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Duncan GD, Ellis AG, Forest F, Verboom GA. Strong habitat and seasonal phenology effects on the evolution of self-compatibility, clonality and pollinator shifts in Lachenalia (Asparagaceae: Scilloideae). New Phytol 2024. [PMID: 38702970 DOI: 10.1111/nph.19786] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/09/2024] [Indexed: 05/06/2024]
Abstract
Plants employ a diversity of reproductive safeguarding strategies to circumvent the challenge of pollen limitation. Focusing on southern African Lachenalia (Asparagaceae: Scilloideae), we test the hypothesis that the evolution of reproductive safeguarding traits (self-compatibility, autonomous selfing, bird pollination and clonal propagation) is favoured in species occupying conditions of low insect abundance imposed by critically infertile fynbos heathland vegetation and by flowering outside the austral spring insect abundance peak. We trace the evolution of these traits and selective regimes on a dated, multi-locus phylogeny of Lachenalia and assess their evolutionary associations using ordinary and phylogenetic regression. Ancestral state reconstructions identify an association with non-fynbos vegetation and spring flowering as ancestral in Lachenalia, the transition to fynbos vegetation and non-spring flowering taking place multiple times. They also show that self-compatibility, autofertility, bird pollination and production of multiple clonal offsets have evolved repeatedly. Regression models suggest that bird pollination and self-compatibility are selected for in fynbos and in non-spring flowering lineages, with autofertility being positively associated with non-spring flowering. These patterns support the interpretation of these traits as reproductive safeguarding adaptations under reduced insect pollinator abundance. We find no evidence to support the interpretation of clonal propagation as a reproductive safeguarding strategy.
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Affiliation(s)
- Graham D Duncan
- Bolus Herbarium and Department of Biological Sciences, University of Cape Town, 7701, Rhodes Gift, South Africa
- Kirstenbosch National Botanical Garden, South African National Biodiversity Institute, 99 Rhodes Ave, Newlands, Cape Town, 7700, South Africa
| | - Allan G Ellis
- Department of Botany and Zoology, Stellenbosch University, Matieland, 7602, South Africa
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, Surrey, UK
| | - G Anthony Verboom
- Bolus Herbarium and Department of Biological Sciences, University of Cape Town, 7701, Rhodes Gift, South Africa
- Department of Biology and Environmental Science, University of Gothenburg, 40530, Gothenburg, Sweden
- Gothenburg Botanical Garden (Botaniska), 41319, Gothenburg, Sweden
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2
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Zuntini AR, Carruthers T, Maurin O, Bailey PC, Leempoel K, Brewer GE, Epitawalage N, Françoso E, Gallego-Paramo B, McGinnie C, Negrão R, Roy SR, Simpson L, Toledo Romero E, Barber VMA, Botigué L, Clarkson JJ, Cowan RS, Dodsworth S, Johnson MG, Kim JT, Pokorny L, Wickett NJ, Antar GM, DeBolt L, Gutierrez K, Hendriks KP, Hoewener A, Hu AQ, Joyce EM, Kikuchi IABS, Larridon I, Larson DA, de Lírio EJ, Liu JX, Malakasi P, Przelomska NAS, Shah T, Viruel J, Allnutt TR, Ameka GK, Andrew RL, Appelhans MS, Arista M, Ariza MJ, Arroyo J, Arthan W, Bachelier JB, Bailey CD, Barnes HF, Barrett MD, Barrett RL, Bayer RJ, Bayly MJ, Biffin E, Biggs N, Birch JL, Bogarín D, Borosova R, Bowles AMC, Boyce PC, Bramley GLC, Briggs M, Broadhurst L, Brown GK, Bruhl JJ, Bruneau A, Buerki S, Burns E, Byrne M, Cable S, Calladine A, Callmander MW, Cano Á, Cantrill DJ, Cardinal-McTeague WM, Carlsen MM, Carruthers AJA, de Castro Mateo A, Chase MW, Chatrou LW, Cheek M, Chen S, Christenhusz MJM, Christin PA, Clements MA, Coffey SC, Conran JG, Cornejo X, Couvreur TLP, Cowie ID, Csiba L, Darbyshire I, Davidse G, Davies NMJ, Davis AP, van Dijk KJ, Downie SR, Duretto MF, Duvall MR, Edwards SL, Eggli U, Erkens RHJ, Escudero M, de la Estrella M, Fabriani F, Fay MF, Ferreira PDL, Ficinski SZ, Fowler RM, Frisby S, Fu L, Fulcher T, Galbany-Casals M, Gardner EM, German DA, Giaretta A, Gibernau M, Gillespie LJ, González CC, Goyder DJ, Graham SW, Grall A, Green L, Gunn BF, Gutiérrez DG, Hackel J, Haevermans T, Haigh A, Hall JC, Hall T, Harrison MJ, Hatt SA, Hidalgo O, Hodkinson TR, Holmes GD, Hopkins HCF, Jackson CJ, James SA, Jobson RW, Kadereit G, Kahandawala IM, Kainulainen K, Kato M, Kellogg EA, King GJ, Klejevskaja B, Klitgaard BB, Klopper RR, Knapp S, Koch MA, Leebens-Mack JH, Lens F, Leon CJ, Léveillé-Bourret É, Lewis GP, Li DZ, Li L, Liede-Schumann S, Livshultz T, Lorence D, Lu M, Lu-Irving P, Luber J, Lucas EJ, Luján M, Lum M, Macfarlane TD, Magdalena C, Mansano VF, Masters LE, Mayo SJ, McColl K, McDonnell AJ, McDougall AE, McLay TGB, McPherson H, Meneses RI, Merckx VSFT, Michelangeli FA, Mitchell JD, Monro AK, Moore MJ, Mueller TL, Mummenhoff K, Munzinger J, Muriel P, Murphy DJ, Nargar K, Nauheimer L, Nge FJ, Nyffeler R, Orejuela A, Ortiz EM, Palazzesi L, Peixoto AL, Pell SK, Pellicer J, Penneys DS, Perez-Escobar OA, Persson C, Pignal M, Pillon Y, Pirani JR, Plunkett GM, Powell RF, Prance GT, Puglisi C, Qin M, Rabeler RK, Rees PEJ, Renner M, Roalson EH, Rodda M, Rogers ZS, Rokni S, Rutishauser R, de Salas MF, Schaefer H, Schley RJ, Schmidt-Lebuhn A, Shapcott A, Al-Shehbaz I, Shepherd KA, Simmons MP, Simões AO, Simões ARG, Siros M, Smidt EC, Smith JF, Snow N, Soltis DE, Soltis PS, Soreng RJ, Sothers CA, Starr JR, Stevens PF, Straub SCK, Struwe L, Taylor JM, Telford IRH, Thornhill AH, Tooth I, Trias-Blasi A, Udovicic F, Utteridge TMA, Del Valle JC, Verboom GA, Vonow HP, Vorontsova MS, de Vos JM, Al-Wattar N, Waycott M, Welker CAD, White AJ, Wieringa JJ, Williamson LT, Wilson TC, Wong SY, Woods LA, Woods R, Worboys S, Xanthos M, Yang Y, Zhang YX, Zhou MY, Zmarzty S, Zuloaga FO, Antonelli A, Bellot S, Crayn DM, Grace OM, Kersey PJ, Leitch IJ, Sauquet H, Smith SA, Eiserhardt WL, Forest F, Baker WJ. Phylogenomics and the rise of the angiosperms. Nature 2024:10.1038/s41586-024-07324-0. [PMID: 38658746 DOI: 10.1038/s41586-024-07324-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 03/15/2024] [Indexed: 04/26/2024]
Abstract
Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.
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Affiliation(s)
| | | | | | | | | | | | | | - Elaine Françoso
- Royal Botanic Gardens, Kew, Richmond, UK
- Centre for Ecology, Evolution and Behaviour, Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, London, UK
| | | | | | | | | | - Lalita Simpson
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | | | | | - Laura Botigué
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
| | | | | | - Steven Dodsworth
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | | | - Jan T Kim
- School of Physics, Engineering and Computer Science, University of Hertfordshire, Hatfield, UK
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Biodiversity and Conservation, Real Jardín Botánico (RJB-CSIC), Madrid, Spain
| | - Norman J Wickett
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Guilherme M Antar
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Departamento de Ciências Agrárias e Biológicas, Centro Universitário Norte do Espírito Santo, Universidade Federal do Espírito Santo, São Mateus, Brazil
| | | | | | - Kasper P Hendriks
- Department of Biology, University of Osnabrück, Osnabrück, Germany
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Alina Hoewener
- Plant Biodiversity, Technical University Munich, Freising, Germany
| | - Ai-Qun Hu
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Elizabeth M Joyce
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
- Systematic, Biodiversity and Evolution of Plants, Ludwig Maximilian University of Munich, Munich, Germany
| | - Izai A B S Kikuchi
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Drew A Larson
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Elton John de Lírio
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Jing-Xia Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | | | - Natalia A S Przelomska
- Royal Botanic Gardens, Kew, Richmond, UK
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Toral Shah
- Royal Botanic Gardens, Kew, Richmond, UK
| | | | | | - Gabriel K Ameka
- Department of Plant and Environmental Biology, University of Ghana, Accra, Ghana
| | - Rose L Andrew
- Botany and N.C.W. Beadle Herbarium, University of New England, Armidale, New South Wales, Australia
| | - Marc S Appelhans
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute of Plant Sciences, University of Göttingen, Göttingen, Germany
| | - Montserrat Arista
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - María Jesús Ariza
- General Research Services, Herbario SEV, CITIUS, Universidad de Sevilla, Seville, Spain
| | - Juan Arroyo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | | | | | - C Donovan Bailey
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Helen F Barnes
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | - Matthew D Barrett
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | - Russell L Barrett
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Randall J Bayer
- Department of Biological Sciences, University of Memphis, Memphis, TN, USA
| | - Michael J Bayly
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Ed Biffin
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
| | | | - Joanne L Birch
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Diego Bogarín
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Jardín Botánico Lankester, Universidad de Costa Rica, Cartago, Costa Rica
| | | | | | - Peter C Boyce
- Centro Studi Erbario Tropicale, Dipartimento di Biologia, University of Florence, Florence, Italy
| | | | | | - Linda Broadhurst
- Centre for Australian National Biodiversity Research, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Gillian K Brown
- Queensland Herbarium and Biodiversity Science, Brisbane Botanic Gardens, Toowong, Queensland, Australia
| | - Jeremy J Bruhl
- Botany and N.C.W. Beadle Herbarium, University of New England, Armidale, New South Wales, Australia
| | - Anne Bruneau
- Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques, University of Montreal, Montreal, Quebec, Canada
| | - Sven Buerki
- Department of Biological Sciences, Boise State University, Boise, ID, USA
| | - Edie Burns
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Government of Western Australia, Kensington, Western Australia, Australia
| | | | - Ainsley Calladine
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
| | | | - Ángela Cano
- Cambridge University Botanic Garden, Cambridge, UK
| | | | - Warren M Cardinal-McTeague
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Alejandra de Castro Mateo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Mark W Chase
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | | | | | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, China
| | - Maarten J M Christenhusz
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
- Plant Gateway, Den Haag, The Netherlands
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Mark A Clements
- Centre for Australian National Biodiversity Research, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Skye C Coffey
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Government of Western Australia, Kensington, Western Australia, Australia
| | - John G Conran
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Xavier Cornejo
- Herbario GUAY, Facultad de Ciencias Naturales, Universidad de Guayaquil, Guayaquil, Ecuador
| | | | - Ian D Cowie
- Northern Territory Herbarium Department of Environment Parks & Water Security, Northern Territory Government, Palmerston, Northern Territory, Australia
| | | | | | | | | | | | - Kor-Jent van Dijk
- The University of Adelaide, North Terrace Campus, Adelaide, South Australia, Australia
| | - Stephen R Downie
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Marco F Duretto
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Melvin R Duvall
- Department of Biological Sciences and Institute for the Study of the Environment, Sustainability and Energy, Northern Illinois University, DeKalb, IL, USA
| | | | - Urs Eggli
- Sukkulenten-Sammlung Zürich/ Grün Stadt Zürich, Zürich, Switzerland
| | - Roy H J Erkens
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Maastricht Science Programme, Maastricht University, Maastricht, The Netherlands
- System Earth Science, Maastricht University, Venlo, The Netherlands
| | - Marcial Escudero
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Manuel de la Estrella
- Departamento de Botánica, Ecología y Fisiología Vegetal, Facultad de Ciencias, Universidad de Córdoba, Córdoba, Spain
| | | | | | - Paola de L Ferreira
- Departamento de Biologia, Faculdade de Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
- Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Rachael M Fowler
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Sue Frisby
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Lin Fu
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | | | - Mercè Galbany-Casals
- Systematics and Evolution of Vascular Plants (UAB)-Associated Unit to CSIC by IBB, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Elliot M Gardner
- Department of Biology, Case Western Reserve University, Cleveland, OH, USA
| | | | - Augusto Giaretta
- Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados, Dourados, Brazil
| | - Marc Gibernau
- Laboratoire Sciences Pour l'Environnement, Université de Corse, Ajaccio, France
| | | | - Cynthia C González
- Herbario Trelew, Universidad Nacional de la Patagonia San Juan Bosco, Trelew, Argentina
| | | | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Bee F Gunn
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | - Diego G Gutiérrez
- Museo Argentino de Ciencias Naturales (MACN-CONICET), Buenos Aires, Argentina
| | - Jan Hackel
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Biology, Universität Marburg, Marburg, Germany
| | - Thomas Haevermans
- Institut de Systématique, Evolution, Biodiversité, Muséum National d'Histoire Naturelle, Paris, France
| | - Anna Haigh
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Tony Hall
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Melissa J Harrison
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | | | - Oriane Hidalgo
- Institut Botànic de Barcelona (IBB CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | - Trevor R Hodkinson
- Botany, School of Natural Sciences, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Gareth D Holmes
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | | | | | - Shelley A James
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Government of Western Australia, Kensington, Western Australia, Australia
| | - Richard W Jobson
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Gudrun Kadereit
- Prinzessin Therese von Bayern-Lehrstuhl für Systematik, Biodiversität & Evolution der Pflanzen, Ludwig-Maximilians-Universität München, Botanische Staatssammlung München, Botanischer Garten München-Nymphenburg, Munich, Germany
| | | | | | - Masahiro Kato
- National Museum of Nature and Science, Tsukuba, Japan
| | | | - Graham J King
- Southern Cross University, Lismore, New South Wales, Australia
| | | | | | - Ronell R Klopper
- Foundational Biodiversity Science Division, South African National Biodiversity Institute, Pretoria, South Africa
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | | | - Marcus A Koch
- Centre for Organismal Studies, Biodiversity and Plant Systematics, Heidelberg University, Heidelberg, Germany
| | | | - Frederic Lens
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | | | | | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Lan Li
- CSIRO, Canberra, Australian Capital Territory, Australia
| | | | - Tatyana Livshultz
- Department of Biodiversity, Earth and Environmental Sciences, Drexel University, Philadelphia, PA, USA
- Academy of Natural Science, Drexel University, Philadelphia, PA, USA
| | - David Lorence
- National Tropical Botanical Garden, Kalaheo, HI, USA
| | - Meng Lu
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Patricia Lu-Irving
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Jaquelini Luber
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Mabel Lum
- Bioplatforms Australia Ltd, Sydney, New South Wales, Australia
| | - Terry D Macfarlane
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Government of Western Australia, Kensington, Western Australia, Australia
| | | | - Vidal F Mansano
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Kristina McColl
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Angela J McDonnell
- Department of Biological Sciences, Saint Cloud State University, Saint Cloud, MN, USA
| | - Andrew E McDougall
- The University of Adelaide, North Terrace Campus, Adelaide, South Australia, Australia
| | - Todd G B McLay
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | - Hannah McPherson
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Rosa I Meneses
- Instituto de Arqueología y Antropología, Universidad Católica del Norte, San Pedro de Atacama, Chile
| | | | | | | | | | | | - Taryn L Mueller
- Department of Ecology, Evolution & Behavior, University of Minnesota, St. Paul, MN, USA
| | - Klaus Mummenhoff
- Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Jérôme Munzinger
- AMAP Lab, Université Montpellier, IRD, CIRAD, CNRS INRAE, Montpellier, France
| | - Priscilla Muriel
- Laboratorio de Ecofisiología, Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | - Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
- Centre for Australian National Biodiversity Research, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Lars Nauheimer
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | - Francis J Nge
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
| | - Reto Nyffeler
- Department of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland
| | - Andrés Orejuela
- Royal Botanic Garden Edinburgh, Edinburgh, UK
- Grupo de Investigación en Recursos Naturales Amazónicos, Instituto Tecnológico del Putumayo, Mocoa, Colombia
| | - Edgardo M Ortiz
- Plant Biodiversity, Technical University Munich, Freising, Germany
| | - Luis Palazzesi
- Museo Argentino de Ciencias Naturales (MACN-CONICET), Buenos Aires, Argentina
| | - Ariane Luna Peixoto
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Jaume Pellicer
- Institut Botànic de Barcelona (IBB CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | - Darin S Penneys
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | | | - Claes Persson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Marc Pignal
- Institut de Systématique, Evolution, Biodiversité, Muséum National d'Histoire Naturelle, Paris, France
| | - Yohan Pillon
- LSTM Université Montpellier, CIRADIRD, Montpellier, France
| | - José R Pirani
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | - Carmen Puglisi
- Royal Botanic Gardens, Kew, Richmond, UK
- Missouri Botanical Garden, St. Louis, MO, USA
| | - Ming Qin
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Richard K Rabeler
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Matthew Renner
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Eric H Roalson
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michele Rodda
- National Parks Board, Singapore Botanic Gardens, Singapore, Singapore
| | | | - Saba Rokni
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Rolf Rutishauser
- Department of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland
| | - Miguel F de Salas
- Tasmanian Herbarium, University of Tasmania, Sandy Bay, Tasmania, Australia
| | - Hanno Schaefer
- Plant Biodiversity, Technical University Munich, Freising, Germany
| | | | - Alexander Schmidt-Lebuhn
- Centre for Australian National Biodiversity Research, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Alison Shapcott
- School of Science Technology and Engineering, Center for Bioinnovation, University Sunshine Coast, Sippy Downs, Queensland, Australia
| | | | - Kelly A Shepherd
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Government of Western Australia, Kensington, Western Australia, Australia
| | - Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - André O Simões
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Campinas, Brazil
| | | | - Michelle Siros
- Royal Botanic Gardens, Kew, Richmond, UK
- University of California, San Francisco, San Francisco, CA, USA
| | - Eric C Smidt
- Departamento de Botânica, Universidade Federal do Paraná, Curitiba, Brazil
| | - James F Smith
- Department of Biological Sciences, Boise State University, Boise, ID, USA
| | - Neil Snow
- Pittsburg State University, Pittsburg, KS, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | | | | | - Julian R Starr
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | | | | | | | - Ian R H Telford
- Botany and N.C.W. Beadle Herbarium, University of New England, Armidale, New South Wales, Australia
| | - Andrew H Thornhill
- Botany and N.C.W. Beadle Herbarium, University of New England, Armidale, New South Wales, Australia
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Ifeanna Tooth
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | | | - Frank Udovicic
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | | | - Jose C Del Valle
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - G Anthony Verboom
- Department of Biological Sciences and Bolus Herbarium, University of Cape Town, Cape Town, South Africa
| | - Helen P Vonow
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
| | | | - Jurriaan M de Vos
- Department of Environmental Sciences-Botany, University of Basel, Basel, Switzerland
| | | | - Michelle Waycott
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Cassiano A D Welker
- Instituto de Biologia, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Adam J White
- Australian National Herbarium, Centre for Australian National Biodiversity Research, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | | | - Luis T Williamson
- The University of Adelaide, North Terrace Campus, Adelaide, South Australia, Australia
| | - Trevor C Wilson
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Sin Yeng Wong
- Institute of Biodiversity And Environmental Conservation, Universiti Malaysia Sarawak, Samarahan, Malaysia
| | - Lisa A Woods
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | | | - Stuart Worboys
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | | | - Ya Yang
- University of Minnesota-Twin Cities, St. Paul, MN, USA
| | | | - Meng-Yuan Zhou
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | | | | | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Oxford, Oxford, UK
| | | | - Darren M Crayn
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | - Olwen M Grace
- Royal Botanic Gardens, Kew, Richmond, UK
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | | | | | - Hervé Sauquet
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - William J Baker
- Royal Botanic Gardens, Kew, Richmond, UK.
- Department of Biology, Aarhus University, Aarhus, Denmark.
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3
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Anest A, Bouchenak-Khelladi Y, Charles-Dominique T, Forest F, Caraglio Y, Hempson GP, Maurin O, Tomlinson KW. Blocking then stinging as a case of two-step evolution of defensive cage architectures in herbivore-driven ecosystems. Nat Plants 2024; 10:587-597. [PMID: 38438539 DOI: 10.1038/s41477-024-01649-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 01/23/2024] [Indexed: 03/06/2024]
Abstract
Dense branching and spines are common features of plant species in ecosystems with high mammalian herbivory pressure. While dense branching and spines can inhibit herbivory independently, when combined, they form a powerful defensive cage architecture. However, how cage architecture evolved under mammalian pressure has remained unexplored. Here we show how dense branching and spines emerged during the age of mammalian radiation in the Combretaceae family and diversified in herbivore-driven ecosystems in the tropics. Phylogenetic comparative methods revealed that modern plant architectural strategies defending against large mammals evolved via a stepwise process. First, dense branching emerged under intermediate herbivory pressure, followed by the acquisition of spines that supported higher speciation rates under high herbivory pressure. Our study highlights the adaptive value of dense branching as part of a herbivore defence strategy and identifies large mammal herbivory as a major selective force shaping the whole plant architecture of woody plants.
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Affiliation(s)
- Artémis Anest
- Center for Integrative Conservation and Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, China.
- University of Chinese Academy of Sciences, Beijing, China.
- AMAP, Univ Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France.
| | - Yanis Bouchenak-Khelladi
- Agroécologie, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Dijon, France
| | - Tristan Charles-Dominique
- AMAP, Univ Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
- Centre National de la Recherche Scientifique (CNRS), Sorbonne University, Paris, France
| | | | - Yves Caraglio
- AMAP, Univ Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
| | - Gareth P Hempson
- Ecology and Environmental Change, School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | | | - Kyle W Tomlinson
- Center for Integrative Conservation and Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, China.
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4
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Bureš P, Elliott TL, Veselý P, Šmarda P, Forest F, Leitch IJ, Nic Lughadha E, Soto Gomez M, Pironon S, Brown MJM, Šmerda J, Zedek F. The global distribution of angiosperm genome size is shaped by climate. New Phytol 2024; 242:744-759. [PMID: 38264772 DOI: 10.1111/nph.19544] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/03/2024] [Indexed: 01/25/2024]
Abstract
Angiosperms, which inhabit diverse environments across all continents, exhibit significant variation in genome sizes, making them an excellent model system for examining hypotheses about the global distribution of genome size. These include the previously proposed large genome constraint, mutational hazard, polyploidy-mediated, and climate-mediated hypotheses. We compiled the largest genome size dataset to date, encompassing 16 017 (> 5% of known) angiosperm species, and analyzed genome size distribution using a comprehensive geographic distribution dataset for all angiosperms. We observed that angiosperms with large range sizes generally had small genomes, supporting the large genome constraint hypothesis. Climate was shown to exert a strong influence on genome size distribution along the global latitudinal gradient, while the frequency of polyploidy and the type of growth form had negligible effects. In contrast to the unimodal patterns along the global latitudinal gradient shown by plant size traits and polyploid proportions, the increase in angiosperm genome size from the equator to 40-50°N/S is probably mediated by different (mostly climatic) mechanisms than the decrease in genome sizes observed from 40 to 50°N northward. Our analysis suggests that the global distribution of genome sizes in angiosperms is mainly shaped by climatically mediated purifying selection, genetic drift, relaxed selection, and environmental filtering.
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Affiliation(s)
- Petr Bureš
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - Tammy L Elliott
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
- Department of Biological Sciences, University of Cape Town, Cape Town, 7700, South Africa
| | - Pavel Veselý
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - Petr Šmarda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
| | | | | | | | - Samuel Pironon
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, UK
- UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, CB3 0DL, UK
| | | | - Jakub Šmerda
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
| | - František Zedek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, 611 37, Brno, Czech Republic
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5
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Elliott TL, Spalink D, Larridon I, Zuntini AR, Escudero M, Hackel J, Barrett RL, Martín-Bravo S, Márquez-Corro JI, Granados Mendoza C, Mashau AC, Romero-Soler KJ, Zhigila DA, Gehrke B, Andrino CO, Crayn DM, Vorontsova MS, Forest F, Baker WJ, Wilson KL, Simpson DA, Muasya AM. Global analysis of Poales diversification - parallel evolution in space and time into open and closed habitats. New Phytol 2024; 242:727-743. [PMID: 38009920 DOI: 10.1111/nph.19421] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 11/03/2023] [Indexed: 11/29/2023]
Abstract
Poales are one of the most species-rich, ecologically and economically important orders of plants and often characterise open habitats, enabled by unique suites of traits. We test six hypotheses regarding the evolution and assembly of Poales in open and closed habitats throughout the world, and examine whether diversification patterns demonstrate parallel evolution. We sampled 42% of Poales species and obtained taxonomic and biogeographic data from the World Checklist of Vascular Plants database, which was combined with open/closed habitat data scored by taxonomic experts. A dated supertree of Poales was constructed. We integrated spatial phylogenetics with regionalisation analyses, historical biogeography and ancestral state estimations. Diversification in Poales and assembly of open and closed habitats result from dynamic evolutionary processes that vary across lineages, time and space, most prominently in tropical and southern latitudes. Our results reveal parallel and recurrent patterns of habitat and trait transitions in the species-rich families Poaceae and Cyperaceae. Smaller families display unique and often divergent evolutionary trajectories. The Poales have achieved global dominance via parallel evolution in open habitats, with notable, spatially and phylogenetically restricted divergences into strictly closed habitats.
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Affiliation(s)
- Tammy L Elliott
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlarska 2, Brno, 611 37, Czech Republic
- Department of Biological Sciences, University of Cape Town, Cape Town, 7700, South Africa
| | - Daniel Spalink
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, Texas, TX, 77843-2258, USA
| | - Isabel Larridon
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Gent, Belgium
| | | | - Marcial Escudero
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Reina Mercedes 6, Seville, 41012, Spain
| | - Jan Hackel
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Department of Biology, University of Marburg, Karl-von-Frisch-Str. 8, 35043, Marburg, Germany
| | - Russell L Barrett
- National Herbarium of New South Wales, Botanic Gardens of Sydney, Australian Botanic Garden, Locked Bag 6002, Mount Annan, NSW, 2567, Australia
| | - Santiago Martín-Bravo
- Botany Area, Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, ctra. de Utrera km 1, 41013, Seville, Spain
| | - José Ignacio Márquez-Corro
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Botany Area, Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, ctra. de Utrera km 1, 41013, Seville, Spain
| | - Carolina Granados Mendoza
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, CP 04510, Mexico
| | - Aluoneswi C Mashau
- Foundational Research and Services, South African National Biodiversity Institute (SANBI), Private Bag X101, Pretoria, 0184, South Africa
| | - Katya J Romero-Soler
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, CP 04510, Mexico
| | - Daniel A Zhigila
- Department of Botany, Gombe State University, Tudun Wada, Gombe, 760001, Nigeria
| | - Berit Gehrke
- Universitetet i Bergen, Universitetsmuseet, Postboks 7800, NO-5020, Bergen, Norway
| | - Caroline Oliveira Andrino
- Departamento de Botânica, Universidade de Brasília, Brasília, Distrito Federal, CEP 70910-900, Brazil
| | - Darren M Crayn
- Sir Robert Norman Building (E2), James Cook University, PO Box 6811, Cairns, QLD, 4870, Australia
| | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | | | - Karen L Wilson
- National Herbarium of New South Wales, Botanic Gardens of Sydney, Australian Botanic Garden, Locked Bag 6002, Mount Annan, NSW, 2567, Australia
| | - David A Simpson
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Botany Department, School of Natural Sciences, Trinity College, The University of Dublin, Dublin 2, Ireland
| | - A Muthama Muasya
- Department of Biological Sciences, University of Cape Town, Cape Town, 7700, South Africa
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6
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Anest A, Bouchenak-Khelladi Y, Charles-Dominique T, Forest F, Caraglio Y, Hempson GP, Maurin O, Tomlinson KW. Author Correction: Blocking then stinging as a case of two-step evolution of defensive cage architectures in herbivore-driven ecosystems. Nat Plants 2024; 10:689. [PMID: 38509223 DOI: 10.1038/s41477-024-01675-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Affiliation(s)
- Artémis Anest
- Center for Integrative Conservation and Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, China.
- University of Chinese Academy of Sciences, Beijing, China.
- AMAP, Univ Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France.
| | - Yanis Bouchenak-Khelladi
- Agroécologie, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, INRAE, Institut Agro, Dijon, France
| | - Tristan Charles-Dominique
- AMAP, Univ Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
- Centre National de la Recherche Scientifique (CNRS), Sorbonne University, Paris, France
| | | | - Yves Caraglio
- AMAP, Univ Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
| | - Gareth P Hempson
- Ecology and Environmental Change, School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | | | - Kyle W Tomlinson
- Center for Integrative Conservation and Yunnan Key Laboratory for Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, China.
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7
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Pérez-Calle V, Bellot S, Kuhnhäuser BG, Pillon Y, Forest F, Leitch IJ, Baker WJ. Phylogeny, biogeography and ecological diversification of New Caledonian palms (Arecaceae). Ann Bot 2024:mcae043. [PMID: 38527418 DOI: 10.1093/aob/mcae043] [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] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Indexed: 03/27/2024]
Abstract
BACKGROUND AND AIMS The geographic origin and evolutionary mechanisms underpinning the rich and distinctive New Caledonian flora remain poorly understood. This is due to the complex geological past of the island and to the scarcity of well-resolved species-level phylogenies. Here, we infer phylogenetic relationships and divergence times of New Caledonian palms, which comprise 40 species. We use this framework to elucidate the biogeography of New Caledonian palm lineages, and to explore how extant species may have formed. METHODS A phylogenetic tree including 37 New Caledonian palm species and 77 relatives from tribe Areceae was inferred from 151 nuclear genes obtained by targeted sequencing. Fossil-calibrated divergence times were estimated, and ancestral ranges were inferred. Ancestral and extant ecological preferences in terms of elevation, precipitation and substrate were compared between New Caledonian sister species to explore their possible roles as drivers of speciation. KEY RESULTS New Caledonian palms form four well-supported clades, inside which relationships are well resolved. Our results support the current classification, but suggest that Veillonia and Campecarpus should be resurrected, and fail to clarify whether Rhopalostylidinae is sister to or nested in Basseliniinae. New Caledonian palm lineages derive from New Guinean and Australian ancestors, which reached the island through at least three independent dispersal events between the Eocene and Miocene. Palms then dispersed out of New Caledonia at least five times, mainly towards Pacific islands. Geographic and ecological transitions associated with speciation events differed across time and genera. Substrate transitions were more frequently associated with older than younger events. CONCLUSIONS Neighbouring areas and a mosaic of local habitats shaped New Caledonia's palm flora, and the island played a significant role in generating palm diversity across the Pacific region. This new spatio-temporal framework will enable population-level ecological and genetic studies to further unpick the mechanisms underpinning New Caledonian palm endemism.
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Affiliation(s)
- Victor Pérez-Calle
- Department of Biology, Memorial University of Newfoundland, St John's, NL A1B 3X9, Canada
| | - Sidonie Bellot
- Royal Botanic Gardens, Kew, Richmond TW9 3AE, United Kingdom
| | | | - Yohan Pillon
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond TW9 3AE, United Kingdom
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond TW9 3AE, United Kingdom
| | - William J Baker
- Royal Botanic Gardens, Kew, Richmond TW9 3AE, United Kingdom
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8
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Gumbs R, Scott O, Bates R, Böhm M, Forest F, Gray CL, Hoffmann M, Kane D, Low C, Pearse WD, Pipins S, Tapley B, Turvey ST, Jetz W, Owen NR, Rosindell J. Global conservation status of the jawed vertebrate Tree of Life. Nat Commun 2024; 15:1101. [PMID: 38424441 PMCID: PMC10904806 DOI: 10.1038/s41467-024-45119-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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 01/16/2024] [Indexed: 03/02/2024] Open
Abstract
Human-driven extinction threatens entire lineages across the Tree of Life. Here we assess the conservation status of jawed vertebrate evolutionary history, using three policy-relevant approaches. First, we calculate an index of threat to overall evolutionary history, showing that we expect to lose 86-150 billion years (11-19%) of jawed vertebrate evolutionary history over the next 50-500 years. Second, we rank jawed vertebrate species by their EDGE scores to identify the highest priorities for species-focused conservation of evolutionary history, finding that chondrichthyans, ray-finned fish and testudines rank highest of all jawed vertebrates. Third, we assess the conservation status of jawed vertebrate families. We found that species within monotypic families are more likely to be threatened and more likely to be in decline than other species. We provide a baseline for the status of families at risk of extinction to catalyse conservation action. This work continues a trend of highlighting neglected groups-such as testudines, crocodylians, amphibians and chondrichthyans-as conservation priorities from a phylogenetic perspective.
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Affiliation(s)
- Rikki Gumbs
- Zoological Society of London, London, NW1 4RY, UK.
- Science and Solutions for a Changing Planet DTP, Grantham Institute, Imperial College London, London, SW7 2AZ, UK.
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, SL5 7PY, UK.
| | - Oenone Scott
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, SL5 7PY, UK
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
| | - Ryan Bates
- Zoological Society of London, London, NW1 4RY, UK
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, SL5 7PY, UK
| | - Monika Böhm
- Global Center for Species Survival, Indianapolis Zoological Society, Indianapolis, IN, 46222, USA
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | | | | | - Daniel Kane
- Zoological Society of London, London, NW1 4RY, UK
| | - Christopher Low
- Department of Genetics, Evolution and Environment, Centre for Biodiversity and Environment Research, University College London, London, WC1E 6BT, UK
| | - William D Pearse
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, SL5 7PY, UK
| | - Sebastian Pipins
- Science and Solutions for a Changing Planet DTP, Grantham Institute, Imperial College London, London, SW7 2AZ, UK
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- On the Edge, London, SW3 2JJ, UK
| | | | - Samuel T Turvey
- Institute of Zoology, Zoological Society of London, London, NW1 4RY, UK
| | - Walter Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
- Center for Biodiversity and Global Change, Yale University, New Haven, CT, 06511, USA
| | | | - James Rosindell
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, SL5 7PY, UK
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9
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Gumbs R, Chaudhary A, Daru BH, Faith DP, Forest F, Gray CL, Kowalska A, Lee WS, Pellens R, Pipins S, Pollock LJ, Rosindell J, Scherson RA, Owen NR. Indicators to monitor the status of the tree of life. Conserv Biol 2023; 37:e14138. [PMID: 37377164 DOI: 10.1111/cobi.14138] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/21/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023]
Abstract
Following the failure to fully achieve any of the 20 Aichi biodiversity targets, the future of biodiversity rests in the balance. The Convention on Biological Diversity's Kunming-Montreal Global Biodiversity Framework (GBF) presents the opportunity to preserve nature's contributions to people (NCPs) for current and future generations by conserving biodiversity and averting extinctions. There is a need to safeguard the tree of life-the unique and shared evolutionary history of life on Earth-to maintain the benefits it bestows into the future. Two indicators have been adopted within the GBF to monitor progress toward safeguarding the tree of life: the phylogenetic diversity (PD) indicator and the evolutionarily distinct and globally endangered (EDGE) index. We applied both to the world's mammals, birds, and cycads to show their utility at the global and national scale. The PD indicator can be used to monitor the overall conservation status of large parts of the evolutionary tree of life, a measure of biodiversity's capacity to maintain NCPs for future generations. The EDGE index is used to monitor the performance of efforts to conserve the most distinctive species. The risk to PD of birds, cycads, and mammals increased, and mammals exhibited the greatest relative increase in threatened PD over time. These trends appeared robust to the choice of extinction risk weighting. EDGE species had predominantly worsening extinction risk. A greater proportion of EDGE mammals (12%) had increased extinction risk compared with threatened mammals in general (7%). By strengthening commitments to safeguarding the tree of life, biodiversity loss can be reduced and thus nature's capacity to provide benefits to humanity now and in the future can be preserved.
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Affiliation(s)
- Rikki Gumbs
- EDGE of Existence Programme, Zoological Society of London, London, UK
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, UK
- IUCN SSC Phylogenetic Diversity Task Force, London, UK
| | - Abhishek Chaudhary
- Department of Civil Engineering, Indian Institute of Technology (IIT) Kanpur, Kanpur, India
| | - Barnabas H Daru
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, Texas, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Daniel P Faith
- The Australian Museum Research Institute, The Australian Museum, Sydney, New South Wales, Australia
| | - Félix Forest
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - Claudia L Gray
- EDGE of Existence Programme, Zoological Society of London, London, UK
| | | | - Who-Seung Lee
- Environmental Assessment Group, Korea Environment Institute, Sejong, Republic of Korea
| | - Roseli Pellens
- Institut de Systématique, Evolution, et Biodiversité (Muséum National d'Histoire Naturelle, Centre National pour la Recherche Scientifique, Sorbonne Université, Ecole Pratique de Hautes Etudes, Université des Antilles), Paris, France
| | - Sebastian Pipins
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, UK
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - Laura J Pollock
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - James Rosindell
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, UK
| | - Rosa A Scherson
- Departamento de Silvicultura y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
| | - Nisha R Owen
- IUCN SSC Phylogenetic Diversity Task Force, London, UK
- On the EDGE Conservation, Chelsea, UK
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10
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Tietje M, Antonelli A, Forest F, Govaerts R, Smith SA, Sun M, Baker WJ, Eiserhardt WL. Global hotspots of plant phylogenetic diversity. New Phytol 2023; 240:1636-1646. [PMID: 37496281 DOI: 10.1111/nph.19151] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/24/2023] [Indexed: 07/28/2023]
Abstract
Regions harbouring high unique phylogenetic diversity (PD) are priority targets for conservation. Here, we analyse the global distribution of plant PD, which remains poorly understood despite plants being the foundation of most terrestrial habitats and key to human livelihoods. Capitalising on a recently completed, comprehensive global checklist of vascular plants, we identify hotspots of unique plant PD and test three hypotheses: (1) PD is more evenly distributed than species diversity; (2) areas of highest PD (often called 'hotspots') do not maximise cumulative PD; and (3) many biomes are needed to maximise cumulative PD. Our results support all three hypotheses: more than twice as many regions are required to cover 50% of global plant PD compared to 50% of species; regions that maximise cumulative PD substantially differ from the regions with outstanding individual PD; and while (sub-)tropical moist forest regions dominate across PD hotspots, other forest types and open biomes are also essential. Safeguarding PD in the Anthropocene (including the protection of some comparatively species-poor areas) is a global, increasingly recognised responsibility. Having highlighted countries with outstanding unique plant PD, further analyses are now required to fully understand the global distribution of plant PD and associated conservation imperatives across spatial scales.
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Affiliation(s)
- Melanie Tietje
- Department of Biology, Aarhus University, Aarhus, 8000, Denmark
| | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Göteborg, 413 19, Sweden
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | | | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Miao Sun
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agriculture University, Wuhan, Hubei, 430070, China
| | | | - Wolf L Eiserhardt
- Department of Biology, Aarhus University, Aarhus, 8000, Denmark
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Aarhus Institute of Advanced Studies, Aarhus University, Aaarhus, 8000, Denmark
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11
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Tovar C, Hudson L, Cuesta F, Meneses RI, Muriel P, Hidalgo O, Palazzesi L, Suarez Ballesteros C, Hammond Hunt E, Diazgranados M, Hind DJN, Forest F, Halloy S, Aguirre N, Baker WJ, Beck S, Carilla J, Eguiguren P, Françoso E, Gámez LE, Jaramillo R, Llambí LD, Maurin O, Melcher I, Muller G, Roy S, Viñas P, Yager K, Viruel J. Strategies of diaspore dispersal investment in Compositae: the case of the Andean highlands. Ann Bot 2023; 132:255-267. [PMID: 37501620 PMCID: PMC10583198 DOI: 10.1093/aob/mcad099] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 07/26/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND AND AIMS Understanding diaspore morphology and how much a species invests on dispersal appendages is key for improving our knowledge of dispersal in fragmented habitats. We investigate diaspore morphological traits in high-Andean Compositae and their main abiotic and biotic drivers and test whether they play a role in species distribution patterns across the naturally fragmented high-Andean grasslands. METHODS We collected diaspore trait data for 125 Compositae species across 47 tropical high-Andean summits, focusing on achene length and pappus-to-achene length ratio, with the latter as a proxy of dispersal investment. We analysed the role of abiotic (temperature, elevation and latitude) and biotic factors (phylogenetic signal and differences between tribes) on diaspore traits and whether they are related to distribution patterns across the Andes, using phylogenomics, distribution modelling and community ecology analyses. KEY RESULTS Seventy-five percent of the studied species show small achenes (length <3.3 mm) and 67% have high dispersal investment (pappus length at least two times the achene length). Dispersal investment increases with elevation, possibly to compensate for lower air density, and achene length increases towards the equator, where non-seasonal climate prevails. Diaspore traits show significant phylogenetic signal, and higher dispersal investment is observed in Gnaphalieae, Astereae and Senecioneae, which together represent 72% of our species. High-Andean-restricted species found across the tropical Andes have, on average, the pappus four times longer than the achene, a significantly higher dispersal investment than species present only in the northern Andes or only in the central Andes. CONCLUSIONS Small achenes and high diaspore dispersal investment dominate among high-Andean Compositae, traits typical of mostly three tribes of African origin; but traits are also correlated with the environmental gradients within the high-Andean grasslands. Our results also suggest that diaspore dispersal investment is likely to shape species distribution patterns in naturally fragmented habitats.
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Affiliation(s)
| | | | - Francisco Cuesta
- Grupo de Investigación en Biodiversidad, Medio Ambiente y Salud – BIOMAS, Universidad de las Américas, Quito, Ecuador
| | - Rosa Isela Meneses
- Universidad Católica del Norte, San Pedro de Atacama, Chile
- Herbario Nacional de Bolivia, Instituto de Ecología, Universidad Mayor de San Andrés, Bolivia
| | - Priscilla Muriel
- Laboratorio de Ecofisiología, Escuela de Ciencias Biológicas, Pontificia Universidad Católica de Ecuador, Quito, Ecuador
| | - Oriane Hidalgo
- Royal Botanic Gardens, Kew, Richmond, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
| | - Luis Palazzesi
- Museo Argentino de Ciencias Naturales (CONICET), Buenos Aires, Argentina
| | | | | | | | | | | | - Stephan Halloy
- Biosecurity New Zealand, Ministry for Primary Industries, Wellington, New Zealand
| | - Nikolay Aguirre
- Centro de Investigaciones Tropicales del Ambiente y Biodiversidad, Carrera de Ingeniería Forestal, Universidad Nacional de Loja, Loja, Ecuador
| | | | - Stephan Beck
- Herbario Nacional de Bolivia, Instituto de Ecología, Universidad Mayor de San Andrés, Bolivia
| | - Julieta Carilla
- Instituto de Ecología Regional (IER), Universidad Nacional de Tucumán (UNT), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Tucumán, Argentina
| | - Paúl Eguiguren
- Centro de Investigaciones Tropicales del Ambiente y Biodiversidad, Carrera de Ingeniería Forestal, Universidad Nacional de Loja, Loja, Ecuador
| | | | - Luis E Gámez
- Laboratorio de Dendrología, Facultad de Ciencias Forestales y Ambientales, Universidad de Los Andes, Mérida, Venezuela
| | - Ricardo Jaramillo
- Laboratorio de Ecofisiología, Escuela de Ciencias Biológicas, Pontificia Universidad Católica de Ecuador, Quito, Ecuador
| | - Luis Daniel Llambí
- Instituto de Ciencias Ambientales y Ecologicas, Universidad de Los Andes, Mérida 5101, Venezuela
- Consorcio para el Desarrollo Sostenible de la Ecorregión Andina, Germán Alemán E12-123, Quito, Ecuador
| | | | - Inga Melcher
- Institute for Biodiversity & Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | | | | | - Karina Yager
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
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12
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Hendriks KP, Kiefer C, Al-Shehbaz IA, Bailey CD, Hooft van Huysduynen A, Nikolov LA, Nauheimer L, Zuntini AR, German DA, Franzke A, Koch MA, Lysak MA, Toro-Núñez Ó, Özüdoğru B, Invernón VR, Walden N, Maurin O, Hay NM, Shushkov P, Mandáková T, Schranz ME, Thulin M, Windham MD, Rešetnik I, Španiel S, Ly E, Pires JC, Harkess A, Neuffer B, Vogt R, Bräuchler C, Rainer H, Janssens SB, Schmull M, Forrest A, Guggisberg A, Zmarzty S, Lepschi BJ, Scarlett N, Stauffer FW, Schönberger I, Heenan P, Baker WJ, Forest F, Mummenhoff K, Lens F. Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset. Curr Biol 2023; 33:4052-4068.e6. [PMID: 37659415 DOI: 10.1016/j.cub.2023.08.026] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/22/2023] [Accepted: 08/08/2023] [Indexed: 09/04/2023]
Abstract
The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data. We found cytonuclear discordance between the two, which is likely a result of rampant hybridization among closely and more distantly related lineages. To evaluate the impact of such hybridization on the nuclear phylogeny reconstruction, we performed five different gene sampling routines, which increasingly removed putatively paralog genes. Our cleaned subset of 297 genes revealed high support for the tribes, whereas support for the main lineages (supertribes) was moderate. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene origin of the family. Finally, our results strongly support a recently published new family classification, dividing the family into two subfamilies (one with five supertribes), together representing 58 tribes. This includes five recently described or re-established tribes, including Arabidopsideae, a monogeneric tribe accommodating Arabidopsis without any close relatives. With a worldwide community of thousands of researchers working on Brassicaceae and its diverse members, our new genus-level family phylogeny will be an indispensable tool for studies on biodiversity and plant biology.
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Affiliation(s)
- Kasper P Hendriks
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany; Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands.
| | - Christiane Kiefer
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | | | - C Donovan Bailey
- Department of Biology, New Mexico State University, PO Box 30001, MSC 3AF, Las Cruces, NM 88003, USA
| | - Alex Hooft van Huysduynen
- Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands; Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Lachezar A Nikolov
- Department of Molecular, Cell and Developmental Biology, University of California, 610 Charles E. Young Dr. S., Los Angeles, CA 90095, USA
| | - Lars Nauheimer
- Australian Tropical Herbarium, James Cook University, PO Box 6811, Cairns, QLD 4870, Australia
| | | | - Dmitry A German
- South-Siberian Botanical Garden, Altai State University, Barnaul, Lesosechnaya Ulitsa, 25, Barnaul, Altai Krai, Russia
| | - Andreas Franzke
- Heidelberg Botanic Garden, Heidelberg University, Im Neuenheimer Feld 361, 69120 Heidelberg, Germany
| | - Marcus A Koch
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Óscar Toro-Núñez
- Departamento de Botánica, Universidad de Concepción, Barrio Universitario, Concepción, Chile
| | - Barış Özüdoğru
- Department of Biology, Hacettepe University, Beytepe, Ankara 06800, Türkiye
| | - Vanessa R Invernón
- Sorbonne Université, Muséum National d'Histoire Naturelle, Institut de Systématique, Évolution, Biodiversité (ISYEB), CP 39, 57 rue Cuvier, 75231 Paris Cedex 05, France
| | - Nora Walden
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Nikolai M Hay
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Philip Shushkov
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, IN 47405, USA
| | - Terezie Mandáková
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Mats Thulin
- Department of Organismal Biology, Uppsala University, Norbyvägen 18, 752 36 Uppsala, Sweden
| | | | - Ivana Rešetnik
- Department of Biology, University of Zagreb, Marulićev trg 20/II, 10000 Zagreb, Croatia
| | - Stanislav Španiel
- Institute of Botany, Slovak Academy of Sciences, Plant Science and Biodiversity Centre, Dúbravská cesta 9, 845 23 Bratislava, Slovakia
| | - Elfy Ly
- Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands; Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - J Chris Pires
- Soil and Crop Sciences, Colorado State University, 307 University Ave., Fort Collins, CO 80523-1170, USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Barbara Neuffer
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Robert Vogt
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195 Berlin, Germany
| | - Christian Bräuchler
- Department of Botany, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Heimo Rainer
- Department of Botany, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Steven B Janssens
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31 - box 2435, 3001 Leuven, Belgium; Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium
| | - Michaela Schmull
- Harvard University Herbaria, 22 Divinity Ave., Cambridge, MA 02138, USA
| | - Alan Forrest
- Centre for Middle Eastern Plants, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Alessia Guggisberg
- ETH Zürich, Institut für Integrative Biologie, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Sue Zmarzty
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Brendan J Lepschi
- Australian National Herbarium, Centre for Australian National Biodiversity Research, Clunies Ross St, Acton, ACT 2601, Australia
| | - Neville Scarlett
- La Trobe University, Plenty Road and Kingsbury Dr., Bundoora, VIC 3086, Australia
| | - Fred W Stauffer
- Conservatory and Botanic Gardens of Geneva, CP 60, Chambésy, 1292 Geneva, Switzerland
| | - Ines Schönberger
- Manaaki Whenua Landcare Research, Allan Herbarium, PO Box 69040, Lincoln, New Zealand
| | - Peter Heenan
- Manaaki Whenua Landcare Research, Allan Herbarium, PO Box 69040, Lincoln, New Zealand
| | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany.
| | - Frederic Lens
- Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands; Institute of Biology Leiden, Plant Sciences, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands.
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13
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Hofman P, Calabrese F, Kern I, Adam J, Alarcão A, Alborelli I, Anton NT, Arndt A, Avdalyan A, Barberis M, Bégueret H, Bisig B, Blons H, Boström P, Brcic L, Bubanovic G, Buisson A, Caliò A, Cannone M, Carvalho L, Caumont C, Cayre A, Chalabreysse L, Chenard MP, Conde E, Copin MC, Côté JF, D'Haene N, Dai HY, de Leval L, Delongova P, Denčić-Fekete M, Fabre A, Ferenc F, Forest F, de Fraipont F, Garcia-Martos M, Gauchotte G, Geraghty R, Guerin E, Guerrero D, Hernandez S, Hurník P, Jean-Jacques B, Kashofer K, Kazdal D, Lantuejoul S, Leonce C, Lupo A, Malapelle U, Matej R, Merlin JL, Mertz KD, Morel A, Mutka A, Normanno N, Ovidiu P, Panizo A, Papotti MG, Parobkova E, Pasello G, Pauwels P, Pelosi G, Penault-Llorca F, Picot T, Piton N, Pittaro A, Planchard G, Poté N, Radonic T, Rapa I, Rappa A, Roma C, Rot M, Sabourin JC, Salmon I, Prince SS, Scarpa A, Schuuring E, Serre I, Siozopoulou V, Sizaret D, Smojver-Ježek S, Solassol J, Steinestel K, Stojšić J, Syrykh C, Timofeev S, Troncone G, Uguen A, Valmary-Degano S, Vigier A, Volante M, Wahl SGF, Stenzinger A, Ilié M. Real-world EGFR testing practices for non-small-cell lung cancer by thoracic pathology laboratories across Europe. ESMO Open 2023; 8:101628. [PMID: 37713929 PMCID: PMC10594022 DOI: 10.1016/j.esmoop.2023.101628] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/14/2023] [Accepted: 08/02/2023] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND Testing for epidermal growth factor receptor (EGFR) mutations is an essential recommendation in guidelines for metastatic non-squamous non-small-cell lung cancer, and is considered mandatory in European countries. However, in practice, challenges are often faced when carrying out routine biomarker testing, including access to testing, inadequate tissue samples and long turnaround times (TATs). MATERIALS AND METHODS To evaluate the real-world EGFR testing practices of European pathology laboratories, an online survey was set up and validated by the Pulmonary Pathology Working Group of the European Society of Pathology and distributed to 64 expert testing laboratories. The retrospective survey focussed on laboratory organisation and daily EGFR testing practice of pathologists and molecular biologists between 2018 and 2021. RESULTS TATs varied greatly both between and within countries. These discrepancies may be partly due to reflex testing practices, as 20.8% of laboratories carried out EGFR testing only at the request of the clinician. Many laboratories across Europe still favour single-test sequencing as a primary method of EGFR mutation identification; 32.7% indicated that they only used targeted techniques and 45.1% used single-gene testing followed by next-generation sequencing (NGS), depending on the case. Reported testing rates were consistent over time with no significant decrease in the number of EGFR tests carried out in 2020, despite the increased pressure faced by testing facilities during the COVID-19 pandemic. ISO 15189 accreditation was reported by 42.0% of molecular biology laboratories for single-test sequencing, and by 42.3% for NGS. 92.5% of laboratories indicated they regularly participate in an external quality assessment scheme. CONCLUSIONS These results highlight the strong heterogeneity of EGFR testing that still occurs within thoracic pathology and molecular biology laboratories across Europe. Even among expert testing facilities there is variability in testing capabilities, TAT, reflex testing practice and laboratory accreditation, stressing the need to harmonise reimbursement technologies and decision-making algorithms in Europe.
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Affiliation(s)
- P Hofman
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Biobank Côte d'Azur BB-0033-00025, Louis Pasteur Hospital, IRCAN, Université Côte d'Azur, Nice, France.
| | - F Calabrese
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padova, Italy
| | - I Kern
- Department of Pathology, University Clinic Golnik, Golnik, Slovenia
| | - J Adam
- Department of Pathology, Groupe Hospitalier Paris Saint-Joseph, Paris, France
| | - A Alarcão
- IAP-PM, Institute of Anatomical and Molecular Pathology, Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
| | - I Alborelli
- Department of Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - N T Anton
- Department of Genetics, University Hospital Bichat-Claude Bernard, Paris University, Paris, France
| | - A Arndt
- Institute of Pathology and Molecular Pathology, Bundeswehrkrankenhaus Ulm, Oberer Eselsberg 40, 89081 Ulm, Germany
| | - A Avdalyan
- Multidisciplinary Clinical Center "Kommunarka" of the Moscow Health Department, Moscow, Russia
| | - M Barberis
- Oncogenomics Unit, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - H Bégueret
- Department of Pathology, University Hospital of Bordeaux, Hôpital Haut-Lévêque, Pessac, France
| | - B Bisig
- Institute of Pathology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - H Blons
- Pharmacogenomics and Molecular Oncology Unit, Biochemistry Department, Assistance Publique-Hopitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France
| | - P Boström
- Department of Pathology, Turku University Hospital, Turku, Finland
| | - L Brcic
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - G Bubanovic
- Laboratory for Molecular Pathology, Department of Pathology, University of Zagreb School of Medicine and University Hospital Centre Zagreb, Zagreb, Croatia
| | - A Buisson
- Department of Biopathology, Centre Léon Bérard, Lyon, France
| | - A Caliò
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - M Cannone
- Inter-Hospital Pathology Division, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), MultiMedica, Milan, Italy
| | - L Carvalho
- IAP-PM, Institute of Anatomical and Molecular Pathology, Faculty of Medicine, University of Coimbra, 3004-504 Coimbra, Portugal
| | - C Caumont
- Department of Tumor Biology, University Hospital of Bordeaux, Hospital Haut-Lévêque, Pessac, France
| | - A Cayre
- Department of Biopathology, Jean Perrin Centre, Clermont-Ferrand, France
| | - L Chalabreysse
- Department of Pathology, Groupement Hospitalier Est, Bron, France
| | - M P Chenard
- Department of Pathology, University Hospital of Strasbourg, 67098 Strasbourg, France
| | - E Conde
- Department of Pathology, 12 de Octubre University Hospital, Universidad Complutense de Madrid, Research Institute 12 de Octubre University Hospital (i+12), CIBERONC, Madrid, Spain
| | - M C Copin
- Department of Pathology, Université d'Angers, Centre Hospitalier Universitaire d'Angers, Angers, France
| | - J F Côté
- Department of Pathology, Institut Mutualiste Montsouris, Paris, France
| | - N D'Haene
- Department of Pathology, Erasme Hospital, HUB ULB, Brussels, Belgium
| | - H Y Dai
- Department of Pathology, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
| | - L de Leval
- Institute of Pathology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - P Delongova
- Institute of Molecular and Clinical Pathology and Medical Genetics, Faculty of Medicine, University Hospital Ostrava, Ostrava, Czech Republic
| | | | - A Fabre
- Department of Histopathology, St. Vincent's University Hospital, University College Dublin School of Medicine, Dublin, Ireland
| | - F Ferenc
- Department of Pathology, University of Oradea, Oradea, Romania
| | - F Forest
- Department of Pathology, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - F de Fraipont
- Medical Unit of Molecular Genetic (Hereditary Diseases and Oncology), Grenoble University Hospital, Grenoble, France
| | - M Garcia-Martos
- Department of Pathology, Gregorio Marañón General University Hospital, Madrid, Spain
| | - G Gauchotte
- Department of Biopathology, CHRU-ICL, CHRU Nancy, Vandoeuvre-lès-Nancy, France
| | - R Geraghty
- Department of Histopathology, St. Vincent's University Hospital, University College Dublin School of Medicine, Dublin, Ireland
| | - E Guerin
- Department of Molecular Cancer Genetics, Laboratory of Biochemistry and Molecular Biology, University Hospital of Strasbourg, Strasbourg, France
| | - D Guerrero
- Biomedical Research Centre, Navarra Health Service, Pamplona, Navarra, Spain
| | - S Hernandez
- Department of Pathology, 12 de Octubre University Hospital, Universidad Complutense de Madrid, Research Institute 12 de Octubre University Hospital (i+12), CIBERONC, Madrid, Spain
| | - P Hurník
- Institute of Molecular and Clinical Pathology and Medical Genetics, Faculty of Medicine, University Hospital Ostrava, Ostrava, Czech Republic
| | - B Jean-Jacques
- Department of Pathology, CHU de Caen Côte de Nacre, Caen, France
| | - K Kashofer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - D Kazdal
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC-H), member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - S Lantuejoul
- Department of Biopathology, Centre Leon Berard Unicancer and Pathology Research Platform, Cancer Research Center of Lyon (CRCL), Lyon, France
| | - C Leonce
- Department of Pathology, Groupement Hospitalier Est, Bron, France
| | - A Lupo
- Department of Pathology, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
| | - U Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - R Matej
- Department of Pathology and Molecular Medicine, Thomayer University Hospital, Prague, Czech Republic
| | - J L Merlin
- Department of Biopathology, Institut de Cancérologie de Lorraine, University of Lorraine, Vandoeuvre-Les-Nancy, France
| | - K D Mertz
- Institute of Pathology, Cantonal Hospital Baselland, Liestal, Switzerland
| | - A Morel
- Department of Innate Immunity and Immunotherapy, Institut de Cancérologie de l'Ouest - Centre Paul Papin, Angers, France
| | - A Mutka
- HUSLAB, Department of Pathology, Helsinki University Hospital, Helsinki, Finland
| | - N Normanno
- Cell Biology and Biotherapy Unit, INT-Fondazione Pascale, Via M. Semmola, Naples, Italy
| | - P Ovidiu
- Department of Pathology, University of Oradea, Oradea, Romania
| | - A Panizo
- Department of Pathology, Complejo Hospitalario de Navarra, Pamplona, Navarra, Spain
| | - M G Papotti
- Division of Pathology, University Hospital Città Della Salute, Turin, Italy
| | - E Parobkova
- Department of Pathology and Molecular Medicine, Thomayer University Hospital, Prague, Czech Republic
| | - G Pasello
- Division of Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padova, Italy
| | - P Pauwels
- Department of Pathology, University Hospital Antwerp and University of Antwerp, Antwerp, Belgium
| | - G Pelosi
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - F Penault-Llorca
- Department of Pathology, Clermont Auvergne University, "Molecular Imaging and Theranostic Strategies", Center Jean Perrin, Montalembert, Clermont-Ferrand, France
| | - T Picot
- Department of Pathology, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - N Piton
- Department of Pathology, Rouen University Hospital, France and Normandie University, UNIROUEN, Inserm U1245, Rouen, France
| | - A Pittaro
- Division of Pathology, University Hospital Città Della Salute, Turin, Italy
| | - G Planchard
- Department of Pathology, CHU de Caen Côte de Nacre, Caen, France
| | - N Poté
- Department of Pathology, Hospital Bichat Bichat, Assistance Publique Hôpitaux de Paris; Université Paris Cité, Paris, France
| | - T Radonic
- Department of Pathology, Amsterdam University Medical Center, VUMC, University of Amsterdam, Amsterdam, Netherlands
| | - I Rapa
- Pathology Unit, San Luigi Hospital, Orbassano Turin, Italy
| | - A Rappa
- Oncogenomics Unit, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | - C Roma
- Cell Biology and Biotherapy Unit, INT-Fondazione Pascale, Via M. Semmola, Naples, Italy
| | - M Rot
- Department of Pathology, University Clinic Golnik, Golnik, Slovenia
| | - J C Sabourin
- Department of Pathology, Rouen University Hospital, France and Normandie University, UNIROUEN, Inserm U1245, Rouen, France
| | - I Salmon
- Department of Pathology, Erasme Hospital, HUB ULB, Brussels, Belgium; CurePath, Jumet, Belgium
| | - S Savic Prince
- Department of Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - A Scarpa
- Department of Diagnostics and Public Health, Section of Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - E Schuuring
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - I Serre
- Department of Pathology, Gui de Chauliac Hospital, Montpellier University Medical Center, University of Montpellier, 80 Avenue Augustin Fliche, Montpellier, France
| | - V Siozopoulou
- Department of Pathology, University Hospital Antwerp and University of Antwerp, Antwerp, Belgium
| | - D Sizaret
- Department of Pathology, CHRU Tours - Hôpital Trousseau, Chambray-lès-Tours, France
| | - S Smojver-Ježek
- Division for Pulmonary Cytology, Department of Pathology and Cytology, University Hospital Centre Zagreb, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - J Solassol
- Solid Tumour Laboratory, Pathology and Oncobiology Department, CHU Montpellier, University of Montpellier, Montpellier, France
| | - K Steinestel
- Institute of Pathology and Molecular Pathology, Bundeswehrkrankenhaus Ulm, Oberer Eselsberg 40, 89081 Ulm, Germany
| | - J Stojšić
- Department of Thoracic Pathology, Section of Pathology, University Clinical Centre of Serbia, Belgrade, Serbia
| | - C Syrykh
- Department of Pathology, IUC-T-Oncopole, Toulouse, France
| | - S Timofeev
- Multidisciplinary Clinical Center "Kommunarka" of the Moscow Health Department, Moscow, Russia
| | - G Troncone
- Department of Pathology, University of Oradea, Oradea, Romania
| | - A Uguen
- Department of Pathological Anatomy and Cytology, CHRU de Brest, Brest, France; LBAI, UMR1227, INSERM, University of Brest, CHU de Brest, Brest, France
| | - S Valmary-Degano
- Department of Pathology, Institute for Advanced Biosciences, CHU Grenoble Alpes, Université Grenoble Alpes, Grenoble, France
| | - A Vigier
- Department of Pathology, IUC-T-Oncopole, Toulouse, France
| | - M Volante
- Department of Oncology, University of Turin, San Luigi Hospital, Orbassano, Turin, Italy
| | - S G F Wahl
- Department of Pathology, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
| | - A Stenzinger
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC-H), member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - M Ilié
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Biobank Côte d'Azur BB-0033-00025, Louis Pasteur Hospital, IRCAN, Université Côte d'Azur, Nice, France
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14
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Wootton LM, Forest F, Verboom GA. Consilience Across Multiple, Independent Genomic Data Sets Reveals Species in a Complex with Limited Phenotypic Variation. Syst Biol 2023; 72:753-766. [PMID: 37098166 DOI: 10.1093/sysbio/syad024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 04/27/2023] Open
Abstract
Species delimitation in the genomic era has focused predominantly on the application of multiple analytical methodologies to a single massive parallel sequencing (MPS) data set, rather than leveraging the unique but complementary insights provided by different classes of MPS data. In this study, we demonstrate how the use of two independent MPS data sets, a sequence capture data set and a single-nucleotide polymorphism (SNP) data set generated via genotyping-by-sequencing, enables the resolution of species in three complexes belonging to the grass genus Ehrharta, whose strong population structure and subtle morphological variation limit the effectiveness of traditional species delimitation approaches. Sequence capture data are used to construct a comprehensive phylogenetic tree of Ehrharta and to resolve population relationships within the focal clades, while SNP data are used to detect patterns of gene pool sharing across populations, using a novel approach that visualizes multiple values of K. Given that the two genomic data sets are independent, the strong congruence in the clusters they resolve provides powerful ratification of species boundaries in all three complexes studied. Our approach is also able to resolve a number of single-population species and a probable hybrid species, both of which would be difficult to detect and characterize using a single MPS data set. Overall, the data reveal the existence of 11 and five species in the E. setacea and E. rehmannii complexes, with the E. ramosa complex requiring further sampling before species limits are finalized. Despite phenotypic differentiation being generally subtle, true crypsis is limited to just a few species pairs and triplets. We conclude that, in the absence of strong morphological differentiation, the use of multiple, independent genomic data sets is necessary in order to provide the cross-data set corroboration that is foundational to an integrative taxonomic approach. [Species delimitation; genotyping-by-sequencing; population structure; integrative taxonomy; cryptic species; Ehrharta (Poaceae).].
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Affiliation(s)
- Lara M Wootton
- Department of Biological Sciences and Bolus Herbarium, University of Cape Town, 7701, Rondebosch, South Africa
- Laboratoire d'Ecologie Alpine, Université Grenoble Alpes, FR-38000 Grenoble, France
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - G Anthony Verboom
- Department of Biological Sciences and Bolus Herbarium, University of Cape Town, 7701, Rondebosch, South Africa
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15
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Ramírez-Verdugo P, Tapia A, Forest F, Scherson RA. Evolutionary diversity of the endemic genera of the vascular flora of Chile and its implications for conservation. PLoS One 2023; 18:e0287957. [PMID: 37406022 DOI: 10.1371/journal.pone.0287957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 06/19/2023] [Indexed: 07/07/2023] Open
Abstract
As a direct consequence of global change, both natural and human-induced, a high percentage of biodiversity is now under threat worldwide. This has urged conservation planners to formulate and/or improve existing strategies to preserve species and their ecosystems. In this context, the present study focuses on two strategies using phylogeny-based measures of biodiversity to account for the processes that led to the biodiversity patterns observed today. It will contribute additional information that can aid decision-making regarding the assignment of threat status for some species, thus strengthening measures currently in use and facilitate the allocation of often scarce conservation resources. The Evolutionarily Distinct (ED) index prioritises species that are on long branches of the tree of life with few descendants, and the Evolutionarily Distinct and Globally Endangered (EDGE) index integrates evolutionary history with IUCN Red List threat status of species. It has been used mostly in animal groups, but since the threats faced by many plants have not been evaluated, it has been more difficult to compile for plants worldwide. Here, we apply the EDGE metric to species of the endemic genera of Chile. However, more than 50% of the endemic flora of the country are still lacking official threat status. We thus used an alternative measure (Relative Evolutionary Distinctness-RED), based on a range-weighted phylogenetic tree, which uses geographic ranges to adjust branch lengths, and calculate ED. The RED index was shown to be a suitable measure, yielding similar results compared to EDGE, at least for this group of species. Given the urgency to halt biodiversity loss and the time it would take to evaluate all species, we propose that this index is used to set conservation priorities until we can calculate EDGE for these unique endemic species. This would allow guiding decision-making until we can gather more data to assess and assign conservation status to new species.
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Affiliation(s)
- Pamela Ramírez-Verdugo
- Herbario VALPL y Laboratorio de Botánica, Departamento de Ciencias y Geografía, Universidad de Playa Ancha, Valparaíso, Chile
- Jardín Botánico Nacional, Viña del Mar, Chile
- Laboratorio de Evolución y Sistemática, Departamento de Silvicultura y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
| | - Alexis Tapia
- Departamento de Matemática, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Félix Forest
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Rosa A Scherson
- Laboratorio de Evolución y Sistemática, Departamento de Silvicultura y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
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16
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Larson DA, Chanderbali AS, Maurin O, Gonçalves DJP, Dick CW, Soltis DE, Soltis PS, Fritsch PW, Clarkson JJ, Grall A, Davies NMJ, Larridon I, Kikuchi IABS, Forest F, Baker WJ, Smith SA, Utteridge TMA. The phylogeny and global biogeography of Primulaceae based on high-throughput DNA sequence data. Mol Phylogenet Evol 2023; 182:107702. [PMID: 36781032 DOI: 10.1016/j.ympev.2023.107702] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 12/13/2022] [Accepted: 01/04/2023] [Indexed: 02/13/2023]
Abstract
The angiosperm family Primulaceae is morphologically diverse and distributed nearly worldwide. However, phylogenetic uncertainty has obstructed the identification of major morphological and biogeographic transitions within the clade. We used target capture sequencing with the Angiosperms353 probes, taxon-sampling encompassing nearly all genera of the family, tree-based sequence curation, and multiple phylogenetic approaches to investigate the major clades of Primulaceae and their relationship to other Ericales. We generated dated phylogenetic trees and conducted broad-scale biogeographic analyses as well as stochastic character mapping of growth habit. We show that Ardisia, a pantropical genus and the largest in the family, is not monophyletic, with at least 19 smaller genera nested within it. Neotropical members of Ardisia and several smaller genera form a clade, an ancestor of which arrived in the Neotropics and began diversifying about 20 Ma. This Neotropical clade is most closely related to Elingamita and Tapeinosperma, which are most diverse on islands of the Pacific. Both Androsace and Primula are non-monophyletic by the inclusion of smaller genera. Ancestral state reconstructions revealed that there have either been parallel transitions to an herbaceous habit in Primuloideae, Samolus, and at least three lineages of Myrsinoideae, or a common ancestor of nearly all Primulaceae was herbaceous. Our results provide a robust estimate of phylogenetic relationships across Primulaceae and show that a revised classification of Myrsinoideae and several other clades within the family is necessary to render all genera monophyletic.
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Affiliation(s)
- Drew A Larson
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biology, Indiana University, Bloomington, IN 47405, USA.
| | - Andre S Chanderbali
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, United Kingdom
| | - Deise J P Gonçalves
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christopher W Dick
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA; Smithsonian Tropical Research Institute, Panama City, Republic of Panama
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Biodiversity Institute, University of Florida, Gainesville, FL 32611, USA
| | - Peter W Fritsch
- Botanical Research Institute of Texas, Fort Worth, TX 76107, USA
| | - James J Clarkson
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, United Kingdom
| | - Aurélie Grall
- Department of Environmental Sciences - Botany, University of Basel, Switzerland
| | - Nina M J Davies
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, United Kingdom
| | - Isabel Larridon
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, United Kingdom
| | - Izai A B S Kikuchi
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, United Kingdom
| | - William J Baker
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, United Kingdom
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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17
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Campos M, Kelley E, Gravendeel B, Médail F, Maarten Christenhusz JM, Fay MF, Catalán P, Leitch IJ, Forest F, Wilkin P, Viruel J. Genomic, spatial and morphometric data for discrimination of four species in the Mediterranean Tamus clade of yams (Dioscorea, Dioscoreaceae). Ann Bot 2023; 131:635-654. [PMID: 36681900 PMCID: PMC10147332 DOI: 10.1093/aob/mcad018] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/23/2023] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Among the numerous pantropical species of the yam genus, Dioscorea, only a small group occurs in the Mediterranean basin, including two narrow Pyrenean endemics (Borderea clade) and two Mediterranean-wide species (D. communis and D. orientalis, Tamus clade). However, several currently unrecognized species and infraspecific taxa have been described in the Tamus clade due to significant morphological variation associated with D. communis. Our overarching aim was to investigate taxon delimitation in the Tamus clade using an integrative approach combining phylogenomic, spatial and morphological data. METHODS We analysed 76 herbarium samples using Hyb-Seq genomic capture to sequence 260 low-copy nuclear genes and plastomes, together with morphometric and environmental modelling approaches. KEY RESULTS Phylogenomic reconstructions confirmed that the two previously accepted species of the Tamus clade, D. communis and D. orientalis, are monophyletic and form sister clades. Three subclades showing distinctive geographic patterns were identified within D. communis. These subclades were also identifiable from morphometric and climatic data, and introgression patterns were inferred between subclades in the eastern part of the distribution of D. communis. CONCLUSIONS We propose a taxonomy that maintains D. orientalis, endemic to the eastern Mediterranean region, and splits D. communis sensu lato into three species: D. edulis, endemic to Macaronesia (Canary Islands and Madeira); D. cretica, endemic to the eastern Mediterranean region; and D. communis sensu stricto, widespread across western and central Europe. Introgression inferred between D. communis s.s. and D. cretica is likely to be explained by their relatively recent speciation at the end of the Miocene, disjunct isolation in eastern and western Mediterranean glacial refugia and a subsequent westward recolonization of D. communis s.s. Our study shows that the use of integrated genomic, spatial and morphological approaches allows a more robust definition of species boundaries and the identification of species that previous systematic studies failed to uncover.
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Affiliation(s)
- Miguel Campos
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
- Department of Plant Biology and Ecology, University of Seville, 41012, Spain
- Universidad de Zaragoza-Escuela Politécnica Superior de Huesca, 22071, Huesca, Spain
| | - Emma Kelley
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
| | - Barbara Gravendeel
- Naturalis Biodiversity Center, Leiden 2333 CR, The Netherlands
- Radboud Institute for Biological and Environmental Sciences, RIBES 6500 GL, Nijmegen, The Netherlands
| | - Frédéric Médail
- Institut Méditerranéen de Biodiversité et d’Écologie marine et continentale (IMBE), Aix Marseille University, Avignon University, CNRS, IRD, Campus Aix, Technopôle de l’Environnement Arbois-Méditerranée, F-13545 Aix-en-Provence cedex 4, France
| | | | - Michael F Fay
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Pilar Catalán
- Universidad de Zaragoza-Escuela Politécnica Superior de Huesca, 22071, Huesca, Spain
- Grupo de Bioquímica, Biofísica y Biología Computacional (BIFI, UNIZAR), Unidad Asociada al CSIC, Zaragoza 50018, Spain
| | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
| | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
| | - Juan Viruel
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
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18
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Joyce EM, Appelhans MS, Buerki S, Cheek M, de Vos JM, Pirani JR, Zuntini AR, Bachelier JB, Bayly MJ, Callmander MW, Devecchi MF, Pell SK, Groppo M, Lowry PP, Mitchell J, Siniscalchi CM, Munzinger J, Orel HK, Pannell CM, Nauheimer L, Sauquet H, Weeks A, Muellner-Riehl AN, Leitch IJ, Maurin O, Forest F, Nargar K, Thiele KR, Baker WJ, Crayn DM. Phylogenomic analyses of Sapindales support new family relationships, rapid Mid-Cretaceous Hothouse diversification, and heterogeneous histories of gene duplication. Front Plant Sci 2023; 14:1063174. [PMID: 36959945 PMCID: PMC10028101 DOI: 10.3389/fpls.2023.1063174] [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: 10/06/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Sapindales is an angiosperm order of high economic and ecological value comprising nine families, c. 479 genera, and c. 6570 species. However, family and subfamily relationships in Sapindales remain unclear, making reconstruction of the order's spatio-temporal and morphological evolution difficult. In this study, we used Angiosperms353 target capture data to generate the most densely sampled phylogenetic trees of Sapindales to date, with 448 samples and c. 85% of genera represented. The percentage of paralogous loci and allele divergence was characterized across the phylogeny, which was time-calibrated using 29 rigorously assessed fossil calibrations. All families were supported as monophyletic. Two core family clades subdivide the order, the first comprising Kirkiaceae, Burseraceae, and Anacardiaceae, the second comprising Simaroubaceae, Meliaceae, and Rutaceae. Kirkiaceae is sister to Burseraceae and Anacardiaceae, and, contrary to current understanding, Simaroubaceae is sister to Meliaceae and Rutaceae. Sapindaceae is placed with Nitrariaceae and Biebersteiniaceae as sister to the core Sapindales families, but the relationships between these families remain unclear, likely due to their rapid and ancient diversification. Sapindales families emerged in rapid succession, coincident with the climatic change of the Mid-Cretaceous Hothouse event. Subfamily and tribal relationships within the major families need revision, particularly in Sapindaceae, Rutaceae and Meliaceae. Much of the difficulty in reconstructing relationships at this level may be caused by the prevalence of paralogous loci, particularly in Meliaceae and Rutaceae, that are likely indicative of ancient gene duplication events such as hybridization and polyploidization playing a role in the evolutionary history of these families. This study provides key insights into factors that may affect phylogenetic reconstructions in Sapindales across multiple scales, and provides a state-of-the-art phylogenetic framework for further research.
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Affiliation(s)
- Elizabeth M. Joyce
- Systematics, Biodiversity and Evolution of Plants, Ludwig-Maximilians-Universität München, Munich, Germany
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
| | - Marc S. Appelhans
- Department of Systematics, Biodiversity and Evolution of Plants, University of Göttingen, Goettingen, Germany
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Sven Buerki
- Department of Biological Sciences, Boise State University, Boise, ID, United States
| | - Martin Cheek
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Jurriaan M. de Vos
- Department of Environmental Sciences, University Basel, Basel, Switzerland
| | - José R. Pirani
- Departamento de Botaênica, Universidade de Saão Paulo, Herbário SPF, Saão Paulo, Brazil
| | | | | | - Michael J. Bayly
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | | | - Marcelo F. Devecchi
- Departamento de Botaênica, Universidade de Saão Paulo, Herbário SPF, Saão Paulo, Brazil
| | - Susan K. Pell
- United States Botanic Garden, Washington, DC, United States
| | - Milton Groppo
- Departamento de Botaênica, Universidade de Saão Paulo, Herbário SPF, Saão Paulo, Brazil
| | - Porter P. Lowry
- Missouri Botanical Garden, St. Louis, MO, United States
- Institut de Systématique, Évolution, et Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, École Pratique des Hautes Études, Université des Antilles, Paris, France
| | - John Mitchell
- New York Botanical Garden, New York, NY, United States
| | - Carolina M. Siniscalchi
- Department of Biological Sciences, Harned Hall, Mississippi State University, Mississippi State, MS, United States
| | - Jérôme Munzinger
- AMAP, Université Montpellier, Institut de Recherche pour le Développement (IRD), Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Centre National de la Recherche Scientifique (CNRS), Institut national de la recherche agronomique (INRAE), Montpellier, France
| | - Harvey K. Orel
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Caroline M. Pannell
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Biology, Oxford University, Oxford, United Kingdom
- Marine Laboratory, Queen’s University Belfast, Portaferry, United Kingdom
| | - Lars Nauheimer
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
| | - Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia
| | - Andrea Weeks
- Department of Biology, George Mason University, Fairfax, VA, United States
| | - Alexandra N. Muellner-Riehl
- Department of Molecular Evolution and Plant Systematics & Herbarium, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | | | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organization (CSIRO), Canberra, ACT, Australia
| | - Kevin R. Thiele
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | | | - Darren M. Crayn
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
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19
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Gumbs R, Gray CL, Böhm M, Burfield IJ, Couchman OR, Faith DP, Forest F, Hoffmann M, Isaac NJB, Jetz W, Mace GM, Mooers AO, Safi K, Scott O, Steel M, Tucker CM, Pearse WD, Owen NR, Rosindell J. The EDGE2 protocol: Advancing the prioritisation of Evolutionarily Distinct and Globally Endangered species for practical conservation action. PLoS Biol 2023; 21:e3001991. [PMID: 36854036 PMCID: PMC9974121 DOI: 10.1371/journal.pbio.3001991] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
The conservation of evolutionary history has been linked to increased benefits for humanity and can be captured by phylogenetic diversity (PD). The Evolutionarily Distinct and Globally Endangered (EDGE) metric has, since 2007, been used to prioritise threatened species for practical conservation that embody large amounts of evolutionary history. While there have been important research advances since 2007, they have not been adopted in practice because of a lack of consensus in the conservation community. Here, building from an interdisciplinary workshop to update the existing EDGE approach, we present an "EDGE2" protocol that draws on a decade of research and innovation to develop an improved, consistent methodology for prioritising species conservation efforts. Key advances include methods for dealing with uncertainty and accounting for the extinction risk of closely related species. We describe EDGE2 in terms of distinct components to facilitate future revisions to its constituent parts without needing to reconsider the whole. We illustrate EDGE2 by applying it to the world's mammals. As we approach a crossroads for global biodiversity policy, this Consensus View shows how collaboration between academic and applied conservation biologists can guide effective and practical priority-setting to conserve biodiversity.
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Affiliation(s)
- Rikki Gumbs
- Conservation and Policy, Zoological Society of London, Regent’s Park, London, United Kingdom
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom
- IUCN SSC Phylogenetic Diversity Task Force, London, United Kingdom
- Science and Solutions for a Changing Planet DTP, Grantham Institute, Imperial College London, South Kensington, London, United Kingdom
- * E-mail:
| | - Claudia L. Gray
- Conservation and Policy, Zoological Society of London, Regent’s Park, London, United Kingdom
| | - Monika Böhm
- Institute of Zoology, Zoological Society of London, Regent’s Park, London, United Kingdom
- Global Center for Species Survival, Indianapolis Zoological Society, Indianapolis, Indiana, United States of America
| | - Ian J. Burfield
- BirdLife International, David Attenborough Building, Cambridge, United Kingdom
| | - Olivia R. Couchman
- Conservation and Policy, Zoological Society of London, Regent’s Park, London, United Kingdom
| | - Daniel P. Faith
- School of Philosophical and Historical Inquiry, The University of Sydney, Sydney, Australia
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Michael Hoffmann
- Conservation and Policy, Zoological Society of London, Regent’s Park, London, United Kingdom
| | - Nick J. B. Isaac
- UK Centre for Ecology & Hydrology, Crowmarsh Gifford, Wallingford, United Kingdom
| | - Walter Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, United States of America
| | - Georgina M. Mace
- Department of Genetics, Evolution & Environment, University College London, London, United Kingdom
| | - Arne O. Mooers
- Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Kamran Safi
- Max-Planck Institute of Animal Behavior, Department of Migration, Radolfzell, Germany
- University of Konstanz, Department of Biology, Konstanz, Germany
| | - Oenone Scott
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Mike Steel
- Biomathematics Research Centre, University of Canterbury, Christchurch, New Zealand
| | - Caroline M. Tucker
- Environment, Ecology and Energy Program, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - William D. Pearse
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom
- Department of Biology and Ecology Center, Utah State University, Logan, Utah, United States of America
| | - Nisha R. Owen
- Conservation and Policy, Zoological Society of London, Regent’s Park, London, United Kingdom
- IUCN SSC Phylogenetic Diversity Task Force, London, United Kingdom
- On the EDGE Conservation, London, United Kingdom
| | - James Rosindell
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom
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Haigh AL, Gibernau M, Maurin O, Bailey P, Carlsen MM, Hay A, Leempoel K, McGinnie C, Mayo S, Morris S, Pérez-Escobar OA, Yeng WS, Zuluaga A, Zuntini AR, Baker WJ, Forest F. Target sequence data shed new light on the infrafamilial classification of Araceae. Am J Bot 2023; 110:e16117. [PMID: 36480380 DOI: 10.1002/ajb2.16117] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
PREMISE Recent phylogenetic studies of the Araceae have confirmed the position of the duckweeds nested within the aroids, and the monophyly of a clade containing all the unisexual flowered aroids plus the bisexual-flowered Calla palustris. The main objective of the present study was to better resolve the deep phylogenetic relationships among the main lineages within the family, particularly the relationships between the eight currently recognized subfamilies. We also aimed to confirm the phylogenetic position of the enigmatic genus Calla in relation to the long-debated evolutionary transition between bisexual and unisexual flowers in the family. METHODS Nuclear DNA sequence data were generated for 128 species across 111 genera (78%) of Araceae using target sequence capture and the Angiosperms 353 universal probe set. RESULTS The phylogenomic data confirmed the monophyly of the eight Araceae subfamilies, but the phylogenetic position of subfamily Lasioideae remains uncertain. The genus Calla is included in subfamily Aroideae, which has also been expanded to include Zamioculcadoideae. The tribe Aglaonemateae is newly defined to include the genera Aglaonema and Boycea. CONCLUSIONS Our results strongly suggest that new research on African genera (Callopsis, Nephthytis, and Anubias) and Calla will be important for understanding the early evolution of the Aroideae. Also of particular interest are the phylogenetic positions of the isolated genera Montrichardia, Zantedeschia, and Anchomanes, which remain only moderately supported here.
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Affiliation(s)
- Anna L Haigh
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Marc Gibernau
- Laboratory of Sciences for the Environment (UMR 6134), CNRS-University of Corsica, Ajaccio, 20000, France
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Paul Bailey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | | | - Alistair Hay
- Australian Institute of Botanical Science, Royal Botanic Gardens & Domain Trust, Mrs Macquarie's Road, Sydney, 2000, Australia
| | - Kevin Leempoel
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | | | - Simon Mayo
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Sarah Morris
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | | | - Wong Sin Yeng
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak (UNIMAS), 94300, Kota Samarahan, Sarawak, Malaysia
| | - Alejandro Zuluaga
- Departamento de Biología, Universidad del Valle, Calle 13 #100-00, Cali, Colombia
| | | | - William J Baker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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21
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Viruel J, Hidalgo O, Pokorny L, Forest F, Gravendeel B, Wilkin P, Leitch IJ. A Bioinformatic Pipeline to Estimate Ploidy Level from Target Capture Sequence Data Obtained from Herbarium Specimens. Methods Mol Biol 2023; 2672:115-126. [PMID: 37335471 DOI: 10.1007/978-1-0716-3226-0_5] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Whole genome duplications (WGD) are frequent in many plant lineages; however, ploidy level variation is unknown in most species. The most widely used methods to estimate ploidy levels in plants are chromosome counts, which require living specimens, and flow cytometry estimates, which necessitate living or relatively recently collected samples. Newly described bioinformatic methods have been developed to estimate ploidy levels using high-throughput sequencing data, and these have been optimized in plants by calculating allelic ratio values from target capture data. This method relies on the maintenance of allelic ratios from the genome to the sequence data. For example, diploid organisms will generate allelic data in a 1:1 proportion, with an increasing number of possible allelic ratio combinations occurring in individuals with higher ploidy levels. In this chapter, we explain step-by-step this bioinformatic approach for the estimation of ploidy level.
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Affiliation(s)
| | - Oriane Hidalgo
- Royal Botanic Gardens, Kew, Richmond, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Catalonia, Spain
- Real Jardín Botánico (RJB-CSIC), Madrid, Spain
| | | | - Barbara Gravendeel
- Naturalis Biodiversity Center, Evolutionary Ecology, Leiden, Netherlands
- Radboud Institute for Biological and Environmental Sciences, Leiden University, Leiden, Netherlands
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22
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Pironon S, Cantwell-Jones A, Forest F, Ball J, Diazgranados M, Douglas R, Hawkins J, Howes MJR, Ulian T, Vaitla B, Collar D. Towards an action plan for characterizing food plant diversity. Nat Plants 2023; 9:34-35. [PMID: 36543935 DOI: 10.1038/s41477-022-01300-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Affiliation(s)
- S Pironon
- Royal Botanic Gardens, Kew, Richmond, UK.
- UN Environment Programme World Conservation Monitoring Centre, Cambridge, UK.
| | - A Cantwell-Jones
- Science and Solutions for a Changing Planet DTP, Imperial College London, Ascot, UK
- Department of Life Sciences, Imperial College London, Ascot, UK
| | - F Forest
- Royal Botanic Gardens, Kew, Richmond, UK
| | - J Ball
- Royal Botanic Gardens, Kew, Richmond, UK
| | | | | | - J Hawkins
- School of Biological Sciences, University of Reading, Reading, UK
| | | | - T Ulian
- Royal Botanic Gardens, Kew, Richmond, UK
| | - B Vaitla
- Department of Nutrition, Harvard TH Chan School of Public Health, Harvard University, Boston, MA, USA
| | - D Collar
- Department of Organismal and Environmental Biology, Christopher Newport University, Newport News, VA, USA
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23
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Antonelli A, Smith RJ, Perrigo AL, Crottini A, Hackel J, Testo W, Farooq H, Torres Jiménez MF, Andela N, Andermann T, Andriamanohera AM, Andriambololonera S, Bachman SP, Bacon CD, Baker WJ, Belluardo F, Birkinshaw C, Borrell JS, Cable S, Canales NA, Carrillo JD, Clegg R, Clubbe C, Cooke RSC, Damasco G, Dhanda S, Edler D, Faurby S, de Lima Ferreira P, Fisher BL, Forest F, Gardiner LM, Goodman SM, Grace OM, Guedes TB, Henniges MC, Hill R, Lehmann CER, Lowry PP, Marline L, Matos-Maraví P, Moat J, Neves B, Nogueira MGC, Onstein RE, Papadopulos AST, Perez-Escobar OA, Phelps LN, Phillipson PB, Pironon S, Przelomska NAS, Rabarimanarivo M, Rabehevitra D, Raharimampionona J, Rajaonah MT, Rajaonary F, Rajaovelona LR, Rakotoarinivo M, Rakotoarisoa AA, Rakotoarisoa SE, Rakotomalala HN, Rakotonasolo F, Ralaiveloarisoa BA, Ramirez-Herranz M, Randriamamonjy JEN, Randriamboavonjy T, Randrianasolo V, Rasolohery A, Ratsifandrihamanana AN, Ravololomanana N, Razafiniary V, Razanajatovo H, Razanatsoa E, Rivers M, Sayol F, Silvestro D, Vorontsova MS, Walker K, Walker BE, Wilkin P, Williams J, Ziegler T, Zizka A, Ralimanana H. Madagascar’s extraordinary biodiversity: Evolution, distribution, and use. Science 2022; 378:eabf0869. [DOI: 10.1126/science.abf0869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Madagascar’s biota is hyperdiverse and includes exceptional levels of endemicity. We review the current state of knowledge on Madagascar’s past and current terrestrial and freshwater biodiversity by compiling and presenting comprehensive data on species diversity, endemism, and rates of species description and human uses, in addition to presenting an updated and simplified map of vegetation types. We report a substantial increase of records and species new to science in recent years; however, the diversity and evolution of many groups remain practically unknown (e.g., fungi and most invertebrates). Digitization efforts are increasing the resolution of species richness patterns and we highlight the crucial role of field- and collections-based research for advancing biodiversity knowledge and identifying gaps in our understanding, particularly as species richness corresponds closely to collection effort. Phylogenetic diversity patterns mirror that of species richness and endemism in most of the analyzed groups. We highlight humid forests as centers of diversity and endemism because of their role as refugia and centers of recent and rapid radiations. However, the distinct endemism of other areas, such as the grassland-woodland mosaic of the Central Highlands and the spiny forest of the southwest, is also biologically important despite lower species richness. The documented uses of Malagasy biodiversity are manifold, with much potential for the uncovering of new useful traits for food, medicine, and climate mitigation. The data presented here showcase Madagascar as a unique “living laboratory” for our understanding of evolution and the complex interactions between people and nature. The gathering and analysis of biodiversity data must continue and accelerate if we are to fully understand and safeguard this unique subset of Earth’s biodiversity.
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Affiliation(s)
- Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Oxford, Oxford, UK
| | - Rhian J. Smith
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Allison L. Perrigo
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Jan Hackel
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Weston Testo
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Field Museum of Natural History, Chicago, Illinois, USA
| | - Harith Farooq
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Faculty of Natural Sciences, Lúrio University, Pemba, Cabo Delgado Province, Mozambique
| | - Maria F. Torres Jiménez
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Institute of Biosciences, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Niels Andela
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, UK
| | - Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Organismal Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | | | | | - Christine D. Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | | | - Francesco Belluardo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Chris Birkinshaw
- Missouri Botanical Garden, Madagascar Program, Antananarivo, Madagascar
- Missouri Botanical Garden, St. Louis, Missouri, USA
| | | | - Stuart Cable
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Nataly A. Canales
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Juan D. Carrillo
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- CR2P, Muséum National d’Histoire Naturelle, Paris, France
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Rosie Clegg
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Geography, University of Exeter, Exeter, Devon, UK
| | - Colin Clubbe
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Robert S. C. Cooke
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- UK Centre for Ecology and Hydrology, Wallingford, UK
| | - Gabriel Damasco
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Sonia Dhanda
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Daniel Edler
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, Sweden
| | - Søren Faurby
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Paola de Lima Ferreira
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic
| | - Brian L. Fisher
- California Academy of Sciences, San Francisco, California, USA
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Lauren M. Gardiner
- Cambridge University Herbarium, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Steven M. Goodman
- Field Museum of Natural History, Chicago, Illinois, USA
- Association Vahatra, Antananarivo, Madagascar
| | | | - Thaís B. Guedes
- Instituto de Biologia, Universidade Estadual de Campinas, Unicamp, Campinas, São Paulo, Brazil
| | - Marie C. Henniges
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Rowena Hill
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Caroline E. R. Lehmann
- Royal Botanic Garden Edinburgh, Edinburgh, UK
- School of GeoSciences, University of Edinburgh, Edinburgh, UK
| | - Porter P. Lowry
- Missouri Botanical Garden, St. Louis, Missouri, USA
- Institut de Systématique, Évolution, et Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Paris, France
| | - Lovanomenjanahary Marline
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
- Association Vahatra, Antananarivo, Madagascar
| | - Pável Matos-Maraví
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic
| | - Justin Moat
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Beatriz Neves
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Matheus G. C. Nogueira
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renske E. Onstein
- Naturalis Biodiversity Center, Darwinweg 2, 2333CR Leiden, the Netherlands
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | | | | | - Leanne N. Phelps
- Royal Botanic Garden Edinburgh, Edinburgh, UK
- School of GeoSciences, University of Edinburgh, Edinburgh, UK
| | - Peter B. Phillipson
- Missouri Botanical Garden, St. Louis, Missouri, USA
- Institut de Systématique, Évolution, et Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Paris, France
| | - Samuel Pironon
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, UK
| | - Natalia A. S. Przelomska
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Anthropology, Smithsonian National Museum of Natural History, Washington, DC, USA
| | | | - David Rabehevitra
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | | | - Mamy Tiana Rajaonah
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Fano Rajaonary
- Missouri Botanical Garden, Madagascar Program, Antananarivo, Madagascar
| | - Landy R. Rajaovelona
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Mijoro Rakotoarinivo
- Department of Plant Biology and Ecology, University of Antananarivo, Antananarivo, Madagascar
| | - Amédée A. Rakotoarisoa
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Solofo E. Rakotoarisoa
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Herizo N. Rakotomalala
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Franck Rakotonasolo
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | | | - Myriam Ramirez-Herranz
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Instituto de Ecología y Biodiversidad, University of La Serena, La Serena, Chile
- Programa de Doctorado en Biología y Ecología Aplicada, Universidad Católica del Norte, Universidad de La Serena, La Serena, Chile
| | | | | | - Vonona Randrianasolo
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | | | | | | | - Velosoa Razafiniary
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Henintsoa Razanajatovo
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Estelle Razanatsoa
- Plant Conservation Unit, Department of Biological Sciences, University of Cape Town, South Africa
| | - Malin Rivers
- Botanic Gardens Conservation International, Kew, Richmond, Surrey, UK
| | - Ferran Sayol
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | | | - Kim Walker
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Royal Holloway, University of London, Egham, Surrey, UK
| | | | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | | | - Thomas Ziegler
- Cologne Zoo, Cologne, Germany
- Institute of Zoology, University of Cologne, Cologne, Germany
| | - Alexander Zizka
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Hélène Ralimanana
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
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24
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Ralimanana H, Perrigo AL, Smith RJ, Borrell JS, Faurby S, Rajaonah MT, Randriamboavonjy T, Vorontsova MS, Cooke RSC, Phelps LN, Sayol F, Andela N, Andermann T, Andriamanohera AM, Andriambololonera S, Bachman SP, Bacon CD, Baker WJ, Belluardo F, Birkinshaw C, Cable S, Canales NA, Carrillo JD, Clegg R, Clubbe C, Crottini A, Damasco G, Dhanda S, Edler D, Farooq H, de Lima Ferreira P, Fisher BL, Forest F, Gardiner LM, Goodman SM, Grace OM, Guedes TB, Hackel J, Henniges MC, Hill R, Lehmann CER, Lowry PP, Marline L, Matos-Maraví P, Moat J, Neves B, Nogueira MGC, Onstein RE, Papadopulos AST, Perez-Escobar OA, Phillipson PB, Pironon S, Przelomska NAS, Rabarimanarivo M, Rabehevitra D, Raharimampionona J, Rajaonary F, Rajaovelona LR, Rakotoarinivo M, Rakotoarisoa AA, Rakotoarisoa SE, Rakotomalala HN, Rakotonasolo F, Ralaiveloarisoa BA, Ramirez-Herranz M, Randriamamonjy JEN, Randrianasolo V, Rasolohery A, Ratsifandrihamanana AN, Ravololomanana N, Razafiniary V, Razanajatovo H, Razanatsoa E, Rivers M, Silvestro D, Testo W, Torres Jiménez MF, Walker K, Walker BE, Wilkin P, Williams J, Ziegler T, Zizka A, Antonelli A. Madagascar’s extraordinary biodiversity: Threats and opportunities. Science 2022; 378:eadf1466. [DOI: 10.1126/science.adf1466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Madagascar’s unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar’s terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevant threats, ex situ collections and programs, and the coverage and comprehensiveness of protected areas. The existing terrestrial protected area network in Madagascar covers 10.4% of its land area and includes at least part of the range of the majority of described native species of vertebrates with known distributions (97.1% of freshwater fishes, amphibians, reptiles, birds, and mammals combined) and plants (67.7%). The overall figures are higher for threatened species (97.7% of threatened vertebrates and 79.6% of threatened plants occurring within at least one protected area). International Union for Conservation of Nature (IUCN) Red List assessments and Bayesian neural network analyses for plants identify overexploitation of biological resources and unsustainable agriculture as the most prominent threats to biodiversity. We highlight five opportunities for action at multiple levels to ensure that conservation and ecological restoration objectives, programs, and activities take account of complex underlying and interacting factors and produce tangible benefits for the biodiversity and people of Madagascar.
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Affiliation(s)
- Hélène Ralimanana
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Allison L. Perrigo
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Rhian J. Smith
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | | | - Søren Faurby
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Mamy Tiana Rajaonah
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | | | | | - Robert S. C. Cooke
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- UK Centre for Ecology and Hydrology, Wallingford, UK
| | - Leanne N. Phelps
- School of GeoSciences, University of Edinburgh, Edinburgh, UK
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - Ferran Sayol
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Niels Andela
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, UK
| | - Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Organismal Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | | | | | - Christine D. Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | | | - Francesco Belluardo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Chris Birkinshaw
- Missouri Botanical Garden, Madagascar Program, Antananarivo, Madagascar
- Missouri Botanical Garden, St. Louis, MO, USA
| | - Stuart Cable
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Nataly A. Canales
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Juan D. Carrillo
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- CR2P, Muséum National d’Histoire Naturelle, Paris, France
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Rosie Clegg
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Geography, University of Exeter, Exeter, Devon, UK
| | - Colin Clubbe
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Gabriel Damasco
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Sonia Dhanda
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Daniel Edler
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, Sweden
| | - Harith Farooq
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Faculty of Natural Sciences, Lúrio University, Pemba, Cabo Delgado Province, Mozambique
| | - Paola de Lima Ferreira
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic
| | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Lauren M. Gardiner
- Cambridge University Herbarium, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Steven M. Goodman
- Association Vahatra, Antananarivo, Madagascar
- Field Museum of Natural History, Chicago, IL, USA
| | | | - Thaís B. Guedes
- Instituto de Biologia, Universidade Estadual de Campinas, Unicamp, Campinas, São Paulo, Brazil
| | - Jan Hackel
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Marie C. Henniges
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Rowena Hill
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Caroline E. R. Lehmann
- School of GeoSciences, University of Edinburgh, Edinburgh, UK
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - Porter P. Lowry
- Missouri Botanical Garden, St. Louis, MO, USA
- Institut de Systématique, Évolution, et Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Paris, France
| | - Lovanomenjanahary Marline
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Association Vahatra, Antananarivo, Madagascar
| | - Pável Matos-Maraví
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic
| | - Justin Moat
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Beatriz Neves
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Matheus G. C. Nogueira
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renske E. Onstein
- Naturalis Biodiversity Center, Leiden, Netherlands
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | | | | | - Peter B. Phillipson
- Missouri Botanical Garden, St. Louis, MO, USA
- Institut de Systématique, Évolution, et Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Paris, France
| | - Samuel Pironon
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, UK
| | - Natalia A. S. Przelomska
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Anthropology, Smithsonian National Museum of Natural History, Washington, DC, USA
| | | | - David Rabehevitra
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | | | - Fano Rajaonary
- Missouri Botanical Garden, Madagascar Program, Antananarivo, Madagascar
| | - Landy R. Rajaovelona
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Mijoro Rakotoarinivo
- Department of Plant Biology and Ecology, University of Antananarivo, Antananarivo, Madagascar
| | - Amédée A. Rakotoarisoa
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Solofo E. Rakotoarisoa
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Herizo N. Rakotomalala
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Franck Rakotonasolo
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | | | - Myriam Ramirez-Herranz
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Instituto de Ecología y Biodiversidad, University of La Serena, La Serena, Chile
- Programa de Doctorado en Biología y Ecología Aplicada, Universidad Católica del Norte, Universidad de La Serena, La Serena, Chile
| | | | - Vonona Randrianasolo
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | | | | | | | - Velosoa Razafiniary
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Henintsoa Razanajatovo
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Estelle Razanatsoa
- Plant Conservation Unit, Department of Biological Sciences, University of Cape Town, South Africa
| | - Malin Rivers
- Botanic Gardens Conservation International, Kew, Richmond, Surrey, UK
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Weston Testo
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Field Museum of Natural History, Chicago, IL, USA
| | - Maria F. Torres Jiménez
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Institute of Biosciences, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Kim Walker
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Royal Holloway, University of London, Egham, Surrey, UK
| | | | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | | | - Thomas Ziegler
- Cologne Zoo, Cologne, Germany
- Institute of Zoology, University of Cologne, Cologne, Germany
| | - Alexander Zizka
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Biology, University of Oxford, Oxford, UK
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Simmons MP, Maurin O, Bailey P, Brewer GE, Roy S, Lombardi JA, Forest F, Baker WJ. Benefits of alignment quality-control processing steps and an Angiosperms353 phylogenomics pipeline applied to the Celastrales. Cladistics 2022; 38:595-611. [PMID: 35569142 DOI: 10.1111/cla.12507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2022] [Indexed: 01/31/2023] Open
Abstract
We examined the impact of successive alignment quality-control steps on downstream phylogenomic analyses. We applied a recently published phylogenomics pipeline that was developed for the Angiosperms353 target-sequence-capture probe set to the flowering plant order Celastrales. Our final dataset consists of 158 species, including at least one exemplar from all 109 currently recognized Celastrales genera. We performed nine quality-control steps and compared the inferred resolution, branch support, and topological congruence of the inferred gene and species trees with those generated after each of the first six steps. We describe and justify each of our quality-control steps, including manual masking, in detail so that they may be readily applied to other lineages. We found that highly supported clades could generally be relied upon even if stringent orthology and alignment quality-control measures had not been applied. But separate instances were identified, for both concatenation and coalescence, wherein a clade was highly supported before manual masking but then subsequently contradicted. These results are generally reassuring for broad-scale analyses that use phylogenomics pipelines, but also indicate that we cannot rely exclusively on these analyses to conclude how challenging phylogenetic problems are best resolved.
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Affiliation(s)
- Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523-1878, USA
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Paul Bailey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Grace E Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Shyamali Roy
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Julio A Lombardi
- Departamento de Botânica, Instituto de Biociências de Rio Claro, Universidade Estadual Paulista - UNESP, Av. 24-A 1515 - Bela Vista, Caixa Postal 199, São Paulo, Brazil
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
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Perquis MP, Tissot C, Bouleftour W, Bayle-Bleuez S, Vercherin P, Forest F, Fournel P. Analyse de la prise en charge des cancers bronchiques avec mutation du gène de l’EGFR. Rev Mal Respir 2022; 39:731-739. [DOI: 10.1016/j.rmr.2022.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 08/01/2022] [Indexed: 11/06/2022]
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Aygören Uluer D, Forest F, Hawkins JA. Dataset of pollination traits in Fabales. Data Brief 2022; 43:108480. [PMID: 35935709 PMCID: PMC9352444 DOI: 10.1016/j.dib.2022.108480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Deniz Aygören Uluer
- School of Biological Sciences, University of Reading, Lyle Building, Whiteknights, Reading, Berkshire RG6 6BX, United Kingdom
- Department of Plant and Animal Production, Cicekdagi Vocational College, Ahi Evran University, Cicekdagi, Kirsehir 40700, Turkiye
- Corresponding authors at: School of Biological Sciences, University of Reading, Lyle Building, Whiteknights, Reading, Berkshire RG6 6BX, United Kingdom.
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, United Kingdom
| | - Julie A. Hawkins
- School of Biological Sciences, University of Reading, Lyle Building, Whiteknights, Reading, Berkshire RG6 6BX, United Kingdom
- Corresponding authors at: School of Biological Sciences, University of Reading, Lyle Building, Whiteknights, Reading, Berkshire RG6 6BX, United Kingdom.
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Simões ARG, Eserman LA, Zuntini AR, Chatrou LW, Utteridge TMA, Maurin O, Rokni S, Roy S, Forest F, Baker WJ, Stefanović S. A Bird's Eye View of the Systematics of Convolvulaceae: Novel Insights From Nuclear Genomic Data. Front Plant Sci 2022; 13:889988. [PMID: 35909765 PMCID: PMC9331175 DOI: 10.3389/fpls.2022.889988] [Citation(s) in RCA: 3] [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] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Convolvulaceae is a family of c. 2,000 species, distributed across 60 currently recognized genera. It includes species of high economic importance, such as the crop sweet potato (Ipomoea batatas L.), the ornamental morning glories (Ipomoea L.), bindweeds (Convolvulus L.), and dodders, the parasitic vines (Cuscuta L.). Earlier phylogenetic studies, based predominantly on chloroplast markers or a single nuclear region, have provided a framework for systematic studies of the family, but uncertainty remains at the level of the relationships among subfamilies, tribes, and genera, hindering evolutionary inferences and taxonomic advances. One of the enduring enigmas has been the relationship of Cuscuta to the rest of Convolvulaceae. Other examples of unresolved issues include the monophyly and relationships within Merremieae, the "bifid-style" clade (Dicranostyloideae), as well as the relative positions of Erycibe Roxb. and Cardiochlamyeae. In this study, we explore a large dataset of nuclear genes generated using Angiosperms353 kit, as a contribution to resolving some of these remaining phylogenetic uncertainties within Convolvulaceae. For the first time, a strongly supported backbone of the family is provided. Cuscuta is confirmed to belong within family Convolvulaceae. "Merremieae," in their former tribal circumscription, are recovered as non-monophyletic, with the unexpected placement of Distimake Raf. as sister to the clade that contains Ipomoeeae and Decalobanthus Ooststr., and Convolvuleae nested within the remaining "Merremieae." The monophyly of Dicranostyloideae, including Jacquemontia Choisy, is strongly supported, albeit novel relationships between genera are hypothesized, challenging the current tribal delimitation. The exact placements of Erycibe and Cuscuta remain uncertain, requiring further investigation. Our study explores the benefits and limitations of increasing sequence data in resolving higher-level relationships within Convolvulaceae, and highlights the need for expanded taxonomic sampling, to facilitate a much-needed revised classification of the family.
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Affiliation(s)
| | - Lauren A. Eserman
- Conservation & Research Department, Atlanta Botanical Garden, Atlanta, GA, United States
| | | | - Lars W. Chatrou
- Systematic and Evolutionary Botany Lab, University of Ghent, Ghent, Belgium
| | | | | | - Saba Rokni
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Shyamali Roy
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Saša Stefanović
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
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Ellestad P, Farrera MAP, Forest F, Buerki S. Uncovering haplotype diversity in cultivated Mexican vanilla species. Am J Bot 2022; 109:1120-1138. [PMID: 35709340 DOI: 10.1002/ajb2.16024] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
PREMISE Although vanilla is one of the best-known spices, there is only a limited understanding of its biology and genetics within Mexico, where its cultivation originated and where phenotypic variability is high. This study aims to augment our understanding of vanilla's genetic resources by assessing species delimitation and genetic, geographic, and climatic variability within Mexican cultivated vanilla. METHODS Using nuclear and plastid DNA sequence data from 58 Mexican samples collected from three regions and 133 ex situ accessions, we assessed species monophyly using phylogenetic analyses and genetic distances. Intraspecific genetic variation was summarized through the identification of haplotypes. Within the primarily cultivated species, Vanilla planifolia, haplotype relationships were further verified using plastome and rRNA gene sequences. Climatic niche and haplotype composition were assessed across the landscape. RESULTS Three species (Vanilla planifolia, V. pompona, and V. insignis) and 13 haplotypes were identified among Mexican vanilla. Within V. planifolia haplotypes, hard phylogenetic incongruences between plastid and nuclear sequences suggest past hybridization events. Eight haplotypes consisted exclusively of Mexican samples. The dominant V. planifolia haplotype occurred throughout all three regions as well as outside of its country of origin. Haplotype richness was found to be highest in regions around Papantla and Chinantla. CONCLUSIONS Long histories of regional cultivation support the consideration of endemic haplotypes as landraces shaped by adaptation to local conditions and/or hybridization. Results may aid further genomic investigations of vanilla's genetic resources and ultimately support the preservation of genetic diversity within the economically important crop.
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Affiliation(s)
- Paige Ellestad
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, Idaho, 83725, USA
| | - Miguel Angel Perez Farrera
- Herbario Eizi Matuda, Laboratorio de Ecología Evolutiva, Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes, Chiapas, Mexico, Libramiento Norte Poniente 1151, Col. Lajas Maciel, Tuxtla Gutiérrez, Chiapas, CP, 29039, Mexico
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Sven Buerki
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, Idaho, 83725, USA
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Uluer DA, Forest F, Armbruster S, Hawkins JA. Reconstructing an historical pollination syndrome: keel flowers. BMC Ecol Evol 2022; 22:45. [PMID: 35413792 PMCID: PMC9004149 DOI: 10.1186/s12862-022-02003-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 04/05/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Keel flowers are bilaterally symmetrical, pentamerous flowers with three different petal types and reproductive organs enclosed by keel petals; generally there is also connation of floral parts such as stamens and keel petals. In this study, the evolution of keel flowers within the order Fabales is explored to investigate whether the establishment of this flower type within one of the species-rich families, the Fabaceae (Leguminosae), preceded and could have influenced the evolution of keel flowers in the Polygalaceae. We conducted molecular dating, and ancestral area and ancestral state analyses for a phylogeny constructed for 678 taxa using published matK, rbcL and trnL plastid gene regions.
Results
We reveal the temporal and spatial origins of keel flowers and traits associated with pollinators, specifically floral symmetry, the presence or absence of a pentamerous corolla and three distinct petal types, the presence or absence of enclosed reproductive organs, androecium types, inflorescence types, inflorescence size, flower size, plant height and habit. Ancestral area reconstructions show that at the time keel flowers appeared in the Polygaleae, subfamily Papilionoideae of the Fabaceae was already distributed almost globally; at least eight clades of the Papilionoideae had keel flowers with a functional morphology broadly similar to the morphology of the first evolving Polygaleae flowers.
Conclusions
The multiple origins of keel flowers within angiosperms likely represent convergence due to bee specialization, and therefore pollinator pressure. In the case of the Fabales, the first evolving keel flowers of Polygaleae have a functional morphology that corresponds with keel flowers of species of the Papilionoideae already present in the environment. These findings are consistent with the keel-flowered Polygaleae exploiting pollinators of keel-flowered Papilionoideae. The current study is the first to use ancestral reconstructions of traits associated with pollination to demonstrate that the multiple evolutionary origins of the keel flower pollinator syndrome in Fabales are consistent with, though do not prove, mimicry.
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Cantwell-Jones A, Ball J, Collar D, Diazgranados M, Douglas R, Forest F, Hawkins J, Howes MJR, Ulian T, Vaitla B, Pironon S. Global plant diversity as a reservoir of micronutrients for humanity. Nat Plants 2022; 8:225-232. [PMID: 35210559 DOI: 10.1038/s41477-022-01100-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
With more than two billion people suffering from malnutrition and diets homogenizing globally, it is vital to identify and conserve nutrient-rich species that may contribute to improving food security and diversifying diets. Of the approximately 390,000 vascular plant species known to science, thousands have been reported to be edible, yet their nutritional content remains poorly characterized. Here we use phylogenetic information to identify plants with the greatest potential to support strategies alleviating B-vitamin deficiencies. We predict the B-vitamin profiles of >6,400 edible plants lacking nutritional data and identify 1,044 species as promising key sources of B vitamins. Several of these source species should become conservation priorities, as 63 (6%) are threatened in the wild and 272 (26%) are absent from seed banks. Moreover, many of these conservation-priority source species overlap with hotspots of malnutrition, highlighting the need for safeguarding strategies to ensure that edible plant diversity remains a reservoir of nutrition for future generations, particularly in countries needing it most. Although by no means a silver bullet to tackling malnutrition, conserving a diverse portfolio of edible plants, unravelling their nutritional potentials, and promoting their sustainable use are essential strategies to enhance global nutritional resilience.
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Affiliation(s)
- Aoife Cantwell-Jones
- Science and Solutions for a Changing Planet DTP, and the Department of Life Sciences, Imperial College London, Ascot, UK.
| | - Jenny Ball
- Royal Botanic Gardens, Richmond, Surrey, UK
| | - David Collar
- Department of Organismal and Environmental Biology, Christopher Newport University, Newport News, VA, USA
| | | | | | | | - Julie Hawkins
- School of Biological Sciences, University of Reading, Reading, Berkshire, UK
| | - Melanie-Jayne R Howes
- Royal Botanic Gardens, Richmond, Surrey, UK
- Institute of Pharmaceutical Science, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | | | - Bapu Vaitla
- Department of Nutrition, Harvard TH Chan School of Public Health, Harvard University, Boston, MA, USA
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Lu M, Fradera-Soler M, Forest F, Barraclough TG, Grace OM. Evidence linking life-form to a major shift in diversification rate in Crassula. Am J Bot 2022; 109:272-290. [PMID: 34730230 DOI: 10.1002/ajb2.1797] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 05/04/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Plants have evolved different ecological strategies in response to environmental challenges, and a higher lability of such strategies is more common in plant groups that adapt to various niches. Crassula (Crassulaceae), occurring in varied mesic to xeric habitats, exhibits a remarkable diversity of life-forms. However, whether any particular life-form trait has shaped species diversification in Crassula has remained unexplored. This study aims to investigate diversification patterns within Crassula and identify potential links to its life-form evolution. METHODS A phylogenetic tree of 140 Crassula taxa was reconstructed using plastid and nuclear loci and dated based on the nuclear DNA information only. We reconstructed ancestral life-form characters to estimate the evolutionary trends of ecophysiological change, and subsequently estimated net diversification rates. Multiple diversification models were applied to examine the association between certain life-forms and net diversification rates. RESULTS Our findings confirm a radiation within Crassula in the last 10 million years. A configuration of net diversification rate shifts was detected, which coincides with the emergence of a speciose lineage during the late Miocene. The results of ancestral state reconstruction demonstrate a high lability of life-forms in Crassula, and the trait-dependent diversification analyses revealed that the increased diversification is strongly associated with a compact growth form. CONCLUSIONS Transitions between life-forms in Crassula seem to have driven adaptation and shaped diversification of this genus across various habitats. The diversification patterns we inferred are similar to those observed in other major succulent lineages, with the most-speciose clades originating in the late Miocene.
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Affiliation(s)
- Meng Lu
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, UK
| | - Marc Fradera-Soler
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Timothy G Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, UK
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Olwen M Grace
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
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Palazzesi L, Hidalgo O, Barreda VD, Forest F, Höhna S. The rise of grasslands is linked to atmospheric CO 2 decline in the late Palaeogene. Nat Commun 2022; 13:293. [PMID: 35022396 PMCID: PMC8755714 DOI: 10.1038/s41467-021-27897-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 06/09/2017] [Accepted: 12/13/2021] [Indexed: 01/25/2023] Open
Abstract
Grasslands are predicted to experience a major biodiversity change by the year 2100. A better understanding of how grasslands have responded to past environmental changes will help predict the outcome of current and future environmental changes. Here, we explore the relationship between past atmospheric CO2 and temperature fluctuations and the shifts in diversification rate of Poaceae (grasses) and Asteraceae (daisies), two exceptionally species-rich grassland families (~11,000 and ~23,000 species, respectively). To this end, we develop a Bayesian approach that simultaneously estimates diversification rates through time from time-calibrated phylogenies and correlations between environmental variables and diversification rates. Additionally, we present a statistical approach that incorporates the information of the distribution of missing species in the phylogeny. We find strong evidence supporting a simultaneous increase in diversification rates for grasses and daisies after the most significant reduction of atmospheric CO2 in the Cenozoic (~34 Mya). The fluctuations of paleo-temperatures, however, appear not to have had a significant relationship with the diversification of these grassland families. Overall, our results shed new light on our understanding of the origin of grasslands in the context of past environmental changes. A better understanding of how grasslands have responded to past environmental changes will help predict the outcomes of future changes. This study explores past climatic fluctuations and shifts in the diversification rate of grasses and daisies, finding strong evidence for a simultaneous increase in their diversification rates following a reduction of atmospheric CO2 in the Cenozoic.
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Affiliation(s)
- Luis Palazzesi
- Museo Argentino de Ciencias Naturales & Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, C1405DJR, Argentina. .,Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK.
| | - Oriane Hidalgo
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK.,Institut Botánic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Catalonia, Spain
| | - Viviana D Barreda
- Museo Argentino de Ciencias Naturales & Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, C1405DJR, Argentina
| | - Félix Forest
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK
| | - Sebastian Höhna
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany. .,Department of Earth and Environmental Sciences, Paleontology & Geobiology, Ludwig-Maximilians-Universität München, Richard-Wagner-Str. 10, 80333, Munich, Germany.
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Milliken W, Walker BE, Howes MJR, Forest F, Nic Lughadha E. Plants used traditionally as antimalarials in Latin America: Mining the tree of life for potential new medicines. J Ethnopharmacol 2021; 279:114221. [PMID: 34029639 DOI: 10.1016/j.jep.2021.114221] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 03/01/2021] [Revised: 05/11/2021] [Accepted: 05/17/2021] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Malaria remains a serious and challenging disease. Traditional antimalarial medicines are largely based on plants, and ethnopharmacological research has inspired the development of antimalarial pharmaceuticals such as artemisinin. Antimalarial drug resistance is an increasing problem in Plasmodium species, and new therapeutic strategies to combat malaria are needed. Although the number of malaria cases has been decreasing in Latin America, malaria remains a significant threat in many regions. Local people in Latin America have been using numerous plant species to treat malaria, some of which have been scientifically studied, but many others have not. AIM OF THE STUDY Our principal objective is to harness ethnobotanical data on species used traditionally to treat malaria, combined with phylogenetic approaches, to understand how ethnobotany could help identify plant genera as potential sources of new medicines. MATERIALS AND METHODS Plants used to treat malaria in Latin America were compiled from published and grey literature, unpublished data, and herbarium specimens. Initial assessment of potentially important species/genera/families included compiling the number of species used within the genus, the number of use reports per genus and species, and the geographic distribution of their use. The analysis of taxonomic distribution of species reported as antimalarial in Latin America (excluding the Southern Cone) was conducted, to determine which genera and families with reputed antimalarial properties are over-represented, and phylogenetic analyses were performed to identify if there was evidence for antimalarial species being dispersed/clustered throughout the tree or at its tips. This approach enabled 'hot-nodes' in certain families to be identified, to predict new genera with potential antimalarial properties. RESULTS Over 1000 plant species have been used to treat malaria in Latin America, of which over 600 species were cited only once. The genera with the highest number of antimalarial species were Aspidosperma, Solanum, Piper, Croton and Aristolochia. In terms of geographic distribution, the most widely used genera were Aspidosperma, Momordica, Cinchona, Senna and Stachytarpheta. Significant phylogenetic signal was detected in the distribution of native species used for malaria, analysed in a genus-level phylogenetic framework. The eudicot and magnoliidae lineages were over-represented, while monocots were not. CONCLUSION Analysis of ethnobotanical use reports in a phylogenetic framework reveals the existence of hot nodes for malaria across the Latin American flora. We demonstrate how species and genera currently lacking such reports could be pinpointed as of potential interest based on their evolutionary history. Extending this approach to other regions of the world and other diseases could accelerate the discovery of novel medicines and enhance healthcare in areas where new therapeutic strategies are needed.
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Affiliation(s)
| | | | - Melanie-Jayne R Howes
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK; Institute of Pharmaceutical Science, Faculty of Life Sciences and Medicine, King's College London, SE1 9NH, UK.
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK.
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Boukhiar S, Tiffet O, Bayle-Bleuez S, Picot T, Yvorel V, Forest F. [Multiple synchronous lung adenocarcinoma: Interest of molecular biology for staging]. Rev Mal Respir 2021; 38:942-945. [PMID: 34565641 DOI: 10.1016/j.rmr.2021.09.001] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 06/30/2021] [Indexed: 10/20/2022]
Abstract
INTRODUCTION The presence of multiple synchronous lung tumors is not a rare event. Distinguishing intra-pulmonary metastases from multiple synchronous lung adenocarcinoma is a challenge for pathologists and physicians. We present observation of a patient with three lung tumors corresponding to three adenocarcinomas for which molecular analysis had a significant impact on tumor staging. OBSERVATION Three suspect lesions were discovered in a 61-year-old patient, a smoker, in each lobe of the right lung. Right pneumonectomy with lymph node dissection was performed. Pathological examination showed that each tumor was in fact an adenocarcinoma. In order to more precisely indicate tumor staging, molecular analysis was performed with next generation sequencing showing a different point mutation in a driver gene on each tumor. The final diagnosis is that the three tumors are distinct synchronous tumors, which must be staged separately. CONCLUSIONS In modern-day practice of thoracic oncology and of surgical pathology, molecular biology represents a complement for tumor staging in the event of multiple lung tumors.
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Affiliation(s)
- S Boukhiar
- Centre Hospitalier Universitaire de Saint Étienne, Hôpital Nord. Laboratoire d'Anatomie et Cytologie Pathologiques, avenue Albert-Raimond, 42055 Saint Étienne cedex 2, France
| | - O Tiffet
- Centre Hospitalier Universitaire de Saint-Étienne, Hôpital Nord, Service de Chirurgie Thoracique, avenue Albert-Raimond, 42055 Saint-Étienne cedex 2, France
| | - S Bayle-Bleuez
- Service de Pneumologie, Centre Hospitalier Universitaire de Saint-Étienne, Hôpital Nord, avenue Albert-Raimond, 42055 Saint-Étienne cedex 2, France
| | - T Picot
- Centre Hospitalier Universitaire de Saint Étienne, Hôpital Nord. Laboratoire d'Anatomie et Cytologie Pathologiques, avenue Albert-Raimond, 42055 Saint Étienne cedex 2, France; Centre Hospitalier Universitaire de Saint-Étienne, Hôpital Nord, Plateforme de biologie moléculaire des tumeurs solides, avenue Albert-Raimond, 42055 Saint-Étienne cedex 2, France
| | - V Yvorel
- Centre Hospitalier Universitaire de Saint Étienne, Hôpital Nord. Laboratoire d'Anatomie et Cytologie Pathologiques, avenue Albert-Raimond, 42055 Saint Étienne cedex 2, France; Centre Hospitalier Universitaire de Saint-Étienne, Hôpital Nord, Plateforme de biologie moléculaire des tumeurs solides, avenue Albert-Raimond, 42055 Saint-Étienne cedex 2, France
| | - F Forest
- Centre Hospitalier Universitaire de Saint Étienne, Hôpital Nord. Laboratoire d'Anatomie et Cytologie Pathologiques, avenue Albert-Raimond, 42055 Saint Étienne cedex 2, France; Centre Hospitalier Universitaire de Saint-Étienne, Hôpital Nord, Plateforme de biologie moléculaire des tumeurs solides, avenue Albert-Raimond, 42055 Saint-Étienne cedex 2, France.
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Bertholon S, Grange S, Grange R, Forest F, Tetard MC, Boutet C, Vassal F. Spinal Arachnoid Web: A didactic report of two cases with clinical, radiological, surgical and pathological correlations. Neurochirurgie 2021; 68:11-15. [PMID: 34329657 DOI: 10.1016/j.neuchi.2021.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 05/20/2021] [Revised: 07/01/2021] [Accepted: 07/12/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Arachnoid web (AW) is a rare but probably underestimated cause of spinal cord injury that is complex to diagnose due to subtle MRI findings and similarities to other better-known diseases such as arachnoid cyst (AC) or transdural spinal cord herniation (TSCH). Increased recognition of AW is mandatory since delay in diagnosis can lead to potentially serious neurological sequelae. CASE PRESENTATIONS We report two additional cases of AW for didactic purposes, with special emphasis on the distinctive MRI and intraoperative findings. Both patients presented with progressively worsening neurological symptoms, including proprioceptive ataxia, motor weakness, numbness and neuropathic pain. The diagnosis of AW was suspected on the basis of specific MRI criteria, especially the so-called "scalpel sign". Formal confirmation of the diagnosis was obtained in two patients that were managed surgically. Postoperative follow-up demonstrated significant functional recovery. DISCUSSION There is a need for better recognition of AW by the medical community. Careful analysis of MRI semiology is crucial for the distinction between AW, AC and TSCH. Prompt and accurate diagnosis is mandatory to conserve functional prognosis, since appropriate surgical treatment with AW resection is curative, halting or even resolving the neurological symptoms.
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Affiliation(s)
- S Bertholon
- Department of Radiology, University Hospital of Saint-Etienne, 42055 Saint-Etienne cedex 2, France
| | - S Grange
- Department of Radiology, University Hospital of Saint-Etienne, 42055 Saint-Etienne cedex 2, France.
| | - R Grange
- Department of Radiology, University Hospital of Saint-Etienne, 42055 Saint-Etienne cedex 2, France
| | - F Forest
- Department of Pathology, University Hospital of Saint-Etienne, 42055 Saint-Etienne cedex 2, France
| | - M-C Tetard
- Department of Neurosurgery, University Hospital of Saint-Etienne, 42055 Saint-Etienne cedex 2, France
| | - C Boutet
- Department of Radiology, University Hospital of Saint-Etienne, 42055 Saint-Etienne cedex 2, France
| | - F Vassal
- Department of Neurosurgery, University Hospital of Saint-Etienne, 42055 Saint-Etienne cedex 2, France
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Hendriks KP, Mandáková T, Hay NM, Ly E, Hooft van Huysduynen A, Tamrakar R, Thomas SK, Toro‐Núñez O, Pires JC, Nikolov LA, Koch MA, Windham MD, Lysak MA, Forest F, Mummenhoff K, Baker WJ, Lens F, Bailey CD. The best of both worlds: Combining lineage-specific and universal bait sets in target-enrichment hybridization reactions. Appl Plant Sci 2021; 9:APS311438. [PMID: 34336398 PMCID: PMC8312739 DOI: 10.1002/aps3.11438] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 03/16/2021] [Indexed: 05/03/2023]
Abstract
PREMISE Researchers adopting target-enrichment approaches often struggle with the decision of whether to use universal or lineage-specific probe sets. To circumvent this quandary, we investigate the efficacy of a simultaneous enrichment by combining universal probes and lineage-specific probes in a single hybridization reaction, to benefit from the qualities of both probe sets with little added cost or effort. METHODS AND RESULTS Using 26 Brassicaceae libraries and standard enrichment protocols, we compare results from three independent data sets. A large average fraction of reads mapping to the Angiosperms353 (24-31%) and Brassicaceae (35-59%) targets resulted in a sizable reconstruction of loci for each target set (x̄ ≥ 70%). CONCLUSIONS High levels of enrichment and locus reconstruction for the two target sets demonstrate that the sampling of genomic regions can be easily extended through the combination of probe sets in single enrichment reactions. We hope that these findings will facilitate the production of expanded data sets that answer individual research questions and simultaneously allow wider applications by the research community as a whole.
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Affiliation(s)
- Kasper P. Hendriks
- Naturalis Biodiversity CenterResearch Group Functional TraitsP.O. Box 95172300RALeidenThe Netherlands
- Department of Biology/BotanyOsnabrück UniversityOsnabrück49076Germany
| | | | - Nikolai M. Hay
- Department of BiologyDuke UniversityDurhamNorth Carolina27708USA
| | - Elfy Ly
- Naturalis Biodiversity CenterResearch Group Functional TraitsP.O. Box 95172300RALeidenThe Netherlands
| | - Alex Hooft van Huysduynen
- Naturalis Biodiversity CenterResearch Group Functional TraitsP.O. Box 95172300RALeidenThe Netherlands
| | - Rubin Tamrakar
- Department of BiologyNew Mexico State UniversityLas CrucesNew Mexico88001USA
| | - Shawn K. Thomas
- Division of Biological SciencesUniversity of MissouriColumbiaMissouri65211USA
| | - Oscar Toro‐Núñez
- Departamento de BotánicaUniversidad de ConcepciónConcepciónChile
| | - J. Chris Pires
- Division of Biological SciencesUniversity of MissouriColumbiaMissouri65211USA
| | - Lachezar A. Nikolov
- Department of Molecular, Cell and Developmental BiologyUniversity of California Los AngelesLos AngelesCalifornia90095USA
| | - Marcus A. Koch
- Centre for Organismal Studies COS, Biodiversity and Plant SystematicsHeidelberg University69120HeidelbergGermany
| | | | | | - Félix Forest
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
| | - Klaus Mummenhoff
- Department of Biology/BotanyOsnabrück UniversityOsnabrück49076Germany
| | | | - Frederic Lens
- Naturalis Biodiversity CenterResearch Group Functional TraitsP.O. Box 95172300RALeidenThe Netherlands
- Institute of Biology LeidenPlant SciencesLeiden UniversitySylviusweg 722333 BELeidenThe Netherlands
| | - C. Donovan Bailey
- Department of BiologyNew Mexico State UniversityLas CrucesNew Mexico88001USA
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McLay TGB, Birch JL, Gunn BF, Ning W, Tate JA, Nauheimer L, Joyce EM, Simpson L, Schmidt‐Lebuhn AN, Baker WJ, Forest F, Jackson CJ. New targets acquired: Improving locus recovery from the Angiosperms353 probe set. Appl Plant Sci 2021; 9:APS311420. [PMID: 34336399 PMCID: PMC8312740 DOI: 10.1002/aps3.11420] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 03/15/2021] [Indexed: 05/10/2023]
Abstract
PREMISE Universal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a cost-efficient kit. The Angiosperms353 kit has been successfully used to capture loci throughout the angiosperms, but the default target reference file includes sequence information from only 6-18 taxa per locus. Consequently, reads sequenced from on-target DNA molecules may fail to map to references, resulting in fewer on-target reads for assembly, and reducing locus recovery. METHODS We expanded the Angiosperms353 target file, incorporating sequences from 566 transcriptomes to produce a 'mega353' target file, with each locus represented by 17-373 taxa. This mega353 file is a drop-in replacement for the original Angiosperms353 file in HybPiper analyses. We provide tools to subsample the file based on user-selected taxon groups, and to incorporate other transcriptome or protein-coding gene data sets. RESULTS Compared to the default Angiosperms353 file, the mega353 file increased the percentage of on-target reads by an average of 32%, increased locus recovery at 75% length by 49%, and increased the total length of the concatenated loci by 29%. DISCUSSION Increasing the phylogenetic density of the target reference file results in improved recovery of target capture loci. The mega353 file and associated scripts are available at: https://github.com/chrisjackson-pellicle/NewTargets.
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Affiliation(s)
- Todd G. B. McLay
- National Herbarium of VictoriaRoyal Botanic Gardens VictoriaMelbourneAustralia
- School of BiosciencesUniversity of MelbourneMelbourneAustralia
- Centre for Australian National Biodiversity ResearchCSIROCanberraAustralia
| | - Joanne L. Birch
- School of BiosciencesUniversity of MelbourneMelbourneAustralia
| | - Bee F. Gunn
- National Herbarium of VictoriaRoyal Botanic Gardens VictoriaMelbourneAustralia
- School of BiosciencesUniversity of MelbourneMelbourneAustralia
| | - Weixuan Ning
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Jennifer A. Tate
- School of Fundamental SciencesMassey UniversityPalmerston NorthNew Zealand
| | - Lars Nauheimer
- James Cook UniversityCairnsAustralia
- Australian Tropical HerbariumJames Cook UniversityCairnsAustralia
| | - Elizabeth M. Joyce
- James Cook UniversityCairnsAustralia
- Australian Tropical HerbariumJames Cook UniversityCairnsAustralia
| | - Lalita Simpson
- James Cook UniversityCairnsAustralia
- Australian Tropical HerbariumJames Cook UniversityCairnsAustralia
| | | | | | - Félix Forest
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
| | - Chris J. Jackson
- National Herbarium of VictoriaRoyal Botanic Gardens VictoriaMelbourneAustralia
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Clarkson JJ, Zuntini AR, Maurin O, Downie SR, Plunkett GM, Nicolas AN, Smith JF, Feist MAE, Gutierrez K, Malakasi P, Bailey P, Brewer GE, Epitawalage N, Zmarzty S, Forest F, Baker WJ. A higher-level nuclear phylogenomic study of the carrot family (Apiaceae). Am J Bot 2021; 108:1252-1269. [PMID: 34287829 DOI: 10.1002/ajb2.1701] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 11/16/2020] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
PREMISE The carrot family (Apiaceae) comprises 466 genera, which include many well-known crops (e.g., aniseed, caraway, carrots, celery, coriander, cumin, dill, fennel, parsley, and parsnips). Higher-level phylogenetic relationships among subfamilies, tribes, and other major clades of Apiaceae are not fully resolved. This study aims to address this important knowledge gap. METHODS Target sequence capture with the universal Angiosperms353 probe set was used to examine phylogenetic relationships in 234 genera of Apiaceae, representing all four currently recognized subfamilies (Apioideae, Azorelloideae, Mackinlayoideae, and Saniculoideae). Recovered nuclear genes were analyzed using both multispecies coalescent and concatenation approaches. RESULTS We recovered hundreds of nuclear genes even from old and poor-quality herbarium specimens. Of particular note, we placed with strong support three incertae sedis genera (Platysace, Klotzchia, and Hermas); all three occupy isolated positions, with Platysace resolved as sister to all remaining Apiaceae. We placed nine genera (Apodicarpum, Bonannia, Grafia, Haplosciadium, Microsciadium, Physotrichia, Ptychotis, Tricholaser, Xatardia) that have never previously been included in any molecular phylogenetic study. CONCLUSIONS We provide support for the maintenance of the four existing subfamilies of Apiaceae, while recognizing that Hermas, Klotzschia, and the Platysace clade may each need to be accommodated in additional subfamilies (pending improved sampling). The placement of the currently apioid genus Phlyctidocarpa can be accommodated by the expansion of subfamily Saniculoideae, although adequate morphological synapomorphies for this grouping are yet to be defined. This is the first phylogenetic study of the Apiaceae using high-throughput sequencing methods and represents an unprecedented evolutionary framework for the group.
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Affiliation(s)
| | | | - Olivier Maurin
- Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AE, UK
| | - Stephen R Downie
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Gregory M Plunkett
- Cullman Program for Molecular Systematics, New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY, 10458, USA
| | | | - James F Smith
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, ID, 83725-1515, USA
| | - Mary Ann E Feist
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Karime Gutierrez
- Department of Biology, Smith College, Burton Hall 115, Northampton, MA, 01063, USA
| | | | - Paul Bailey
- Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AE, UK
| | - Grace E Brewer
- Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AE, UK
| | | | - Sue Zmarzty
- Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AE, UK
| | - Félix Forest
- Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AE, UK
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Buerki S, Callmander MW, Acevedo‐Rodriguez P, Lowry PP, Munzinger J, Bailey P, Maurin O, Brewer GE, Epitawalage N, Baker WJ, Forest F. An updated infra-familial classification of Sapindaceae based on targeted enrichment data. Am J Bot 2021; 108:1234-1251. [PMID: 34219219 PMCID: PMC8361682 DOI: 10.1002/ajb2.1693] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 10/30/2020] [Accepted: 03/17/2021] [Indexed: 05/02/2023]
Abstract
PREMISE The economically important, cosmopolitan soapberry family (Sapindaceae) comprises ca. 1900 species in 144 genera. Since the seminal work of Radlkofer, several authors have attempted to overcome challenges presented by the family's complex infra-familial classification. With the advent of molecular systematics, revisions of the various proposed groupings have provided significant momentum, but we still lack a formal classification system rooted in an evolutionary framework. METHODS Nuclear DNA sequence data were generated for 123 genera (86%) of Sapindaceae using target sequence capture with the Angiosperms353 universal probe set. HybPiper was used to produce aligned DNA matrices. Phylogenetic inferences were obtained using coalescence-based and concatenated methods. The clades recovered are discussed in light of both benchmark studies to identify synapomorphies and distributional evidence to underpin an updated infra-familial classification. KEY RESULTS Coalescence-based and concatenated phylogenetic trees had identical topologies and node support, except for the placement of Melicoccus bijugatus Jacq. Twenty-one clades were recovered, which serve as the basis for a revised infra-familial classification. CONCLUSIONS Twenty tribes are recognized in four subfamilies: two tribes in Hippocastanoideae, two in Dodonaeoideae, and 16 in Sapindoideae (no tribes are recognized in the monotypic subfamily Xanthoceratoideae). Within Sapindoideae, six new tribes are described: Blomieae Buerki & Callm.; Guindilieae Buerki, Callm. & Acev.-Rodr.; Haplocoeleae Buerki & Callm.; Stadmanieae Buerki & Callm.; Tristiropsideae Buerki & Callm.; and Ungnadieae Buerki & Callm. This updated classification provides a backbone for further research and conservation efforts on this family.
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Affiliation(s)
- Sven Buerki
- Department of Biological SciencesBoise State University1910 University DriveBoiseID83725USA
| | - Martin W. Callmander
- Conservatoire et Jardin botaniques de Genèvech. de l’Impératrice 1, CP 711292ChambésySwitzerland
| | - Pedro Acevedo‐Rodriguez
- Department of BotanyNational Museum of Natural HistorySmithsonian InstitutionP.O. Box 37012WashingtonD.C.20013‐7012USA
| | - Porter P. Lowry
- Missouri Botanical Garden4344 Shaw Blvd.St. LouisMissouri63110USA
- Institut de Systématique, Évolution, et Biodiversité (ISYEB)Muséum National d’Histoire NaturelleCentre National de la Recherche ScientifiqueSorbonne UniversitéÉcole Pratique des Hautes ÉtudesUniversité des AntillesC.P. 39, 57 rue Cuvier75005ParisFrance
| | | | - Paul Bailey
- Royal Botanic GardensKew, RichmondSurreyTW9 3AEUK
| | | | | | | | | | - Félix Forest
- Royal Botanic GardensKew, RichmondSurreyTW9 3AEUK
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Pillon Y, Hopkins HCF, Maurin O, Epitawalage N, Bradford J, Rogers ZS, Baker WJ, Forest F. Phylogenomics and biogeography of Cunoniaceae (Oxalidales) with complete generic sampling and taxonomic realignments. Am J Bot 2021; 108:1181-1200. [PMID: 34278558 PMCID: PMC8361763 DOI: 10.1002/ajb2.1688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 11/25/2020] [Accepted: 04/16/2021] [Indexed: 05/28/2023]
Abstract
PREMISE Cunoniaceae are a family of shrubs and trees with 27 genera and ca. 335 species, mostly confined to tropical and wet temperate zones of the southern hemisphere. There are several known issues regarding generic limits, and the family also displays a number of intriguing long-range disjunctions. METHODS We performed a phylogenomic study using the universal Angiosperms353 probe set for targeted sequence capture. We sampled 37 species covering all genera in the Cunoniaceae, and those in the three closely related families of the crown Oxalidales (Brunelliaceae, Cephalotaceae, and Elaeocarpaceae). We also performed analyses for molecular dating and ancestral area reconstruction. RESULTS We recovered the topology (Cunoniaceae, (Cephalotaceae, (Brunelliaceae, Elaeocarpaceae))) and a well-resolved genus-level phylogeny of Cunoniaceae with strongly supported clades corresponding to all previously recognized tribes. As previously suspected, the genera Ackama and Weinmannia were recovered as paraphyletic. Australasia was inferred as the likely ancestral area for the family. CONCLUSIONS The current distribution of Cunoniaceae is best explained by long-distance dispersal with a few possible cases of Australasian-American vicariance events. Extinctions may have been important in determining the mostly Oceanian distribution of this family while some genera in the tribe Cunonieae and in New Caledonia have undergone recent bursts of diversification. New generic diagnoses, 80 new combinations, and one new name are provided for a recircumscribed Ackama (including Spiraeopsis), a much smaller Weinmannia (mostly New World), and a resurrected Pterophylla to accommodate Old World taxa previously in Weinmannia.
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Affiliation(s)
- Yohan Pillon
- LSTMIRDINRAE, CIRADInstitut AgroUniv. MontpellierMontpellierFrance
| | | | | | | | | | - Zachary S. Rogers
- New Mexico State UniversityBox 30003MSC 3‐ILas CrucesNM88003‐8003USA
| | | | - Félix Forest
- Royal Botanic GardensKew, RichmondSurreyTW9 3AEUK
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Pérez-Escobar OA, Dodsworth S, Bogarín D, Bellot S, Balbuena JA, Schley RJ, Kikuchi IA, Morris SK, Epitawalage N, Cowan R, Maurin O, Zuntini A, Arias T, Serna-Sánchez A, Gravendeel B, Torres Jimenez MF, Nargar K, Chomicki G, Chase MW, Leitch IJ, Forest F, Baker WJ. Hundreds of nuclear and plastid loci yield novel insights into orchid relationships. Am J Bot 2021; 108:1166-1180. [PMID: 34250591 DOI: 10.1002/ajb2.1702] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 11/17/2020] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
PREMISE The inference of evolutionary relationships in the species-rich family Orchidaceae has hitherto relied heavily on plastid DNA sequences and limited taxon sampling. Previous studies have provided a robust plastid phylogenetic framework, which was used to classify orchids and investigate the drivers of orchid diversification. However, the extent to which phylogenetic inference based on the plastid genome is congruent with the nuclear genome has been only poorly assessed. METHODS We inferred higher-level phylogenetic relationships of orchids based on likelihood and ASTRAL analyses of 294 low-copy nuclear genes sequenced using the Angiosperms353 universal probe set for 75 species (representing 69 genera, 16 tribes, 24 subtribes) and a concatenated analysis of 78 plastid genes for 264 species (117 genera, 18 tribes, 28 subtribes). We compared phylogenetic informativeness and support for the nuclear and plastid phylogenetic hypotheses. RESULTS Phylogenetic inference using nuclear data sets provides well-supported orchid relationships that are highly congruent between analyses. Comparisons of nuclear gene trees and a plastid supermatrix tree showed that the trees are mostly congruent, but revealed instances of strongly supported phylogenetic incongruence in both shallow and deep time. The phylogenetic informativeness of individual Angiosperms353 genes is in general better than that of most plastid genes. CONCLUSIONS Our study provides the first robust nuclear phylogenomic framework for Orchidaceae and an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely thoroughly documented: nuclear and plastid phylogenetic trees can contain strongly supported discordances, and this incongruence must be reconciled prior to interpretation in evolutionary studies, such as taxonomy, biogeography, and character evolution.
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Affiliation(s)
| | - Steven Dodsworth
- School of Biological Sciences, University of Portsmouth, Portsmouth, PO1 2UP, UK
| | - Diego Bogarín
- Lankester Botanic Garden, University of Costa Rica, Cartago, Costa Rica
| | | | | | | | | | | | | | - Robyn Cowan
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
| | | | | | | | | | | | | | - Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Australia
- National Research Collections, Commonwealth Industrial and Scientific Research Organization, Australia
| | - Guillaume Chomicki
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Mark W Chase
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, 6102, Australia
| | | | - Félix Forest
- Royal Botanic Gardens Kew, Richmond, TW9 3AE, UK
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Baker WJ, Dodsworth S, Forest F, Graham SW, Johnson MG, McDonnell A, Pokorny L, Tate JA, Wicke S, Wickett NJ. Exploring Angiosperms353: An open, community toolkit for collaborative phylogenomic research on flowering plants. Am J Bot 2021; 108:1059-1065. [PMID: 34293179 DOI: 10.1002/ajb2.1703] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/14/2021] [Indexed: 06/13/2023]
Affiliation(s)
| | - Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, University Square, Luton, LU1 3JU, UK
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79409, USA
| | - Angela McDonnell
- Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Jennifer A Tate
- School of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Susann Wicke
- Plant Evolutionary Biology, Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
- Plant Systematics and Biodiversity, Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Norman J Wickett
- Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
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Antonelli A, Clarkson JJ, Kainulainen K, Maurin O, Brewer GE, Davis AP, Epitawalage N, Goyder DJ, Livshultz T, Persson C, Pokorny L, Straub SCK, Struwe L, Zuntini AR, Forest F, Baker WJ. Settling a family feud: a high-level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes. Am J Bot 2021; 108:1143-1165. [PMID: 34254285 DOI: 10.1002/ajb2.1697] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 10/06/2020] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Comprising five families that vastly differ in species richness-ranging from Gelsemiaceae with 13 species to the Rubiaceae with 13,775 species-members of the Gentianales are often among the most species-rich and abundant plants in tropical forests. Despite considerable phylogenetic work within particular families and genera, several alternative topologies for family-level relationships within Gentianales have been presented in previous studies. METHODS Here we present a phylogenomic analysis based on nuclear genes targeted by the Angiosperms353 probe set for approximately 150 species, representing all families and approximately 85% of the formally recognized tribes. We were able to retrieve partial plastomes from off-target reads for most taxa and infer phylogenetic trees for comparison with the nuclear-derived trees. RESULTS We recovered high support for over 80% of all nodes. The plastid and nuclear data are largely in agreement, except for some weakly to moderately supported relationships. We discuss the implications of our results for the order's classification, highlighting points of increased support for previously uncertain relationships. Rubiaceae is sister to a clade comprising (Gentianaceae + Gelsemiaceae) + (Apocynaceae + Loganiaceae). CONCLUSIONS The higher-level phylogenetic relationships within Gentianales are confidently resolved. In contrast to recent studies, our results support the division of Rubiaceae into two subfamilies: Cinchonoideae and Rubioideae. We do not formally recognize Coptosapelteae and Luculieae within any particular subfamily but treat them as incertae sedis. Our framework paves the way for further work on the phylogenetics, biogeography, morphological evolution, and macroecology of this important group of flowering plants.
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Affiliation(s)
- Alexandre Antonelli
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 405 30, Sweden
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | | | - Kent Kainulainen
- Gothenburg Botanical Garden, Carl Skottsbergs gata 22 A, Gothenburg, 413 19, Sweden
| | | | | | | | | | | | - Tatyana Livshultz
- Department of Biodiversity Earth and Environmental Sciences and Academy of Natural Sciences, Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA, 19103, USA
| | - Claes Persson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 405 30, Sweden
| | | | - Shannon C K Straub
- Department of Biology, Hobart and William Smith Colleges, 300 Pulteney Street, Geneva, NY, 14456, USA
| | - Lena Struwe
- Department of Ecology, Evolution, and Natural Resources & Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, NJ, 08901, USA
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Ottenlips MV, Mansfield DH, Buerki S, Feist MAE, Downie SR, Dodsworth S, Forest F, Plunkett GM, Smith JF. Resolving species boundaries in a recent radiation with the Angiosperms353 probe set: the Lomatium packardiae/L. anomalum clade of the L. triternatum (Apiaceae) complex. Am J Bot 2021; 108:1217-1233. [PMID: 34105148 PMCID: PMC8362113 DOI: 10.1002/ajb2.1676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 10/01/2020] [Accepted: 02/26/2021] [Indexed: 05/29/2023]
Abstract
PREMISE Speciation not associated with morphological shifts is challenging to detect unless molecular data are employed. Using Sanger-sequencing approaches, the Lomatium packardiae/L. anomalum subcomplex within the larger Lomatium triternatum complex could not be resolved. Therefore, we attempt to resolve these boundaries here. METHODS The Angiosperms353 probe set was employed to resolve the ambiguity within Lomatium triternatum species complex using 48 accessions assigned to L. packardiae, L. anomalum, or L. triternatum. In addition to exon data, 54 nuclear introns were extracted and were complete for all samples. Three approaches were used to estimate evolutionary relationships and define species boundaries: STACEY, a Bayesian coalescent-based species tree analysis that takes incomplete lineage sorting into account; ASTRAL-III, another coalescent-based species tree analysis; and a concatenated approach using MrBayes. Climatic factors, morphological characters, and soil variables were measured and analyzed to provide additional support for recovered groups. RESULTS The STACEY analysis recovered three major clades and seven subclades, all of which are geographically structured, and some correspond to previously named taxa. No other analysis had full agreement between recovered clades and other parameters. Climatic niche and leaflet width and length provide some predictive ability for the major clades. CONCLUSIONS The results suggest that these groups are in the process of incipient speciation and incomplete lineage sorting has been a major barrier to resolving boundaries within this lineage previously. These results are hypothesized through sequencing of multiple loci and analyzing data using coalescent-based processes.
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Affiliation(s)
| | | | - Sven Buerki
- Department of Biological SciencesBoise State UniversityBoiseID83725USA
| | | | - Stephen R. Downie
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIL61801USA
| | - Steven Dodsworth
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUK
- School of Life SciencesUniversity of BedfordshireLutonLU1 3JUUK
| | - Félix Forest
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUK
| | - Gregory M. Plunkett
- Cullman Program for Molecular SystematicsNew York Botanical Garden2900 Southern BoulevardBronxNY10458USA
| | - James F. Smith
- Department of Biological SciencesBoise State UniversityBoiseID83725USA
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Shah T, Schneider JV, Zizka G, Maurin O, Baker W, Forest F, Brewer GE, Savolainen V, Darbyshire I, Larridon I. Joining forces in Ochnaceae phylogenomics: a tale of two targeted sequencing probe kits. Am J Bot 2021; 108:1201-1216. [PMID: 34180046 DOI: 10.1002/ajb2.1682] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 09/29/2020] [Accepted: 02/23/2021] [Indexed: 05/10/2023]
Abstract
PREMISE Both universal and family-specific targeted sequencing probe kits are becoming widely used for reconstruction of phylogenetic relationships in angiosperms. Within the pantropical Ochnaceae, we show that with careful data filtering, universal kits are equally as capable in resolving intergeneric relationships as custom probe kits. Furthermore, we show the strength in combining data from both kits to mitigate bias and provide a more robust result to resolve evolutionary relationships. METHODS We sampled 23 Ochnaceae genera and used targeted sequencing with two probe kits, the universal Angiosperms353 kit and a family-specific kit. We used maximum likelihood inference with a concatenated matrix of loci and multispecies-coalescence approaches to infer relationships in the family. We explored phylogenetic informativeness and the impact of missing data on resolution and tree support. RESULTS For the Angiosperms353 data set, the concatenation approach provided results more congruent with those of the Ochnaceae-specific data set. Filtering missing data was most impactful on the Angiosperms353 data set, with a relaxed threshold being the optimum scenario. The Ochnaceae-specific data set resolved consistent topologies using both inference methods, and no major improvements were obtained after data filtering. Merging of data obtained with the two kits resulted in a well-supported phylogenetic tree. CONCLUSIONS The Angiosperms353 data set improved upon data filtering, and missing data played an important role in phylogenetic reconstruction. The Angiosperms353 data set resolved the phylogenetic backbone of Ochnaceae as equally well as the family specific data set. All analyses indicated that both Sauvagesia L. and Campylospermum Tiegh. as currently circumscribed are polyphyletic and require revised delimitation.
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Affiliation(s)
- Toral Shah
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Department of Life Sciences, Imperial College, Silwood Park Campus, Ascot, Berks, SL5 7PY, UK
| | - Julio V Schneider
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, Frankfurt am Main, D-60325, Germany
| | - Georg Zizka
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, Frankfurt am Main, D-60325, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, Frankfurt am Main, 60438, Germany
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - William Baker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Grace E Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Vincent Savolainen
- Department of Life Sciences, Imperial College, Silwood Park Campus, Ascot, Berks, SL5 7PY, UK
| | | | - Isabel Larridon
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, K.L., Ledeganckstraat 35, Gent, 9000, Belgium
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McDonnell AJ, Baker WJ, Dodsworth S, Forest F, Graham SW, Johnson MG, Pokorny L, Tate J, Wicke S, Wickett NJ. Exploring Angiosperms353: Developing and applying a universal toolkit for flowering plant phylogenomics. Appl Plant Sci 2021; 9:APS311443. [PMID: 34336400 PMCID: PMC8312743 DOI: 10.1002/aps3.11443] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 06/25/2021] [Indexed: 05/30/2023]
Affiliation(s)
- Angela J. McDonnell
- Negaunee Institute for Plant Conservation Science and ActionChicago Botanic Garden1000 Lake Cook RoadGlencoeIllinois60022USA
| | | | - Steven Dodsworth
- School of Life SciencesUniversity of BedfordshireUniversity SquareLutonLU1 3JUUnited Kingdom
| | - Félix Forest
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
| | - Sean W. Graham
- Department of BotanyUniversity of British Columbia6270 University BoulevardVancouverBritish ColumbiaV6T 1Z4Canada
| | - Matthew G. Johnson
- Department of Biological SciencesTexas Tech UniversityLubbockTexas79409USA
| | - Lisa Pokorny
- Royal Botanic Gardens, KewRichmondSurreyTW9 3AEUnited Kingdom
- Centre for Plant Biotechnology and Genomics (CBGP) UPM‐INIA‐CSIC28223Pozuelo de Alarcón (Madrid)Spain
| | - Jennifer Tate
- School of Fundamental SciencesMassey UniversityPalmerston North4442New Zealand
| | - Susann Wicke
- Plant Evolutionary BiologyInstitute for Evolution and BiodiversityUniversity of MünsterMünsterGermany
- Plant Systematics and BiodiversityInstitute for BiologyHumboldt‐Universität zu BerlinBerlinGermany
| | - Norman J. Wickett
- Negaunee Institute for Plant Conservation Science and ActionChicago Botanic Garden1000 Lake Cook RoadGlencoeIllinois60022USA
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Zuntini AR, Frankel LP, Pokorny L, Forest F, Baker WJ. A comprehensive phylogenomic study of the monocot order Commelinales, with a new classification of Commelinaceae. Am J Bot 2021; 108:1066-1086. [PMID: 34278560 DOI: 10.1002/ajb2.1698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 11/30/2020] [Accepted: 06/02/2021] [Indexed: 05/03/2023]
Abstract
PREMISE Resolving relationships within order Commelinales has posed quite a challenge, as reflected in its unstable infra-familial classification. Thus, we investigated (1) relationships across families and genera of Commelinales; (2) phylogenetic placement of never-before sequenced genera; (3) how well off-target plastid data integrate with other plastid-based data sets; and (4) how the novel inferences coincide with the infra-familial classification. METHODS We generated two large data sets (nuclear and plastome) by means of target sequence capture using the Angiosperms353 probe set, with additional sequences mined from publicly available transcriptomes and full plastomes. A third extended-plastid data set was considered, including all species with sequences in public repositories. Species trees were inferred under a multispecies coalescent framework from individual gene trees and also using maximum likelihood analyses from concatenated and partitioned data. RESULTS The nuclear, plastome, and extended-plastid data sets include 52, 53, and 58 genera, respectively, and up to 290 species of Commelinales, representing the most comprehensive molecular sampling for the order to date, which includes seven never-before sequenced genera. CONCLUSIONS We inferred robust phylogenies supporting the monophyly of Commelinales and its five constituent families, and we recovered the clades Pontederiaceae-Haemodoraceae and Hanguanaceae-Commelinaceae, as previously reported. The placement of Philydraceae remains contentious. Relationships within the two largest families, Commelinaceae and Haemodoraceae, are resolved. Based on the latter results, we confirm the subfamilial classification of Haemodoraceae and propose a new classification for Commelinaceae, which includes the synonymization of Tapheocarpa in Commelina.
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Affiliation(s)
| | - Lorna P Frankel
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Faculty of Life and Environmental Sciences, University of Southampton Highfield Campus, Southampton, SO17 1BJ, UK
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Centre for Plant Biotechnology and Genomics (CBGP UPM - INIA), Autopista M-40, Km 38, Pozuelo de Alarcón (Madrid), 28223, Spain
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Maurin O, Anest A, Bellot S, Biffin E, Brewer G, Charles-Dominique T, Cowan RS, Dodsworth S, Epitawalage N, Gallego B, Giaretta A, Goldenberg R, Gonçalves DJP, Graham S, Hoch P, Mazine F, Low YW, McGinnie C, Michelangeli FA, Morris S, Penneys DS, Pérez Escobar OA, Pillon Y, Pokorny L, Shimizu G, Staggemeier VG, Thornhill AH, Tomlinson KW, Turner IM, Vasconcelos T, Wilson PG, Zuntini AR, Baker WJ, Forest F, Lucas E. A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set. Am J Bot 2021; 108:1087-1111. [PMID: 34297852 DOI: 10.1002/ajb2.1699] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 10/29/2020] [Accepted: 05/29/2021] [Indexed: 06/13/2023]
Abstract
PREMISE To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit. METHODS We combined high-throughput sequencing and target enrichment with the Angiosperms353 probe kit to evaluate a sample of 485 species across 305 genera (76% of all genera in the order). RESULTS Results provide the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks, such as the relationship of the early-diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. Technical considerations for processing HTS data are also discussed. CONCLUSIONS High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events.
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Affiliation(s)
- Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Artemis Anest
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sidonie Bellot
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Edward Biffin
- School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- State Herbarium of South Australia, PO Box 1047, Adelaide, South Australia, 5001, Australia
| | - Grace Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Tristan Charles-Dominique
- Centre National de la Recherche Scientifique (CNRS), Sorbonne University, 4 Place Jussieu, Paris, 75005, France
| | - Robyn S Cowan
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, University Square, Luton, LU1 3JU, UK
| | | | - Berta Gallego
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Augusto Giaretta
- Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados - UFGD, Dourados, MS, Brazil
| | - Renato Goldenberg
- Departamento de Botânica, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | | | | | - Peter Hoch
- Missouri Botanical Garden, St. Louis, MO, 63110, USA
| | - Fiorella Mazine
- Departamento de Ciências Ambientais, Centro de Ciências e Tecnologias para a Sustentabilidade, Universidade Federal de São Carlos - campus Sorocaba, Sorocaba, SP, 18052-780, Brazil
| | - Yee Wen Low
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, 259569, Singapore
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | | | - Fabián A Michelangeli
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY, 10458-5126, USA
| | - Sarah Morris
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Darin S Penneys
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28403, USA
| | | | - Yohan Pillon
- LSTM, IRD, INRAE, CIRAD, Institut Agro, Univ. Montpellier, Montpellier, France
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Centre for Plant Biotechnology and Genomics (CBGP UPM - INIA), Autopista M-40, Km 38, Pozuelo de Alarcón (Madrid), 28223, Spain
| | - Gustavo Shimizu
- Department of Plant Biology, University of Campinas, Campinas, São Paulo, 13083-970, Brazil
| | - Vanessa G Staggemeier
- Departamento de Ecologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078-970, Brazil
| | - Andrew H Thornhill
- School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- State Herbarium of South Australia, PO Box 1047, Adelaide, South Australia, 5001, Australia
| | - Kyle W Tomlinson
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Ian M Turner
- Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, 259569, Singapore
- Singapore Botanical Liaison Officer, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Thais Vasconcelos
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Peter G Wilson
- Royal Botanic Gardens Sydney, Mrs Macquaries Rd, Sydney, NSW, 2000, Australia
| | | | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Eve Lucas
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
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Baker WJ, Bailey P, Barber V, Barker A, Bellot S, Bishop D, Botigué LR, Brewer G, Carruthers T, Clarkson JJ, Cook J, Cowan RS, Dodsworth S, Epitawalage N, Françoso E, Gallego B, Johnson MG, Kim JT, Leempoel K, Maurin O, McGinnie C, Pokorny L, Roy S, Stone M, Toledo E, Wickett NJ, Zuntini AR, Eiserhardt WL, Kersey PJ, Leitch IJ, Forest F. A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life. Syst Biol 2021; 71:301-319. [PMID: 33983440 PMCID: PMC8830076 DOI: 10.1093/sysbio/syab035] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [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: 02/23/2021] [Revised: 05/06/2021] [Accepted: 05/08/2021] [Indexed: 12/22/2022] Open
Abstract
The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this article are to (i) document our methods, (ii) describe our first data release, and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic data set for angiosperms to date, comprising 3099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96\documentclass[12pt]{minimal}
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}{}$\%$\end{document}). A “first pass” angiosperm tree of life was inferred from the data, which totaled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated data set, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone toward a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardized nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections. [Angiosperms; Angiosperms353; genomics; herbariomics; museomics; nuclear phylogenomics; open access; target sequence capture; tree of life.]
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Affiliation(s)
- William J Baker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Paul Bailey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Vanessa Barber
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Abigail Barker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Sidonie Bellot
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - David Bishop
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Laura R Botigué
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Centre for Research in Agricultural Genomics, Campus UAB, Edifici CRAG, Bellaterra Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Grace Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Tom Carruthers
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - James J Clarkson
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Jeffrey Cook
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Robyn S Cowan
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Steven Dodsworth
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,School of Life Sciences, University of Bedfordshire, University Square, Luton LU1 3JU, United Kingdom
| | | | - Elaine Françoso
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Berta Gallego
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Jan T Kim
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Department of Computer Science, School of Physics, Engineering and Computer Science, University of Hertfordshire, Hatfield, Hertfordshire, AL10 9AB, United Kingdom
| | - Kevin Leempoel
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | | | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Centre for Plant Biotechnology and Genomics (CBGP) UPM-INIA, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Shyamali Roy
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Malcolm Stone
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Eduardo Toledo
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Norman J Wickett
- Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL 60022, USA
| | | | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Paul J Kersey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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