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Attikora AJP, Silué S, Yao SDM, De Clerck C, Shumbe L, Diarrassouba N, Fofana IJ, Alabi T, Lassois L. An innovative optimized protocol for high-quality genomic DNA extraction from recalcitrant Shea tree (Vitellaria paradoxa, C.F. Gaertn) plant and its suitability for downstream applications. Mol Biol Rep 2024; 51:171. [PMID: 38252378 DOI: 10.1007/s11033-023-09098-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/04/2023] [Indexed: 01/23/2024]
Abstract
BACKGROUND It is not always easy to find a universal protocol for the extraction of genomic DNA (gDNA) from plants. Extraction of gDNA from plants such as shea with a lot of polysaccharides in their leaves is done in two steps: a first step to remove the polysaccharides and a second step for the extraction of the gDNA. In this work, we designed a protocol for extracting high-quality gDNA from shea tree and demonstrate its suitability for downstream molecular applications. METHODS Fifty milligrams of leaf and root tissues were used to test the efficiency of our protocol. The quantity of gDNA was measured with the NanoDrop spectrometer and the quality was checked on agarose gel. Its suitability for use in downstream applications was tested with restriction enzymes, SSRs and RAPD polymerase chain reactions and Sanger sequencing. RESULTS The average yield of gDNA was 5.17; 3.96; 2.71 and 2.41 µg for dry leaves, dry roots, fresh leaves and fresh roots respectively per 100 mg of tissue. Variance analysis of the yield showed significant difference between all tissue types. Leaf gDNA quality was better compared to root gDNA at the absorbance ratio A260/280 and A260/230. The minimum amplifiable concentration of leaf gDNA was 1 pg/µl while root gDNA remained amplifiable at 10 pg/µl. Genomic DNA obtained was also suitable for sequencing. CONCLUSION This protocol provides an efficient, convenient and cost effective DNA extraction method suitable for use in various vitellaria paradoxa genomic studies.
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Affiliation(s)
- Affi Jean Paul Attikora
- Plant Genetics and Rhizosphere Processes Lab, Gembloux Agro Bio-Tech, Terra Research Center, University of Liege, Passage des déportés 2, 5030, Gembloux, Belgium.
| | - Souleymane Silué
- Department of Biochemistry-Genetics, Faculty of Biological Sciences, Educational and Research Unit of Genetic, University of Peleforo Gon Coulibaly (UPGC), BP 1328, Korhogo, Côte d'Ivoire
| | - Saraka Didier Martial Yao
- Department of Biochemistry-Genetics, Faculty of Biological Sciences, Educational and Research Unit of Genetic, University of Peleforo Gon Coulibaly (UPGC), BP 1328, Korhogo, Côte d'Ivoire
| | - Caroline De Clerck
- AgricultureIsLife, Gembloux Agro Bio-Tech, University of Liege, Passage des déportés 2, 5030, Gembloux, Belgium
| | - Leonard Shumbe
- Plant Genetics and Rhizosphere Processes Lab, Gembloux Agro Bio-Tech, Terra Research Center, University of Liege, Passage des déportés 2, 5030, Gembloux, Belgium
| | - Nafan Diarrassouba
- Department of Biochemistry-Genetics, Faculty of Biological Sciences, Educational and Research Unit of Genetic, University of Peleforo Gon Coulibaly (UPGC), BP 1328, Korhogo, Côte d'Ivoire
| | - Inza Jésus Fofana
- Department of Biochemistry-Genetics, Faculty of Biological Sciences, Educational and Research Unit of Genetic, University of Peleforo Gon Coulibaly (UPGC), BP 1328, Korhogo, Côte d'Ivoire
| | - Taofic Alabi
- Department of Biochemistry-Genetics, Faculty of Biological Sciences, Educational and Research Unit of Genetic, University of Peleforo Gon Coulibaly (UPGC), BP 1328, Korhogo, Côte d'Ivoire
- Functional and Evolutive Entomology, Gembloux Agro Bio-Tech, University of Liege, Passage des déportés 2, 5030, Gembloux, Belgium
| | - Ludivine Lassois
- Plant Genetics and Rhizosphere Processes Lab, Gembloux Agro Bio-Tech, Terra Research Center, University of Liege, Passage des déportés 2, 5030, Gembloux, Belgium
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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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Hale I, Ma X, Melo ATO, Padi FK, Hendre PS, Kingan SB, Sullivan ST, Chen S, Boffa JM, Muchugi A, Danquah A, Barnor MT, Jamnadass R, Van de Peer Y, Van Deynze A. Genomic Resources to Guide Improvement of the Shea Tree. FRONTIERS IN PLANT SCIENCE 2021; 12:720670. [PMID: 34567033 PMCID: PMC8459026 DOI: 10.3389/fpls.2021.720670] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/04/2021] [Indexed: 05/25/2023]
Abstract
A defining component of agroforestry parklands across Sahelo-Sudanian Africa (SSA), the shea tree (Vitellaria paradoxa) is central to sustaining local livelihoods and the farming environments of rural communities. Despite its economic and cultural value, however, not to mention the ecological roles it plays as a dominant parkland species, shea remains semi-domesticated with virtually no history of systematic genetic improvement. In truth, shea's extended juvenile period makes traditional breeding approaches untenable; but the opportunity for genome-assisted breeding is immense, provided the foundational resources are available. Here we report the development and public release of such resources. Using the FALCON-Phase workflow, 162.6 Gb of long-read PacBio sequence data were assembled into a 658.7 Mbp, chromosome-scale reference genome annotated with 38,505 coding genes. Whole genome duplication (WGD) analysis based on this gene space revealed clear signatures of two ancient WGD events in shea's evolutionary past, one prior to the Astrid-Rosid divergence (116-126 Mya) and the other at the root of the order Ericales (65-90 Mya). In a first genome-wide look at the suite of fatty acid (FA) biosynthesis genes that likely govern stearin content, the primary determinant of shea butter quality, relatively high copy numbers of six key enzymes were found (KASI, KASIII, FATB, FAD2, FAD3, and FAX2), some likely originating in shea's more recent WGD event. To help translate these findings into practical tools for characterization, selection, and genome-wide association studies (GWAS), resequencing data from a shea diversity panel was used to develop a database of more than 3.5 million functionally annotated, physically anchored SNPs. Two smaller, more curated sets of suggested SNPs, one for GWAS (104,211 SNPs) and the other targeting FA biosynthesis genes (90 SNPs), are also presented. With these resources, the hope is to support national programs across the shea belt in the strategic, genome-enabled conservation and long-term improvement of the shea tree for SSA.
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Affiliation(s)
- Iago Hale
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH, United States
| | - Xiao Ma
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Arthur T. O. Melo
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH, United States
| | - Francis Kwame Padi
- Plant Breeding Division, Cocoa Research Institute of Ghana, Ghana Cocoa Board, New Tafo, Ghana
| | - Prasad S. Hendre
- AOCC Genomics Laboratory and Tree Genebank Research Unit, World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
| | | | | | - Shiyu Chen
- Seed Biotechnology Center, University of California, Davis, Davis, CA, United States
| | - Jean-Marc Boffa
- AOCC Genomics Laboratory and Tree Genebank Research Unit, World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
| | - Alice Muchugi
- AOCC Genomics Laboratory and Tree Genebank Research Unit, World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
- The Forage Genebank, Feed and Forage Development Program, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Agyemang Danquah
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Michael Teye Barnor
- Plant Breeding Division, Cocoa Research Institute of Ghana, Ghana Cocoa Board, New Tafo, Ghana
| | - Ramni Jamnadass
- AOCC Genomics Laboratory and Tree Genebank Research Unit, World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Allen Van Deynze
- AOCC Genomics Laboratory and Tree Genebank Research Unit, World Agroforestry (CIFOR-ICRAF), Nairobi, Kenya
- Seed Biotechnology Center, University of California, Davis, Davis, CA, United States
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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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Sousa EC, Raizada MN. Contributions of African Crops to American Culture and Beyond: The Slave Trade and Other Journeys of Resilient Peoples and Crops. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.586340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
There is a general unawareness of food crops indigenous to the African continent that have contributed to Western culture. This under-appreciation is particularly relevant in the current context of societal movements to end historic racism and value the contributions of peoples of African origin and African skin colors. Lack of awareness of the contributions of Africa's crops has negative practical consequences, including inadequate investments in preserving and maximizing the use of crop diversity to facilitate breeding. This paper provides an overview and analysis of African crops that have made significant contributions to the United States and globally, and/or hold potential in the twenty-first century. The paper specifically discusses watermelon, coffee, kola, rooibos, oil palm, shea, cowpea/black eyed pea, leafy greens, okra, yam, sorghum, pearl millet, finger millet, teff, and fonio. The review focuses on the intersection of these crops with racialized peoples, with a particular focus on African-Americans starting with slavery. The analysis includes the sites of domestication of African crops, their historical migration out of Africa, their sociocultural contributions to cuisines and products around the world, their uses today, and the indigenous knowledge associated with traditional cultivation and landrace selection. The untapped potential of local genetic resources and indigenous agronomic strategies are also described. The review demonstrates that African crops played an important role in the development of American cuisine, beverages and household products. Many of these crops are nutritious, high value and stress tolerant. The paper concludes that African crops hold significant promise in improving the resiliency of global food production systems, to mitigate climate change and alleviate food insecurity and rural poverty, especially in dry regions of the world. It is hoped that this review contributes to teaching the next generation of agriculturalists, food scientists and international development professionals about the valuable contributions of Africa's resilient crops and peoples.
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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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Lompo D, Vinceti B, Konrad H, Gaisberger H, Geburek T. Phylogeography of African Locust Bean (Parkia biglobosa) Reveals Genetic Divergence and Spatially Structured Populations in West and Central Africa. J Hered 2019; 109:811-824. [PMID: 30247720 PMCID: PMC6208456 DOI: 10.1093/jhered/esy047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 09/20/2018] [Indexed: 01/03/2023] Open
Abstract
The evolutionary history of African savannah tree species is crucial for the management of their genetic resources. In this study, we investigated the phylogeography of Parkia biglobosa and its modeled distribution under past and present climate conditions. This tree species is very valued and widespread in West Africa, providing edible and medicinal products. A large sample of 1610 individuals from 84 populations, distributed across 12 countries in Western and Central Africa, were genotyped using 8 nuclear microsatellites. Individual-based assignments clearly distinguished 3 genetic clusters, extreme West Africa (EWA), center of West Africa (CWA), and Central Africa (CA). Overall, estimates of genetic diversity were moderate to high, with lower values for populations in EWA (allelic richness after rarefaction [AR] = 6.4, expected heterozygosity [HE] = 0.78, and observed heterozygosity [HO] = 0.7) and CA (AR = 5.9, HE = 0.67, and HO = 0.61) compared with populations in CWA (AR = 7.3, HE = 0.79, and HO = 0.75). The overall population differentiation was found to be moderate (FST = 0.09). A highly significant isolation by distance pattern was detected, with a marked phylogeographic signature suggesting possible effects of past climate and geographic barriers to migration. Modeling the potential distribution of the species showed a contraction during the last glaciations followed by expansion events. The exploratory approximate Bayesian computation conducted suggests a best-supported scenario in which the cluster CWA traced back to the ancestral populations and a first split between EWA and CWA took place about 160000 years before present (BP), then a second split divided CA and CWA, about 100000 years BP. However, our genetic data do not enable us to conclusively distinguish among a few alternative possible scenarios.
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Affiliation(s)
- Djingdia Lompo
- Centre National de Semences Forestières, Ouagadougou, Burkina Faso
| | | | - Heino Konrad
- Austrian Research and Training Centre for Forests, Department of Forest Genetics, Vienna, Austria
| | | | - Thomas Geburek
- Austrian Research and Training Centre for Forests, Department of Forest Genetics, Vienna, Austria
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Cornejo-Romero A, Vargas-Mendoza CF, Aguilar-Martínez GF, Medina-Sánchez J, Rendón-Aguilar B, Valverde PL, Zavala-Hurtado JA, Serrato A, Rivas-Arancibia S, Pérez-Hernández MA, López-Ortega G, Jiménez-Sierra C. Alternative glacial-interglacial refugia demographic hypotheses tested on Cephalocereus columna-trajani (Cactaceae) in the intertropical Mexican drylands. PLoS One 2017; 12:e0175905. [PMID: 28426818 PMCID: PMC5398652 DOI: 10.1371/journal.pone.0175905] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/02/2017] [Indexed: 12/27/2022] Open
Abstract
Historic demography changes of plant species adapted to New World arid environments could be consistent with either the Glacial Refugium Hypothesis (GRH), which posits that populations contracted to refuges during the cold-dry glacial and expanded in warm-humid interglacial periods, or with the Interglacial Refugium Hypothesis (IRH), which suggests that populations contracted during interglacials and expanded in glacial times. These contrasting hypotheses are developed in the present study for the giant columnar cactus Cephalocereus columna-trajani in the intertropical Mexican drylands where the effects of Late Quaternary climatic changes on phylogeography of cacti remain largely unknown. In order to determine if the historic demography and phylogeographic structure of the species are consistent with either hypothesis, sequences of the chloroplast regions psbA-trnH and trnT-trnL from 110 individuals from 10 populations comprising the full distribution range of this species were analysed. Standard estimators of genetic diversity and structure were calculated. The historic demography was analysed using a Bayesian approach and the palaeodistribution was derived from ecological niche modelling to determine if, in the arid environments of south-central Mexico, glacial-interglacial cycles drove the genetic divergence and diversification of this species. Results reveal low but statistically significant population differentiation (FST = 0.124, P < 0.001), although very clear geographic clusters are not formed. Genetic diversity, haplotype network and Approximate Bayesian Computation (ABC) demographic analyses suggest a population expansion estimated to have taken place in the Last Interglacial (123.04 kya, 95% CI 115.3–130.03). The species palaeodistribution is consistent with the ABC analyses and indicates that the potential area of palaedistribution and climatic suitability were larger during the Last Interglacial and Holocene than in the Last Glacial Maximum. Overall, these results suggest that C. columna-trajani experienced an expansion following the warm conditions of interglacials, in accordance with the GRH.
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Affiliation(s)
- Amelia Cornejo-Romero
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, CD México, México
| | - Carlos Fabián Vargas-Mendoza
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, CD México, México
- * E-mail:
| | - Gustavo F. Aguilar-Martínez
- Departamento de Zoología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, CD México, México
| | | | - Beatriz Rendón-Aguilar
- Departamento de Biología, Universidad Autónoma Metropolitana-Iztapalapa, CD México, México
| | - Pedro Luis Valverde
- Departamento de Biología, Universidad Autónoma Metropolitana-Iztapalapa, CD México, México
| | | | - Alejandra Serrato
- Departamento de Hidrobiología, Universidad Autónoma Metropolitana-Iztapalapa, CD México, México
| | | | | | - Gerardo López-Ortega
- Departamento de Biología, Universidad Autónoma Metropolitana-Iztapalapa, CD México, México
| | - Cecilia Jiménez-Sierra
- Departamento de Biología, Universidad Autónoma Metropolitana-Iztapalapa, CD México, México
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Leaché AD, Grummer JA, Miller M, Krishnan S, Fujita MK, Böhme W, Schmitz A, Lebreton M, Ineich I, Chirio L, Ofori-boateng C, Eniang EA, Greenbaum E, Rödel MO, Wagner P. Bayesian inference of species diffusion in the West African Agama agama species group (Reptilia, Agamidae). SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1238018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Adam D. Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, 98195-1800, USA
| | - Jared A. Grummer
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, 98195-1800, USA
| | - Michael Miller
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, 98195-1800, USA
| | - Sneha Krishnan
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, 98195-1800, USA
| | - Matthew K. Fujita
- Department of Biology, University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Wolfgang Böhme
- Zoologisches Forschungsmuseum Alexander Koenig, Adenauerallee 160, D53113, Bonn, Germany
| | - Andreas Schmitz
- Natural History Museum of Geneva, Department of Herpetology and Ichthyology, C.P. 6434, CH-1211, Geneva 6, Switzerland
| | - Matthew Lebreton
- Muséum National d'Histoire Naturelle & Sorbonne Universités, Département Systématique et Évolution (Reptiles), ISyEB (Institut de Systématique, Évolution, Biodiversité, UMR 7205 CNRS/UPMC/EPHE/MNHN), Paris, France
| | - Ivan Ineich
- Muséum National d'Histoire Naturelle & Sorbonne Universités, Département Systématique et Évolution (Reptiles), ISyEB (Institut de Systématique, Évolution, Biodiversité, UMR 7205 CNRS/UPMC/EPHE/MNHN), Paris, France
| | - Laurent Chirio
- Muséum National d'Histoire Naturelle & Sorbonne Universités, Département Systématique et Évolution (Reptiles), ISyEB (Institut de Systématique, Évolution, Biodiversité, UMR 7205 CNRS/UPMC/EPHE/MNHN), Paris, France
| | | | - Edem A. Eniang
- Department of Forestry and Wildlife, University of Uyo, Akwa Ibom State, Nigeria
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, 500 West University Ave., El Paso, TX, 79968, USA
| | - Mark-Oliver Rödel
- Museum für Naturkunde, Leibniz Institute for Research on Evolution and Biodiversity, 10115, Berlin, Germany
| | - Philipp Wagner
- Zoologische Staatssammlung München, Münchhausenstr. 21, D81247, München, Germany
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11
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Gutiérrez-Tapia P, Palma RE. Integrating phylogeography and species distribution models: cryptic distributional responses to past climate change in an endemic rodent from the central Chile hotspot. DIVERS DISTRIB 2016; 22:638-650. [PMID: 27453686 PMCID: PMC4950956 DOI: 10.1111/ddi.12433] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
AIM Biodiversity losses under the species level may have been severely underestimated in future global climate change scenarios. Therefore, it is important to characterize the diversity units at this level, as well as to understand their ecological responses to climatic forcings. We have chosen an endemic rodent from a highly endangered ecogeographic area as a model to look for distributional responses below the species level: Phyllotis darwini. LOCATION The central Chile biodiversity hotspot: This area harbours a high number of endemic species, and it is known to have experienced vegetational displacements between two mountain systems during and after the Last Glacial Maximum. METHODS We have characterized cryptic lineages inside P. darwini in a classic phylogeographic approach; those intraspecific lineages were considered as relevant units to construct distribution models at Last Glacial Maximum and at present, as border climatic conditions. Differences in distribution between border conditions for each lineage were interpreted as distributional responses to post-glacial climate change. RESULTS The species is composed of two major phylogroups: one of them has a broad distribution mainly across the valley but also in mountain ranges, whereas the other displays a disjunct distribution across both mountain ranges and always above 1500 m. The lineage distribution model under LGM climatic conditions suggests that both lineages were co-distributed in the southern portion of P. darwini's current geographic range, mainly at the valley and at the coast. MAIN CONCLUSIONS Present distribution of lineages in P. darwini is the consequence of a cryptic distributional response to climate change after LGM: postglacial northward colonization, with strict altitudinal segregation of both phylogroups.
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Affiliation(s)
- Pablo Gutiérrez-Tapia
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago 6513677, Chile
| | - R Eduardo Palma
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Pontificia Universidad Católica de Chile, Casilla 114-D, Santiago 6513677, Chile
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12
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Cunningham SW, Shirley MH, Hekkala ER. Fine scale patterns of genetic partitioning in the rediscovered African crocodile, Crocodylus suchus (Saint-Hilaire 1807). PeerJ 2016; 4:e1901. [PMID: 27114867 PMCID: PMC4841213 DOI: 10.7717/peerj.1901] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/15/2016] [Indexed: 11/20/2022] Open
Abstract
Landscape heterogeneity, phylogenetic history, and stochasticity all influence patterns of geneflow and connectivity in wild vertebrates. Fine-scale patterns of genetic partitioning may be particularly important for the sustainable management of widespread species in trade, such as crocodiles. We examined genetic variation within the rediscovered African crocodile, Crocodylus suchus, across its distribution in West and Central Africa. We genotyped 109 individuals at nine microsatellite loci from 16 sampling localities and used three Bayesian clustering techniques and an analysis of contemporary gene flow to identify population structure across the landscape. We identified up to eight genetic clusters that largely correspond to populations isolated in coastal wetland systems and across large distances. Crocodile population clusters from the interior were readily distinguished from coastal areas, which were further subdivided by distance and drainage basin. Migration analyses indicated contemporary migration only between closely positioned coastal populations. These findings indicate high levels of population structure throughout the range of C. suchus and we use our results to suggest a role for molecular tools in identifying crocodile conservation units for this species. Further research, including additional sampling throughout the Congo and Niger drainages, would clarify both the landscape connectivity and management of this species.
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Affiliation(s)
- Seth W Cunningham
- Department of Biological Sciences, Fordham University , Bronx, NY , United States
| | - Matthew H Shirley
- Department of Wildlife Ecology & Conservation, University of Florida, Gainesville, FL, United States; Rare Species Conservatory Foundation, Loxahatchee, FL, United States
| | - Evon R Hekkala
- Department of Biological Sciences, Fordham University , Bronx, NY , United States
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13
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Ley A, Hardy O. Contrasting patterns of gene flow between sister plant species in the understorey of African moist forests – The case of sympatric and parapatric Marantaceae species. Mol Phylogenet Evol 2014; 77:264-74. [DOI: 10.1016/j.ympev.2014.04.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 02/20/2014] [Accepted: 04/17/2014] [Indexed: 11/29/2022]
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14
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Australia's arid-adapted butcherbirds experienced range expansions during Pleistocene glacial maxima. Nat Commun 2014; 5:3994. [PMID: 24876071 DOI: 10.1038/ncomms4994] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/29/2014] [Indexed: 11/08/2022] Open
Abstract
A model of range expansions during glacial maxima (GM) for cold-adapted species is generally accepted for the Northern Hemisphere. Given that GM in Australia largely resulted in the expansion of arid zones, rather than glaciation, it could be expected that arid-adapted species might have had expanded ranges at GM, as cold-adapted species did in the Northern Hemisphere. For Australian biota, however, it remains paradigmatic that arid-adapted species contracted to refugia at GM. Here we use multilocus data and ecological niche models (ENMs) to test alternative GM models for butcherbirds. ENMs, mtDNA and estimates of nuclear introgression and past population sizes support a model of GM expansion in the arid-tolerant Grey Butcherbird that resulted in secondary contact with its close relative--the savanna-inhabiting Silver-backed Butcherbird--whose contemporary distribution is widely separated. Together, these data reject the universal use of a GM contraction model for Australia's dry woodland and arid biota.
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15
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Dupas S, le Ru B, Branca A, Faure N, Gigot G, Campagne P, Sezonlin M, Ndemah R, Ong'amo G, Calatayud PA, Silvain JF. Phylogeography in continuous space: coupling species distribution models and circuit theory to assess the effect of contiguous migration at different climatic periods on genetic differentiation inBusseola fusca(Lepidoptera: Noctuidae). Mol Ecol 2014; 23:2313-25. [DOI: 10.1111/mec.12730] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 03/05/2014] [Accepted: 03/13/2014] [Indexed: 11/27/2022]
Affiliation(s)
- S. Dupas
- Laboratoire Evolution, Génomes et Spéciation; UPR 9034; Centre National de la Recherche Scientifique; Institut de Recherche pour le Développement; UR 072; 91198 Gif sur Yvette France
- Université Paris-Sud 11; 91405 Orsay France
| | - B. le Ru
- Laboratoire Evolution, Génomes et Spéciation; UPR 9034; Centre National de la Recherche Scientifique; Institut de Recherche pour le Développement; UR 072; 91198 Gif sur Yvette France
- Université Paris-Sud 11; 91405 Orsay France
- Icipe - African Insect Science for Food and Health; PO Box 30772-00100 Nairobi Kenya
| | - A. Branca
- Ecologie, Systématique et Evolution, Bâtiment 360; Université Paris-Sud; F-91405 Orsay France
| | - N. Faure
- Laboratoire Evolution, Génomes et Spéciation; UPR 9034; Centre National de la Recherche Scientifique; Institut de Recherche pour le Développement; UR 072; 91198 Gif sur Yvette France
| | - G. Gigot
- Laboratoire Evolution, Génomes et Spéciation; UPR 9034; Centre National de la Recherche Scientifique; Institut de Recherche pour le Développement; UR 072; 91198 Gif sur Yvette France
| | - P. Campagne
- Laboratoire Evolution, Génomes et Spéciation; UPR 9034; Centre National de la Recherche Scientifique; Institut de Recherche pour le Développement; UR 072; 91198 Gif sur Yvette France
| | - M. Sezonlin
- Département de Zoologie et de Génétique; Faculté des Sciences et Techniques; Université d'Abomey - Calavi; 01 BP 526 Cotonou Bénin
| | - R. Ndemah
- International Institute of Tropical Agriculture; PO Box 2008 Messa Yaoundé Cameroon
| | - G. Ong'amo
- Icipe - African Insect Science for Food and Health; PO Box 30772-00100 Nairobi Kenya
- School of Biological Sciences; University of Nairobi; PO Box 30197 Nairobi Kenya
| | - P.-A. Calatayud
- Laboratoire Evolution, Génomes et Spéciation; UPR 9034; Centre National de la Recherche Scientifique; Institut de Recherche pour le Développement; UR 072; 91198 Gif sur Yvette France
- Université Paris-Sud 11; 91405 Orsay France
- Icipe - African Insect Science for Food and Health; PO Box 30772-00100 Nairobi Kenya
| | - J.-F. Silvain
- Laboratoire Evolution, Génomes et Spéciation; UPR 9034; Centre National de la Recherche Scientifique; Institut de Recherche pour le Développement; UR 072; 91198 Gif sur Yvette France
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16
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Alvarado-Serrano DF, Knowles LL. Ecological niche models in phylogeographic studies: applications, advances and precautions. Mol Ecol Resour 2013; 14:233-48. [DOI: 10.1111/1755-0998.12184] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 10/02/2013] [Accepted: 10/04/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Diego F. Alvarado-Serrano
- Department of Ecology and Evolutionary Biology; Museum of Zoology; University of Michigan; Ann Arbor MI 48109-1079 USA
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology; Museum of Zoology; University of Michigan; Ann Arbor MI 48109-1079 USA
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Parks DH, Mankowski T, Zangooei S, Porter MS, Armanini DG, Baird DJ, Langille MGI, Beiko RG. GenGIS 2: geospatial analysis of traditional and genetic biodiversity, with new gradient algorithms and an extensible plugin framework. PLoS One 2013; 8:e69885. [PMID: 23922841 PMCID: PMC3726740 DOI: 10.1371/journal.pone.0069885] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 06/14/2013] [Indexed: 12/21/2022] Open
Abstract
GenGIS is free and open source software designed to integrate biodiversity data with a digital map and information about geography and habitat. While originally developed with microbial community analyses and phylogeography in mind, GenGIS has been applied to a wide range of datasets. A key feature of GenGIS is the ability to test geographic axes that can correspond to routes of migration or gradients that influence community similarity. Here we introduce GenGIS version 2, which extends the linear gradient tests introduced in the first version to allow comprehensive testing of all possible linear geographic axes. GenGIS v2 also includes a new plugin framework that supports the development and use of graphically driven analysis packages: initial plugins include implementations of linear regression and the Mantel test, calculations of alpha-diversity (e.g., Shannon Index) for all samples, and geographic visualizations of dissimilarity matrices. We have also implemented a recently published method for biomonitoring reference condition analysis (RCA), which compares observed species richness and diversity to predicted values to determine whether a given site has been impacted. The newest version of GenGIS supports vector data in addition to raster files. We demonstrate the new features of GenGIS by performing a full gradient analysis of an Australian kangaroo apple data set, by using plugins and embedded statistical commands to analyze human microbiome sample data, and by applying RCA to a set of samples from Atlantic Canada. GenGIS release versions, tutorials and documentation are freely available at http://kiwi.cs.dal.ca/GenGIS, and source code is available at https://github.com/beiko-lab/gengis.
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Affiliation(s)
- Donovan H. Parks
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Timothy Mankowski
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Somayyeh Zangooei
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Michael S. Porter
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
| | - David G. Armanini
- Prothea srl, Milan, Italy
- Environment Canada @ Canadian Rivers Institute, University of New Brunswick, Fredericton, Canada
| | - Donald J. Baird
- Environment Canada @ Canadian Rivers Institute, University of New Brunswick, Fredericton, Canada
| | | | - Robert G. Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, Nova Scotia, Canada
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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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Odee DW, Telford A, Wilson J, Gaye A, Cavers S. Plio-Pleistocene history and phylogeography of Acacia senegal in dry woodlands and savannahs of sub-Saharan tropical Africa: evidence of early colonisation and recent range expansion. Heredity (Edinb) 2012; 109:372-82. [PMID: 22929152 DOI: 10.1038/hdy.2012.52] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Drylands are extensive across sub-Saharan Africa, socio-economically and ecologically important yet highly sensitive to environmental changes. Evolutionary history, as revealed by contemporary intraspecific genetic variation, can provide valuable insight into how species have responded to past environmental and population changes and guide strategies to promote resilience to future changes. The gum arabic tree (Acacia senegal) is an arid-adapted, morphologically diverse species native to the sub-Saharan drylands. We used variation in nuclear sequences (internal transcribed spacer (ITS)) and two types of chloroplast DNA (cpDNA) markers (PCR-RFLP, cpSSR) to study the phylogeography of the species with 293 individuals from 66 populations sampled across its natural range. cpDNA data showed high regional and rangewide haplotypic diversity (h(T(cpSSR))=0.903-0.948) and population differentiation (G(ST(RFLP))=0.700-0.782) with a phylogeographic pattern that indicated extensive historical gene flow via seed dispersal. Haplotypes were not restricted to any of the four varieties, but showed significant geographic structure (G(ST(cpSSR))=0.392; R(ST)=0.673; R(ST)>R(ST) (permuted)), with the major division separating East and Southern Africa populations from those in West and Central Africa. Phylogenetic analysis of ITS data indicated a more recent origin for the clade including West and Central African haplotypes, suggesting range expansion in this region, possibly during the Holocene humid period. In conjunction with paleobotanical evidence, our data suggest dispersal to West Africa, and across to the Arabian Peninsula and Indian subcontinent, from source populations located in the East African region during climate oscillations of the Plio-Pleistocene.
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Affiliation(s)
- D W Odee
- Centre for Ecology & Hydrology, Bush Estate, Penicuik, Midlothian, Scotland, UK.
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20
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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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