columnaris have a monophyletic origin, subdivided into three plastomes-geographic clades. The plastid phylogenomic results and age of the sky islands indicate that L. columnaris colonized first along with the Cameroon Volcanic Line's young sky islands of Bioko. The crown group (1.54 Ma) split the population in Bioko and mainland Cameroon. It is possible that Bioko was the ancestral area and likely isolated during cold and dry conditions in forest refugia. Presumably, the colonization history occurred during the middle-late Pleistocene from South Bioko's young sky island to North Bioko and the northern old sky islands in Cameroon. Furthermore, the central depression with lowland forest between North and South Bioko is a current geographic barrier that keeps separating the populations of Bioko from each other. Also, the shallow sea channel keeps isolated the populations of Bioko and the mainland populations. The Pleistocene climatic oscillations led to the divergence of the Cameroon and Bioko populations into three clades. L. columnaris colonized the older sky islands in mainland Cameroon after establishment in Bioko's younger sky islands. Contrary to expectations, the biogeography history was an inverse progression with respect to the age of the Afromontane sky islands.
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Affiliation(s)
- Miguel A. Pérez‐Pérez
- Department of Biological SciencesNorthern Arizona UniversityFlagstaffArizonaUSA
- Department of Biodiversity, Earth & Environmental ScienceDrexel UniversityPhiladelphiaPennsylvaniaUSA
| | - Wen‐Bin Yu
- Center for Integrative ConservationXishuangbanna Tropical Botanical GardenMenglaChina
- Center of Conservation Biology, Core Botanical GardensChinese Academy of SciencesMenglaChina
- Southeast Asia Biodiversity Research InstituteChinese Academy of ScienceYezinMyanmar
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Gene flow in phylogenomics: Sequence capture resolves species limits and biogeography of Afromontane forest endemic frogs from the Cameroon Highlands. Mol Phylogenet Evol 2021; 163:107258. [PMID: 34252546 DOI: 10.1016/j.ympev.2021.107258] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 06/28/2021] [Accepted: 07/07/2021] [Indexed: 11/21/2022]
Abstract
Puddle frogs of the Phrynobatrachus steindachneri species complex are a useful group for investigating speciation and phylogeography in Afromontane forests of the Cameroon Volcanic Line, western Central Africa. The species complex is represented by six morphologically relatively cryptic mitochondrial DNA lineages, only two of which are distinguished at the species level - southern P. jimzimkusi and Lake Oku endemic P. njiomock, leaving the remaining four lineages identified as 'P. steindachneri'. In this study, the six mtDNA lineages are subjected to genomic sequence capture analyses and morphological examination to delimit species and to study biogeography. The nuclear DNA data (387 loci; 571,936 aligned base pairs) distinguished all six mtDNA lineages, but the topological pattern and divergence depths supported only four main clades: P. jimzimkusi, P. njiomock, and only two divergent evolutionary lineages within the four 'P. steindachneri' mtDNA lineages. One of the two lineages is herein described as a new species, P. amieti sp. nov. Reticulate evolution (hybridization) was detected within the species complex with morphologically intermediate hybrid individuals placed between the parental species in phylogenomic analyses, forming a ladder-like phylogenetic pattern. The presence of hybrids is undesirable in standard phylogenetic analyses but is essential and beneficial in the network multispecies coalescent. This latter approach provided insight into the reticulate evolutionary history of these endemic frogs. Introgressions likely occurred during the Middle and Late Pleistocene climatic oscillations, due to the cyclic connections (likely dominating during cold glacials) and separations (during warm interglacials) of montane forests. The genomic phylogeographic pattern supports the separation of the southern (Mt. Manengouba to Mt. Oku) and northern mountains at the onset of the Pleistocene. Further subdivisions occurred in the Early Pleistocene, separating populations from the northernmost (Tchabal Mbabo, Gotel Mts.) and middle mountains (Mt. Mbam, Mt. Oku, Mambilla Plateau), as well as the microendemic lineage restricted to Lake Oku (Mt. Oku). This unique model system is highly threatened as all the species within the complex have exhibited severe population declines in the past decade, placing them on the brink of extinction. In addition, Mount Oku is identified to be of particular conservation importance because it harbors three species of this complex. We, therefore, urge for conservation actions in the Cameroon Highlands to preserve their diversity before it is too late.
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Migliore J, Lézine AM, Hardy OJ. The recent colonization history of the most widespread Podocarpus tree species in Afromontane forests. ANNALS OF BOTANY 2020; 126:73-83. [PMID: 32193530 PMCID: PMC7304463 DOI: 10.1093/aob/mcaa049] [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: 09/18/2019] [Accepted: 03/18/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND AND AIMS Afromontane forests host a unique biodiversity distributed in isolated high-elevation habitats within a matrix of rain forests or savannahs, yet they share a remarkable flora that raises questions about past connectivity between currently isolated forests. Here, we focused on the Podocarpus latifolius-P. milanjianus complex (Podocarpaceae), the most widely distributed conifers throughout sub-Saharan African highlands, to infer its demographic history from genetic data. METHODS We sequenced the whole plastid genome, mitochondrial DNA regions and nuclear ribosomal DNA of 88 samples from Cameroon to Angola in western Central Africa and from Kenya to the Cape region in eastern and southern Africa to reconstruct time-calibrated phylogenies and perform demographic inferences. KEY RESULTS We show that P. latifolius and P. milanjianus form a single species, whose lineages diverged during the Pleistocene, mostly between approx, 200 000 and 300 000 years BP, after which they underwent a wide range expansion leading to their current distributions. Confronting phylogenomic and palaeoecological data, we argue that the species originated in East Africa and reached the highlands of the Atlantic side of Africa through two probable latitudinal migration corridors: a northern one towards the Cameroon volcanic line, and a southern one towards Angola. Although the species is now rare in large parts of its range, no demographic decline was detected, probably because it occurred too recently to have left a genetic signature in our DNA sequences. CONCLUSIONS Despite the ancient and highly fluctuating history of podocarps in Africa revealed by palaeobotanical records, the extended distribution of current P. latifolius/milanjianus lineages is shown to result from a more recent history, mostly during the mid-late Pleistocene, when Afromontane forests were once far more widespread and continuous.
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Affiliation(s)
- Jérémy Migliore
- Sorbonne Université, Laboratoire d’Océanographie et du Climat: Expérimentations et Approches Numériques (LOCEAN/IPSL), CNRS UMR, Paris, France
- Université Libre de Bruxelles, Faculté des Sciences, Service Evolution Biologique et Ecologie, Bruxelles, Belgium
- Muséum départemental du Var, Toulon, France
| | - Anne-Marie Lézine
- Sorbonne Université, Laboratoire d’Océanographie et du Climat: Expérimentations et Approches Numériques (LOCEAN/IPSL), CNRS UMR, Paris, France
| | - Olivier J Hardy
- Université Libre de Bruxelles, Faculté des Sciences, Service Evolution Biologique et Ecologie, Bruxelles, Belgium
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Helmstetter AJ, Kamga SM, Bethune K, Lautenschläger T, Zizka A, Bacon CD, Wieringa JJ, Stauffer F, Antonelli A, Sonké B, Couvreur TLP. Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus Raphia (Calamoideae, Arecaceae). PLANTS (BASEL, SWITZERLAND) 2020; 9:E549. [PMID: 32340211 PMCID: PMC7238857 DOI: 10.3390/plants9040549] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 03/27/2020] [Accepted: 04/08/2020] [Indexed: 11/16/2022]
Abstract
Palms are conspicuous floristic elements across the tropics. In continental Africa, even though there are less than 70 documented species, they are omnipresent across the tropical landscape. The genus Raphia has 20 accepted species in Africa and one species endemic to the Neotropics. It is the most economically important genus of African palms with most of its species producing food and construction material. Raphia is divided into five sections based on inflorescence morphology. Nevertheless, the taxonomy of Raphia is problematic with no intra-generic phylogenetic study available. We present a phylogenetic study of the genus using a targeted exon capture approach sequencing of 56 individuals representing 18 out of the 21 species. Our results recovered five well supported clades within the genus. Three sections correspond to those based on inflorescence morphology. R. regalis is strongly supported as sister to all other Raphia species and is placed into a newly described section: Erectae. Overall, morphological based identifications agreed well with our phylogenetic analyses, with 12 species recovered as monophyletic based on our sampling. Species delimitation analyses recovered 17 or 23 species depending on the confidence level used. Species delimitation is especially problematic in the Raphiate and Temulentae sections. In addition, our clustering analysis using SNP data suggested that individual clusters matched geographic distribution. The Neotropical species R. taedigera is supported as a distinct species, rejecting the hypothesis of a recent introduction into South America. Our analyses support the hypothesis that the Raphia individuals from Madagascar are potentially a distinct species different from the widely distributed R. farinifera. In conclusion, our results support the infra generic classification of Raphia based on inflorescence morphology, which is shown to be phylogenetically useful. Classification and species delimitation within sections remains problematic even with our phylogenomic approach. Certain widely distributed species could potentially contain cryptic species. More in-depth studies should be undertaken using morphometrics, increased sampling, and more variable markers. Our study provides a robust phylogenomic framework that enables further investigation on the biogeographic history, morphological evolution, and other eco-evolutionary aspects of this charismatic, socially, and economically important palm genus.
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Affiliation(s)
| | - Suzanne Mogue Kamga
- Laboratoire de Botanique systématique et d’Ecologie, Department of Biological Sciences, University of Yaoundé I, Higher Teacher Training College, Yaoundé B.P. 047, Cameroon; (S.M.K.); (B.S.)
| | - Kevin Bethune
- IRD, DIADE, University Montpellier, 34394 Montpellier, France; (A.J.H.); (K.B.)
| | - Thea Lautenschläger
- Institute of Botany, Department of Biology, Faculty of Science, Technische Universität Dresden, 01062 Dresden, Germany;
| | - Alexander Zizka
- German Center for Integrative Biodiversity Research (iDiv) Halle-Leipzig-Jena, 04103 Leipzig, Germany;
| | - Christine D. Bacon
- Department of Biological and Environmental Sciences and Gothenburg Global Biodiversity Centre, University of Gothenburg, 405 30 Gothenburg, Sweden; (C.D.B.); (A.A.)
- Gothenburg Global Biodiversity Centre, Box 461, SE 40530 Goteborg, Sweden
| | - Jan J. Wieringa
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands;
| | - Fred Stauffer
- Department of Botany and Plant Biology, Conservatory and Botanical Garden of the City of Geneva, University of Geneva, 1205 Geneva, Switzerland;
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences and Gothenburg Global Biodiversity Centre, University of Gothenburg, 405 30 Gothenburg, Sweden; (C.D.B.); (A.A.)
- Gothenburg Global Biodiversity Centre, Box 461, SE 40530 Goteborg, Sweden
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Bonaventure Sonké
- Laboratoire de Botanique systématique et d’Ecologie, Department of Biological Sciences, University of Yaoundé I, Higher Teacher Training College, Yaoundé B.P. 047, Cameroon; (S.M.K.); (B.S.)
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11
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Tchiechoua YH, Kinyua J, Ngumi VW, Odee DW. Effect of Indigenous and Introduced Arbuscular Mycorrhizal Fungi on Growth and Phytochemical Content of Vegetatively Propagated Prunus Africana (Hook. f.) Kalkman Provenances. PLANTS (BASEL, SWITZERLAND) 2019; 9:E37. [PMID: 31881729 PMCID: PMC7020206 DOI: 10.3390/plants9010037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 11/03/2019] [Accepted: 11/20/2019] [Indexed: 11/22/2022]
Abstract
Prunus africana bark contains phytochemical compounds used in the treatment of benign prostatic hyperplasia and prostate cancer. It has been shown that this plant establishes association with arbuscular mycorrhizal fungi (AMF). AMF are involved in nutrient uptake, which may also affect plant growth and secondary metabolites composition. However, there is no information regarding the role of AMF in the growth and phytochemical content of P. africana. A pot experiment was carried out to assess the response of 8 months old vegetatively propagated P. africana seedlings inoculated with indigenous AMF collected from Mount Cameroon (MC) and Mount Manengumba (MM) in Cameroon, Malava near Kakamega (MK) and Chuka Tharaka-Nithi (CT) in Kenya. Mycorrhizal (frequency, abundance and intensity), growth (height, shoot weight, total weight, number of leaf, leaf surface) and phytochemical (total phenol, tannin and flavonoids) parameters were measured three months after growth of seedlings from two provenances (Muguga and Chuka) with the following inoculation treatments: MK, CT, MC, MM, non-sterilized soil (NS) and sterilized sand as non-inoculated control. Results showed that seedling heights were significantly increased by inoculation and associated with high root colonization (>80%) compared to non-inoculated seedlings. We also found that AMF promoted leaf formation, whereas inoculation did not have any effect on the seedling total weight. AMF inoculum from MM had a higher tannin content, while no significant difference was observed on the total phenol and flavonoid contents due to AMF inoculation. Pearson's correlation was positive between mycorrhizal parameters and the growth parameters, and negative with phytochemical parameters. This study is the first report on the effect of AMF on the growth and phytochemical in P. africana. Further investigations are necessary to determine the effect of single AMF strains to provide better understanding of the role of AMF on the growth performance and physiology of this important medicinal plant species.
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Affiliation(s)
- Yves H. Tchiechoua
- Department of Molecular Biology and Biotechnology, Pan African University Institute for Basic Sciences, Technology and Innovation (PAUSTI), P.O. Box 62000, Nairobi 00200, Kenya
| | - Johnson Kinyua
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology (JKUAT), P.O. Box 62000, Nairobi 00200, Kenya;
| | - Victoria Wambui Ngumi
- Department of Botany, Jomo Kenyatta University of Agriculture and Technology (JKUAT), P.O. Box 62000, Nairobi 00200, Kenya;
| | - David Warambo Odee
- Biotechnology Laboratory, Kenya Forestry Research Institute (KEFRI), P.O. Box 20412, Nairobi 00200, Kenya;
- Centre for Ecology & Hydrology, Bush Estate, Penicuik EH26 0QB, UK
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12
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Mairal M, Caujapé-Castells J, Pellissier L, Jaén-Molina R, Álvarez N, Heuertz M, Sanmartín I. A tale of two forests: ongoing aridification drives population decline and genetic diversity loss at continental scale in Afro-Macaronesian evergreen-forest archipelago endemics. ANNALS OF BOTANY 2018; 122:1005-1017. [PMID: 29905771 PMCID: PMC6266103 DOI: 10.1093/aob/mcy107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 05/25/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND AND AIMS Various studies and conservationist reports have warned about the contraction of the last subtropical Afro-Macaronesian forests. These relict vegetation zones have been restricted to a few oceanic and continental islands around the edges of Africa, due to aridification. Previous studies on relict species have generally focused on glacial effects on narrow endemics; however, little is known about the effects of aridification on the fates of previously widespread subtropical lineages. METHODS Nuclear microsatellites and ecological niche modelling were used to understand observed patterns of genetic diversity in two emblematic species, widely distributed in these ecosystems: Canarina eminii (a palaeoendemic of the eastern Afromontane forests) and Canarina canariensis (a palaeoendemic of the Canarian laurel forests). The software DIYABC was used to test alternative demographic scenarios and an ensemble method was employed to model potential distributions of the selected plants from the end of the deglaciation to the present. KEY RESULTS All the populations assessed experienced a strong and recent population decline, revealing that locally widespread endemisms may also be alarmingly threatened. CONCLUSIONS The detected extinction debt, as well as the extinction spiral to which these populations are subjected, demands urgent conservation measures for the unique, biodiversity-rich ecosystems that they inhabit.
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Affiliation(s)
- Mario Mairal
- Real Jardín Botánico (RJB), CSIC, Plaza de Murillo, Madrid, Spain
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico ‘Viera y Clavijo’ – Unidad Asociada CSIC (Cabildo de Gran Canaria), Las Palmas de Gran Canaria, Spain
| | - Juli Caujapé-Castells
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico ‘Viera y Clavijo’ – Unidad Asociada CSIC (Cabildo de Gran Canaria), Las Palmas de Gran Canaria, Spain
| | - Loïc Pellissier
- Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zürich, Zürich, Switzerland
- Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Ruth Jaén-Molina
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico ‘Viera y Clavijo’ – Unidad Asociada CSIC (Cabildo de Gran Canaria), Las Palmas de Gran Canaria, Spain
| | - Nadir Álvarez
- Department of Ecology and Evolution, Institute of Biology, University of Lausanne, Biophore Dorigny, Lausanne, Switzerland
| | | | - Isabel Sanmartín
- Real Jardín Botánico (RJB), CSIC, Plaza de Murillo, Madrid, Spain
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13
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Bell RC, Parra JL, Badjedjea G, Barej MF, Blackburn DC, Burger M, Channing A, Dehling JM, Greenbaum E, Gvoždík V, Kielgast J, Kusamba C, Lötters S, McLaughlin PJ, Nagy ZT, Rödel M, Portik DM, Stuart BL, VanDerWal J, Zassi‐Boulou AG, Zamudio KR. Idiosyncratic responses to climate‐driven forest fragmentation and marine incursions in reed frogs from Central Africa and the Gulf of Guinea Islands. Mol Ecol 2017; 26:5223-5244. [DOI: 10.1111/mec.14260] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 07/03/2017] [Accepted: 07/12/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Rayna C. Bell
- Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution Washington DC USA
- Museum of Vertebrate Zoology University of California, Berkeley CA USA
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
| | - Juan L. Parra
- Grupo de Ecología y Evolución de Vertebrados Instituto de Biología Universidad de Antioquia Medellín Colombia
| | - Gabriel Badjedjea
- Département d'Ecologie et Biodiversité des ressources Aquatiques Centre de Surveillance de la Biodiversité Kisangani Democratic Republic of the Congo
| | - Michael F. Barej
- Museum für Naturkunde ‐ Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
| | - David C. Blackburn
- Florida Museum of Natural History University of Florida Gainesville FL USA
- Department of Herpetology California Academy of Sciences San Francisco CA USA
| | - Marius Burger
- African Amphibian Conservation Research Group Unit for Environmental Sciences and Management North‐West University Potchefstroom South Africa
- Flora Fauna & Man, Ecological Services Ltd. Tortola British Virgin Islands
| | - Alan Channing
- Biodiversity and Conservation Biology Department University of the Western Cape Bellville South Africa
| | - Jonas Maximilian Dehling
- Abteilung Biologie Institut für Integrierte Naturwissenschaften Universität Koblenz‐Landau Koblenz Germany
| | - Eli Greenbaum
- Department of Biological Sciences University of Texas at El Paso El Paso TX USA
| | - Václav Gvoždík
- Institute of Vertebrate Biology Czech Academy of Sciences Brno Czech Republic
- Department of Zoology National Museum Prague Czech Republic
| | - Jos Kielgast
- Section of Freshwater Biology Department of Biology University of Copenhagen Copenhagen Denmark
- Center for Macroecology, Evolution and Climate Natural History Museum of Denmark Copenhagen Denmark
| | - Chifundera Kusamba
- Laboratoire d'Herpétologie Département de Biologie Centre de Recherche en Sciences Naturelles Lwiro Democratic Republic of the Congo
| | | | | | - Zoltán T. Nagy
- Museum für Naturkunde ‐ Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
- Royal Belgian Institute of Natural Sciences Brussels Belgium
| | - Mark‐Oliver Rödel
- Museum für Naturkunde ‐ Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
| | - Daniel M. Portik
- Museum of Vertebrate Zoology University of California, Berkeley CA USA
- Department of Biology University of Texas Arlington TX USA
| | | | - Jeremy VanDerWal
- Centre for Tropical Biodiveristy & Climate Change College of Science and Engineering James Cook University Townsville Qld Australia
- Division of Research and Innovation eResearch Centre James Cook University Townsville Qld Australia
| | | | - Kelly R. Zamudio
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
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14
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Anco C, Kolokotronis SO, Henschel P, Cunningham SW, Amato G, Hekkala E. Historical mitochondrial diversity in African leopards (Panthera pardus) revealed by archival museum specimens. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:455-473. [PMID: 28423965 DOI: 10.1080/24701394.2017.1307973] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Once found throughout Africa and Eurasia, the leopard (Panthera pardus) was recently uplisted from Near Threatened to Vulnerable by the International Union for the Conservation of Nature (IUCN). Historically, more than 50% of the leopard's global range occurred in continental Africa, yet sampling from this part of the species' distribution is only sparsely represented in prior studies examining patterns of genetic variation at the continental or global level. Broad sampling to determine baseline patterns of genetic variation throughout the leopard's historical distribution is important, as these measures are currently used by the IUCN to direct conservation priorities and management plans. By including data from 182 historical museum specimens, faecal samples from ongoing field surveys, and published sequences representing sub-Saharan Africa, we identify previously unrecognized genetic diversity in African leopards. Our mtDNA data indicates high levels of divergence among regional populations and strongly differentiated lineages in West Africa on par with recent studies of other large vertebrates. We provide a reference benchmark of genetic diversity in African leopards against which future monitoring can be compared. These findings emphasize the utility of historical museum collections in understanding the processes that shape present biodiversity. Additionally, we suggest future research to clarify African leopard taxonomy and to differentiate between delineated units requiring monitoring or conservation action.
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Affiliation(s)
- Corey Anco
- a Department of Biological Sciences , Fordham University , Bronx , USA.,b Sackler Institute for Comparative Genomics, American Museum of Natural History , New York , USA
| | - Sergios-Orestis Kolokotronis
- b Sackler Institute for Comparative Genomics, American Museum of Natural History , New York , USA.,c Department of Epidemiology and Biostatistics, School of Public Health , SUNY Downstate Medical Center , Brooklyn , USA
| | | | - Seth W Cunningham
- a Department of Biological Sciences , Fordham University , Bronx , USA
| | - George Amato
- b Sackler Institute for Comparative Genomics, American Museum of Natural History , New York , USA
| | - Evon Hekkala
- a Department of Biological Sciences , Fordham University , Bronx , USA.,b Sackler Institute for Comparative Genomics, American Museum of Natural History , New York , USA
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15
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Mairal M, Sanmartín I, Herrero A, Pokorny L, Vargas P, Aldasoro JJ, Alarcón M. Geographic barriers and Pleistocene climate change shaped patterns of genetic variation in the Eastern Afromontane biodiversity hotspot. Sci Rep 2017; 7:45749. [PMID: 28397796 PMCID: PMC5387718 DOI: 10.1038/srep45749] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/02/2017] [Indexed: 12/02/2022] Open
Abstract
The Eastern African Afromontane forest is getting increased attention in conservation studies because of its high endemicity levels and shrinking geographic distribution. Phylogeographic studies have found evidence of high levels of genetic variation structured across the Great Rift System. Here, we use the epiphytic plant species Canarina eminii to explore causal explanations for this pattern. Phylogeographic analyses were undertaken using plastid regions and AFLP fragments. Population genetic analyses, Statistical Parsimony, and Bayesian methods were used to infer genetic diversity, genealogical relationships, structure, gene flow barriers, and the spatiotemporal evolution of populations. A strong phylogeographic structure was found, with two reciprocally monophyletic lineages on each side of the Great Rift System, high genetic exclusivity, and restricted gene flow among mountain ranges. We explain this pattern by topographic and ecological changes driven by geological rifting in Eastern Africa. Subsequent genetic structure is attributed to Pleistocene climatic changes, in which sky-islands acted as long-term refuges and cradles of genetic diversity. Our study highlights the importance of climate change and geographic barriers associated with the African Rift System in shaping population genetic patterns, as well as the need to preserve the high levels of exclusive and critically endangered biodiversity harboured by current patches of the Afromontane forest.
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Affiliation(s)
- Mario Mairal
- Real Jardín Botánico (RJB-CSIC), 28014 Madrid, Spain
| | | | | | - Lisa Pokorny
- Royal Botanic Gardens, Kew (RBGK), Richmond, Surrey, TW9 3DS, UK
| | - Pablo Vargas
- Real Jardín Botánico (RJB-CSIC), 28014 Madrid, Spain
| | - Juan J Aldasoro
- Instituto Botánico de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Spain.,Universidad Rey Juan Carlos, Móstoles, Spain
| | - Marisa Alarcón
- Instituto Botánico de Barcelona (IBB-CSIC-ICUB), 08038 Barcelona, Spain
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16
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Hamon P, Grover CE, Davis AP, Rakotomalala JJ, Raharimalala NE, Albert VA, Sreenath HL, Stoffelen P, Mitchell SE, Couturon E, Hamon S, de Kochko A, Crouzillat D, Rigoreau M, Sumirat U, Akaffou S, Guyot R. Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content. Mol Phylogenet Evol 2017; 109:351-361. [PMID: 28212875 DOI: 10.1016/j.ympev.2017.02.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 12/30/2022]
Abstract
A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) as the most likely ancestral locality for the origin of the coffee genus, with independent radiations across Africa, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolution of caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. High and consistent caffeine content is found only in species from the equatorial, fully humid environments of West and Central Africa, possibly as an adaptive response to increased levels of pest predation. Moderate caffeine production, however, evolved at least one additional time recently (between 2 and 4Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already in place during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subject to convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate.
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Affiliation(s)
- Perla Hamon
- UMR DIADE, IRD, BP 64501, F-34394 Montpellier cedex 5, France.
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
| | - Aaron P Davis
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom.
| | | | | | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA.
| | - Hosahalli L Sreenath
- Plant Biotechnology Division, Unit of Central Coffee Research Institute, Coffee Board, Manasagangothri, Mysore 570006, India.
| | - Piet Stoffelen
- Herbarium Plantentuin Meise, Nieuwelaan 38, 1860 Meise, Belgium.
| | - Sharon E Mitchell
- Cornell University, Institute of Biotechnology, Genomic Diversity Facility, Ithaca, NY, USA.
| | | | - Serge Hamon
- UMR DIADE, IRD, BP 64501, F-34394 Montpellier cedex 5, France.
| | | | | | - Michel Rigoreau
- Nestlé Centre R&D Tours, BP 49716, F-37097 Tours cedex 2, France.
| | - Ucu Sumirat
- Indonesian Coffee and Cocoa Research Institute Jl. PB Sudirman 90, Jember 68118, Indonesia.
| | | | - Romain Guyot
- UMR IPME, IRD, BP 64501, F-34394 Montpellier cedex 5, France.
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17
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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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18
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Nantongo JS, Eilu G, Geburek T, Schueler S, Konrad H. Detection of Self Incompatibility Genotypes in Prunus africana: Characterization, Evolution and Spatial Analysis. PLoS One 2016; 11:e0155638. [PMID: 27348423 PMCID: PMC4922633 DOI: 10.1371/journal.pone.0155638] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 05/02/2016] [Indexed: 11/29/2022] Open
Abstract
In flowering plants, self-incompatibility is an effective genetic mechanism that prevents self-fertilization. Most Prunus tree species exhibit a homomorphic gametophytic self-incompatibility (GSI) system, in which the pollen phenotype is encoded by its own haploid genome. To date, no identification of S-alleles had been done in Prunus africana, the only member of the genus in Africa. To identify S-RNase alleles and hence determine S-genotypes in African cherry (Prunus africana) from Mabira Forest Reserve, Uganda, primers flanking the first and second intron were designed and these amplified two bands in most individuals. PCR bands on agarose indicated 26 and 8 different S-alleles for second and first intron respectively. Partial or full sequences were obtained for all these fragments. Comparison with published S-RNase data indicated that the amplified products were S-RNase alleles with very high interspecies homology despite the high intraspecific variation. Against expectations for a locus under balancing selection, frequency and spatial distribution of the alleles in a study plot was not random. Implications of the results to breeding efforts in the species are discussed, and mating experiments are strongly suggested to finally prove the functionality of SI in P. africana.
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Affiliation(s)
| | | | - Thomas Geburek
- Austrian Federal Office and Research Centre for Forests (BFW), Vienna, Austria
| | - Silvio Schueler
- Austrian Federal Office and Research Centre for Forests (BFW), Vienna, Austria
| | - Heino Konrad
- Austrian Federal Office and Research Centre for Forests (BFW), Vienna, Austria
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19
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Cunningham A, Anoncho VF, Sunderland T. Power, policy and the Prunus africana bark trade, 1972-2015. JOURNAL OF ETHNOPHARMACOLOGY 2016; 178:323-33. [PMID: 26631758 DOI: 10.1016/j.jep.2015.11.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 11/24/2015] [Accepted: 11/24/2015] [Indexed: 05/25/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE After almost 50 years of international trade in wild harvested medicinal bark from Africa and Madagascar, the example of Prunus africana holds several lessons for both policy and practice in the fields of forestry, conservation and rural development. Due to recent CITES restrictions on P. africana exports from Burundi, Kenya and Madagascar, coupled with the lifting of the 2007 European Union (EU) ban in 2011, Cameroon's share of the global P. africana bark trade has risen from an average of 38% between 1995 and 2004, to 72.6% (658.6 metric tons) in 2012. Cameroon is therefore at the center of this international policy arena. METHODS AND MATERIALS This paper draws upon several approaches, combining knowledge in working with P. africana over a 30-year period with a thorough literature review and updated trade data with "ground-truthing" in the field in 2013 and 2014. This enabled the construction of a good perspective on trade volumes (1991-2012), bark prices (and value-chain data) and the gaps between research reports and practice. Two approaches provided excellent lenses for a deeper understanding of policy failure and the "knowing-doing gap" in the P. africana case. A similar approach to Médard's (1992) analyses of power, politics and African development was taken and secondly, studies of commodity chains that assess the power relations that coalesce around different commodities (Ribot, 1998; Ribot and Peluso, 2003). RESULTS Despite the need to conserve genetically and chemically diverse P. africana, wild populations are vulnerable, even in several "protected areas" in Burundi, Cameroon, the Democratic Republic of Congo and in the forest reserves of Madagascar. Secondly, hopes of decentralized governance of this forest product are misplaced due to elite capture, market monopolies and subsidized management regimes. At the current European price, for P. africana bark (US$6 per kg) for example, the 2012 bark quota (658.675t) from Cameroon alone was worth over US$3.9 million, with the majority of this accruing to a single company. In contrast to lucrative bark exports, the livelihood benefits and financial returns to local harvesters from wild harvest are extremely low. For example, in 2012, the 48 active harvesters working within Mount Cameroon National Park (MCNP) received less than 1US$ per day from bark harvests, due to a net bark price of 0.33 US$ per kg (or 43% of the farm gate price for wild harvested bark). In addition, the costs of inventory, monitoring and managing sustainable wild harvests are far greater than the benefits to harvesters. CONCLUSION Without the current substantial international donor subsidies, sustainable harvest cannot be sustained. What is required to supply the current and future market is to develop separate, traceable P. africana bark supply chains based on cultivated stocks. On-farm production would benefit thousands of small-scale farmers cultivating P. africana, including local women, for whom wild harvesting is too onerous. This change requires CITES and EU support and would catalyze P. africana cultivation in across several montane African countries and Madagascar, increasing farm-gate prices to harvesters compared to economic returns from wild harvest.
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Affiliation(s)
- A Cunningham
- School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley Perth, Western Australia 6009, Australia.
| | | | - T Sunderland
- CIFOR, Jalan CIFOR, Situ Gede, Bogor, Jawa Barat, 16000 Indonesia
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Yineger H, Schmidt DJ, Teketay D, Zalucki J, Hughes JM. Gene dispersal inference across forest patches in an endangered medicinal tree: comparison of model-based approaches. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Haile Yineger
- Australian Rivers Institute; School of Environment; Griffith University; 170 Kessels Road Nathan QLD 4111 Australia
| | - Daniel J. Schmidt
- Australian Rivers Institute; School of Environment; Griffith University; 170 Kessels Road Nathan QLD 4111 Australia
| | - Demel Teketay
- Department of Crop Science and Production; Botswana College of Agriculture; Private Bag 0027 Gaborone Botswana
| | - Jacinta Zalucki
- Environmental Futures Centre; School of Environment; Griffith University; 170 Kessels Road Nathan QLD 4111 Australia
| | - Jane M. Hughes
- Australian Rivers Institute; School of Environment; Griffith University; 170 Kessels Road Nathan QLD 4111 Australia
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Jump AS, Carr M, Ahrends A, Marchant R. Genetic Divergence During Long-term Isolation in Highly Diverse Populations of Tropical Trees Across the Eastern Arc Mountains of Tanzania. Biotropica 2014. [DOI: 10.1111/btp.12139] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Alistair S. Jump
- Tropical Ecology and Conservation Group; Biological and Environmental Sciences; School of Natural Sciences; University of Stirling; Stirling FK9 4LA U.K
| | - Martin Carr
- School of Applied Sciences; University of Huddersfield; Huddersfield HD1 3DH U.K
| | - Antje Ahrends
- Royal Botanic Garden Edinburgh; 20A Inverleith Row Edinburgh EH3 5LR U.K
| | - Rob Marchant
- York Institute for Tropical Ecosystem Dynamics; Environment Department; University of York; York YO10 5DD U.K
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Russell JR, Hedley PE, Cardle L, Dancey S, Morris J, Booth A, Odee D, Mwaura L, Omondi W, Angaine P, Machua J, Muchugi A, Milne I, Kindt R, Jamnadass R, Dawson IK. tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species. PLoS One 2014; 9:e102502. [PMID: 25025376 PMCID: PMC4099372 DOI: 10.1371/journal.pone.0102502] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 06/18/2014] [Indexed: 01/24/2023] Open
Abstract
The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data.
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Affiliation(s)
- Joanne R. Russell
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom
| | - Peter E. Hedley
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom
| | - Linda Cardle
- Information and Computational Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom
| | - Siobhan Dancey
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom
- College of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Jenny Morris
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom
| | - Allan Booth
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom
| | - David Odee
- Headquarters, Kenya Forestry Research Institute, Nairobi, Kenya
- Centre for Ecology & Hydrology at Edinburgh, Centre for Ecology & Hydrology, Penicuik, Scotland, United Kingdom
| | - Lucy Mwaura
- Headquarters, World Agroforestry Centre, Nairobi, Kenya
| | - William Omondi
- Headquarters, Kenya Forestry Research Institute, Nairobi, Kenya
| | - Peter Angaine
- Headquarters, Kenya Forestry Research Institute, Nairobi, Kenya
| | - Joseph Machua
- Headquarters, Kenya Forestry Research Institute, Nairobi, Kenya
| | - Alice Muchugi
- Headquarters, World Agroforestry Centre, Nairobi, Kenya
| | - Iain Milne
- Information and Computational Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom
| | - Roeland Kindt
- Headquarters, World Agroforestry Centre, Nairobi, Kenya
| | | | - Ian K. Dawson
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Scotland, United Kingdom
- Headquarters, World Agroforestry Centre, Nairobi, Kenya
- * E-mail:
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Diversification of almonds, peaches, plums and cherries – Molecular systematics and biogeographic history of Prunus (Rosaceae). Mol Phylogenet Evol 2014; 76:34-48. [DOI: 10.1016/j.ympev.2014.02.024] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 12/15/2013] [Accepted: 02/27/2014] [Indexed: 11/20/2022]
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Yineger H, Schmidt DJ, Hughes JM. Genetic structuring of remnant forest patches in an endangered medicinal tree in North-western Ethiopia. BMC Genet 2014; 15:31. [PMID: 24602239 PMCID: PMC4021171 DOI: 10.1186/1471-2156-15-31] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 02/28/2014] [Indexed: 11/10/2022] Open
Abstract
Background Habitat loss and fragmentation may have detrimental impacts on genetic diversity, population structure and overall viability of tropical trees. The response of tropical trees to fragmentation processes may, however, be species, cohort or region-specific. Here we test the hypothesis that forest fragmentation is associated with lower genetic variability and higher genetic differentiation in adult and seedling populations of Prunus africana in North-western Ethiopia. This is a floristically impoverished region where all but a few remnant forest patches have been destroyed, mostly by anthropogenic means. Results Genetic diversity (based on allelic richness) was significantly greater in large and less-isolated forest patches as well as in adults than seedlings. Nearly all pairwise FST comparisons showed evidence for significant population genetic differentiation. Mean FST values were significantly greater in seedlings than adults, even after correction for within population diversity, but varied little with patch size or isolation. Conclusions Analysis of long-lived adult trees suggests the formerly contiguous forest in North-western Ethiopia probably exhibited strong spatial patterns of genetic structure. This means that protecting a range of patches including small and isolated ones is needed to conserve the extant genetic resources of the valuable forests in this region. However, given the high livelihood dependence of the local community and the high impact of foreign investors on forest resources of this region, in situ conservation efforts alone may not be helpful. Therefore, these efforts should be supported with ex situ gene conservation actions.
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Affiliation(s)
- Haile Yineger
- Australian Rivers Institute, Griffith School of Environment, Griffith University, 170 Kessels Road, Nathan QLD 4111, Australia.
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Vinceti B, Loo J, Gaisberger H, van Zonneveld MJ, Schueler S, Konrad H, Kadu CAC, Geburek T. Conservation priorities for Prunus africana defined with the aid of spatial analysis of genetic data and climatic variables. PLoS One 2013; 8:e59987. [PMID: 23544118 PMCID: PMC3609728 DOI: 10.1371/journal.pone.0059987] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 02/25/2013] [Indexed: 12/04/2022] Open
Abstract
Conservation priorities for Prunus africana, a tree species found across Afromontane regions, which is of great commercial interest internationally and of local value for rural communities, were defined with the aid of spatial analyses applied to a set of georeferenced molecular marker data (chloroplast and nuclear microsatellites) from 32 populations in 9 African countries. Two approaches for the selection of priority populations for conservation were used, differing in the way they optimize representation of intra-specific diversity of P. africana across a minimum number of populations. The first method (S1) was aimed at maximizing genetic diversity of the conservation units and their distinctiveness with regard to climatic conditions, the second method (S2) at optimizing representativeness of the genetic diversity found throughout the species' range. Populations in East African countries (especially Kenya and Tanzania) were found to be of great conservation value, as suggested by previous findings. These populations are complemented by those in Madagascar and Cameroon. The combination of the two methods for prioritization led to the identification of a set of 6 priority populations. The potential distribution of P. africana was then modeled based on a dataset of 1,500 georeferenced observations. This enabled an assessment of whether the priority populations identified are exposed to threats from agricultural expansion and climate change, and whether they are located within the boundaries of protected areas. The range of the species has been affected by past climate change and the modeled distribution of P. africana indicates that the species is likely to be negatively affected in future, with an expected decrease in distribution by 2050. Based on these insights, further research at the regional and national scale is recommended, in order to strengthen P. africana conservation efforts.
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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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Kadu CAC, Parich A, Schueler S, Konrad H, Muluvi GM, Eyog-Matig O, Muchugi A, Williams VL, Ramamonjisoa L, Kapinga C, Foahom B, Katsvanga C, Hafashimana D, Obama C, Vinceti B, Schumacher R, Geburek T. Bioactive constituents in Prunus africana: geographical variation throughout Africa and associations with environmental and genetic parameters. PHYTOCHEMISTRY 2012; 83:70-8. [PMID: 22795601 DOI: 10.1016/j.phytochem.2012.06.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 05/31/2012] [Accepted: 06/03/2012] [Indexed: 06/01/2023]
Abstract
Prunus africana--an evergreen tree found in Afromontane forests--is used in traditional medicine to cure benign prostate hyperplasia. Different bioactive constituents derived from bark extracts from 20 tree populations sampled throughout the species' natural range in Africa were studied by means of GC-MSD. The average concentration [mg/kgw/w] in increasing order was: lauric acid (18), myristic acid (22), n-docosanol (25), ferulic acid (49), β-sitostenone (198), β-sitosterol (490), and ursolic acid (743). The concentrations of many bark constituents were significantly correlated and concentration of n-docosanol was highly significantly correlated with all other analytes. Estimates of variance components revealed the highest variation among populations for ursolic acid (66%) and the lowest for β-sitosterol (20%). In general, environmental parameters recorded (temperature, precipitation, altitude) for the samples sites were not correlated with the concentration of most constituents; however, concentration of ferulic acid was significantly correlated with annual precipitation. Because the concentration of compounds in bark extracts may be affected by tree size, the diameter of sampled plants at 1.3m tree height (as proxy of age) was recorded. The only relationship with tree diameter was a negative correlation with ursolic acid. Under the assumption that genetically less variable populations have less variable concentrations of bark compounds, correlations between variation parameters of the concentration and the respective genetic composition based on chloroplast and nuclear DNA markers were assessed. Only variation of β-sitosterol concentration was significantly correlated with haplotypic diversity. The fixation index (F(IS)) was positively correlated with the variation in concentration of ferulic acid. Principal Components Analysis (PCA) indicated a weak geographic pattern. Mantel tests, however, revealed associations between the geographic patterns of bioactive constituents and the phylogenetic relationship among the populations sampled. This suggests an independent evolution of bark metabolism within different phylogeographical lineages, and the molecular phylogeographic pattern is partly reflected in the variation in concentration of bark constituents. The results have important implications for the design of strategies for the sustainable use and conservation of this important African tree species.
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Affiliation(s)
- Caroline A C Kadu
- Federal Research Centre for Forests-BFW, Department of Forest Genetics, Hauptstraße 7, A-1140 Vienna, Austria
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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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