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Gaudeul M, Sweeney P, Munzinger J. An updated infrageneric classification of the pantropical species-rich genus Garcinia L. (Clusiaceae) and some insights into the systematics of New Caledonian species, based on molecular and morphological evidence. PhytoKeys 2024; 239:73-105. [PMID: 38523734 PMCID: PMC10960151 DOI: 10.3897/phytokeys.239.112563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 02/08/2024] [Indexed: 03/26/2024]
Abstract
Garcinia L. is a pantropically distributed genus comprised of at least 250 species of shrubs and trees and has centers of diversity located in Africa/Madagascar, Australasia, and Southeast Asia. The genus is notable due to its extreme diversity of floral form, common presence in lowland tropical rainforests worldwide, and potential pharmacological value. Across its entire geographic range, Garcinia lacks a recent taxonomic revision, with the last genus-level taxonomic treatment of Garcinia conducted over 40 years ago. In order to provide an evolutionary-based framework for a revised infrageneric classification of the genus and to investigate in more detail the systematics of New Caledonian species, we conducted molecular phylogenetic analyses using DNA sequence data for the nuclear ITS region on all samples, and for three chloroplast intergenic spacers (psbM-trnD, trnQ-rps16 and rps16-trnK) on a subset of our overall sampling. Our phylogenetic analyses are the most comprehensive to date for the genus, containing 111 biogeographically and morphologically diverse Garcinia species. The analyses support a broad circumscription of Garcinia, including several previously segregated genera (e.g. Allanblackia, Clusianthemum, Ochrocarpos p.p., Pentaphalangium, Rheedia, and Tripetalum). We recovered nine major clades falling within two major lineages, and we delimit 11 sections. We discuss each of the clades, assign them sectional names, discuss their distinguishing morphological features, compare our taxonomic treatment with the most recent sectional treatment, list representative species, note geographic distribution, and highlight some questions that deserve future investigations. We propose nine new nomenclatural combinations, four new names, and three new lectotypes. In New Caledonia (NC), a total of ten, all endemic, species are recognized and were included in our phylogenetic analyses, with several replicates per species (with the exception of G.virgata and G.urceolata, represented by a single accession each). New Caledonian species were retrieved within three separate clades, respectively including 1) G.balansae; 2) G.comptonii, G.neglecta, G.urceolata, G.virgata; and 3) G.amplexicaulis, G.densiflora, G.pedicellata, G.puat, G.vieillardii. Within NC, the phylogenies did not support the distinction between a putative undescribed species and G.balansae. However, it confirmed the distinction between NC species and both G.vitiensis (found in Fiji and Vanuatu) and G.adinantha (found in Fiji), suggesting that all NC species should be considered as endemics.
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Affiliation(s)
- Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle-CNRS-SU-EPHE-UA, 57 rue Cuvier, CP 39, 75231 Paris, Cedex 05, FranceMuséum National d’Histoire Naturelle-CNRS-SU-EPHE-UAParisFrance
| | - Patrick Sweeney
- Yale Peabody Museum, Yale University, 170 Whitney Avenue, New Haven, CT 06511, USAYale UniversityNew HavenUnited States of America
| | - Jérôme Munzinger
- AMAP, University of Montpellier, IRD, INRAE, CIRAD, CNRS, Montpellier, FranceUniversity of MontpellierMontpellierFrance
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Dagallier LPMJ, Mbago FM, Couderc M, Gaudeul M, Grall A, Loup C, Wieringa JJ, Sonké B, Couvreur TLP. Phylogenomic inference of the African tribe Monodoreae (Annonaceae) and taxonomic revision of Dennettia, Uvariodendron and Uvariopsis. PhytoKeys 2023; 233:1-200. [PMID: 37811332 PMCID: PMC10552675 DOI: 10.3897/phytokeys.233.103096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/16/2023] [Indexed: 10/10/2023]
Abstract
Monodoreae (Annonaceae) is a tribe composed of 11 genera and 90 species restricted to the tropical African rain forests. All the genera are taxonomically well circumscribed except the species rich genera Uvariodendron and Uvariopsis which lack a recent taxonomic revision. Here, we used a robust phylogenomic approach, including all the 90 currently accepted species, with several specimens per species, and based on more than 300 Annonaceae-specific nuclear genes, to infer the phylogenetic tree of the Monodoreae and test the limits between the genera and species. We recover all the genera as monophyletic, except the genus Uvariopsis for which the species Uvariopsistripetala falls outside this clade. We thus reinstate the monotypic genus Dennettia for its single species Dennettiatripetala. We also erect a new tribe, Ophrypetaleae trib. nov., to accommodate the genera Ophrypetalum and Sanrafaelia, as we recover them excluded from the Monodoreae tribe with good support. Below the genus level, the genera Isolona, Monodora, Uvariastrum, Uvariodendron and Uvariopsis show weakly supported nodes and phylogenetic conflicts, suggesting that population level processes of evolution might occur in these clades. Our results also support, at the molecular level, the description of several new species of Uvariodendron and Uvariopsis, as well as several new synonymies. Finally, we present a taxonomic revision of the genera Dennettia, Uvariodendron and Uvariopsis, which contain one, 18 and 17 species respectively. We provide a key to the 11 genera of the Monodoraeae and describe four new species to science: Uvariodendronkimbozaense Dagallier & Couvreur, sp. nov., Uvariodendronmossambicense Robson ex Dagallier & Couvreur, sp. nov., Uvariodendronpilosicarpum Dagallier & Couvreur, sp. nov. and Uvariopsisoligocarpa Dagallier & Couvreur, sp. nov., and provide provisional descriptions of three putatively new species. We also present lectotypifications and nomenclatural changes implying synonymies and new combinations (Uvariodendroncitriodorum (Le Thomas) Dagallier & Couvreur, comb. et stat. nov., Uvariodendronfuscumvar.magnificum (Verdc.) Dagallier & Couvreur, comb. et stat. nov., Uvariopsiscongensisvar.angustifolia Dagallier & Couvreur, var. nov., Uvariopsisguineensisvar.globiflora (Keay) Dagallier & Couvreur, comb. et stat. nov., and Uvariopsissolheidiivar.letestui (Pellegr.) Dagallier & Couvreur, comb. et stat. nov.).
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Affiliation(s)
- Léo-Paul M. J. Dagallier
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, New York 10458, USA
| | - Frank M. Mbago
- The Herbarium, Botany Department, Box 35060, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Marie Couderc
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle-CNRS-SU-EPHE-UA, 57 rue Cuvier, CP 39, 75231 Paris, Cedex 05, France
| | - Aurélie Grall
- Herbaria Basel, Department of Environmental Sciences, University of Basel, Basel, Switzerland
- Herbarium, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Caroline Loup
- DIADE, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Jan J. Wieringa
- Herbier MPU, DCSPH – CC 99010, Université de Montpellier, 163 rue A. Broussonnet, F-34090 Montpellier, France
| | - Bonaventure Sonké
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, Netherlands
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Campos PE, Pruvost O, Boyer K, Chiroleu F, Cao TT, Gaudeul M, Baider C, Utteridge TMA, Becker N, Rieux A, Gagnevin L. Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history. Nat Commun 2023; 14:4306. [PMID: 37474518 PMCID: PMC10359311 DOI: 10.1038/s41467-023-39950-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/15/2023] [Indexed: 07/22/2023] Open
Abstract
Herbarium collections are an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography can shed light on the emergence and evolutionary history of plant pathogens. Here, we reconstruct 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected Citrus herbarium specimens. Following authentication based on ancient DNA damage patterns, we compare them with a large set of modern genomes to estimate their phylogenetic relationships, pathogenicity-associated gene content and several evolutionary parameters. Our results indicate that Xci originated in Southern Asia ~11,500 years ago (perhaps in relation to Neolithic climate change and the development of agriculture) and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world (probably via human-driven expansion of citriculture through early East-West trade and colonization).
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Affiliation(s)
- Paola E Campos
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
| | | | - Karine Boyer
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
| | | | - Thuy Trang Cao
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France
| | - Myriam Gaudeul
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
- Herbier national, Muséum national d'Histoire naturelle, CP39, 57 rue Cuvier, 75005, Paris, France
| | - Cláudia Baider
- The Mauritius Herbarium, Agricultural Services, Ministry of Agro-Industry and Food Security, R.E. Vaughan Building (MSIRI Compound), Reduit, 80835, Mauritius
| | | | - Nathalie Becker
- Institut de Systématique, Évolution, Biodiversité (ISyEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 50, 75005, Paris, France
| | - Adrien Rieux
- CIRAD, UMR PVBMT, F-97410, St Pierre, La Réunion, France.
| | - Lionel Gagnevin
- PHIM Plant Health Institute, Univ. Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France.
- CIRAD, UMR PHIM, Montpellier, France.
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Ringelberg JJ, Koenen EJ, Sauter B, Aebli A, Rando JG, Iganci JR, de Queiroz LP, Murphy DJ, Gaudeul M, Bruneau A, Luckow M, Lewis GP, Miller JT, Simon MF, Jordão LS, Morales M, Bailey CD, Nageswara-Rao M, Nicholls JA, Loiseau O, Pennington RT, Dexter KG, Zimmermann NE, Hughes CE. Precipitation is the main axis of tropical plant phylogenetic turnover across space and time. Sci Adv 2023; 9:eade4954. [PMID: 36800419 PMCID: PMC10957106 DOI: 10.1126/sciadv.ade4954] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Early natural historians-Comte de Buffon, von Humboldt, and De Candolle-established environment and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and global species distribution data for Mimosoid legumes, a pantropical plant clade of c. 3500 species, we show that the water availability gradient from deserts to rain forests dictates turnover of lineages within continents across the tropics. We demonstrate that 95% of speciation occurs within a precipitation niche, showing profound phylogenetic niche conservatism, and that lineage turnover boundaries coincide with isohyets of precipitation. We reveal similar patterns on different continents, implying that evolution and dispersal follow universal processes.
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Affiliation(s)
- Jens J. Ringelberg
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
| | - Erik J. M. Koenen
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
| | - Benjamin Sauter
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
| | - Anahita Aebli
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
| | - Juliana G. Rando
- Programa de Pós Graduação em Ciências Ambientais, Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Rua Prof. José Seabra de Lemos, 316, Bairro Recanto dos Pássaros, 47808-021 Barreiras-BA, Brazil
| | - João R. Iganci
- Instituto de Biologia, Universidade Federal de Pelotas, Campus Universitário Capão do Leão, Travessa André Dreyfus s/n, 96010-900 Capão do Leão-RS, Brazil
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, 91501-970 Porto Alegre-RS, Brazil
| | - Luciano P. de Queiroz
- Departamento Ciências Biológicas, Universidade Estadual de Feira de Santana, Avenida Transnordestina s/n, Novo Horizonte, 44036-900 Feira de Santana-BA, Brazil
| | - Daniel J. Murphy
- Royal Botanic Gardens Victoria, Birdwood Ave., Melbourne, VIC 3004, Australia
- School of Biological, Earth and Environmental Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), MNHN-CNRS-SU-EPHE-UA, 57 rue Cuvier, CP 39, 75231 Paris, Cedex 05, France
| | - Anne Bruneau
- Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montreal, QC H1X 2B2, Canada
| | - Melissa Luckow
- School of Integrative Plant Science, Plant Biology Section, Cornell University, 215 Garden Avenue, Roberts Hall 260, Ithaca, NY 14853, USA
| | - Gwilym P. Lewis
- Accelerated Taxonomy Department, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Joseph T. Miller
- Global Biodiversity Information Facility, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Marcelo F. Simon
- Embrapa Recursos Genéticos e Biotecnologia, 70770-901 Brasília-DF, Brazil
| | - Lucas S. B. Jordão
- Programa de Pós-Graduação em Botânica, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, 22460-030 Rua Pacheco Leão-RJ, Brazil
| | - Matías Morales
- Instituto de Recursos Biológicos, CIRN-CNIA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham 1686, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1425FQB Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Agronomía y Ciencias Agroalimentarias, Universidad de Morón, B1708JPD Morón, Buenos Aires, Argentina
| | - C. Donovan Bailey
- Department of Biology, New Mexico State University, Las Cruces, NM 88001, USA
| | - Madhugiri Nageswara-Rao
- United States Department of Agriculture - Agricultural Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Road, Miami, FL 33158, USA
| | - James A. Nicholls
- Australian National Insect Collection, CSIRO, Clunies Ross Street, Acton, ACT 2601, Australia
| | - Oriane Loiseau
- School of Geosciences, University of Edinburgh, Old College, South Bridge, Edinburgh EH8 9YL, UK
| | - R. Toby Pennington
- Department of Geography, University of Exeter, Laver Building, North Park Road, Exeter EX4 4QE, UK
- Tropical Diversity Section, Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, UK
| | - Kyle G. Dexter
- School of Geosciences, University of Edinburgh, Old College, South Bridge, Edinburgh EH8 9YL, UK
- Tropical Diversity Section, Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, UK
| | - Niklaus E. Zimmermann
- Department of Environmental System Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Colin E. Hughes
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
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Bieker VC, Battlay P, Petersen B, Sun X, Wilson J, Brealey JC, Bretagnolle F, Nurkowski K, Lee C, Barreiro FS, Owens GL, Lee JY, Kellner FL, van Boheeman L, Gopalakrishnan S, Gaudeul M, Mueller-Schaerer H, Lommen S, Karrer G, Chauvel B, Sun Y, Kostantinovic B, Dalén L, Poczai P, Rieseberg LH, Gilbert MTP, Hodgins KA, Martin MD. Uncovering the genomic basis of an extraordinary plant invasion. Sci Adv 2022; 8:eabo5115. [PMID: 36001672 PMCID: PMC9401624 DOI: 10.1126/sciadv.abo5115] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/11/2022] [Indexed: 05/31/2023]
Abstract
Invasive species are a key driver of the global biodiversity crisis, but the drivers of invasiveness, including the role of pathogens, remain debated. We investigated the genomic basis of invasiveness in Ambrosia artemisiifolia (common ragweed), introduced to Europe in the late 19th century, by resequencing 655 ragweed genomes, including 308 herbarium specimens collected up to 190 years ago. In invasive European populations, we found selection signatures in defense genes and lower prevalence of disease-inducing plant pathogens. Together with temporal changes in population structure associated with introgression from closely related Ambrosia species, escape from specific microbial enemies likely favored the plant's remarkable success as an invasive species.
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Affiliation(s)
- Vanessa C. Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Paul Battlay
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Bent Petersen
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, 08100 Kedah, Malaysia
| | - Xin Sun
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Jonathan Wilson
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Jaelle C. Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - François Bretagnolle
- UMR CNRS/uB 6282 Biogéosciences, Université de Bourgogne-Franche-Comté, Dijon, France
| | - Kristin Nurkowski
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Chris Lee
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Fátima Sánchez Barreiro
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Jacqueline Y. Lee
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Fabian L. Kellner
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | | | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Myriam Gaudeul
- Institut de Systématique Evolution Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, SU, EPHE, UA, National Herbarium (P), 57 rue Cuvier, CP39, 75005 Paris, France
| | | | - Suzanne Lommen
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Institute of Biology, Section Plant Ecology and Phytochemistry, Leiden University, P.O. Box 9505, 2300 RA Leiden, Netherlands
- Koppert Biological Systems, Department R&D Macrobiology, Veilingweg 14, 2651 BE Berkel en Rodenrijs, Netherlands
| | - Gerhard Karrer
- Department of Integrative Biology and Biodiversity Research, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Bruno Chauvel
- UMR Agroécologie, Institut Agro, INRAE, Univ. Bourgogne, Univ. Bourgogne-Franche-Comté, F-21000 Dijon, France
| | - Yan Sun
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Bojan Kostantinovic
- Department of Environmental and Plant Protection, Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Péter Poczai
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Institute of Advanced Studies Kőszeg (iASK), Kőszeg, Hungary
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, Canada
| | - M. Thomas P. Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Michael D. Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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Ringelberg JJ, Koenen EJM, Iganci JR, de Queiroz LP, Murphy DJ, Gaudeul M, Bruneau A, Luckow M, Lewis GP, Hughes CE. Phylogenomic analysis of 997 nuclear genes reveals the need for extensive generic re-delimitation in Caesalpinioideae (Leguminosae). PhytoKeys 2022; 205:3-58. [PMID: 36762007 PMCID: PMC9848904 DOI: 10.3897/phytokeys.205.85866] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/27/2022] [Indexed: 05/05/2023]
Abstract
Subfamily Caesalpinioideae with ca. 4,600 species in 152 genera is the second-largest subfamily of legumes (Leguminosae) and forms an ecologically and economically important group of trees, shrubs and lianas with a pantropical distribution. Despite major advances in the last few decades towards aligning genera with clades across Caesalpinioideae, generic delimitation remains in a state of considerable flux, especially across the mimosoid clade. We test the monophyly of genera across Caesalpinioideae via phylogenomic analysis of 997 nuclear genes sequenced via targeted enrichment (Hybseq) for 420 species and 147 of the 152 genera currently recognised in the subfamily. We show that 22 genera are non-monophyletic or nested in other genera and that non-monophyly is concentrated in the mimosoid clade where ca. 25% of the 90 genera are found to be non-monophyletic. We suggest two main reasons for this pervasive generic non-monophyly: (i) extensive morphological homoplasy that we document here for a handful of important traits and, particularly, the repeated evolution of distinctive fruit types that were historically emphasised in delimiting genera and (ii) this is an artefact of the lack of pantropical taxonomic syntheses and sampling in previous phylogenies and the consequent failure to identify clades that span the Old World and New World or conversely amphi-Atlantic genera that are non-monophyletic, both of which are critical for delimiting genera across this large pantropical clade. Finally, we discuss taxon delimitation in the phylogenomic era and especially how assessing patterns of gene tree conflict can provide additional insights into generic delimitation. This new phylogenomic framework provides the foundations for a series of papers reclassifying genera that are presented here in Advances in Legume Systematics (ALS) 14 Part 1, for establishing a new higher-level phylogenetic tribal and clade-based classification of Caesalpinioideae that is the focus of ALS14 Part 2 and for downstream analyses of evolutionary diversification and biogeography of this important group of legumes which are presented elsewhere.
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Affiliation(s)
- Jens J. Ringelberg
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008, Zurich, SwitzerlandUniversity of ZurichZurichSwitzerland
| | - Erik J. M. Koenen
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008, Zurich, SwitzerlandUniversity of ZurichZurichSwitzerland
- Present address: Evolutionary Biology & Ecology, Université Libre de Bruxelles, Faculté des Sciences, Campus du Solbosch - CP 160/12, Avenue F.D. Roosevelt, 50, 1050 Bruxelles, BelgiumUniversité Libre de BruxellesBruxellesBelgium
| | - João R. Iganci
- Instituto de Biologia, Universidade Federal de Pelotas, Campus Universitário Capão do Leão, Travessa André Dreyfus s/n, Capão do Leão 96010-900, Rio Grande do Sul, BrazilUniversidade Federal de PelotasRio Grande do SulBrazil
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, Porto Alegre, Rio Grande do Sul, 91501-970, BrazilUniversidade Federal do Rio Grande do SulRio Grande do SulBrazil
| | - Luciano P. de Queiroz
- Departamento Ciências Biológicas, Universidade Estadual de Feira de Santana, Avenida Transnordestina s/n – Novo Horizonte, 44036-900, Feira de Santana, BrazilUniversidade Estadual de Feira de SantanaFeira de SantanaBrazil
| | - Daniel J. Murphy
- Royal Botanic Gardens Victoria, Birdwood Ave., Melbourne, VIC 3004, AustraliaRoyal Botanic Gardens VictoriaMelbourneAustralia
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), MNHN-CNRS-SU-EPHE-UA, 57 rue Cuvier, CP 39, 75231 Paris, Cedex 05, FranceInstitut de Systématique, Evolution, Biodiversité (ISYEB)ParisFrance
| | - Anne Bruneau
- Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montreal, QC H1X 2B2, CanadaUniversité de MontréalMontrealCanada
| | - Melissa Luckow
- School of Integrative Plant Science, Plant Biology Section, Cornell University, 215 Garden Avenue, Roberts Hall 260, Ithaca, NY 14853, USACornell UniversityIthacaUnited States of America
| | - Gwilym P. Lewis
- Accelerated Taxonomy Department, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UKAccelerated Taxonomy Department, Royal Botanic GardensRichmondUnited Kingdom
| | - Colin E. Hughes
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008, Zurich, SwitzerlandUniversity of ZurichZurichSwitzerland
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Rieux A, Campos P, Duvermy A, Scussel S, Martin D, Gaudeul M, Lefeuvre P, Becker N, Lett JM. Contribution of historical herbarium small RNAs to the reconstruction of a cassava mosaic geminivirus evolutionary history. Sci Rep 2021; 11:21280. [PMID: 34711837 PMCID: PMC8553777 DOI: 10.1038/s41598-021-00518-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/13/2021] [Indexed: 12/30/2022] Open
Abstract
Emerging viral diseases of plants are recognised as a growing threat to global food security. However, little is known about the evolutionary processes and ecological factors underlying the emergence and success of viruses that have caused past epidemics. With technological advances in the field of ancient genomics, it is now possible to sequence historical genomes to provide a better understanding of viral plant disease emergence and pathogen evolutionary history. In this context, herbarium specimens represent a valuable source of dated and preserved material. We report here the first historical genome of a crop pathogen DNA virus, a 90-year-old African cassava mosaic virus (ACMV), reconstructed from small RNA sequences bearing hallmarks of small interfering RNAs. Relative to tip-calibrated dating inferences using only modern data, those performed with the historical genome yielded both molecular evolution rate estimates that were significantly lower, and lineage divergence times that were significantly older. Crucially, divergence times estimated without the historical genome appeared in discordance with both historical disease reports and the existence of the historical genome itself. In conclusion, our study reports an updated time-frame for the history and evolution of ACMV and illustrates how the study of crop viral diseases could benefit from natural history collections.
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Affiliation(s)
- Adrien Rieux
- CIRAD, UMR PVBMT, 97410, St Pierre, La Réunion, France.
| | - Paola Campos
- CIRAD, UMR PVBMT, 97410, St Pierre, La Réunion, France
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, CP 50, 75005, Paris, France
| | | | - Sarah Scussel
- CIRAD, UMR PVBMT, 97410, St Pierre, La Réunion, France
| | - Darren Martin
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, CP 50, 75005, Paris, France
- Herbier national (P), Muséum national d'Histoire Naturelle, CP39, 57 Rue Cuvier, 75005, Paris, France
| | | | - Nathalie Becker
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 Rue Cuvier, CP 50, 75005, Paris, France
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8
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Campos PE, Groot Crego C, Boyer K, Gaudeul M, Baider C, Richard D, Pruvost O, Roumagnac P, Szurek B, Becker N, Gagnevin L, Rieux A. First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence. PLoS Pathog 2021; 17:e1009714. [PMID: 34324594 PMCID: PMC8320980 DOI: 10.1371/journal.ppat.1009714] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 06/14/2021] [Indexed: 12/30/2022] Open
Abstract
Over the past decade, ancient genomics has been used in the study of various pathogens. In this context, herbarium specimens provide a precious source of dated and preserved DNA material, enabling a better understanding of plant disease emergences and pathogen evolutionary history. We report here the first historical genome of a crop bacterial pathogen, Xanthomonas citri pv. citri (Xci), obtained from an infected herbarium specimen dating back to 1937. Comparing the 1937 genome within a large set of modern genomes, we reconstructed their phylogenetic relationships and estimated evolutionary parameters using Bayesian tip-calibration inferences. The arrival of Xci in the South West Indian Ocean islands was dated to the 19th century, probably linked to human migrations following slavery abolishment. We also assessed the metagenomic community of the herbarium specimen, showed its authenticity using DNA damage patterns, and investigated its genomic features including functional SNPs and gene content, with a focus on virulence factors.
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Affiliation(s)
- Paola E. Campos
- CIRAD, UMR PVBMT, Saint-Pierre, La Réunion, France
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, SU, EPHE, UA, Paris, France
| | | | - Karine Boyer
- CIRAD, UMR PVBMT, Saint-Pierre, La Réunion, France
| | - Myriam Gaudeul
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, SU, EPHE, UA, Paris, France
- Herbier national (P), Muséum national d’Histoire naturelle, Paris, France
| | - Claudia Baider
- Ministry of Agro Industry and Food Security, Mauritius Herbarium, R.E. Vaughan Building (MSIRI compound), Agricultural Services, Réduit, Mauritius
| | | | | | - Philippe Roumagnac
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Boris Szurek
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Nathalie Becker
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum national d’Histoire naturelle, CNRS, SU, EPHE, UA, Paris, France
| | - Lionel Gagnevin
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Adrien Rieux
- CIRAD, UMR PVBMT, Saint-Pierre, La Réunion, France
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9
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Abstract
Taxonomy is the science that explores, describes, names, and classifies all organisms. In this introductory chapter, we highlight the major historical steps in the elaboration of this science, which provides baseline data for all fields of biology and plays a vital role for society but is also an independent, complex, and sound hypothesis-driven scientific discipline.In a first part, we underline that plant taxonomy is one of the earliest scientific disciplines that emerged thousands of years ago, even before the important contributions of the Greeks and Romans (e.g., Theophrastus, Pliny the Elder, and Dioscorides). In the fifteenth-sixteenth centuries, plant taxonomy benefited from the Great Navigations, the invention of the printing press, the creation of botanic gardens, and the use of the drying technique to preserve plant specimens. In parallel with the growing body of morpho-anatomical data, subsequent major steps in the history of plant taxonomy include the emergence of the concept of natural classification , the adoption of the binomial naming system (with the major role of Linnaeus) and other universal rules for the naming of plants, the formulation of the principle of subordination of characters, and the advent of the evolutionary thought. More recently, the cladistic theory (initiated by Hennig) and the rapid advances in DNA technologies allowed to infer phylogenies and to propose true natural, genealogy-based classifications.In a second part, we put the emphasis on the challenges that plant taxonomy faces nowadays. The still very incomplete taxonomic knowledge of the worldwide flora (the so-called taxonomic impediment) is seriously hampering conservation efforts that are especially crucial as biodiversity has entered its sixth extinction crisis. It appears mainly due to insufficient funding, lack of taxonomic expertise, and lack of communication and coordination. We then review recent initiatives to overcome these limitations and to anticipate how taxonomy should and could evolve. In particular, the use of molecular data has been era-splitting for taxonomy and may allow an accelerated pace of species discovery. We examine both strengths and limitations of such techniques in comparison to morphology-based investigations, we give broad recommendations on the use of molecular tools for plant taxonomy, and we highlight the need for an integrative taxonomy based on evidence from multiple sources.
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Affiliation(s)
- Germinal Rouhan
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, Sorbonne Université, Ecole Pratique des Hautes Etudes, Université des Antilles, CNRS, Paris, France.
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, Sorbonne Université, Ecole Pratique des Hautes Etudes, Université des Antilles, CNRS, Paris, France
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10
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Mariem SB, Gámez AL, Larraya L, Fuertes-Mendizabal T, Cañameras N, Araus JL, McGrath SP, Hawkesford MJ, Murua CG, Gaudeul M, Medina L, Paton A, Cattivelli L, Fangmeier A, Bunce J, Tausz-Posch S, Macdonald AJ, Aranjuelo I. Assessing the evolution of wheat grain traits during the last 166 years using archived samples. Sci Rep 2020; 10:21828. [PMID: 33311545 PMCID: PMC7733497 DOI: 10.1038/s41598-020-78504-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 11/20/2020] [Indexed: 11/09/2022] Open
Abstract
The current study focuses on yield and nutritional quality changes of wheat grain over the last 166 years. It is based on wheat grain quality analyses carried out on samples collected between 1850 and 2016. Samples were obtained from the Broadbalk Continuous Wheat Experiment (UK) and from herbaria from 16 different countries around the world. Our study showed that, together with an increase in carbohydrate content, an impoverishment of mineral composition and protein content occurred. The imbalance in carbohydrate/protein content was specially marked after the 1960's, coinciding with strong increases in ambient [CO2] and temperature and the introduction of progressively shorter straw varieties. The implications of altered crop physiology are discussed.
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Affiliation(s)
- Sinda Ben Mariem
- Spanish National Research Council (CSIC)-Government of Navarre, AgroBiotechnology Institute (IdAB), Av. Pamplona 123, 31006, Mutilva, Spain
| | - Angie L Gámez
- Spanish National Research Council (CSIC)-Government of Navarre, AgroBiotechnology Institute (IdAB), Av. Pamplona 123, 31006, Mutilva, Spain
| | - Luis Larraya
- Institute for Multidisciplinary Applied Biology, Dpto. Agronomía, Biotecnología y Alimentación, Universidad Pública de Navarra, Campus Arrosadia, 31006, Pamplona, Spain
| | | | - Nuria Cañameras
- Universitat Politècnica de Catalunya, EsteveTerrades 8, Building 4, Castelldefels, Spain
| | - José L Araus
- Integrative Crop Ecophysiology Group, Plant Physiology Section, Faculty of Biology, University of Barcelona, Barcelona, and AGROTECNIO Center, Lleida, Spain
| | - Steve P McGrath
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
| | | | - Carmen Gonzalez Murua
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Myriam Gaudeul
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National D'Histoire Naturelle, CNRS, EPHE, UA, Sorbonne Université, 57 rue Cuvier, CP 39, 75005, Paris, France
| | - Leopoldo Medina
- Spanish National Research Council (CSIC), Real Jardín Botánico, C/ Claudio Moyano 1, Madrid, Spain
| | - Alan Paton
- Royal Botanic Gardens Kew, Kew Richmond, TW9 3AB, UK
| | - Luigi Cattivelli
- Agricultural Research Council (CREA), Centre for Genomics and Bioinformatics, Via San Protaso 302, Fiorenzuolad'Arda, Italy
| | - Andreas Fangmeier
- Institute of Landscape and Plant Ecology, University of Hohenheim, August-von-Hartmann-Str. 3, 70599, Stuttgart, Germany
| | - James Bunce
- Adaptive Cropping Systems Lab (Retired), Beltsville Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Sabine Tausz-Posch
- Department of Agriculture, Science and the Environment, School of Health, Medical and Applied Sciences, CQ University Australia, Rockhampton, QLD, Australia
| | - Andy J Macdonald
- Sustainable Agriculture Sciences, Rothamsted Research, Harpenden, AL5 2JQ, Hertfordshire, UK
| | - Iker Aranjuelo
- Spanish National Research Council (CSIC)-Government of Navarre, AgroBiotechnology Institute (IdAB), Av. Pamplona 123, 31006, Mutilva, Spain.
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11
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Robène I, Maillot-Lebon V, Chabirand A, Moreau A, Becker N, Moumène A, Rieux A, Campos P, Gagnevin L, Gaudeul M, Baider C, Chiroleu F, Pruvost O. Development and comparative validation of genomic-driven PCR-based assays to detect Xanthomonas citri pv. citri in citrus plants. BMC Microbiol 2020; 20:296. [PMID: 33004016 PMCID: PMC7528614 DOI: 10.1186/s12866-020-01972-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/08/2020] [Indexed: 01/07/2023] Open
Abstract
Background Asiatic Citrus Canker, caused by Xanthomonas citri pv. citri, severely impacts citrus production worldwide and hampers international trade. Considerable regulatory procedures have been implemented to prevent the introduction and establishment of X. citri pv. citri into areas where it is not present. The effectiveness of this surveillance largely relies on the availability of specific and sensitive detection protocols. Although several PCR- or real-time PCR-based methods are available, most of them showed analytical specificity issues. Therefore, we developed new conventional and real-time quantitative PCR assays, which target a region identified by comparative genomic analyses, and compared them to existing protocols. Results Our assays target the X. citri pv. citri XAC1051 gene that encodes for a putative transmembrane protein. The real-time PCR assay includes an internal plant control (5.8S rDNA) for validating the assay in the absence of target amplification. A receiver-operating characteristic approach was used in order to determine a reliable cycle cut-off for providing accurate qualitative results. Repeatability, reproducibility and transferability between real-time devices were demonstrated for this duplex qPCR assay (XAC1051-2qPCR). When challenged with an extensive collection of target and non-target strains, both assays displayed a high analytical sensitivity and specificity performance: LOD95% = 754 CFU ml− 1 (15 cells per reaction), 100% inclusivity, 97.2% exclusivity for XAC1051-2qPCR; LOD95% = 5234 CFU ml− 1 (105 cells per reaction), 100% exclusivity and inclusivity for the conventional PCR. Both assays can detect the target from naturally infected citrus fruit. Interestingly, XAC1051-2qPCR detected X. citri pv. citri from herbarium citrus samples. The new PCR-based assays displayed enhanced analytical sensitivity and specificity when compared with previously published PCR and real-time qPCR assays. Conclusions We developed new valuable detection assays useful for routine diagnostics and surveillance of X. citri pv. citri in citrus material. Their reliability was evidenced through numerous trials on a wide range of bacterial strains and plant samples. Successful detection of the pathogen was achieved from both artificially and naturally infected plants, as well as from citrus herbarium samples, suggesting that these assays will have positive impact both for future applied and academic research on this bacterium.
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Affiliation(s)
| | | | - Aude Chabirand
- Unit for Tropical Pests and Diseases, Plant Health Laboratory (LSV), French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Saint-Pierre, Reunion Island, France
| | - Aurélie Moreau
- Unit for Tropical Pests and Diseases, Plant Health Laboratory (LSV), French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Saint-Pierre, Reunion Island, France
| | - Nathalie Becker
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Sorbonne Université, EPHE, Université des Antilles, CNRS, Paris, France
| | - Amal Moumène
- Université de La Réunion, UMR PVBMT, Saint-Pierre, Reunion Island, France
| | - Adrien Rieux
- CIRAD, UMR PVBMT, Saint-Pierre, Reunion Island, France
| | - Paola Campos
- CIRAD, UMR PVBMT, Saint-Pierre, Reunion Island, France.,Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, Sorbonne Université, EPHE, Université des Antilles, CNRS, Paris, France
| | | | - Myriam Gaudeul
- Herbier national (P), Muséum National d'Histoire Naturelle, Paris, France
| | - Claudia Baider
- Ministry of Agro Industry and Food Security, Mauritius Herbarium, R.E. Vaughan Building (MSIRI compound) Agricultural Services, Réduit, Mauritius
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12
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Bauret L, Field AR, Gaudeul M, Selosse MA, Rouhan G. First insights on the biogeographical history of Phlegmariurus (Lycopodiaceae), with a focus on Madagascar. Mol Phylogenet Evol 2018; 127:488-501. [DOI: 10.1016/j.ympev.2018.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 05/01/2018] [Accepted: 05/03/2018] [Indexed: 10/17/2022]
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13
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Jabbour F, Gaudeul M, Lambourdière J, Ramstein G, Hassanin A, Labat JN, Sarthou C. Phylogeny, biogeography and character evolution in the tribe Desmodieae (Fabaceae: Papilionoideae), with special emphasis on the New Caledonian endemic genera. Mol Phylogenet Evol 2017; 118:108-121. [PMID: 28966123 DOI: 10.1016/j.ympev.2017.09.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 09/21/2017] [Accepted: 09/22/2017] [Indexed: 01/18/2023]
Abstract
The nearly cosmopolitan tribe Desmodieae (Fabaceae) includes many important genera for medicine and forage. However, the phylogenetic relationships among the infratribal groups circumscribed using morphological traits are still poorly known. In this study, we used chloroplast (rbcL, psbA-trnH) and nuclear (ITS-1) DNA sequences to investigate the molecular phylogeny and historical biogeography of Desmodieae, and infer ancestral states for several vegetative and reproductive traits. Three groups, corresponding to the Desmodium, Lespedeza, and Phyllodium groups sensu Ohashi were retrieved in the phylogenetic analyses. Conflicts in the topologies inferred from the chloroplast and nuclear datasets were detected. For instance, the Lespedeza clade was sister to the groups Phyllodium+Desmodium based on chloroplast DNA, but nested within the Desmodium group based on ITS-1. Moreover, the New Caledonian endemic genera Arthroclianthus and Nephrodesmus were not monophyletic but together formed a clade, which also included Hanslia and Ohwia based on chloroplast DNA. The hypothetical common ancestor of Desmodieae was dated to the Middle Oligocene (ca. 28.3Ma) and was likely an Asian shrub or tree producing indehiscent loments. Several colonization events towards Oceania, America, and Africa occurred (all less than ca. 17.5Ma), most probably through long distance dispersal. The fruits of Desmodieae repeatedly evolved from indehiscence to dehiscence. We also showed that indehiscent loments allow for more variability in the number of seeds per fruit than indehiscent legumes. Modularity seems here to allow variability in the number of ovules produced in a single ovary.
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Affiliation(s)
- Florian Jabbour
- Muséum national d'Histoire naturelle, Institut de Systématique, Évolution, Biodiversité, UMR 7205 ISYEB MNHN/CNRS/UPMC/EPHE, Sorbonne Universités, 57 rue Cuvier, CP 39, 75005 Paris, France
| | - Myriam Gaudeul
- Muséum national d'Histoire naturelle, Institut de Systématique, Évolution, Biodiversité, UMR 7205 ISYEB MNHN/CNRS/UPMC/EPHE, Sorbonne Universités, 57 rue Cuvier, CP 39, 75005 Paris, France
| | - Josie Lambourdière
- Muséum national d'Histoire naturelle, Service de Systématique Moléculaire, UMS CNRS 2700, CP 26, 75005 Paris, France
| | - Guillaume Ramstein
- Muséum national d'Histoire naturelle, Institut de Systématique, Évolution, Biodiversité, UMR 7205 ISYEB MNHN/CNRS/UPMC/EPHE, Sorbonne Universités, 57 rue Cuvier, CP 39, 75005 Paris, France
| | - Alexandre Hassanin
- Muséum national d'Histoire naturelle, Institut de Systématique, Évolution, Biodiversité, UMR 7205 ISYEB MNHN/CNRS/UPMC/EPHE, Sorbonne Universités, 57 rue Cuvier, CP 39, 75005 Paris, France
| | - Jean-Noël Labat
- Muséum national d'Histoire naturelle, Institut de Systématique, Évolution, Biodiversité, UMR 7205 ISYEB MNHN/CNRS/UPMC/EPHE, Sorbonne Universités, 57 rue Cuvier, CP 39, 75005 Paris, France
| | - Corinne Sarthou
- Muséum national d'Histoire naturelle, Institut de Systématique, Évolution, Biodiversité, UMR 7205 ISYEB MNHN/CNRS/UPMC/EPHE, Sorbonne Universités, 57 rue Cuvier, CP 39, 75005 Paris, France.
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14
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Le Bras G, Pignal M, Jeanson ML, Muller S, Aupic C, Carré B, Flament G, Gaudeul M, Gonçalves C, Invernón VR, Jabbour F, Lerat E, Lowry PP, Offroy B, Pimparé EP, Poncy O, Rouhan G, Haevermans T. The French Muséum national d'histoire naturelle vascular plant herbarium collection dataset. Sci Data 2017; 4:170016. [PMID: 28195585 PMCID: PMC5308200 DOI: 10.1038/sdata.2017.16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 01/04/2017] [Indexed: 11/10/2022] Open
Abstract
We provide a quantitative description of the French national herbarium vascular plants collection dataset. Held at the Muséum national d’histoire naturelle, Paris, it currently comprises records for 5,400,000 specimens, representing 90% of the estimated total of specimens. Ninety nine percent of the specimen entries are linked to one or more images and 16% have field-collecting information available. This major botanical collection represents the results of over three centuries of exploration and study. The sources of the collection are global, with a strong representation for France, including overseas territories, and former French colonies. The compilation of this dataset was made possible through numerous national and international projects, the most important of which was linked to the renovation of the herbarium building. The vascular plant collection is actively expanding today, hence the continuous growth exhibited by the dataset, which can be fully accessed through the GBIF portal or the MNHN database portal (available at: https://science.mnhn.fr/institution/mnhn/collection/p/item/search/form). This dataset is a major source of data for systematics, global plants macroecological studies or conservation assessments.
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Affiliation(s)
- Gwenaël Le Bras
- Direction des collections, Muséum national d'histoire naturelle, CP 39, 57 rue Cuvier, Paris, Cedex 05 75231, France
| | - Marc Pignal
- Direction des collections, Muséum national d'histoire naturelle, CP 39, 57 rue Cuvier, Paris, Cedex 05 75231, France.,Sorbonne Université, UPMC Univ Paris 06, MNHN, CNRS, EPHE, Institut de Systématique, Évolution, Biodiversité (ISYEB), CP39, 57 rue Cuvier, Paris, Cedex 05 75231, France
| | - Marc L Jeanson
- Direction des collections, Muséum national d'histoire naturelle, CP 39, 57 rue Cuvier, Paris, Cedex 05 75231, France
| | - Serge Muller
- Sorbonne Université, UPMC Univ Paris 06, MNHN, CNRS, EPHE, Institut de Systématique, Évolution, Biodiversité (ISYEB), CP39, 57 rue Cuvier, Paris, Cedex 05 75231, France
| | - Cécile Aupic
- Direction des collections, Muséum national d'histoire naturelle, CP 39, 57 rue Cuvier, Paris, Cedex 05 75231, France
| | - Benoît Carré
- Archéozoologie, archéobotanique UMR 7209 (LaBex BCDiv) Centre National de la Recherche Scientifique-CNRS, Muséum national d'histoire naturelle, CP 39, 57 rue Cuvier, Paris, Cedex 05 75231, France
| | - Grégoire Flament
- Direction des collections, Muséum national d'histoire naturelle, CP 39, 57 rue Cuvier, Paris, Cedex 05 75231, France
| | - Myriam Gaudeul
- Sorbonne Université, UPMC Univ Paris 06, MNHN, CNRS, EPHE, Institut de Systématique, Évolution, Biodiversité (ISYEB), CP39, 57 rue Cuvier, Paris, Cedex 05 75231, France
| | - Claudia Gonçalves
- Direction des collections, Muséum national d'histoire naturelle, CP 39, 57 rue Cuvier, Paris, Cedex 05 75231, France
| | - Vanessa R Invernón
- Direction des collections, Muséum national d'histoire naturelle, CP 39, 57 rue Cuvier, Paris, Cedex 05 75231, France
| | - Florian Jabbour
- Sorbonne Université, UPMC Univ Paris 06, MNHN, CNRS, EPHE, Institut de Systématique, Évolution, Biodiversité (ISYEB), CP39, 57 rue Cuvier, Paris, Cedex 05 75231, France
| | - Elodie Lerat
- Direction des collections, Muséum national d'histoire naturelle, CP 39, 57 rue Cuvier, Paris, Cedex 05 75231, France
| | - Porter P Lowry
- Sorbonne Université, UPMC Univ Paris 06, MNHN, CNRS, EPHE, Institut de Systématique, Évolution, Biodiversité (ISYEB), CP39, 57 rue Cuvier, Paris, Cedex 05 75231, France.,Missouri Botanical Garden, P O Box 299, St Louis, Missouri 63166, USA
| | - Bérangère Offroy
- Direction des collections, Muséum national d'histoire naturelle, CP 39, 57 rue Cuvier, Paris, Cedex 05 75231, France
| | - Eva Pérez Pimparé
- Direction des collections, Muséum national d'histoire naturelle, CP 39, 57 rue Cuvier, Paris, Cedex 05 75231, France
| | - Odile Poncy
- Sorbonne Université, UPMC Univ Paris 06, MNHN, CNRS, EPHE, Institut de Systématique, Évolution, Biodiversité (ISYEB), CP39, 57 rue Cuvier, Paris, Cedex 05 75231, France
| | - Germinal Rouhan
- Sorbonne Université, UPMC Univ Paris 06, MNHN, CNRS, EPHE, Institut de Systématique, Évolution, Biodiversité (ISYEB), CP39, 57 rue Cuvier, Paris, Cedex 05 75231, France
| | - Thomas Haevermans
- Sorbonne Université, UPMC Univ Paris 06, MNHN, CNRS, EPHE, Institut de Systématique, Évolution, Biodiversité (ISYEB), CP39, 57 rue Cuvier, Paris, Cedex 05 75231, France
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Lallemand F, Gaudeul M, Lambourdière J, Matsuda Y, Hashimoto Y, Selosse MA. The elusive predisposition to mycoheterotrophy in Ericaceae. New Phytol 2016; 212:314-319. [PMID: 27400967 DOI: 10.1111/nph.14092] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 06/08/2016] [Indexed: 06/06/2023]
Affiliation(s)
- Félix Lallemand
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205 CNRS MNHN UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, CP39, Paris, F-75005, France
- Master BioSciences, Département de Biologie, École Normale Supérieure de Lyon, Université de Lyon, UCB Lyon1, 46 Allée d'Italie, Lyon, France
| | - Myriam Gaudeul
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205 CNRS MNHN UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, CP39, Paris, F-75005, France
| | - Josie Lambourdière
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205 CNRS MNHN UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, CP39, Paris, F-75005, France
| | - Yosuke Matsuda
- Laboratory of Forest Mycology, Graduate School of Bioresources, Mie University, Kurimamachiya 1577, Tsu, Mie, 514-8507, Japan
| | - Yasushi Hashimoto
- Department of Life Science and Agriculture, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido, 080-8555, Japan
| | - Marc-André Selosse
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205 CNRS MNHN UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, CP39, Paris, F-75005, France.
- Department of Plant Taxonomy and Nature Conservation, University of Gdansk, ul. Wita Stwosza 59, Gdańsk, 80-308, Poland.
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Ruhsam M, Clark A, Finger A, Wulff AS, Mill RR, Thomas PI, Gardner MF, Gaudeul M, Ennos RA, Hollingsworth PM. Hidden in plain view: Cryptic diversity in the emblematic Araucaria of New Caledonia. Am J Bot 2016; 103:888-898. [PMID: 27208357 DOI: 10.3732/ajb.1500487] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 03/30/2016] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Cryptic species represent a conservation challenge, because distributions and threats cannot be accurately assessed until species are recognized and defined. Cryptic species are common in diminutive and morphologically simple organisms, but are rare in charismatic and/or highly visible groups such as conifers. New Caledonia, a small island in the southern Pacific is a hotspot of diversity for the emblematic conifer genus Araucaria (Araucariaceae, Monkey Puzzle trees) where 13 of the 19 recognized species are endemic. METHODS We sampled across the entire geographical distribution of two closely related species (Araucaria rulei and A. muelleri) and screened them for genetic variation at 12 nuclear and 14 plastid microsatellites and one plastid minisatellite; a subset of the samples was also examined using leaf morphometrics. KEY RESULTS The genetic data show that populations of the endangered A. muelleri fall into two clearly distinct genetic groups: one corresponding to montane populations, the other corresponding to trees from lower elevation populations from around the Goro plateau. These Goro plateau populations are more closely related to A. rulei, but are sufficiently genetically and morphological distinct to warrant recognition as a new species. CONCLUSIONS Our study shows the presence of a previously unrecognized species in this flagship group, and that A. muelleri has 30% fewer individuals than previously thought. Combined, this clarification of species diversity and distributions provides important information to aid conservation planning for New Caledonian Araucaria.
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Affiliation(s)
- Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Alexandra Clark
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Aline Finger
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Adrien S Wulff
- SoREco-NC, 57 Route de l'Anse Vata 98800 Nouméa, New Caledonia Institut Agronomique néo-Calédonien (IAC), Axe II "Diversités biologique et fonctionnelle des écosystèmes, BP 73 98890 Païta, New Caledonia
| | - Robert R Mill
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Philip I Thomas
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Martin F Gardner
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Myriam Gaudeul
- Institut de Systématique, Évolution, Biodiversité (ISYEB), UMR 7205 CNRS MNHN UPMC EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, 57 rue Cuvier, CP39, F-75005 Paris, France
| | - Richard A Ennos
- University of Edinburgh, Institute of Evolutionary Biology, West Mains Road, Edinburgh, EH3 9JT, UK
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Gaudeul M, Véla E, Rouhan G. Eastward colonization of the Mediterranean Basin by two geographically structured clades: The case of Odontites Ludw. (Orobanchaceae). Mol Phylogenet Evol 2016; 96:140-149. [DOI: 10.1016/j.ympev.2015.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 12/09/2015] [Accepted: 12/14/2015] [Indexed: 11/16/2022]
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Soulebeau A, Aubriot X, Gaudeul M, Rouhan G, Hennequin S, Haevermans T, Dubuisson JY, Jabbour F. The hypothesis of adaptive radiation in evolutionary biology: hard facts about a hazy concept. ORG DIVERS EVOL 2015. [DOI: 10.1007/s13127-015-0220-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Kranitz ML, Biffin E, Clark A, Hollingsworth ML, Ruhsam M, Gardner MF, Thomas P, Mill RR, Ennos RA, Gaudeul M, Lowe AJ, Hollingsworth PM. Evolutionary diversification of new Caledonian Araucaria. PLoS One 2014; 9:e110308. [PMID: 25340350 PMCID: PMC4207703 DOI: 10.1371/journal.pone.0110308] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 09/11/2014] [Indexed: 11/19/2022] Open
Abstract
New Caledonia is a global biodiversity hotspot. Hypotheses for its biotic richness suggest either that the island is a 'museum' for an old Gondwana biota or alternatively it has developed following relatively recent long distance dispersal and in situ radiation. The conifer genus Araucaria (Araucariaceae) comprises 19 species globally with 13 endemic to this island. With a typically Gondwanan distribution, Araucaria is particularly well suited to testing alternative biogeographic hypotheses concerning the origins of New Caledonian biota. We derived phylogenetic estimates using 11 plastid and rDNA ITS2 sequence data for a complete sampling of Araucaria (including multiple accessions of each of the 13 New Caledonian Araucaria species). In addition, we developed a dataset comprising 4 plastid regions for a wider taxon sample to facilitate fossil based molecular dating. Following statistical analyses to identify a credible and internally consistent set of fossil constraints, divergence times estimated using a Bayesian relaxed clock approach were contrasted with geological scenarios to explore the biogeographic history of Araucaria. The phylogenetic data resolve relationships within Araucariaceae and among the main lineages in Araucaria, but provide limited resolution within the monophyletic New Caledonian species group. Divergence time estimates suggest a Late Cretaceous-Cenozoic radiation of extant Araucaria and a Neogene radiation of the New Caledonian lineage. A molecular timescale for the evolution of Araucariaceae supports a relatively recent radiation, and suggests that earlier (pre-Cenozoic) fossil types assigned to Araucaria may have affinities elsewhere in Araucariaceae. While additional data will be required to adequately resolve relationships among the New Caledonian species, their recent origin is consistent with overwater dispersal following Eocene emersion of New Caledonia but is too old to support a single dispersal from Australia to Norfolk Island for the radiation of the Pacific Araucaria sect. Eutacta clade.
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Affiliation(s)
| | - Edward Biffin
- Australian Centre for Evolutionary Biology and Biodiversity, Environment Institute, School of Earth and Environmental Science, University of Adelaide, Adelaide, Australia
| | | | | | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | | | - Philip Thomas
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | - Robert R. Mill
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
| | - Richard A. Ennos
- University of Edinburgh, Institute of Evolutionary Biology, Edinburgh, United Kingdom
| | - Myriam Gaudeul
- UMR CNRS MNHN UPMC EPHE 7205 Institut de Systématique, Evolution, Biodiversité, Muséum National d'Histoire Naturelle, Paris, France
| | - Andrew J. Lowe
- Australian Centre for Evolutionary Biology and Biodiversity, Environment Institute, School of Earth and Environmental Science, University of Adelaide, Adelaide, Australia
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20
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Gaudeul M, Gardner MF, Thomas P, Ennos RA, Hollingsworth PM. Evolutionary dynamics of emblematic Araucaria species (Araucariaceae) in New Caledonia: nuclear and chloroplast markers suggest recent diversification, introgression, and a tight link between genetics and geography within species. BMC Evol Biol 2014; 14:171. [PMID: 25189104 PMCID: PMC4182765 DOI: 10.1186/s12862-014-0171-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 07/23/2014] [Indexed: 11/21/2022] Open
Abstract
Background New Caledonia harbours a highly diverse and endemic flora, and 13 (out of the 19 worldwide) species of Araucaria are endemic to this territory. Their phylogenetic relationships remain largely unresolved. Using nuclear microsatellites and chloroplast DNA sequencing, we focused on five closely related Araucaria species to investigate among-species relationships and the distribution of within-species genetic diversity across New Caledonia. Results The species could be clearly distinguished here, except A. montana and A. laubenfelsii that were not differentiated and, at most, form a genetic cline. Given their apparent morphological and ecological similarity, we suggested that these two species may be considered as a single evolutionary unit. We observed cases of nuclear admixture and incongruence between nuclear and chloroplast data, probably explained by introgression and shared ancestral polymorphism. Ancient hybridization was evidenced between A. biramulata and A. laubenfelsii in Mt Do, and is strongly suspected between A. biramulata and A. rulei in Mt Tonta. In both cases, extensive asymmetrical backcrossing eliminated the influence of one parent in the nuclear DNA composition. Shared ancestral polymorphism was also observed for cpDNA, suggesting that species diverged recently, have large effective sizes and/or that cpDNA experienced slow rates of molecular evolution. Within-species genetic structure was pronounced, probably because of low gene flow and significant inbreeding, and appeared clearly influenced by geography. This may be due to survival in distinct refugia during Quaternary climatic oscillations. Conclusions The study species probably diverged recently and/or are characterized by a slow rate of cpDNA sequence evolution, and introgression is strongly suspected. Within-species genetic structure is tightly linked with geography. We underline the conservation implications of our results, and highlight several perspectives. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0171-6) contains supplementary material, which is available to authorized users.
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Hinsinger DD, Gaudeul M, Couloux A, Bousquet J, Frascaria-Lacoste N. The phylogeography of Eurasian Fraxinus species reveals ancient transcontinental reticulation. Mol Phylogenet Evol 2014; 77:223-37. [PMID: 24795215 DOI: 10.1016/j.ympev.2014.04.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 04/14/2014] [Accepted: 04/18/2014] [Indexed: 01/16/2023]
Abstract
To investigate the biogeographical history of ashes species of the Eurasian section Fraxinus and to test the hypothesis of ancient reticulations, we sequenced nuclear DNA (nETS and nITS, 1075 bp) for 533 samples and scored AFLP for 63 samples of Eurasian ashes within the section Fraxinus. The nITS phylogeny retrieved the classical view of the evolution of the section, whereas nETS phylogeny indicated an unexpected separation of F. angustifolia in two paraphyletic groups, respectively found in southeastern Europe and in the other parts of the Mediterranean basin. In the nETS phylogeny, the former group was closely related to F. excelsior, whereas the later was closely related to F. mandshurica, a species which is restricted nowadays to northeastern Asia. This topological incongruence between the two loci indicated the occurrence of an ancient reticulation between European and Asian ash species. Several other ancient reticulation events between the two European species and the other species of the section were supported by the posterior predictive checking method. Some of these reticulation events would have occurred during the Miocene, when climatic variations may have lead these species to expand their distribution range and come into contact. The recurrent reticulations observed among Eurasian ash species indicate that they should be considered as conspecific taxa, with subspecific status for some groups. Altogether, the results of the present study provide a rare documented evidence for the occurrence of multiple ancient reticulations within a group of temperate tree taxa with modern disjunct distributions in Eurasia. These ancient reticulation events indicate that the speciation process is slow in ashes, necessitating long periods of geographical isolation. The implications for speciation processes in temperate trees with similar life history and reproductive biology are discussed.
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Affiliation(s)
- Damien D Hinsinger
- AgroParisTech, UMR 8079, 91405 Orsay, France; Centre national de la recherche scientifique, UMR 8079, 910405 Orsay, France; Université Paris-Sud, UMR 8079, F-91000 Orsay, France; Chaire de recherche du Canada en génomique forestière et environnementale, Centre d'étude de la forêt et Institut de biologie intégrative et des systèmes, Université Laval, Québec, Québec G1V 0A6, Canada.
| | - Myriam Gaudeul
- Muséum National d'Histoire Naturelle, UMR CNRS 7205 'Origine, Structure et Evolution de la Biodiversité', 16 rue Buffon, CP 39, F-75005 Paris, France.
| | - Arnaud Couloux
- Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP 5706, F-91057 Evry Cedex, France.
| | - Jean Bousquet
- Chaire de recherche du Canada en génomique forestière et environnementale, Centre d'étude de la forêt et Institut de biologie intégrative et des systèmes, Université Laval, Québec, Québec G1V 0A6, Canada.
| | - Nathalie Frascaria-Lacoste
- AgroParisTech, UMR 8079, 91405 Orsay, France; Centre national de la recherche scientifique, UMR 8079, 910405 Orsay, France; Université Paris-Sud, UMR 8079, F-91000 Orsay, France.
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22
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Hinsinger DD, Basak J, Gaudeul M, Cruaud C, Bertolino P, Frascaria-Lacoste N, Bousquet J. The phylogeny and biogeographic history of ashes (fraxinus, oleaceae) highlight the roles of migration and vicariance in the diversification of temperate trees. PLoS One 2013; 8:e80431. [PMID: 24278282 PMCID: PMC3837005 DOI: 10.1371/journal.pone.0080431] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 10/03/2013] [Indexed: 11/18/2022] Open
Abstract
The cosmopolitan genus Fraxinus, which comprises about 40 species of temperate trees and shrubs occupying various habitats in the Northern Hemisphere, represents a useful model to study speciation in long-lived angiosperms. We used nuclear external transcribed spacers (nETS), phantastica gene sequences, and two chloroplast loci (trnH-psbA and rpl32-trnL) in combination with previously published and newly obtained nITS sequences to produce a time-calibrated multi-locus phylogeny of the genus. We then inferred the biogeographic history and evolution of floral morphology. An early dispersal event could be inferred from North America to Asia during the Oligocene, leading to the diversification of the section Melioides sensus lato. Another intercontinental dispersal originating from the Eurasian section of Fraxinus could be dated from the Miocene and resulted in the speciation of F. nigra in North America. In addition, vicariance was inferred to account for the distribution of the other Old World species (sections Sciadanthus, Fraxinus and Ornus). Geographic speciation likely involving dispersal and vicariance could also be inferred from the phylogenetic grouping of geographically close taxa. Molecular dating suggested that the initial divergence of the taxonomical sections occurred during the middle and late Eocene and Oligocene periods, whereas diversification within sections occurred mostly during the late Oligocene and Miocene, which is consistent with the climate warming and accompanying large distributional changes observed during these periods. These various results underline the importance of dispersal and vicariance in promoting geographic speciation and diversification in Fraxinus. Similarities in life history, reproductive and demographic attributes as well as geographical distribution patterns suggest that many other temperate trees should exhibit similar speciation patterns. On the other hand, the observed parallel evolution and reversions in floral morphology would imply a major influence of environmental pressure. The phylogeny obtained and its biogeographical implications should facilitate future studies on the evolution of complex adaptive characters, such as habitat preference, and their possible roles in promoting divergent evolution in trees.
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Affiliation(s)
- Damien Daniel Hinsinger
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, AgroParisTech, Orsay, France
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, Centre national de la recherche scientifique, Orsay, France
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, Université Paris Sud, Orsay, France
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Québec, Canada
- * E-mail:
| | - Jolly Basak
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, Université Paris Sud, Orsay, France
| | - Myriam Gaudeul
- Unité mixte de recherche 7205 ‘Origine, Structure et Evolution de la Biodiversité’, Muséum National d'Histoire Naturelle, Paris, France
| | | | - Paola Bertolino
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, AgroParisTech, Orsay, France
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, Centre national de la recherche scientifique, Orsay, France
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, Université Paris Sud, Orsay, France
| | - Nathalie Frascaria-Lacoste
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, AgroParisTech, Orsay, France
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, Centre national de la recherche scientifique, Orsay, France
- Laboratoire Ecologie, Systématique et Evolution, Unité mixte de recherche 8079, Université Paris Sud, Orsay, France
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec, Québec, Canada
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Gaudeul M, Rouhan G. A plea for modern botanical collections to include DNA-friendly material. Trends Plant Sci 2013; 18:184-5. [PMID: 23312146 DOI: 10.1016/j.tplants.2012.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 11/28/2012] [Accepted: 12/11/2012] [Indexed: 05/12/2023]
Abstract
Botanists have long collected herbarium specimens during their expeditions, and the importance of such collections is broadly acknowledged nowadays. It is largely recognized that material for molecular studies must be accompanied by herbarium material to be deposited in a recognized herbarium (vouchers). By contrast, the collection of herbarium specimens with no material for genetic analyses is unfortunately still common. The evolution of science and the need to face new environmental challenges require some changes in the way science is planned and performed. Here, we highlight some key scientific areas which could greatly benefit from such DNA-friendly collections, and we make a plea - and a call to all botanists - for the routine collection of DNA-friendly material together with herbarium specimens.
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Affiliation(s)
- Myriam Gaudeul
- Muséum National d'Histoire Naturelle, Herbier National (P), UMR CNRS 7205 Origine, Structure et Evolution de la Biodiversité, 16 rue Buffon, CP39, 75231 Paris Cedex 05, France.
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Taberlet P, Zimmermann NE, Englisch T, Tribsch A, Holderegger R, Alvarez N, Niklfeld H, Coldea G, Mirek Z, Moilanen A, Ahlmer W, Marsan PA, Bona E, Bovio M, Choler P, Cieślak E, Colli L, Cristea V, Dalmas J, Frajman B, Garraud L, Gaudeul M, Gielly L, Gutermann W, Jogan N, Kagalo AA, Korbecka G, Küpfer P, Lequette B, Letz DR, Manel S, Mansion G, Marhold K, Martini F, Negrini R, Niño F, Paun O, Pellecchia M, Perico G, Piękoś‐Mirkowa H, Prosser F, Puşcaş M, Ronikier M, Scheuerer M, Schneeweiss GM, Schönswetter P, Schratt‐Ehrendorfer L, Schüpfer F, Selvaggi A, Steinmann K, Thiel‐Egenter C, Loo M, Winkler M, Wohlgemuth T, Wraber T, Gugerli F. Genetic diversity in widespread species is not congruent with species richness in alpine plant communities. Ecol Lett 2012; 15:1439-48. [DOI: 10.1111/ele.12004] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 08/15/2012] [Accepted: 08/20/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Pierre Taberlet
- Laboratoire d'Ecologie Alpine CNRS UMR 5553 Université Joseph Fourier BP 43 38041 Grenoble Cedex 9 France
| | - Niklaus E. Zimmermann
- WSL Swiss Federal Research Institute Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Thorsten Englisch
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | - Andreas Tribsch
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | - Rolf Holderegger
- WSL Swiss Federal Research Institute Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Nadir Alvarez
- Laboratoire de Botanique Evolutive Université de Neuchâtel 11, rue Emile‐Argand 2007 Neuchâtel Switzerland
| | - Harald Niklfeld
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | - Gheorghe Coldea
- Institute of Biological Research Str. Republicii nr. 48 400015 Cluj‐Napoca Romania
| | - Zbigniew Mirek
- Institute of Botany Polish Academy of Sciences Lubicz 46 31‐512 Kraków Poland
| | - Atte Moilanen
- Department of Biosciences P.O. Box 65 (Biocenter III) FI‐00014 University of Helsinki Finland
| | - Wolfgang Ahlmer
- University of Regensburg Institute of Botany 93040 Regensburg Germany
| | - Paolo Ajmone Marsan
- Biodiversity and ancient DNA Research Center – BioDNA – and Institute of Zootechnics Università Cattolica del S. Cuore via E. Parmense, 84 29122 Piacenza Italy
| | - Enzo Bona
- Dipartimento di Biologia Università di Trieste Via L. Giorgieri 10 34127 Trieste Italy
| | - Maurizio Bovio
- Dipartimento di Biologia Università di Trieste Via L. Giorgieri 10 34127 Trieste Italy
| | - Philippe Choler
- Laboratoire d'Ecologie Alpine CNRS UMR 5553 Université Joseph Fourier BP 43 38041 Grenoble Cedex 9 France
| | - Elżbieta Cieślak
- Institute of Botany Polish Academy of Sciences Lubicz 46 31‐512 Kraków Poland
| | - Licia Colli
- Biodiversity and ancient DNA Research Center – BioDNA – and Institute of Zootechnics Università Cattolica del S. Cuore via E. Parmense, 84 29122 Piacenza Italy
| | | | - Jean‐Pierre Dalmas
- Conservatoire Botanique National Alpin ‐ CBNA Domaine de Charance 05000 Gap France
| | - Božo Frajman
- Univerza v Ljubljani Oddelek za biologijo BF Večna pot 111 1000 Ljubljana Slovenia
| | - Luc Garraud
- Conservatoire Botanique National Alpin ‐ CBNA Domaine de Charance 05000 Gap France
| | - Myriam Gaudeul
- Laboratoire d'Ecologie Alpine CNRS UMR 5553 Université Joseph Fourier BP 43 38041 Grenoble Cedex 9 France
| | - Ludovic Gielly
- Laboratoire d'Ecologie Alpine CNRS UMR 5553 Université Joseph Fourier BP 43 38041 Grenoble Cedex 9 France
| | - Walter Gutermann
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | - Nejc Jogan
- Univerza v Ljubljani Oddelek za biologijo BF Večna pot 111 1000 Ljubljana Slovenia
| | - Alexander A. Kagalo
- Institute of Ecology of the Carpathians N.A.S. of Ukraine 4 Kozelnitska str. 79026 Lviv Ukraine
| | - Grażyna Korbecka
- Institute of Botany Polish Academy of Sciences Lubicz 46 31‐512 Kraków Poland
| | - Philippe Küpfer
- Laboratoire de Botanique Evolutive Université de Neuchâtel 11, rue Emile‐Argand 2007 Neuchâtel Switzerland
| | - Benoît Lequette
- Parc national du Mercantour 23 rue d'Italie, BP 1316 06006 Nice Cedex 1 France
| | - Dominik Roman Letz
- Institute of Botany of Slovak Academy of Sciences Department of Vascular Plant Taxonomy Dúbravská cesta 9 845 23 Bratislava Slovakia
| | - Stéphanie Manel
- Laboratoire d'Ecologie Alpine CNRS UMR 5553 Université Joseph Fourier BP 43 38041 Grenoble Cedex 9 France
| | - Guilhem Mansion
- Laboratoire de Botanique Evolutive Université de Neuchâtel 11, rue Emile‐Argand 2007 Neuchâtel Switzerland
| | - Karol Marhold
- Institute of Botany of Slovak Academy of Sciences Department of Vascular Plant Taxonomy Dúbravská cesta 9 845 23 Bratislava Slovakia
| | - Fabrizio Martini
- Dipartimento di Biologia Università di Trieste Via L. Giorgieri 10 34127 Trieste Italy
| | - Riccardo Negrini
- Biodiversity and ancient DNA Research Center – BioDNA – and Institute of Zootechnics Università Cattolica del S. Cuore via E. Parmense, 84 29122 Piacenza Italy
| | - Fernando Niño
- Medias‐France/IRD CNES ‐ BPi 2102, 18, Av. Edouard Belin F‐31401 Toulouse Cedex 9 France
| | - Ovidiu Paun
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | - Marco Pellecchia
- Biodiversity and ancient DNA Research Center – BioDNA – and Institute of Zootechnics Università Cattolica del S. Cuore via E. Parmense, 84 29122 Piacenza Italy
| | - Giovanni Perico
- Dipartimento di Biologia Università di Trieste Via L. Giorgieri 10 34127 Trieste Italy
| | | | | | - Mihai Puşcaş
- Babes‐Bolyai University 400015 Cluj‐Napoca Romania
| | - Michał Ronikier
- Institute of Botany Polish Academy of Sciences Lubicz 46 31‐512 Kraków Poland
| | - Martin Scheuerer
- University of Regensburg Institute of Botany 93040 Regensburg Germany
| | | | - Peter Schönswetter
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | | | - Fanny Schüpfer
- Laboratoire de Botanique Evolutive Université de Neuchâtel 11, rue Emile‐Argand 2007 Neuchâtel Switzerland
| | - Alberto Selvaggi
- Istituto per le Piante da Legno e l'Ambiente c.so Casale, 476 10132 Torino Italy
| | - Katharina Steinmann
- WSL Swiss Federal Research Institute Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Conny Thiel‐Egenter
- WSL Swiss Federal Research Institute Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Marcela Loo
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | - Manuela Winkler
- Faculty Centre of Biodiversity University of Vienna Rennweg 14 1030 Vienna Austria
| | - Thomas Wohlgemuth
- WSL Swiss Federal Research Institute Zürcherstrasse 111 8903 Birmensdorf Switzerland
| | - Tone Wraber
- Univerza v Ljubljani Oddelek za biologijo BF Večna pot 111 1000 Ljubljana Slovenia
| | - Felix Gugerli
- WSL Swiss Federal Research Institute Zürcherstrasse 111 8903 Birmensdorf Switzerland
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Gaudeul M, Rouhan G, Gardner MF, Hollingsworth PM. AFLP markers provide insights into the evolutionary relationships and diversification of New Caledonian Araucaria species (Araucariaceae). Am J Bot 2012; 99:68-81. [PMID: 22184275 DOI: 10.3732/ajb.1100321] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY Despite its small size, New Caledonia is characterized by a very diverse flora and striking environmental gradients, which make it an ideal setting to study species diversification. Thirteen of the 19 Araucaria species are endemic to the territory and form a monophyletic group, but patterns and processes that lead to such a high species richness are largely unexplored. METHODS We used 142 polymorphic AFLP markers and performed analyses based on Bayesian clustering algorithms, genetic distances, and cladistics on 71 samples representing all New Caledonian Araucaria species. We examined correlations between the inferred evolutionary relationships and shared morphological, ecological, or geographic parameters among species, to investigate evolutionary processes that may have driven speciation. KEY RESULTS We showed that genetic divergence among the present New Caledonian Araucaria species is low, suggesting recent diversification rather than pre-existence on Gondwana. We identified three genetic groups that included small-leaved, large-leaved, and coastal species, but detected no association with soil preference, ecological habitat, or rainfall. The observed patterns suggested that speciation events resulted from both differential adaptation and vicariance. Last, we hypothesize that speciation is ongoing and/or there are cryptic species in some genetically (sometimes also morphologically) divergent populations. CONCLUSIONS Further data are required to provide better resolution and understanding of the diversification of New Caledonian Araucaria species. Nevertheless, our study allowed insights into their evolutionary relationships and provides a framework for future investigations on the evolution of this emblematic group of plants in one of the world's biodiversity hotspots.
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Affiliation(s)
- Myriam Gaudeul
- Muséum National d'Histoire Naturelle, UMR CNRS 'Origine, Structure et Evolution de la Biodiversité', Paris, France.
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Gaudeul M, Giraud T, Kiss L, Shykoff JA. Nuclear and chloroplast microsatellites show multiple introductions in the worldwide invasion history of common ragweed, Ambrosia artemisiifolia. PLoS One 2011; 6:e17658. [PMID: 21423697 PMCID: PMC3053376 DOI: 10.1371/journal.pone.0017658] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 02/07/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Ambrosia artemisiifolia is a North American native that has become one of the most problematic invasive plants in Europe and Asia. We studied its worldwide population genetic structure, using both nuclear and chloroplast microsatellite markers and an unprecedented large population sampling. Our goals were (i) to identify the sources of the invasive populations; (ii) to assess whether all invasive populations were founded by multiple introductions, as previously found in France; (iii) to examine how the introductions have affected the amount and structure of genetic variation in Europe; (iv) to document how the colonization of Europe proceeded; (v) to check whether populations exhibit significant heterozygote deficiencies, as previously observed. PRINCIPAL FINDINGS We found evidence for multiple introductions of A. artemisiifolia, within regions but also within populations in most parts of its invasive range, leading to high levels of diversity. In Europe, introductions probably stem from two different regions of the native area: populations established in Central Europe appear to have originated from eastern North America, and Eastern European populations from more western North America. This may result from differential commercial exchanges between these geographic regions. Our results indicate that the expansion in Europe mostly occurred through long-distance dispersal, explaining the absence of isolation by distance and the weak influence of geography on the genetic structure in this area in contrast to the native range. Last, we detected significant heterozygote deficiencies in most populations. This may be explained by partial selfing, biparental inbreeding and/or a Wahlund effect and further investigation is warranted. CONCLUSIONS This insight into the sources and pathways of common ragweed expansion may help to better understand its invasion success and provides baseline data for future studies on the evolutionary processes involved during range expansion in novel environments.
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Affiliation(s)
- Myriam Gaudeul
- UMR CNRS 7205 Origine, Structure et Evolution de la Biodiversité, Muséum National d'Histoire Naturelle, Paris, France.
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Abstract
Populations at the periphery of a species' range are of interest to conservation biologists because they can show marked genetic differentiation from populations at the center of a range and because of potential hybridization among rare and common species. We examined two closely related Cyclamen species. One is a narrow endemic, and the other is more geographically widespread (both protected by law in continental southern France). We used floral traits and genetic variability to test for hybridization among the species in peripheral populations of the rare species. The species co-occurred on Corsica in a disjunct, peripheral part of the distribution of the endemic species and in an ecologically marginal area for the widespread species. The two species have hybridized and the endemic species showed high levels of introgression with its widespread congener. Genetic and floral variability in sites with both species was markedly higher than in sites with a single species. Our results highlight the need for a conservation strategy that integrates hybrid populations because they represent a source of novel diversity that may have adaptive potential.
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Affiliation(s)
- John D Thompson
- UMR 5175 Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, 1919 route de Mende, 34293 Montpellier cedex 5, France.
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Alvarez N, Thiel-Egenter C, Tribsch A, Holderegger R, Manel S, Schönswetter P, Taberlet P, Brodbeck S, Gaudeul M, Gielly L, Küpfer P, Mansion G, Negrini R, Paun O, Pellecchia M, Rioux D, Schüpfer F, Van Loo M, Winkler M, Gugerli F. History or ecology? Substrate type as a major driver of patial genetic structure in Alpine plants. Ecol Lett 2009; 12:632-40. [PMID: 19392716 DOI: 10.1111/j.1461-0248.2009.01312.x] [Citation(s) in RCA: 154] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nadir Alvarez
- Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
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Hollingsworth ML, Andra Clark A, Forrest LL, Richardson J, Pennington RT, Long DG, Cowan R, Chase MW, Gaudeul M, Hollingsworth PM. Selecting barcoding loci for plants: evaluation of seven candidate loci with species-level sampling in three divergent groups of land plants. Mol Ecol Resour 2009. [PMID: 21564673 DOI: 10.1111/j.1755‐0998.2008.02439.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There has been considerable debate, but little consensus regarding locus choice for DNA barcoding land plants. This is partly attributable to a shortage of comparable data from all proposed candidate loci on a common set of samples. In this study, we evaluated the seven main candidate plastid regions (rpoC1, rpoB, rbcL, matK, trnH-psbA, atpF-atpH, psbK-psbI) in three divergent groups of land plants [Inga (angiosperm); Araucaria (gymnosperm); Asterella s.l. (liverwort)]. Across these groups, no single locus showed high levels of universality and resolvability. Interspecific sharing of sequences from individual loci was common. However, when multiple loci were combined, fewer barcodes were shared among species. Evaluation of the performance of previously published suggestions of particular multilocus barcode combinations showed broadly equivalent performance. Minor improvements on these were obtained by various new three-locus combinations involving rpoC1, rbcL, matK and trnH-psbA, but no single combination clearly outperformed all others. In terms of absolute discriminatory power, promising results occurred in liverworts (e.g. c. 90% species discrimination based on rbcL alone). However, Inga (rapid radiation) and Araucaria (slow rates of substitution) represent challenging groups for DNA barcoding, and their corresponding levels of species discrimination reflect this (upper estimate of species discrimination = 69% in Inga and only 32% in Araucaria; mean = 60% averaging all three groups).
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Affiliation(s)
- Michelle L Hollingsworth
- Royal Botanic Garden, 20 Inverleith Row, Edinburgh EH3 5LR, UK Jodrell Laboratory, Royal Botanic Gardens Kew, Richmond, TW9 3DS, UK Département Systématique et Evolution, Museum National d'Histoire Naturelle, 16 Rue Buffon, F-75005 Paris, France
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Ehrich D, Gaudeul M, Assefa A, Koch MA, Mummenhoff K, Nemomissa S, Brochmann C. Genetic consequences of Pleistocene range shifts: contrast between the Arctic, the Alps and the East African mountains. Mol Ecol 2008; 16:2542-59. [PMID: 17561912 DOI: 10.1111/j.1365-294x.2007.03299.x] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In wide-ranging species, the genetic consequences of range shifts in response to climate change during the Pleistocene can be predicted to differ among different parts of the distribution area. We used amplified fragment length polymorphism data to compare the genetic structure of Arabis alpina, a widespread arctic-alpine and afro-alpine plant, in three distinct parts of its range: the North Atlantic region, which was recolonized after the last ice age, the European Alps, where range shifts were probably primarily altitudinal, and the high mountains of East Africa, where the contemporary mountain top populations result from range contraction. Genetic structure was inferred using clustering analyses and estimates of genetic diversity within and between populations. There was virtually no diversity in the vast North Atlantic region, which was probably recolonized from a single refugial population, possibly located between the Alps and the northern ice sheets. In the European mountains, genetic diversity was high and distinct genetic groups had a patchy and sometimes disjunct distribution. In the African mountains, genetic diversity was high, clearly structured and partially in accordance with a previous chloroplast phylogeography. The fragmented structure in the European and African mountains indicated that A. alpina disperses little among established populations. Occasional long-distance dispersal events were, however, suggested in all regions. The lack of genetic diversity in the north may be explained by leading-edge colonization by this pioneer plant in glacier forelands, closely following the retracting glaciers. Overall, the genetic structure observed corresponded to the expectations based on the environmental history of the different regions.
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Affiliation(s)
- Dorothee Ehrich
- National Centre for Biosystematics, Natural History Museum, University of Oslo, NO-0318 Oslo, Norway.
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Manel S, Berthoud F, Bellemain E, Gaudeul M, Luikart G, Swenson JE, Waits LP, Taberlet P. A new individual-based spatial approach for identifying genetic discontinuities in natural populations. Mol Ecol 2008; 16:2031-43. [PMID: 17498230 DOI: 10.1111/j.1365-294x.2007.03293.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The population concept is central in evolutionary and conservation biology, but identifying the boundaries of natural populations is often challenging. Here, we present a new approach for assessing spatial genetic structure without the a priori assumptions on the locations of populations made by adopting an individual-centred approach. Our method is based on assignment tests applied in a moving window over an extensively sampled study area. For each individual, a spatially explicit probability surface is constructed, showing the estimated probability of finding its multilocus genotype across the landscape, and identifying putative migrants. Population boundaries are localized by estimating the mean slope of these probability surfaces over all individuals to identify areas with genetic discontinuities. The significance of the genetic discontinuities is assessed by permutation tests. This new approach has the potential to reveal cryptic population structure and to improve our ability to understand gene flow dynamics across landscapes. We illustrate our approach by simulations and by analysing two empirical datasets: microsatellite data of Ursus arctos in Scandinavia, and amplified fragment length polymorphism (AFLP) data of Rhododendron ferrugineum in the Alps.
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Affiliation(s)
- S Manel
- Laboratoire d'Ecologie Alpine, CNRS UMR 5553, Université Joseph Fourier, BP 53, F-38041 Grenoble Cedex 9, France.
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Abstract
We studied the phylogeography of Eryngium alpinum by sequencing two intergenic chloroplast spacers, trnH-psbA and trnS-trnG (1322 bp). The sampling design included 36 populations and 397 individuals spanning the entire distribution range of the species, from France to Bosnia. Twenty-one haplotypes were characterized and polymorphism was observed both within and among populations. Population differentiation was strong (F(ST) = 0.92) and largely explained by the distinction of five geographic regions: Southwestern, Western, Middle, Eastern Alps and Balkans (F(CT) = 0.62). Moreover, N(ST) was significantly higher than G(ST) (P < 0.05), showing the existence of a phylogeographic pattern. Six major lineages were recognized using samova and median-joining networks. One lineage, highly divergent from the other ones, was only found in the Balkans and probably persisted in situ during last glaciations. All other lineages might have survived in a Southwestern refugium (Mercantour) and colonized the entire Alpine arc (Southwestern, Western, Middle and Eastern Alps) through repeated colonization events at different time periods. This is the first empirical study suggesting Southern refugia for calcareous Alpine plants, although the existence of a secondary refugium in northern Italy/Austria is also suspected. We also observed recent haplotype diversification, especially in the Southwestern Alps.
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Affiliation(s)
- Y Naciri
- Laboratoire de Systématique et de Biodiversité, Unité de Phylogénie et Génétique Moléculaires, Conservatoire et Jardin botaniques, 1 Chemin de l'Impératrice, CP 60, CH-1292 Chambésy, Geneva, Switzerland.
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Gaudeul M, Stenøien HK, Agren J. Landscape structure, clonal propagation, and genetic diversity in Scandinavian populations of Arabidopsis lyrata (Brassicaceae). Am J Bot 2007; 94:1146-1155. [PMID: 21636482 DOI: 10.3732/ajb.94.7.1146] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Colonization history, landscape structure, and environmental conditions may influence patterns of neutral genetic variation because of their effects on gene flow and reproductive mode. We compared variation at microsatellite loci within and among 26 Arabidopsis lyrata populations in two disjunct areas of its distribution in northern Europe (Norway and Sweden). The two areas probably share a common colonization history but differ in size (Norwegian range markedly larger than Swedish range), landscape structure (mountains vs. coast), and habitat conditions likely to affect patterns of gene flow and opportunities for sexual reproduction. Within-population genetic diversity was not related to latitude but was higher in Sweden than in Norway. Population differentiation was stronger among Norwegian than among Swedish populations (F(ST) = 0.23 vs. F(ST) = 0.18). The frequency of clonal propagation (proportion of identical multilocus genotypes) increased with decreasing population size, was higher in Norwegian than in Swedish populations, but was not related to altitude or substrate. Differences in genetic structure are discussed in relation to population characteristics and range size in the two areas. The results demonstrate that the possibility of clonal propagation should be considered when developing strategies for sampling and analyzing data in ecological and genetic studies of this emerging model species.
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Affiliation(s)
- Myriam Gaudeul
- Department of Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Villavägen 14, SE-752 36 Uppsala, Sweden
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Kivimäki M, Kärkkäinen K, Gaudeul M, Løe G, Agren J. Gene, phenotype and function: GLABROUS1 and resistance to herbivory in natural populations of Arabidopsis lyrata. Mol Ecol 2007; 16:453-62. [PMID: 17217357 DOI: 10.1111/j.1365-294x.2007.03109.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The molecular genetic basis of adaptive variation is of fundamental importance for evolutionary dynamics, but is still poorly known. Only in very few cases has the relationship between genetic variation at the molecular level, phenotype and function been established in natural populations. We examined the functional significance and genetic basis of a polymorphism in production of leaf hairs, trichomes, in the perennial herb Arabidopsis lyrata. Earlier studies suggested that trichome production is subject to divergent selection. Here we show that the production of trichomes is correlated with reduced damage from insect herbivores in natural populations, and using statistical methods developed for medical genetics we document an association between loss of trichome production and mutations in the regulatory gene GLABROUS1. Sequence data suggest that independent mutations in this regulatory gene have provided the basis for parallel evolution of reduced resistance to insect herbivores in different populations of A. lyrata and in the closely related Arabidopsis thaliana. The results show that candidate genes identified in model organisms provide a valuable starting point for analysis of the genetic basis of phenotypic variation in natural populations.
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Affiliation(s)
- Maarit Kivimäki
- Finnish Forest Research Institute, Vantaa Research Unit, 01301 Vantaa, Finland.
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Gaudeul M, Till-Bottraud I. Reproductive ecology of the endangered Alpine species Eryngium alpinum L. (Apiaceae): phenology, gene dispersal and reproductive success. Ann Bot 2004; 93:711-21. [PMID: 15102612 PMCID: PMC4242303 DOI: 10.1093/aob/mch098] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
BACKGROUND AND AIMS Eryngium alpinum (Apiaceae) is an endangered perennial, characteristic of the Alpine flora. Because the breeding system influences both demographic (reproductive success) and genetic (inbreeding depression, evolutionary potential) parameters that are crucial for population maintenance, the reproductive ecology of E. alpinum was investigated. Specifically, the aims of the study were (1) to determine the factors (resources and/or pollen) limiting plant fitness; and (2) to assess the potential for gene flow within a plant, within a patch of plants, and across a whole valley where the species is abundant. METHODS Field experiments were performed at two sites in the Fournel valley, France, over three consecutive years. Studies included a phenological survey, observations of pollinators (visitation rates and flight distances), dispersal of a fluorescent powder used as a pollen analogue, the use of seed traps, determination of the pollen/ovule ratio, and an experiment to test whether seed production is limited by pollen and/or by resources. KEY RESULTS E. alpinum is pollinated by generalist pollinators, visitation rates are very high and seed set is resource- rather than pollen-limited. The short flights of honeybees indicate a high potential for geitonogamy, and low pollen and seed dispersals suggest strong genetic structure over short distances. These results are interpreted in the light of previous molecular markers studies, which, in contrast, showed complete outcrossing and high genetic homogeneity. CONCLUSION S. The study highlights the usefulness of adopting several complementary approaches to understanding the dynamic processes at work in natural populations, and the conservation implications for E. alpinum are emphasized. Although the studied populations do not seem threatened in the near future, long-term monitoring appears necessary to assess the impact of habitat fragmentation. Moreover, this study provides useful baseline data for future investigations in smaller and more isolated populations.
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Affiliation(s)
- M Gaudeul
- Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université J. Fourier, BP 53, F-38041 Grenoble Cedex 09, France.
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Gaudeul M, Till-Bottraud I, Barjon F, Manel S. Genetic diversity and differentiation in Eryngium alpinum L. (Apiaceae): comparison of AFLP and microsatellite markers. Heredity (Edinb) 2004; 92:508-18. [PMID: 15014426 DOI: 10.1038/sj.hdy.6800443] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Genetic diversity and structure of 12 populations of Eryngium alpinum L. were investigated using 63 dominant amplified fragment length polymorphism (AFLP) and seven codominant microsatellite (48 alleles) markers. Within-population diversity estimates obtained with both markers were not correlated, but the microsatellite-based fixation index Fis was correlated with both AFLP diversity indices (number of polymorphic bands and Nei's expected heterozygosity). Only AFLP diversity indices increased with the size of populations, although they did not significantly differ among them (Kruskall-Wallis test). The discrepancy between AFLPs and microsatellites may be explained by a better coverage of the genome with numerous AFLPs, the higher mutation rates of microsatellites or the absence of significant difference among within-population diversity estimates. Genetic differentiation was higher with AFLPs (theta=0.40) than with microsatellites (theta=0.23), probably due to the higher polymorphism of microsatellites. Thus, we considered global qualitative patterns rather than absolute estimates to compare the performance of both types of markers. On a large geographic scale, the Mantel test and multivariate analysis showed that genetic patterns were more congruent with the spatial arrangement of populations when inferred from microsatellites than from AFLPs, suggesting higher homoplasy of AFLP markers. On a small spatial scale, AFLPs managed to discriminate individuals from neighboring populations whereas microsatellites did not (multivariate analysis), and the percentage of individuals correctly assigned to their population of origin was higher with AFLPs than with microsatellites. However, dominant AFLPs cannot be used to study heterozygosity-related topics. Thus, distinct molecular markers should be used depending on the biological question and the geographical scale investigated.
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Affiliation(s)
- M Gaudeul
- Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université J Fourier, BP 53, F-38041 Grenoble 09, France.
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Abstract
We investigated the reproductive ecology of an endangered alpine species, Eryngium alpinum L., to determine its selfing rate and to propose possible mechanisms that may shape its breeding system. Whereas pollinators' foraging behavior suggested a high potential for geitonogamy (70% of the flights occur within plants), microsatellite analyses of seed progenies demonstrated that plants are primarily outcrossing (outcrossing rate [tm] = 0.65, 0.96, and 1 in three populations). Given the relatively long pollen viability (at least 4-5 d) and the high number of simultaneously opened flowers on each plant, protandry is not sufficient to eliminate selfing. Second, controlled crosses demonstrated not only auto-fertility, but also partial self-incompatibility. Partial self-incompatibility is probably due to the competitive advantage of cross vs. self-pollen, and, together with protandry, could lead the species to selfing as a reproductive assurance. These results are encouraging for the maintenance of large populations. However, higher selfing was observed in a small population that could suffer inbreeding depression, as observed on experimentally selfed seeds. Thus, these populations should be carefully monitored. Finally, this study shows how molecular markers and field experiments may complement each other in our reaching a global understanding of mating patterns.
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Affiliation(s)
- Myriam Gaudeul
- Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université J. Fourier, BP 53, F-38041 Grenoble Cedex 09, France
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Despres L, Loriot S, Gaudeul M. Geographic pattern of genetic variation in the European globeflower Trollius europaeus L. (Ranunculaceae) inferred from amplified fragment length polymorphism markers. Mol Ecol 2002; 11:2337-47. [PMID: 12406244 DOI: 10.1046/j.1365-294x.2002.01618.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The distribution of genetic variation and the phylogenetic relationships between 18 populations of the arctic-alpine plant Trollius europaeus were analysed in three main regions (Alps, Pyrenees and Fennoscandia) by using dominant AFLP markers. Analysis of molecular variance revealed that most of the genetic variability was found within populations (64%), although variation among regions (17%) and among populations within regions (19%) was highly significant (P < 0.001). Accordingly, the global fixation index FST averaged over loci was high (0.39). The among-population differentiation indicates restricted gene flow, congruent with limited dispersal of specific globeflower's pollinating flies (Chiastocheta spp.). Within-population diversity levels were significantly higher in the Alps (mean Nei's expected heterozygosity HE = 0.229) than in the Pyrenees (HE= 0.197) or in Fennoscandia (HE = 0.158). This finding is congruent with the species-richness of the associated flies, which is maximum in the Alps. We discuss the processes involved in shaping observed patterns of genetic diversity within and among T. europaeus populations. Genetic drift is the major factor acting on the small Pyrenean populations at the southern edge of T. europaeus distribution, while large Fennoscandian populations result probably from a founder effect followed by demographic expansion. The Alpine populations represent moderately fragmented relics of large southern ancestral populations. The patterns of genetic variability observed in the host plant support the hypothesis of sympatric speciation in associated flies, rather than recurrent allopatric speciations.
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Affiliation(s)
- Laurence Despres
- Laboratoire de Biologie des Populations d'Altitude, CNRS-UMR 5553, Université J. Fourier, BP 53-38041 Grenoble Cedex 09, France.
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Gaudeul M, Naciri-Graven Y, Gauthier P, Pompanon F. Isolation and characterization of microsatellites in a perennial Apiaceae, Eryngium alpinum L. ACTA ACUST UNITED AC 2002. [DOI: 10.1046/j.1471-8286.2002.00162.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Gaudeul M, Taberlet P, Till-Bottraud I. Genetic diversity in an endangered alpine plant, Eryngium alpinum L. (Apiaceae), inferred from amplified fragment length polymorphism markers. Mol Ecol 2000; 9:1625-37. [PMID: 11050557 DOI: 10.1046/j.1365-294x.2000.01063.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Eryngium alpinum L. is an endangered species found across the European Alps. In order to obtain base-line data for the conservation of this species, we investigated levels of genetic diversity within and among 14 populations from the French Alps. We used the amplified fragment length polymorphism (AFLP) technique with three primer pairs and scored a total of 62 unambiguous, polymorphic markers in 327 individuals. Because AFLP markers are dominant, within-population genetic structure (e.g. FIS) could not be assessed. Analyses based either on the assumption of random-mating or on complete selfing lead to very similar results. Diversity levels within populations were relatively high (mean Nei's expected heterozygosity = 0.198; mean Shannon index = 0.283), and a positive correlation was detected between both genetic diversity measurements and population size (Spearman rank correlation: P = 0. 005 and P = 0.002, respectively). Moreover, FST values and exact tests of differentiation revealed high differentiation among populations (mean pairwise FST = 0.40), which appeared to be independent of geographical distance (nonsignificant Mantel test). Founder events during postglacial colonizations and/or bottlenecks are proposed to explain this high but random genetic differentiation. By contrast, we detected a pattern of isolation by distance within populations and valleys. Predominant local gene flow by pollen or seed is probably responsible for this pattern. Concerning the management of E. alpinum, the high genetic differentiation leads us to recommend the conservation of a maximum number of populations. This study demonstrates that AFLP markers enable a quick and reliable assessment of intraspecific genetic variability in conservation genetics.
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Affiliation(s)
- M Gaudeul
- Laboratoire de Biologie des Populations d'Altitude, UMR CNRS 5553, Université J. Fourier, BP 53, F-38041 Grenoble Cedex 09, France.
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