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Umesh Kanna S, Parthiban KT, Senthilraja K, Venkatesan S, Udhaya Nandhini D, Mohan Kumar S, Dhasarathan M, Kumaresan P, Sai MJ, Raveendran M, Geethalakshmi V. Genetic Diversity and Structure of Terminalia bellerica (Gaertn. Roxb.) Population in India as Revealed by Genetic Analysis. PLANTS (BASEL, SWITZERLAND) 2024; 13:470. [PMID: 38498452 PMCID: PMC10892032 DOI: 10.3390/plants13040470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/20/2023] [Accepted: 12/29/2023] [Indexed: 03/20/2024]
Abstract
In this study, an extensive exploration survey of wild progeny was conducted which yielded 18 candidate plus trees (CPTs) of Terminalia bellerica. Seeds of these CPTs were collected from diverse locations between 10°54' and 28°07' E longitude, and 76°27' and 95°32' N latitude, covering 18 different locations across 5 states of the Indian subcontinent. The objective of the progeny trial was to assess genetic associations and variability in growth and physio-chemical characteristics. Significant variations (p < 0.05) were observed among the growth traits, encompassing plant height, basal diameter, girth at breast height and volume, as well as physio-chemical characteristics such as leaf length, width, area and chlorophyll content, carotenoids, and protein in the progeny trial. Broad-sense heritability (h2b) estimates were consistently high, exceeding 80% for all growth and physiological related traits under investigation except for plant height, leaf length, and girth at breast height. A correlation study revealed that selecting based on plant height, leaf area, and girth at breast height effectively enhances T. bellerica volume. A moderate genetic advance in percent of the mean (GAM) was observed for most traits, except leaf length, leaf width, girth at breast height, and plant height. Across all 13 traits, phenotypic coefficient of variation (PCV) surpassed genotypic coefficient of variation (GCV). Utilizing principal component analysis (PCA) and dendrogram construction categorized the genotypes into seven distinct groups. In conclusion, the study has demonstrated that targeting girth at breast height and plant height would be a highly effective strategy for the establishment of elite seedling nurseries and clonal seed nurseries for varietal and hybridization programs in the future.
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Affiliation(s)
- Subramani Umesh Kanna
- Directorate of Planning and Monitoring, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India;
| | - Kalappan Thangamuthu Parthiban
- Forest College and Research Institute, Tamil Nadu Agricultural University, Mettupalayam 641 301, Tamil Nadu, India; (K.T.P.); (M.J.S.)
| | - Kandasamy Senthilraja
- Directorate of Research, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India; (K.S.); (S.V.); (M.R.)
| | - Subramanian Venkatesan
- Directorate of Research, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India; (K.S.); (S.V.); (M.R.)
| | - Dhandayuthapani Udhaya Nandhini
- Centre of Excellence in Sustaining Soil Health, Anbil Dharmalingam Agricultural College and Research Institute, Trichy 620 027, Tamil Nadu, India
| | - Shanmugam Mohan Kumar
- Agro-Climatic Research Centre, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India; (S.M.K.); (M.D.)
| | - Manickam Dhasarathan
- Agro-Climatic Research Centre, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India; (S.M.K.); (M.D.)
| | - Palaniyappan Kumaresan
- Centre for Water and Geospatial Studies, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India;
| | - Makkena Jaswanth Sai
- Forest College and Research Institute, Tamil Nadu Agricultural University, Mettupalayam 641 301, Tamil Nadu, India; (K.T.P.); (M.J.S.)
| | - Muthurajan Raveendran
- Directorate of Research, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India; (K.S.); (S.V.); (M.R.)
| | - Vellingiri Geethalakshmi
- Agro-Climatic Research Centre, Tamil Nadu Agricultural University, Coimbatore 641 003, Tamil Nadu, India; (S.M.K.); (M.D.)
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U-thoomporn S, Kongkachana W, Jomchai N, Narong N, Waiyamitra P, Maprasop P, Tangphatsornruang S, Pootakham W. The complete chloroplast genome sequence of Intsia bijuga (Colebr.) Kuntze (Fabaceae: Detaroideae: Afzelieae). Mitochondrial DNA B Resour 2022; 7:1814-1816. [PMID: 36278125 PMCID: PMC9586575 DOI: 10.1080/23802359.2022.2132121] [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] [Indexed: 11/06/2022] Open
Abstract
Intsia bijuga (Colebr.) Kuntze. (1891) is a threatened mangrove species, belonging to the Fabaceae family and is native to the western Pacific coast and Southeast Asia. Here, we applied short-read Illumina technology to sequence and assemble its chloroplast genome. The complete chloroplast genome is 158,363 bp in length, composed of one large single-copy (LSC) region of 87,489 bp, one small single-copy (SSC) region of 19,438 bp, and a pair of inverted repeats (IRs) of 25,719 bp. A total of 129 unique genes were annotated, comprising 84 protein-coding genes, eight rRNA genes, and 37 tRNA genes. Our phylogenetic analysis showed the placement of I. bijuga (OL699920.1) with Afzelia species within Fabaceae family.
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Affiliation(s)
- Sonicha U-thoomporn
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nukoon Jomchai
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nattapol Narong
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Pitchaporn Waiyamitra
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Pasin Maprasop
- Department of Marine and Coastal Resources, Bangkok, Thailand
| | | | - Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand,CONTACT Wirulda Pootakham National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
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Couvreur TL, Dauby G, Blach‐Overgaard A, Deblauwe V, Dessein S, Droissart V, Hardy OJ, Harris DJ, Janssens SB, Ley AC, Mackinder BA, Sonké B, Sosef MS, Stévart T, Svenning J, Wieringa JJ, Faye A, Missoup AD, Tolley KA, Nicolas V, Ntie S, Fluteau F, Robin C, Guillocheau F, Barboni D, Sepulchre P. Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna. Biol Rev Camb Philos Soc 2021; 96:16-51. [PMID: 32924323 PMCID: PMC7821006 DOI: 10.1111/brv.12644] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 08/07/2020] [Accepted: 08/13/2020] [Indexed: 12/30/2022]
Abstract
Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.
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Affiliation(s)
| | - Gilles Dauby
- AMAP Lab, IRD, CIRAD, CNRS, INRAUniversity of MontpellierMontpellierFrance
- Laboratoire d'évolution Biologique et Ecologie, Faculté des SciencesUniversité Libre de BruxellesCP160/12, Avenue F.D. Roosevelt 50Brussels1050Belgium
| | - Anne Blach‐Overgaard
- Section for Ecoinformatics & Biodiversity, Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
| | - Vincent Deblauwe
- Center for Tropical Research (CTR), Institute of the Environment and SustainabilityUniversity of California, Los Angeles (UCLA)Los AngelesCA90095U.S.A.
- International Institute of Tropical Agriculture (IITA)YaoundéCameroon
| | | | - Vincent Droissart
- AMAP Lab, IRD, CIRAD, CNRS, INRAUniversity of MontpellierMontpellierFrance
- Laboratoire de Botanique Systématique et d'Écologie, École Normale SupérieureUniversité de Yaoundé IPO Box 047YaoundéCameroon
- Herbarium et Bibliothèque de Botanique AfricaineUniversité Libre de BruxellesBoulevard du TriompheBrusselsB‐1050Belgium
- Africa & Madagascar DepartmentMissouri Botanical GardenSt. LouisMOU.S.A.
| | - Oliver J. Hardy
- Laboratoire d'évolution Biologique et Ecologie, Faculté des SciencesUniversité Libre de BruxellesCP160/12, Avenue F.D. Roosevelt 50Brussels1050Belgium
| | - David J. Harris
- Royal Botanic Garden Edinburgh20A Inverleith RowEdinburghU.K.
| | | | - Alexandra C. Ley
- Institut für Geobotanik und Botanischer GartenUniversity Halle‐WittenbergNeuwerk 21Halle06108Germany
| | | | - Bonaventure Sonké
- Laboratoire de Botanique Systématique et d'Écologie, École Normale SupérieureUniversité de Yaoundé IPO Box 047YaoundéCameroon
| | | | - Tariq Stévart
- Herbarium et Bibliothèque de Botanique AfricaineUniversité Libre de BruxellesBoulevard du TriompheBrusselsB‐1050Belgium
- Africa & Madagascar DepartmentMissouri Botanical GardenSt. LouisMOU.S.A.
| | - Jens‐Christian Svenning
- Section for Ecoinformatics & Biodiversity, Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Department of BiologyAarhus UniversityNy Munkegade 114Aarhus CDK‐8000Denmark
| | - Jan J. Wieringa
- Naturalis Biodiversity CenterDarwinweg 2Leiden2333 CRThe Netherlands
| | - Adama Faye
- Laboratoire National de Recherches sur les Productions Végétales (LNRPV)Institut Sénégalais de Recherches Agricoles (ISRA)Route des Hydrocarbures, Bel Air BP 1386‐ CP18524DakarSenegal
| | - Alain D. Missoup
- Zoology Unit, Laboratory of Biology and Physiology of Animal Organisms, Faculty of ScienceUniversity of DoualaPO Box 24157DoualaCameroon
| | - Krystal A. Tolley
- South African National Biodiversity InstituteKirstenbosch Research CentrePrivate Bag X7, ClaremontCape Town7735South Africa
- School of Animal, Plant and Environmental SciencesUniversity of the WitwatersrandPrivate Bag 3Wits2050South Africa
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHEUniversité des AntillesCP51, 57 rue CuvierParis75005France
| | - Stéphan Ntie
- Département de Biologie, Faculté des SciencesUniversité des Sciences et Techniques de MasukuFrancevilleBP 941Gabon
| | - Frédiéric Fluteau
- Institut de Physique du Globe de Paris, CNRSUniversité de ParisParisF‐75005France
| | - Cécile Robin
- CNRS, Géosciences Rennes, UMR6118University of RennesRennes35042France
| | | | - Doris Barboni
- CEREGE, Aix‐Marseille University, CNRS, IRD, Collège de France, INRA, Technopole Arbois MéditerranéeBP80Aix‐en‐Provence cedex413545France
| | - Pierre Sepulchre
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA‐CNRS‐UVSQUniversité Paris‐SaclayGif‐sur‐YvetteF‐91191France
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Donkpegan ASL, Doucet JL, Hardy OJ, Heuertz M, Piñeiro R. Miocene Diversification in the Savannahs Precedes Tetraploid Rainforest Radiation in the African Tree Genus Afzelia (Detarioideae, Fabaceae). FRONTIERS IN PLANT SCIENCE 2020; 11:798. [PMID: 32625223 PMCID: PMC7313659 DOI: 10.3389/fpls.2020.00798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
The dating of diversification events, including transitions between biomes, is key to elucidate the processes that underlie the assembly and evolution of tropical biodiversity. Afzelia is a widespread genus of tropical trees, threatened by exploitation for its valuable timber, that presents an interesting system to investigate diversification events in Africa. Africa hosts diploid Afzelia species in the savannahs north and south of the Guineo-Congolian rainforest and autotetraploid species confined to the rainforest. Species delimitation and phylogenetic relationships among the diploid and tetraploid species remained unresolved in previous studies using small amounts of DNA sequence data. We used genotyping-by-sequencing in the five widespread Afzelia species in Africa, the savannah species A. africana and A. quanzensis and the rainforest species A. bipindensis, A. pachyloba, and A. bella. Maximum likelihood and coalescent approaches resolved all species as monophyletic and placed the savannah and rainforest taxa into two separate clades corresponding to contrasted ploidy levels. Our data are thus compatible with a single biome shift in Afzelia in Africa, although we were unable to conclude on its direction. SNAPP calibrated species trees show that the savannah diploids started to diversify early, at 12 (9.09-14.89) Ma, which contrasts with a recent and rapid diversification of the rainforest tetraploid clade, starting at 4.22 (3.12 - 5.36) Ma. This finding of older diversification in a tropical savannah clade vs. its sister rainforest clade is exceptional; it stands in opposition to the predominant observation of young ages for savannahs lineages in tropical regions during the relatively recent expansion of the savannah biome.
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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, Gembloux, Belgium
- Evolutionary Biology and Ecology Unit, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
- INRAE, BFP, University of Bordeaux, Villenave d’Ornon, France
| | - Jean-Louis Doucet
- Forest is Life, TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Olivier J. Hardy
- Evolutionary Biology and Ecology Unit, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Rosalía Piñeiro
- Department of Geography, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
- Evolutionary Genomics, Centre for Geogenetics – Natural History Museum of Denmark, Copenhagen, Denmark
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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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Choo LM, Forest F, Wieringa JJ, Bruneau A, de la Estrella M. Phylogeny and biogeography of the Daniellia clade (Leguminosae: Detarioideae), a tropical tree lineage largely threatened in Africa and Madagascar. Mol Phylogenet Evol 2020; 146:106752. [PMID: 32028029 DOI: 10.1016/j.ympev.2020.106752] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 11/28/2022]
Abstract
The legume subfamily Detarioideae is exceptionally diverse in tropical Africa and Madagascar, compared to South America or Asia, a trend contrary to that shown by most other pantropical plant groups. We aim to elucidate the process of diversification giving rise to these high diversity levels by focussing our investigations on the Daniellia clade, which is present in both Africa and Madagascar. The Daniellia clade is an early-diverging lineage of subfamily Detarioideae (Leguminosae; pea family) and consists of three genera: Daniellia, Brandzeia and Neoapaloxylon. The species belonging to this group exhibit a wide range of habitat types. The Madagascar endemics Brandzeia (1 species) and Neoapaloxylon (3 species) occupy dry woodlands and arid succulent habitats respectively. Daniellia alsteeniana and D. oliveri are found in savannahs while the remaining eight species within Daniellia all occupy rainforest habitats. Phylogenetic analyses were generated from a dense, multi-individual species level sampling of the clade. Divergence time estimates were carried out using a molecular clock method to investigate biogeographical patterns and shifts in habitat types within the Daniellia clade, and conservation assessments were conducted to determine the levels of extinction risks these species are facing. We estimate that the Daniellia clade first emerged during the Early Eocene from an ancestor present in the rainforests of North Africa at that time, reflecting an ancestral habitat preference. There was a first major split over the course of the Eocene, giving rise to both African rainforest and Madagascan savannah lineages. With the emergence of a drier climate and vegetation type in Africa during the Eocene, it is likely that a dry-climate adapted lineage from the Daniellia clade ancestor could have dispersed through suitable savannah or woodland regions to reach Madagascar, subsequently giving rise to the savannah-adapted ancestor of Brandzeia and Neoapaloxylon in the Early Miocene. The African rainforest lineage gave rise to the genus Daniellia, which is postulated to have first diversified in the Middle Miocene, while savannah species of Daniellia emerged independently during the Pliocene, coinciding with the global rise of C4-dominated grasslands. More than half of the species in the Daniellia clade are near threatened or threatened, which highlights the need to understand the threats of anthropogenic pressures and climate change these species are facing to prioritise their conservation.
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Affiliation(s)
- Le Min Choo
- Herbarium, Research & Conservation Branch, Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, 259569 Singapore; Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK.
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
| | - Jan J Wieringa
- Naturalis Biodiversity Centre, National Herbarium of the Netherlands, Darwinweg 2, 2333 CR Leiden, the Netherlands
| | - Anne Bruneau
- Institut de recherche en biologie végétale and Département de Sciences biologiques, Université de Montréal, 4101 Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Manuel de la Estrella
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; Departamento de Botánica, Ecología y Fisiología Vegetal, Universidad de Córdoba, Campus de Rabanales, 14071 Córdoba, Spain
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Gallego-Tévar B, Curado G, Grewell BJ, Figueroa ME, Castillo JM. Realized niche and spatial pattern of native and exotic halophyte hybrids. Oecologia 2018; 188:849-862. [DOI: 10.1007/s00442-018-4251-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 08/20/2018] [Indexed: 11/28/2022]
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de la Estrella M, Forest F, Klitgård B, Lewis GP, Mackinder BA, de Queiroz LP, Wieringa JJ, Bruneau A. A new phylogeny-based tribal classification of subfamily Detarioideae, an early branching clade of florally diverse tropical arborescent legumes. Sci Rep 2018; 8:6884. [PMID: 29720687 PMCID: PMC5932001 DOI: 10.1038/s41598-018-24687-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 03/28/2018] [Indexed: 11/09/2022] Open
Abstract
Detarioideae (81 genera, c. 760 species) is one of the six Leguminosae subfamilies recently reinstated by the Legume Phylogeny Working Group. This subfamily displays high morphological variability and is one of the early branching clades in the evolution of legumes. Using previously published and newly generated sequences from four loci (matK-trnK, rpL16, trnG-trnG2G and ITS), we develop a new densely sampled phylogeny to assess generic relationships and tribal delimitations within Detarioideae. The ITS phylogenetic trees are poorly resolved, but the plastid data recover several strongly supported clades, which also are supported in a concatenated plastid + ITS sequence analysis. We propose a new phylogeny-based tribal classification for Detarioideae that includes six tribes: re-circumscribed Detarieae and Amherstieae, and the four new tribes Afzelieae, Barnebydendreae, Saraceae and Schotieae. An identification key and descriptions for each of the tribes are also provided.
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Affiliation(s)
- Manuel de la Estrella
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK. .,Departamento de Botánica, Ecología y Fisiología Vegetal, Facultad de Ciencias, Campus de Rabanales, Universidad de Córdoba, 14071, Córdoba, Spain.
| | - Félix Forest
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK
| | - Bente Klitgård
- Department for Identification and Naming, Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
| | - Gwilym P Lewis
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK
| | - Barbara A Mackinder
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3DS, UK.,Tropical Diversity, Royal Botanic Garden Edinburgh, 20ª Inverleith Row, EH3 5LR, Edinburgh, UK
| | - Luciano P de Queiroz
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina s.n., Novo Horizonte, 44036-900, Feira de Santana, Bahia, Brazil
| | - Jan J Wieringa
- Naturalis Biodiversity Centre, National Herbarium of the Netherlands, Darwinweg 2, 2333 CR, Leiden, The Netherlands
| | - Anne Bruneau
- Institut de recherche en biologie végétale and Département de Sciences biologiques, Université de Montréal, 4101 Sherbrooke est, Montréal, H1X 2B2, Canada
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9
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Wang YH, Wicke S, Wang H, Jin JJ, Chen SY, Zhang SD, Li DZ, Yi TS. Plastid Genome Evolution in the Early-Diverging Legume Subfamily Cercidoideae (Fabaceae). FRONTIERS IN PLANT SCIENCE 2018; 9:138. [PMID: 29479365 PMCID: PMC5812350 DOI: 10.3389/fpls.2018.00138] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/24/2018] [Indexed: 05/18/2023]
Abstract
The subfamily Cercidoideae is an early-branching legume lineage, which consists of 13 genera distributed in the tropical and warm temperate Northern Hemisphere. A previous study detected two plastid genomic variations in this subfamily, but the limited taxon sampling left the overall plastid genome (plastome) diversification across the subfamily unaddressed, and phylogenetic relationships within this clade remained unresolved. Here, we assembled eight plastomes from seven Cercidoideae genera and conducted phylogenomic-comparative analyses in a broad evolutionary framework across legumes. The plastomes of Cercidoideae all exhibited a typical quadripartite structure with a conserved gene content typical of most angiosperm plastomes. Plastome size ranged from 151,705 to 165,416 bp, mainly due to the expansion and contraction of inverted repeat (IR) regions. The order of genes varied due to the occurrence of several inversions. In Tylosema species, a plastome with a 29-bp IR-mediated inversion was found to coexist with a canonical-type plastome, and the abundance of the two arrangements of isomeric molecules differed between individuals. Complete plastome data were much more efficient at resolving intergeneric relationships of Cercidoideae than the previously used selection of only a few plastid or nuclear loci. In sum, our study revealed novel insights into the structural diversification of plastomes in an early-branching legume lineage, and, thus, into the evolutionary trajectories of legume plastomes in general.
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Affiliation(s)
- Yin-Huan Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Susann Wicke
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Hong Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
| | - Jian-Jun Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Si-Yun Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
| | - Shu-Dong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
| | - De-Zhu Li
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
| | - Ting-Shuang Yi
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan, China
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10
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Males J. Geography, environment and organismal traits in the diversification of a major tropical herbaceous angiosperm radiation. AOB PLANTS 2018; 10:ply008. [PMID: 29479409 PMCID: PMC5814923 DOI: 10.1093/aobpla/ply008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 01/29/2018] [Indexed: 06/08/2023]
Abstract
The generation of plant diversity involves complex interactions between geography, environment and organismal traits. Many macroevolutionary processes and emergent patterns have been identified in different plant groups through the study of spatial data, but rarely in the context of a large radiation of tropical herbaceous angiosperms. A powerful system for testing interrelated biogeographical hypotheses is provided by the terrestrial bromeliads, a Neotropical group of extensive ecological diversity and importance. In this investigation, distributional data for 564 species of terrestrial bromeliads were used to estimate variation in the position and width of species-level hydrological habitat occupancy and test six core hypotheses linking geography, environment and organismal traits. Taxonomic groups and functional types differed in hydrological habitat occupancy, modulated by convergent and divergent trait evolution, and with contrasting interactions with precipitation abundance and seasonality. Plant traits in the Bromeliaceae are intimately associated with bioclimatic differentiation, which is in turn strongly associated with variation in geographical range size and species richness. These results emphasize the ecological relevance of structural-functional innovation in a major plant radiation.
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Affiliation(s)
- Jamie Males
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, UK
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11
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Tosso F, Hardy OJ, Doucet JL, Daïnou K, Kaymak E, Migliore J. Evolution in the Amphi-Atlantic tropical genus Guibourtia (Fabaceae, Detarioideae), combining NGS phylogeny and morphology. Mol Phylogenet Evol 2017; 120:83-93. [PMID: 29222064 DOI: 10.1016/j.ympev.2017.11.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 11/22/2017] [Accepted: 11/30/2017] [Indexed: 11/16/2022]
Abstract
Tropical rain forests support a remarkable diversity of tree species, questioning how and when this diversity arose. The genus Guibourtia (Fabaceae, Detarioideae), characterized by two South American and 13 African tree species growing in various tropical biomes, is an interesting model to address the role of biogeographic processes and adaptation to contrasted environments on species diversification. Combining whole plastid genome sequencing and morphological characters analysis, we studied the timing of speciation and diversification processes in Guibourtia through molecular dating and ancestral habitats reconstruction. All species except G. demeusei and G. copallifera appear monophyletic. Dispersal from Africa to America across the Atlantic Ocean is the most plausible hypothesis to explain the occurrence of Neotropical Guibourtia species, which diverged ca. 11.8 Ma from their closest African relatives. The diversification of the three main clades of African Guibourtia is concomitant to Miocene global climate changes, highlighting pre-Quaternary speciation events. These clades differ by their reproductive characters, which validates the three subgenera previously described: Pseudocopaiva, Guibourtia and Gorskia. Within most monophyletic species, plastid lineages start diverging from each other during the Pliocene or early Pleistocene, suggesting that these species already arose during this period. The multiple transitions between rain forests and dry forests/savannahs inferred here through the plastid phylogeny in each Guibourtia subgenus address thus new questions about the role of phylogenetic relationships in shaping ecological niche and morphological similarity among taxa.
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Affiliation(s)
- Félicien Tosso
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, B-5030 Gembloux, Belgium; Evolutionary Biology and Ecology Unit CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. Roosevelt, B-1050 Brussels, Belgium.
| | - Olivier J Hardy
- Evolutionary Biology and Ecology Unit CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. Roosevelt, B-1050 Brussels, Belgium.
| | - Jean-Louis Doucet
- TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liège, Passage des Déportés 2, B-5030 Gembloux, Belgium.
| | - Kasso Daïnou
- Nature + asbl / TERRA Research Centre, Central African Forests, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, 5030 Gembloux, Belgium; BIOSE Department, Management of Forest Resources, Gembloux Agro-Bio Tech, Université de Liège, Passage des Déportés 2, B-5030 Gembloux, Belgium; Université Nationale d'Agriculture, BP 43 Kétou, Benin.
| | - Esra Kaymak
- Evolutionary Biology and Ecology Unit CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. Roosevelt, B-1050 Brussels, Belgium.
| | - Jérémy Migliore
- Evolutionary Biology and Ecology Unit CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 avenue F. Roosevelt, B-1050 Brussels, Belgium.
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12
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Tedersoo L. Global Biogeography and Invasions of Ectomycorrhizal Plants: Past, Present and Future. BIOGEOGRAPHY OF MYCORRHIZAL SYMBIOSIS 2017. [DOI: 10.1007/978-3-319-56363-3_20] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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