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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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Lozinski M, Lumbers ER, Bowden NA, Martin JH, Fay MF, Pringle KG, Tooney PA. Upregulation of the Renin-Angiotensin System Is Associated with Patient Survival and the Tumour Microenvironment in Glioblastoma. Cells 2024; 13:634. [PMID: 38607073 PMCID: PMC11012120 DOI: 10.3390/cells13070634] [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: 02/28/2024] [Revised: 03/29/2024] [Accepted: 04/03/2024] [Indexed: 04/13/2024] Open
Abstract
Glioblastoma is a highly aggressive disease with poor survival outcomes. An emerging body of literature links the role of the renin-angiotensin system (RAS), well-known for its function in the cardiovascular system, to the progression of cancers. We studied the expression of RAS-related genes (ATP6AP2, AGTR1, AGTR2, ACE, AGT, and REN) in The Cancer Genome Atlas (TCGA) glioblastoma cohort, their relationship to patient survival, and association with tumour microenvironment pathways. The expression of RAS genes was then examined in 12 patient-derived glioblastoma cell lines treated with chemoradiation. In cases of glioblastoma within the TCGA, ATP6AP2, AGTR1, ACE, and AGT had consistent expressions across samples, while AGTR2 and REN were lowly expressed. High expression of AGTR1 was independently associated with lower progression-free survival (PFS) (p = 0.01) and had a non-significant trend for overall survival (OS) after multivariate analysis (p = 0.095). The combined expression of RAS receptors (ATP6AP2, AGTR1, and AGTR2) was positively associated with gene pathways involved in hypoxia, microvasculature, stem cell plasticity, and the molecular characterisation of glioblastoma subtypes. In patient-derived glioblastoma cell lines, ATP6AP2 and AGTR1 were upregulated after chemoradiotherapy and correlated with an increase in HIF1A expression. This data suggests the RAS is correlated with changes in the tumour microenvironment and associated with glioblastoma survival outcomes.
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Affiliation(s)
- Mathew Lozinski
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308, Australia; (M.L.); (N.A.B.); (J.H.M.); (M.F.F.)
- Mark Hughes Foundation Centre for Brain Cancer Research, University of Newcastle, Callaghan, NSW 2308, Australia
- Drug Repurposing and Medicines Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Eugenie R. Lumbers
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308, Australia; (E.R.L.); (K.G.P.)
- Mothers and Babies Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Nikola A. Bowden
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308, Australia; (M.L.); (N.A.B.); (J.H.M.); (M.F.F.)
- Drug Repurposing and Medicines Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Jennifer H. Martin
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308, Australia; (M.L.); (N.A.B.); (J.H.M.); (M.F.F.)
- Drug Repurposing and Medicines Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Michael F. Fay
- School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308, Australia; (M.L.); (N.A.B.); (J.H.M.); (M.F.F.)
- Mark Hughes Foundation Centre for Brain Cancer Research, University of Newcastle, Callaghan, NSW 2308, Australia
- Drug Repurposing and Medicines Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
- GenesisCare, Gateshead, NSW 2290, Australia
| | - Kirsty G. Pringle
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308, Australia; (E.R.L.); (K.G.P.)
- Mothers and Babies Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Paul A. Tooney
- Mark Hughes Foundation Centre for Brain Cancer Research, University of Newcastle, Callaghan, NSW 2308, Australia
- Drug Repurposing and Medicines Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW 2308, Australia; (E.R.L.); (K.G.P.)
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3
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Pérez-Escobar OA, Bogarín D, Przelomska NAS, Ackerman JD, Balbuena JA, Bellot S, Bühlmann RP, Cabrera B, Cano JA, Charitonidou M, Chomicki G, Clements MA, Cribb P, Fernández M, Flanagan NS, Gravendeel B, Hágsater E, Halley JM, Hu AQ, Jaramillo C, Mauad AV, Maurin O, Müntz R, Leitch IJ, Li L, Negrão R, Oses L, Phillips C, Rincon M, Salazar GA, Simpson L, Smidt E, Solano-Gomez R, Parra-Sánchez E, Tremblay RL, van den Berg C, Tamayo BSV, Zuluaga A, Zuntini AR, Chase MW, Fay MF, Condamine FL, Forest F, Nargar K, Renner SS, Baker WJ, Antonelli A. The origin and speciation of orchids. New Phytol 2024; 242:700-716. [PMID: 38382573 DOI: 10.1111/nph.19580] [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: 09/04/2023] [Accepted: 12/04/2023] [Indexed: 02/23/2024]
Abstract
Orchids constitute one of the most spectacular radiations of flowering plants. However, their origin, spread across the globe, and hotspots of speciation remain uncertain due to the lack of an up-to-date phylogeographic analysis. We present a new Orchidaceae phylogeny based on combined high-throughput and Sanger sequencing data, covering all five subfamilies, 17/22 tribes, 40/49 subtribes, 285/736 genera, and c. 7% (1921) of the 29 524 accepted species, and use it to infer geographic range evolution, diversity, and speciation patterns by adding curated geographical distributions from the World Checklist of Vascular Plants. The orchids' most recent common ancestor is inferred to have lived in Late Cretaceous Laurasia. The modern range of Apostasioideae, which comprises two genera with 16 species from India to northern Australia, is interpreted as relictual, similar to that of numerous other groups that went extinct at higher latitudes following the global climate cooling during the Oligocene. Despite their ancient origin, modern orchid species diversity mainly originated over the last 5 Ma, with the highest speciation rates in Panama and Costa Rica. These results alter our understanding of the geographic origin of orchids, previously proposed as Australian, and pinpoint Central America as a region of recent, explosive speciation.
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Affiliation(s)
| | - Diego Bogarín
- Lankester Botanical Garden, University of Costa Rica, P.O. Box 302-7050, Cartago, Costa Rica
- Naturalis Biodiversity Centre, Leiden, CR 2333, the Netherlands
| | - Natalia A S Przelomska
- Royal Botanic Gardens, Kew, London, TW9 3AE, UK
- University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - James D Ackerman
- University of Puerto Rico - Rio Piedras, San Juan, PR, 00925-2537, USA
| | | | | | | | - Betsaida Cabrera
- Jardín Botánico Rafael Maria Moscoso, Santo Domingo, 21-9, Dominican Republic
| | | | | | | | - Mark A Clements
- Centre for Australian National Biodiversity Research (joint venture between Parks Australia and CSIRO), GPO Box 1700, Canberra, ACT, 2601, Australia
| | | | - Melania Fernández
- Lankester Botanical Garden, University of Costa Rica, P.O. Box 302-7050, Cartago, Costa Rica
| | - Nicola S Flanagan
- Universidad Pontificia Javeriana, Seccional Cali, Cali, 760031, Colombia
| | | | | | | | - Ai-Qun Hu
- Singapore Botanic Gardens, 1 Cluny Road, Singapore, 257494, Singapore
| | - Carlos Jaramillo
- Smithsonian Tropical Research Institute, Apartado, Panama City, 0843-03092, Panama
| | | | | | - Robert Müntz
- Reserva Biológica Guaitil, Eisenstadt, 7000, Austria
| | | | - Lan Li
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), GPO Box 1700, Canberra, ACT, 2601, Australia
| | | | - Lizbeth Oses
- Lankester Botanical Garden, University of Costa Rica, P.O. Box 302-7050, Cartago, Costa Rica
| | - Charlotte Phillips
- Royal Botanic Gardens, Kew, London, TW9 3AE, UK
- University of Portsmouth, Portsmouth, PO1 2DY, UK
| | - Milton Rincon
- Jardín Botánico Jose Celestino Mutis, Bogota, 111071, Colombia
| | | | - Lalita Simpson
- Australian Tropical Herbarium, James Cook University, GPO Box 6811, Cairns, Qld, 4878, Australia
| | - Eric Smidt
- Universidade Federal do Paraná, Curitiba, 19031, Brazil
| | | | | | | | - Cassio van den Berg
- Universidade Estadual de Feira de Santana, Feira de Santana, 44036-900, Brazil
| | | | | | | | - Mark W Chase
- Royal Botanic Gardens, Kew, London, TW9 3AE, UK
- Department of Environment and Agriculture, Curtin University, Perth, WA, 6102, Australia
| | | | - Fabien L Condamine
- Institut des Sciences de l'Evolution de Montpellier (Université de Montpellier|CNRS|IRD|EPHE), Place Eugène Bataillon, Montpellier, 34000, France
| | | | - Katharina Nargar
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organisation (CSIRO), GPO Box 1700, Canberra, ACT, 2601, Australia
- Australian Tropical Herbarium, James Cook University, GPO Box 6811, Cairns, Qld, 4878, Australia
- Scientific Research Organisation (CSIRO), GPO Box 1700, Canberra, ACT, 2601, Australia
| | | | | | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, London, TW9 3AE, UK
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, Gothenburg, 417 56, Sweden
- University of Gothenburg, Gothenburg, 417 56, Sweden
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
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4
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Hochkirch A, Bilz M, Ferreira CC, Danielczak A, Allen D, Nieto A, Rondinini C, Harding K, Hilton-Taylor C, Pollock CM, Seddon M, Vié JC, Alexander KN, Beech E, Biscoito M, Braud Y, Burfield IJ, Buzzetti FM, Cálix M, Carpenter KE, Chao NL, Chobanov D, Christenhusz MJM, Collette BB, Comeros-Raynal MT, Cox N, Craig M, Cuttelod A, Darwall WRT, Dodelin B, Dulvy NK, Englefield E, Fay MF, Fettes N, Freyhof J, García S, Criado MG, Harvey M, Hodgetts N, Ieronymidou C, Kalkman VJ, Kell SP, Kemp J, Khela S, Lansdown RV, Lawson JM, Leaman DJ, Brehm JM, Maxted N, Miller RM, Neubert E, Odé B, Pollard D, Pollom R, Pople R, Presa Asensio JJ, Ralph GM, Rankou H, Rivers M, Roberts SPM, Russell B, Sennikov A, Soldati F, Staneva A, Stump E, Symes A, Telnov D, Temple H, Terry A, Timoshyna A, van Swaay C, Väre H, Walls RHL, Willemse L, Wilson B, Window J, Wright EGE, Zuna-Kratky T. A multi-taxon analysis of European Red Lists reveals major threats to biodiversity. PLoS One 2023; 18:e0293083. [PMID: 37939028 PMCID: PMC10631624 DOI: 10.1371/journal.pone.0293083] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 10/04/2023] [Indexed: 11/10/2023] Open
Abstract
Biodiversity loss is a major global challenge and minimizing extinction rates is the goal of several multilateral environmental agreements. Policy decisions require comprehensive, spatially explicit information on species' distributions and threats. We present an analysis of the conservation status of 14,669 European terrestrial, freshwater and marine species (ca. 10% of the continental fauna and flora), including all vertebrates and selected groups of invertebrates and plants. Our results reveal that 19% of European species are threatened with extinction, with higher extinction risks for plants (27%) and invertebrates (24%) compared to vertebrates (18%). These numbers exceed recent IPBES (Intergovernmental Platform on Biodiversity and Ecosystem Services) assumptions of extinction risk. Changes in agricultural practices and associated habitat loss, overharvesting, pollution and development are major threats to biodiversity. Maintaining and restoring sustainable land and water use practices is crucial to minimize future biodiversity declines.
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Affiliation(s)
- Axel Hochkirch
- Musée National d’Histoire Naturelle, Luxembourg, Luxembourg
- Department of Biogeography, Trier University, Trier, Germany
- IUCN SSC Invertebrate Conservation Committee, Trier, Germany
- IUCN SSC Steering Committee, Caracas, Venezuela
- IUCN SSC Grasshopper Specialist Group, Trier, Germany
| | - Melanie Bilz
- Institute of Landscape Architecture and Environmental Planning, Technische Universität Berlin, Berlin, Germany
- IUCN SSC Freshwater Plant Specialist Group, Stroud, United Kingdom
- IUCN European Regional Office, Brussels, Belgium
| | - Catarina C. Ferreira
- IUCN European Regional Office, Brussels, Belgium
- UFZ—Helmholtz Centre for Environmental Research, Department of Conservation Biology, Leipzig, Germany
| | - Anja Danielczak
- Department of Biogeography, Trier University, Trier, Germany
| | - David Allen
- IUCN, Biodiversity Assessment and Knowledge Team, Cambridge, United Kingdom
| | - Ana Nieto
- IUCN European Regional Office, Brussels, Belgium
- IUCN, Species Conservation Action Team, Gland, Switzerland
| | - Carlo Rondinini
- Global Mammal Assessment program, Department of Biology and Biotechnologies, Sapienza University of Rome; Rome, Italy
- Global Wildlife Conservation Center, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States of America
| | - Kate Harding
- IUCN, Biodiversity Assessment and Knowledge Team, Cambridge, United Kingdom
| | | | | | - Mary Seddon
- IUCN SSC Invertebrate Conservation Committee, Trier, Germany
- IUCN SSC Mollusc Specialist Group, Devon, United Kingdom
| | - Jean-Christophe Vié
- IUCN SSC Steering Committee, Caracas, Venezuela
- Fondation Franklinia, Genève, Switzerland
- IUCN SSC Plant Conservation Committee, Pretoria, South Africa
| | | | - Emily Beech
- Botanic Gardens Conservation International, Richmond, United Kingdom
| | - Manuel Biscoito
- Funchal Natural History Museum, Funchal, Portugal
- MARE-Marine and Environmental Sciences Centre, Lisboa, Portugal
| | - Yoan Braud
- IUCN SSC Grasshopper Specialist Group, Trier, Germany
| | - Ian J. Burfield
- BirdLife International, Cambridge, United Kingdom
- IUCN SSC Red List Authority for Birds, Cambridge, United Kingdom
| | - Filippo Maria Buzzetti
- IUCN SSC Grasshopper Specialist Group, Trier, Germany
- Fondazione Museo Civico di Rovereto, Sezione Zoologia, Rovereto, Italy
| | - Marta Cálix
- IUCN European Regional Office, Brussels, Belgium
- Rewilding Portugal, Guarda, Portugal
| | - Kent E. Carpenter
- IUCN Marine Biodiversity Unit, Biological Sciences, Norfolk, VA, United States of America
| | | | - Dragan Chobanov
- IUCN SSC Grasshopper Specialist Group, Trier, Germany
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | - Bruce B. Collette
- IUCN Tuna and Billfish Specialist Group, National Museum of Natural History, Washington, DC, United States of America
| | - Mia T. Comeros-Raynal
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia
- Water Resources Research Center, University of Hawai’i, Honolulu, HI, United States of America
| | - Neil Cox
- IUCN-Conservation International Biodiversity Assessment Unit, Washington, DC, United States of America
| | - Matthew Craig
- National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Southwest Fisheries Science Center, La Jolla, CA, United States of America
| | - Annabelle Cuttelod
- IUCN Red List Unit, IUCN Global Species Programme, Cambridge, United Kingdom
| | | | - Benoit Dodelin
- IUCN Specialist Adviser on European Saproxylic Beetles, Truro, United Kingdom
| | - Nicholas K. Dulvy
- Earth to Ocean Research Group, Department of Biological Sciences, Simon Fraser University, Burnaby, Canada
| | - Eve Englefield
- IUCN European Regional Office, Brussels, Belgium
- Joint Nature Conservation Committee, Peterborough, United Kingdom
| | - Michael F. Fay
- IUCN SSC Orchid Specialist Group, Royal Botanic Gardens; Richmond, United Kingdom
| | - Nicholas Fettes
- IUCN European Regional Office, Brussels, Belgium
- Scott Cawley, Dublin, Ireland
| | - Jörg Freyhof
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | | | - Mariana García Criado
- IUCN European Regional Office, Brussels, Belgium
- School of Geosciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Michael Harvey
- IUCN Marine Biodiversity Unit, Biological Sciences, Norfolk, VA, United States of America
| | - Nick Hodgetts
- European Committee for the Conservation of Bryophytes, Portree, United Kingdom
| | | | | | - Shelagh P. Kell
- The University of Birmingham, School of Biosciences, Birmingham, United Kingdom
| | - James Kemp
- IUCN European Regional Office, Brussels, Belgium
| | - Sonia Khela
- IUCN SSC Cave Invertebrate Specialist Group, Cambridge, United Kingdom
| | | | - Julia M. Lawson
- IUCN Red List Unit, IUCN Global Species Programme, Cambridge, United Kingdom
- Bren School of Environmental Science & Management, University of California, Santa Barbara, Santa Barbara, CA, United States of America
| | | | - Joana Magos Brehm
- The University of Birmingham, School of Biosciences, Birmingham, United Kingdom
- IUCN SSC Crop Wild Relative Specialist Group, Birmingham, United Kingdom
| | - Nigel Maxted
- The University of Birmingham, School of Biosciences, Birmingham, United Kingdom
| | - Rebecca M. Miller
- IUCN Red List Unit, IUCN Global Species Programme, Cambridge, United Kingdom
| | | | - Baudewijn Odé
- IUCN SSC Grasshopper Specialist Group, Trier, Germany
- FLORON Plant Conservation Netherlands, Nijmegen, Netherlands
| | - David Pollard
- Department of Ichthyology, Australian Museum, Sydney, Australia
| | - Riley Pollom
- Species Recovery Program, Seattle Aquarium, Seattle, WA, United States of America
| | - Rob Pople
- BirdLife International, Cambridge, United Kingdom
| | | | - Gina M. Ralph
- IUCN Marine Biodiversity Unit, Biological Sciences, Norfolk, VA, United States of America
| | - Hassan Rankou
- IUCN SSC Orchid Specialist Group, Royal Botanic Gardens; Richmond, United Kingdom
| | - Malin Rivers
- Botanic Gardens Conservation International, Richmond, United Kingdom
- IUCN SSC Global Tree Specialist Group, Richmond, United Kingdom
| | - Stuart P. M. Roberts
- Department of Agroecology, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Barry Russell
- IUCN Snapper, Seabream and Grunt Specialist Group, Museum and Art Gallery of the Northern Territory, Darwin, Australia
| | - Alexander Sennikov
- Botanical Museum, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Fabien Soldati
- Office National des Forêts, Laboratoire National d’Entomologie Forestière, Quillan, France
| | - Anna Staneva
- BirdLife International, Cambridge, United Kingdom
| | - Emilie Stump
- IUCN Marine Biodiversity Unit, Biological Sciences, Norfolk, VA, United States of America
| | - Andy Symes
- BirdLife International, Cambridge, United Kingdom
| | - Dmitry Telnov
- Natural History Museum, Department of Life Sciences, London, United Kingdom
- Coleopterological Research Center, Institute of Life Sciences and Technology, Daugavpils University, Daugavpils, Latvia
- Institute of Biology, University of Latvia, Rīga, Latvia
| | - Helen Temple
- The Biodiversity Consultancy, Cambridge, United Kingdom
| | - Andrew Terry
- Zoological Society of London, London, United Kingdom
| | - Anastasiya Timoshyna
- IUCN SSC Medicinal Plant Specialist Group, Ottawa, Canada
- TRAFFIC, Cambridge, United Kingdom
| | - Chris van Swaay
- Vlinderstichting (Dutch Butterfly Conservation), Wageningen, Netherlands
| | - Henry Väre
- Botanical Museum, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Rachel H. L. Walls
- Reef Environmental Education Foundation, Key Largo, FL, United States of America
| | - Luc Willemse
- IUCN SSC Grasshopper Specialist Group, Trier, Germany
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Brett Wilson
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Jemma Window
- IUCN, Biodiversity Assessment and Knowledge Team, Cambridge, United Kingdom
| | | | - Thomas Zuna-Kratky
- IUCN SSC Grasshopper Specialist Group, Trier, Germany
- Ingenieurbüro für Landschaftsplanung und Landschaftspflege, Vienna, Austria
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5
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Christenhusz MJM, Fay MF. The genome sequence of common fleabane, Pulicaria dysenterica (L.) Bernh. (Asteraceae). Wellcome Open Res 2023; 8:447. [PMID: 38009086 PMCID: PMC10674090 DOI: 10.12688/wellcomeopenres.20003.1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2023] [Indexed: 11/28/2023] Open
Abstract
We present a genome assembly from an individual Pulicaria dysenterica (common fleabane; Tracheophyta; Magnoliopsida; Asterales; Asteraceae). The genome sequence is 833.2 megabases in span. Most of the assembly is scaffolded into 9 chromosomal pseudomolecules. The mitochondrial and plastid genomes were assembled and have lengths of 375.47 kilobases and 150.94 kilobases respectively.
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6
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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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7
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Gargiulo R, Waples RS, Grow AK, Shefferson RP, Viruel J, Fay MF, Kull T. Effective population size in a partially clonal plant is not predicted by the number of genetic individuals. Evol Appl 2023; 16:750-766. [PMID: 36969138 PMCID: PMC10033856 DOI: 10.1111/eva.13535] [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: 07/07/2022] [Revised: 11/22/2022] [Accepted: 02/02/2023] [Indexed: 02/23/2023] Open
Abstract
Estimating effective population size (N e) is important for theoretical and practical applications in evolutionary biology and conservation. Nevertheless, estimates of N e in organisms with complex life-history traits remain scarce because of the challenges associated with estimation methods. Partially clonal plants capable of both vegetative (clonal) growth and sexual reproduction are a common group of organisms for which the discrepancy between the apparent number of individuals (ramets) and the number of genetic individuals (genets) can be striking, and it is unclear how this discrepancy relates to N e. In this study, we analysed two populations of the orchid Cypripedium calceolus to understand how the rate of clonal versus sexual reproduction affected N e. We genotyped >1000 ramets at microsatellite and SNP loci, and estimated contemporary N e with the linkage disequilibrium method, starting from the theoretical expectation that variance in reproductive success among individuals caused by clonal reproduction and by constraints on sexual reproduction would lower N e. We considered factors potentially affecting our estimates, including different marker types and sampling strategies, and the influence of pseudoreplication in genomic data sets on N e confidence intervals. The magnitude of N e/N ramets and N e/N genets ratios we provide may be used as reference points for other species with similar life-history traits. Our findings demonstrate that N e in partially clonal plants cannot be predicted based on the number of genets generated by sexual reproduction, because demographic changes over time can strongly influence N e. This is especially relevant in species of conservation concern in which population declines may not be detected by only ascertaining the number of genets.
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Affiliation(s)
| | - Robin S. Waples
- NOAA Fisheries, Northwest Fisheries Science Center Seattle Washington USA
- University of Washington Seattle Washington USA
| | - Adri K. Grow
- Department of Biological Sciences Smith College Northampton Massachusetts USA
| | | | | | - Michael F. Fay
- Royal Botanic Gardens, Kew Richmond UK
- School of Biological Sciences University of Western Australia Crawley Western Australia Australia
| | - Tiiu Kull
- Estonian University of Life Sciences Tartu Estonia
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8
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Song AJ, Ding K, Alnahhas I, Laperriere NJ, Perry J, Mason WP, Winch C, O'Callaghan CJ, Menten JJ, Brandes AA, Phillips C, Fay MF, Nishikawa R, Osoba D, Cairncross JG, Roa W, Wick W, Shi W. Corrigendum to: Impact of lymphopenia on survival for elderly patients with glioblastoma: A secondary analysis of the CCTG CE.6 (EORTC 26062-22061, TROG 08.02) randomized clinical trial. Neurooncol Adv 2022; 4:vdac011. [PMID: 35098127 PMCID: PMC8794587 DOI: 10.1093/noajnl/vdac011] [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] [Indexed: 11/14/2022] Open
Affiliation(s)
- Andrew J Song
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Keyue Ding
- Department of Public Health Sciences, Canadian Cancer Trials Group, Queen's University, Kingston, Ontario, Canada
| | - Iyad Alnahhas
- Department of Neurological Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Normand J Laperriere
- Department of Radiation Oncology, Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - James Perry
- Department of Medicine, Division of Neurology, University of Toronto, Toronto, Ontario, Canada
| | - Warren P Mason
- Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Chad Winch
- Department of Public Health Sciences, Canadian Cancer Trials Group, Queen's University, Kingston, Ontario, Canada
| | - Chris J O'Callaghan
- Department of Public Health Sciences, Canadian Cancer Trials Group, Queen's University, Kingston, Ontario, Canada
| | - Johan J Menten
- Department of Experimental Radiation Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Alba A Brandes
- Department of Medical oncology, IRCCS Istituto Scienze Neurologiche - Bologna, Italy
| | - Claire Phillips
- Department of Radiation Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Ryo Nishikawa
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, Hidaka, Japan
| | - David Osoba
- QOL Consulting, West Vancouver, British Columbia, Canada
| | - J Gregory Cairncross
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
| | - Wilson Roa
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Wolfgang Wick
- Division of Neurology, Heidelberg University Medical Center, Clinical Cooperation Unit Neurooncology, German Cancer Research Center, Heidelberg, Germany
| | - Wenyin Shi
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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9
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Pellicer J, Fernández P, Fay MF, Michálková E, Leitch IJ. Corrigendum: Genome Size Doubling Arises From the Differential Repetitive DNA Dynamics in the Genus Heloniopsis (Melanthiaceae). Front Genet 2021; 12:799661. [PMID: 34804134 PMCID: PMC8595389 DOI: 10.3389/fgene.2021.799661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jaume Pellicer
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain.,Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Pol Fernández
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | - Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, United Kingdom.,School of Plant Biology, University of Western Australia, Crawley, WA, Australia
| | - Ester Michálková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
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10
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Song AJ, Ding K, Alnahhas I, Laperriere NJ, Perry J, Mason WP, Winch C, O'Callaghan CJ, Menten JJ, Brandes AA, Phillips C, Fay MF, Nishikawa R, Osoba D, Cairncross JG, Roa W, Wick W, Shi W. Impact of lymphopenia on survival for elderly patients with glioblastoma: A secondary analysis of the CCTG CE.6 (EORTC 26062-22061, TROG03.01) randomized clinical trial. Neurooncol Adv 2021; 3:vdab153. [PMID: 34765975 PMCID: PMC8577525 DOI: 10.1093/noajnl/vdab153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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] [Indexed: 12/22/2022] Open
Abstract
Background Lymphopenia may lead to worse outcomes for glioblastoma patients. This study is a secondary analysis of the CCTG CE.6 trial evaluating the impact of chemotherapy and radiation on lymphopenia, and effects of lymphopenia on overall survival (OS). Methods CCTG CE.6 randomized elderly glioblastoma patients (≥ 65 years) to short-course radiation alone (RT) or short-course radiation with temozolomide (RT + TMZ). Lymphopenia (mild-moderate: grade 1–2; severe: grade 3–4) was defined per CTCAE v3.0, and measured at baseline, 1 week and 4 weeks post-RT. Preselected key factors for analysis included age, sex, ECOG, resection extent, MGMT methylation, Mini-Mental State Examination, and steroid use. Multinomial logistic regression and multivariable Cox regression models were used to identify lymphopenia-associated factors and association with survival. Results Five hundred and sixty-two patients were analyzed (281 RT vs 281 RT+TMZ). At baseline, both arms had similar rates of mild-moderate (21.4% vs 21.4%) and severe (3.2% vs 2.9%) lymphopenia. However, at 4 weeks post-RT, RT+TMZ was more likely to develop lymphopenia (mild-moderate: 27.9% vs 18.2%; severe: 9.3% vs 1.8%; p<0.001). Developing any lymphopenia post-RT was associated with baseline lymphopenia (P < .001). Baseline lymphopenia (hazard ratio [HR] 1.3) was associated with worse OS (HR: 1.30, 95% confidence interval [CI] 1.05–1.62; P = .02), regardless of MGMT status. Conclusions Development of post-RT lymphopenia is associated with addition of TMZ and baseline lymphopenia and not with RT alone in patients treated with short-course radiation. However, regardless of MGMT status, only baseline lymphopenia is associated with worse OS, which may be considered as a prognostic biomarker for elderly glioblastoma patients.
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Affiliation(s)
- Andrew J Song
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Keyue Ding
- Department of Public Health Sciences, Canadian Cancer Trials Group, Queen's University, Kingston, Ontario, Canada
| | - Iyad Alnahhas
- Department of Neurological Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Normand J Laperriere
- Department of Radiation Oncology, Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - James Perry
- Department of Medicine, Division of Neurology, University of Toronto, Toronto, Ontario, Canada
| | - Warren P Mason
- Department of Medicine, Princess Margaret Cancer Centre, University of Toronto, Toronto, Ontario, Canada
| | - Chad Winch
- Department of Public Health Sciences, Canadian Cancer Trials Group, Queen's University, Kingston, Ontario, Canada
| | - Chris J O'Callaghan
- Department of Public Health Sciences, Canadian Cancer Trials Group, Queen's University, Kingston, Ontario, Canada
| | - Johan J Menten
- Department of Experimental Radiation Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Alba A Brandes
- Department of Medical oncology, IRCCS Istituto Scienze Neurologiche - Bologna, Italy
| | - Claire Phillips
- Department of Radiation Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Ryo Nishikawa
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, Hidaka, Japan
| | - David Osoba
- QOL Consulting, West Vancouver, British Columbia, Canada
| | - J Gregory Cairncross
- Department of Clinical Neurosciences, University of Calgary, Calgary, Alberta, Canada
| | - Wilson Roa
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Wolfgang Wick
- Division of Neurology, Heidelberg University Medical Center, Clinical Cooperation Unit Neurooncology, German Cancer Research Center, Heidelberg, Germany
| | - Wenyin Shi
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
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11
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Pellicer J, Fernández P, Fay MF, Michálková E, Leitch IJ. Genome Size Doubling Arises From the Differential Repetitive DNA Dynamics in the Genus Heloniopsis (Melanthiaceae). Front Genet 2021; 12:726211. [PMID: 34552621 PMCID: PMC8450539 DOI: 10.3389/fgene.2021.726211] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/19/2021] [Indexed: 12/23/2022] Open
Abstract
Plant genomes are highly diverse in size and repetitive DNA composition. In the absence of polyploidy, the dynamics of repetitive elements, which make up the bulk of the genome in many species, are the main drivers underpinning changes in genome size and the overall evolution of the genomic landscape. The advent of high-throughput sequencing technologies has enabled investigation of genome evolutionary dynamics beyond model plants to provide exciting new insights in species across the biodiversity of life. Here we analyze the evolution of repetitive DNA in two closely related species of Heloniopsis (Melanthiaceae), which despite having the same chromosome number differ nearly twofold in genome size [i.e., H. umbellata (1C = 4,680 Mb), and H. koreana (1C = 2,480 Mb)]. Low-coverage genome skimming and the RepeatExplorer2 pipeline were used to identify the main repeat families responsible for the significant differences in genome sizes. Patterns of repeat evolution were found to correlate with genome size with the main classes of transposable elements identified being twice as abundant in the larger genome of H. umbellata compared with H. koreana. In addition, among the satellite DNA families recovered, a single shared satellite (HeloSAT) was shown to have contributed significantly to the genome expansion of H. umbellata. Evolutionary changes in repetitive DNA composition and genome size indicate that the differences in genome size between these species have been underpinned by the activity of several distinct repeat lineages.
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Affiliation(s)
- Jaume Pellicer
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain.,Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Pol Fernández
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | - Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, United Kingdom.,School of Plant Biology, University of Western Australia, Crawley, WA, Australia
| | | | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
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12
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Gargiulo R, Adamo M, Cribb PJ, Bartolucci F, Sarasan V, Alessandrelli C, Bona E, Ciaschetti G, Conti F, Di Cecco V, Di Martino L, Gentile C, Juan A, Magrini S, Mucciarelli M, Perazza G, Fay MF. Combining current knowledge of
Cypripedium calceolus
with a new analysis of genetic variation in Italian populations to provide guidelines for conservation actions. Conservat Sci and Prac 2021. [DOI: 10.1111/csp2.513] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
| | - Martino Adamo
- Department of Life Sciences and Systems Biology Università di Torino Torino Italy
| | | | - Fabrizio Bartolucci
- Floristic Research Center of the Apennine (University of Camerino – Gran Sasso and Laga Mountains National Park) Barisciano (L'Aquila) Italy
| | | | | | - Enzo Bona
- Centro Studi Naturalistici Bresciani, Museo di Scienze Naturali Brescia (BS) Italy
| | - Giampiero Ciaschetti
- Maiella National Park – Office for Plant Biodiversity Monitoring and Conservation Sulmona (AQ) Italy
| | - Fabio Conti
- Floristic Research Center of the Apennine (University of Camerino – Gran Sasso and Laga Mountains National Park) Barisciano (L'Aquila) Italy
| | - Valter Di Cecco
- Maiella National Park – Office for Plant Biodiversity Monitoring and Conservation Sulmona (AQ) Italy
| | - Luciano Di Martino
- Maiella National Park – Office for Plant Biodiversity Monitoring and Conservation Sulmona (AQ) Italy
| | - Carmelo Gentile
- Abruzzo, Lazio and Molise National Park viale Santa Lucia Pescasseroli (AQ) Italy
| | - Ana Juan
- Ciencias Ambientales y Recursos Naturales University of Alicante Alicante Spain
| | - Sara Magrini
- Tuscia Germplasm Bank, Tuscia University, largo dell'Università blocco C Viterbo Italy
| | - Marco Mucciarelli
- Department of Life Sciences and Systems Biology Università di Torino Torino Italy
| | | | - Michael F. Fay
- Royal Botanic Gardens, Kew Richmond United Kingdom
- School of Plant Biology, University of Western Australia Crawley Western Australia Australia
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13
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Papadopulos AST, Helmstetter AJ, Osborne OG, Comeault AA, Wood DP, Straw EA, Mason L, Fay MF, Parker J, Dunning LT, Foote AD, Smith RJ, Lighten J. Rapid Parallel Adaptation to Anthropogenic Heavy Metal Pollution. Mol Biol Evol 2021; 38:3724-3736. [PMID: 33950261 PMCID: PMC8382892 DOI: 10.1093/molbev/msab141] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The impact of human-mediated environmental change on the evolutionary trajectories of wild organisms is poorly understood. In particular, capacity of species to adapt rapidly (in hundreds of generations or less), reproducibly and predictably to extreme environmental change is unclear. Silene uniflora is predominantly a coastal species, but it has also colonized isolated, disused mines with phytotoxic, zinc-contaminated soils. To test whether rapid, parallel adaptation to anthropogenic pollution has taken place, we used reduced representation sequencing (ddRAD) to reconstruct the evolutionary history of geographically proximate mine and coastal population pairs and found largely independent colonization of mines from different coastal sites. Furthermore, our results show that parallel evolution of zinc tolerance has occurred without gene flow spreading adaptive alleles between mine populations. In genomic regions where signatures of selection were detected across multiple mine-coast pairs, we identified genes with functions linked to physiological differences between the putative ecotypes, although genetic differentiation at specific loci is only partially shared between mine populations. Our results are consistent with a complex, polygenic genetic architecture underpinning rapid adaptation. This shows that even under a scenario of strong selection and rapid adaptation, evolutionary responses to human activities (and other environmental challenges) may be idiosyncratic at the genetic level and, therefore, difficult to predict from genomic data.
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Affiliation(s)
- Alexander S T Papadopulos
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Andrew J Helmstetter
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- FRB-CESAB, Institut Bouisson Bertrand, Rue de l'École de Médecine, Montpellier, France
| | - Owen G Osborne
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Aaron A Comeault
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Daniel P Wood
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Edward A Straw
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Centre for Ecology, Evolution & Behaviour, Department of Biological Sciences, School for Life Sciences and the Environment, Royal Holloway University of London, Egham, United Kingdom
| | | | - Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- School of Plant Biology, University of Western Australia, Crawley, WA, Australia
| | - Joe Parker
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- National Biofilms Innovation Centre, Department of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Luke T Dunning
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Andrew D Foote
- Molecular Ecology and Evolution Bangor, Environment Centre Wales, School of Natural Sciences, Bangor University, Bangor, United Kingdom
- Department of Natural History, Norwegian University of Science and Technology, NTNU University Museum, Trondheim, Norway
| | - Rhian J Smith
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Jackie Lighten
- Biosciences, University of Exeter, Exeter, United Kingdom
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14
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Bersweden L, Viruel J, Schatz B, Harland J, Gargiulo R, Cowan RS, Calevo J, Juan A, Clarkson JJ, Leitch AR, Fay MF. Microsatellites and petal morphology reveal new patterns of admixture in Orchis hybrid zones. Am J Bot 2021; 108:1388-1404. [PMID: 34418070 DOI: 10.1002/ajb2.1710] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 09/30/2020] [Revised: 02/20/2021] [Accepted: 02/23/2021] [Indexed: 05/23/2023]
Abstract
PREMISE The genetic structure of hybrid zones provides insight into the potential for gene flow to occur between plant taxa. Four closely related European orchid species (Orchis anthropophora, O. militaris, O. purpurea, and O. simia) hybridize when they co-occur. We aimed to characterize patterns of hybridization in O. militaris-O. purpurea, O. purpurea-O. simia, and O. anthropophora-O. simia hybrid zones using molecular and morphological data. METHODS We used 11 newly isolated nuclear microsatellites to genotype 695 individuals collected from seven hybrid zones and six allopatric parental populations in France. Geometric morphometric analysis was conducted using 15 labellum landmarks to capture the main aspects of petal shape. RESULTS Backcrossing was asymmetric toward O. militaris in multiple O. militaris-O. purpurea hybrid zones. Hybrids in O. purpurea-O. simia and O. anthropophora-O. simia hybrid zones were largely limited to F1 and F2 generations, but further admixture had occurred. These patterns were reflected in labellum geometric morphometric data, which correlated strongly with nuclear microsatellite data in all three species combinations. CONCLUSIONS The coexistence of parental and admixed individuals in these Orchis hybrid zones implies they are likely to be tension zones being maintained by a balance between gene flow into the hybrid zone and selection acting against admixed individuals. The pattern of admixture in the three species combinations suggests intrinsic selection acting on the hybrids is weaker in more closely related taxa.
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Affiliation(s)
- Leif Bersweden
- Jodrell Laboratory, Royal Botanic Gardens, Kew TW9 3DS, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Juan Viruel
- Jodrell Laboratory, Royal Botanic Gardens, Kew TW9 3DS, UK
| | - Bertrand Schatz
- Centre for Ecology and Evolution, University of Montpellier, Montpellier 34090, France
| | - Joanna Harland
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | | | - Robyn S Cowan
- Jodrell Laboratory, Royal Botanic Gardens, Kew TW9 3DS, UK
| | - Jacopo Calevo
- Department of Life Sciences and Systems Biology, University of Turin, Turin 10125, Italy
| | - Ana Juan
- Department of Environmental Sciences & Natural Resources, University of Alicante, San Vicente, Alicante 03690, Spain
| | | | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Michael F Fay
- Jodrell Laboratory, Royal Botanic Gardens, Kew TW9 3DS, UK
- School of Plant Biology, University of Western Australia, Crawley, WA 6009, Australia
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15
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Christenhusz MJM, Chase MW, Fay MF, Hidalgo O, Leitch IJ, Pellicer J, Viruel J. Biogeography and genome size evolution of the oldest extant vascular plant genus, Equisetum (Equisetaceae). Ann Bot 2021; 127:681-695. [PMID: 33598697 PMCID: PMC8052921 DOI: 10.1093/aob/mcab005] [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: 05/15/2020] [Accepted: 01/09/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Extant plant groups with a long fossil history are key elements in understanding vascular plant evolution. Horsetails (Equisetum, Equisetaceae) have a nearly continuous fossil record dating back to the Carboniferous, but their phylogenetic and biogeographic patterns are still poorly understood. We use here the most extensive phylogenetic analysis to date as a framework to evaluate their age, biogeography and genome size evolution. METHODS DNA sequences of four plastid loci were used to estimate divergence times and investigate the biogeographic history of all extant species of Equisetum. Flow cytometry was used to study genome size evolution against the framework of phylogenetic relationships in Equisetum. KEY RESULTS On a well-supported phylogenetic tree including all extant Equisetum species, a molecular clock calibrated with multiple fossils places the node at which the outgroup and Equisetum diverged at 343 Mya (Early Carboniferous), with the first major split among extant species occurring 170 Mya (Middle Jurassic). These dates are older than those reported in some other recent molecular clock studies but are largely in agreement with a timeline established by fossil appearance in the geological record. Representatives of evergreen subgenus Hippochaete have much larger genome sizes than those of deciduous subgenus Equisetum, despite their shared conserved chromosome number. Subgenus Paramochaete has an intermediate genome size and maintains the same number of chromosomes. CONCLUSIONS The first divergences among extant members of the genus coincided with the break-up of Pangaea and the resulting more humid, warmer climate. Subsequent tectonic activity most likely involved vicariance events that led to species divergences combined with some more recent, long-distance dispersal events. We hypothesize that differences in genome size between subgenera may be related to the number of sperm flagellae.
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Affiliation(s)
- Maarten J M Christenhusz
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Mark W Chase
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Environment and Agriculture, Curtin University, Perth, WA, Australia
| | - Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, UK
- School of Biological Sciences, The University of Western Australia, Perth WA, Australia
| | - Oriane Hidalgo
- Royal Botanic Gardens, Kew, Richmond, UK
- Laboratori de Botànica, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Barcelona, Spain
| | | | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Richmond, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
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16
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Gargiulo R, Kull T, Fay MF. Effective double-digest RAD sequencing and genotyping despite large genome size. Mol Ecol Resour 2021; 21:1037-1055. [PMID: 33351289 DOI: 10.1111/1755-0998.13314] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 12/03/2020] [Accepted: 12/14/2020] [Indexed: 11/28/2022]
Abstract
Obtaining informative data is the ambition of any genomic project, but in nonmodel species with very large genomes, pursuing such a goal requires surmounting a series of analytical challenges. Double-digest RAD sequencing is routinely used in nonmodel organisms and offers some control over the volume of data obtained. However, the volume of data recovered is not always an indication of the reliability of data sets, and quality checks are necessary to ensure that true and artefactual information is set apart. In the present study, we aim to fill the gap existing between the known applicability of RAD sequencing methods in plants with large genomes and the use of the retrieved loci for population genetic inference. By analysing two populations of Cypripedium calceolus, a nonmodel orchid species with a large genome size (1C ~ 31.6 Gbp), we provide a complete workflow from library preparation to bioinformatic filtering and inference of genetic diversity and differentiation. We show how filtering strategies to dismiss potentially misleading data need to be explored and adapted to data set-specific features. Moreover, we suggest that the occurrence of organellar sequences in libraries should not be neglected when planning the experiment and analysing the results. Finally, we explain how, in the absence of prior information about the genome of the species, seeking high standards of quality during library preparation and sequencing can provide an insurance against unpredicted technical or biological constraints.
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Affiliation(s)
| | - Tiiu Kull
- Estonian University of Life Sciences, Tartu, Estonia
| | - Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK.,School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
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17
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Gargiulo R, Worswick G, Arnold C, Pike LJ, Cowan RS, Hardwick KA, Chapman T, Fay MF. Conservation of the Threatened Species, Pulsatilla vulgaris Mill. (Pasqueflower), is Aided by Reproductive System and Polyploidy. J Hered 2020; 110:618-628. [PMID: 31102445 DOI: 10.1093/jhered/esz035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/16/2019] [Indexed: 11/13/2022] Open
Abstract
Population loss due to habitat disturbance is a major concern in biodiversity conservation. Here we investigate the genetic causes of the demographic decline observed in English populations of Pulsatilla vulgaris and the consequences for conservation. Using 10 nuclear microsatellite markers, we compare genetic variation in wild populations with restored and seed-regenerated populations (674 samples). Emergence of genetic structure and loss of allelic variation in natural populations are not as evident as expected from demographic trends. Restored populations show genetic variation comparable to their source populations and, in general, to the wild ones. Genetic homogeneity is observed in regeneration trials, although some alleles not captured in source populations are detected. We infer that polyploidy, longevity, and clonal reproduction have provided P. vulgaris with the standing genetic variation necessary to make the species resilient to the effects of demographic decline, suggesting that the use of multiple sources for reintroduction may be beneficial to mimic natural gene flow and the availability of multiple allele copies typical of polyploid species.
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Affiliation(s)
| | | | | | | | | | - Kate A Hardwick
- Royal Botanic Gardens, Kew, Millennium Seed Bank, Ardingly, UK
| | - Ted Chapman
- Royal Botanic Gardens, Kew, Millennium Seed Bank, Ardingly, UK
| | - Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, UK.,School of Plant Biology, University of Western Australia, Crawley, Western Australia, Australia
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18
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Song AJ, Ding K, Laperriere N, Perry JR, Mason WP, Winch C, O'Callaghan CJ, Menten J, Brandes AA, Phillips C, Fay MF, Nishikawa R, Osoba D, Cairncross G, Roa W, Wick W, Shi W. Impact of lymphopenia on survival for elderly patients with glioblastoma: A secondary analysis of the CCTG CE.6 (EORTC 26062-22061, TROG03.01) randomized clinical trial. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.2547] [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: 11/20/2022] Open
Abstract
2547 Background: Lymphopenia (LMP) may lead to worse outcomes for patients with glioblastoma (GBM). This study is a secondary analysis of the CCTG CE.6 trial evaluating the impact of chemotherapy and radiation on LMP, as well as the association of LMP with overall survival. Methods: CCTG clinical trial CE.6 randomized elderly GBM patients (≥ 65 yrs) to short course radiation alone (RT) or short course radiation with temozolomide (RT + TMZ). In this study LMP (mild-mod: grade 1-2; severe: grade 3-4) was defined per CTCAE v3.0 criteria, and measured at baseline, 1 wk and 4 wks post-RT. Pre-selected key factors for the analysis included age, sex, ECOG, extent of resection, MGMT methylation, MMSE, and steroid use. Multinomial logistic regression models were used to identify factors associated with LMP and multivariable Cox regression models were used to study effect of LMP on survival. Results: A total of 562 patients were included for analysis (281 RT vs 281 RT+TMZ). At baseline, both arms (RT vs RT+TMZ) had similar rates of mild-mod (21.4% vs 21.4%) and severe (3.2% vs 2.9%) LMP. The 1 wk post-RT LMP rates were also similar (p = 0.25). However, RT+TMZ pts were more likely to develop both mild-mod LMP (18.2% vs 27.9%) and severe LMP (1.8% vs 9.3%) [p < 0.001] at 4 wks post-RT. Developing mild-mod and severe LMP post-RT were both associated with baseline LMP (p < 0.001) and RT+TMZ (p < 0.001). Severe LMP at 4 wks post-RT was also associated with biopsy only (p < 0.02). After adjusting for confounding factors, 4 wks post-RT LMP was not significantly associated with PFS or OS regardless of severity. However, baseline LMP (HR 1.3) was significantly associated with worse OS (HR: 1.30, 95% C.I.: 1.05-1.62, p = 0.02), regardless of MGMT status. Other factors significantly associated with worse outcome included: males (HR 1.41), biopsy only (HR 1.59), and lower MMSE (HR 1.03). Conclusions: Short course RT alone does not lead to LMP after treatment. Development of LMP post-RT is associated with addition of TMZ and baseline LMP. However, only baseline LMP is associated with worse OS regardless of MGMT status. This may be considered as a prognostic biomarker for elderly GBM patients and warrants further validation. Clinical trial information: NCT00482677 .
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Affiliation(s)
| | - Keyue Ding
- Canadian Cancer Trials Group, Kingston, ON, Canada
| | - Normand Laperriere
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Warren P. Mason
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Chad Winch
- Canadian Cancer Trials Group (CTTG), Kingston, ON, Canada
| | | | | | | | | | | | - Ryo Nishikawa
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, Saitama, Japan
| | | | - Gregory Cairncross
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - Wilson Roa
- Cross Cancer Institute, Edmonton, AB, Canada
| | - Wolfgang Wick
- National Center for Tumor Diseases (NCT), UKHD and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wenyin Shi
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA
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19
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Davis AP, Gargiulo R, Fay MF, Sarmu D, Haggar J. Lost and Found: Coffea stenophylla and C. affinis, the Forgotten Coffee Crop Species of West Africa. Front Plant Sci 2020; 11:616. [PMID: 32508866 PMCID: PMC7248357 DOI: 10.3389/fpls.2020.00616] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/21/2020] [Indexed: 06/11/2023]
Abstract
Coffea arabica (Arabica) and C. canephora (robusta) almost entirely dominate global coffee production. Various challenges at the production (farm) level, including the increasing prevalence and severity of disease and pests and climate change, indicate that the coffee crop portfolio needs to be substantially diversified in order to ensure resilience and sustainability. In this study, we use a multidisciplinary approach (herbarium and literature review, fieldwork and DNA sequencing) to elucidate the identity, whereabouts, and potential attributes, of two poorly known coffee crop species: C. affinis and C. stenophylla. We show that despite widespread (albeit small-scale) use as a coffee crop species across Upper West Africa and further afield more than 100 years ago, these species are now extremely rare in the wild and are not being farmed. Fieldwork enabled us to rediscover C. stenophylla in Sierra Leone, which previously had not been recorded in the wild there since 1954. We confirm that C. stenophylla is an indigenous species in Guinea, Sierra Leone, and Ivory Coast. Coffea affinis was discovered in the wild in Sierra Leone for the first time, having previously been found only in Guinea and Ivory Coast. Prior to our rediscovery, C. affinis was last seen in the wild in 1941, although sampling of an unidentified herbarium specimen reveals that it was collected in Guinea-Conakry in 2015. DNA sequencing using plastid and ITS markers was used to: (1) confirm the identity of museum and field collected samples of C. stenophylla; (2) identify new accessions of C. affinis; (3) refute hybrid status for C. affinis; (4) identify accessions confused with C. affinis; (5) show that C. affinis and C. stenophylla are closely related, and possibly a single species; (6) substantiate the hybrid C. stenophylla × C. liberica; (7) demonstrate the use of plastid and nuclear markers as a simple means of identifying F1 and early-generation interspecific hybrids in Coffea; (8) infer that C. liberica is not monophyletic; and (9) show that hybridization is possible across all the major groups of key Africa Coffea species (Coffee Crop Wild Relative Priority Groups I and II). Coffea affinis and C. stenophylla may possess useful traits for coffee crop plant development, including taste differentiation, disease resistance, and climate resilience. These attributes would be best accessed via breeding programs, although the species may have niche-market potential via minimal domestication.
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Affiliation(s)
| | | | | | | | - Jeremy Haggar
- Department of Agriculture, Health and Environment, Faculty of Engineering and Science, Natural Resources Institute, University of Greenwich, Medway, United Kingdom
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20
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Hamston TJ, de Vere N, King RA, Pellicer J, Fay MF, Cresswell JE, Stevens JR. Apomixis and Hybridization Drives Reticulate Evolution and Phyletic Differentiation in Sorbus L.: Implications for Conservation. Front Plant Sci 2018; 9:1796. [PMID: 30619388 PMCID: PMC6300497 DOI: 10.3389/fpls.2018.01796] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 11/19/2018] [Indexed: 06/09/2023]
Abstract
Hybridization and polyploidy are major forces in the evolution of plant diversity and the study of these processes is of particular interest to understand how novel taxa are formed and how they maintain genetic integrity. Sorbus is an example of a genus where active diversification and speciation are ongoing and, as such, represents an ideal model to investigate the roles of hybridization, polyploidy and apomixis in a reticulate evolutionary process. To elucidate breeding systems and evolutionary origins of a complex of closely related Sorbus taxa, we assessed genotypic diversity and population structure within and among taxa, combining data from nuclear DNA microsatellite markers and flow cytometry. Clonal analysis and low genotypic diversity within the polyploid taxa suggest apomixis is obligate. However, genetic variation has led to groups of 'clone-mates' within apomictic taxa that strongly suggest mutation is responsible for the genotypic diversity of these apomictic lineages. In addition, microsatellite profiles and site demographics suggest hybridization events among apomictic polyploid Sorbus may have contributed to the extant diversity of recognized taxa in this region. This research demonstrates that both macro- and micro-evolutionary processes are active within this reticulate Sorbus complex. Conservation measures should be aimed at maintaining this process and should therefore be prioritized for those areas of Sorbus species richness where the potential for interspecific gene flow is greatest.
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Affiliation(s)
- Tracey J. Hamston
- Molecular Ecology and Evolution Group, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
- Field Conservation and Research Department, Whitley Wildlife Conservation Trust, Paignton, United Kingdom
| | - Natasha de Vere
- National Botanic Garden of Wales, Llanarthney, United Kingdom
- Faculty of Earth and Life Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - R. Andrew King
- Molecular Ecology and Evolution Group, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Jaume Pellicer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, United Kingdom
| | - Michael F. Fay
- Jodrell Laboratory, Royal Botanic Gardens, Kew, United Kingdom
- School of Plant Biology, University of Western Australia, Crawley, WA, Australia
| | - James E. Cresswell
- Molecular Ecology and Evolution Group, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Jamie R. Stevens
- Molecular Ecology and Evolution Group, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
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21
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Chase MW, Christenhusz MJM, Conran JG, Dodsworth S, Medeiros de Assis FN, Felix LP, Fay MF. UNEXPECTED DIVERSITY OF AUSTRALIAN TOBACCO SPECIES (NICOTIANASECTIONSUAVEOLENTES,SOLANACEAE). ACTA ACUST UNITED AC 2018. [DOI: 10.1111/curt.12241] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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22
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Lee YI, Yap JW, Izan S, Leitch IJ, Fay MF, Lee YC, Hidalgo O, Dodsworth S, Smulders MJM, Gravendeel B, Leitch AR. Satellite DNA in Paphiopedilum subgenus Parvisepalum as revealed by high-throughput sequencing and fluorescent in situ hybridization. BMC Genomics 2018; 19:578. [PMID: 30068293 PMCID: PMC6090851 DOI: 10.1186/s12864-018-4956-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 07/23/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Satellite DNA is a rapidly diverging, largely repetitive DNA component of many eukaryotic genomes. Here we analyse the evolutionary dynamics of a satellite DNA repeat in the genomes of a group of Asian subtropical lady slipper orchids (Paphiopedilum subgenus Parvisepalum and representative species in the other subgenera/sections across the genus). A new satellite repeat in Paphiopedilum subgenus Parvisepalum, SatA, was identified and characterized using the RepeatExplorer pipeline in HiSeq Illumina reads from P. armeniacum (2n = 26). Reconstructed monomers were used to design a satellite-specific fluorescent in situ hybridization (FISH) probe. The data were also analysed within a phylogenetic framework built using the internal transcribed spacer (ITS) sequences of 45S nuclear ribosomal DNA. RESULTS SatA comprises c. 14.5% of the P. armeniacum genome and is specific to subgenus Parvisepalum. It is composed of four primary monomers that range from 230 to 359 bp and contains multiple inverted repeat regions with hairpin-loop motifs. A new karyotype of P. vietnamense (2n = 28) is presented and shows that the chromosome number in subgenus Parvisepalum is not conserved at 2n = 26, as previously reported. The physical locations of SatA sequences were visualised on the chromosomes of all seven Paphiopedilum species of subgenus Parvisepalum (2n = 26-28), together with the 5S and 45S rDNA loci using FISH. The SatA repeats were predominantly localisedin the centromeric, peri-centromeric and sub-telocentric chromosome regions, but the exact distribution pattern was species-specific. CONCLUSIONS We conclude that the newly discovered, highly abundant and rapidly evolving satellite sequence SatA is specific to Paphiopedilum subgenus Parvisepalum. SatA and rDNA chromosomal distributions are characteristic of species, and comparisons between species reveal that the distribution patterns generate a strong phylogenetic signal. We also conclude that the ancestral chromosome number of subgenus Parvisepalum and indeed of all Paphiopedilum could be either 2n = 26 or 28, if P. vietnamense is sister to all species in the subgenus as suggested by the ITS data.
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Affiliation(s)
- Yung-I Lee
- Biology Department, National Museum of Natural Science, No 1, Kuan-Chien Rd, 40453 Taichung, Taiwan, Republic of China
- Department of Life Sciences, National Chung Hsing University, 40227 Taichung, Taiwan, Republic of China
| | - Jing Wei Yap
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS UK
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
- Forest Research Institute Malaysia (FRIM), 52109 Kepong, Selangor Darul Ehsan Malaysia
| | - Shairul Izan
- Plant Breeding, Wageningen University & Research, P.O. Box 386, NL-6700 AJ Wageningen, The Netherlands
- Department of Crop Science, Faculty of Agriculture, University Putra Malaysia (UPM) Serdang, Serdang, Selangor Malaysia
| | - Ilia J. Leitch
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
| | - Michael F. Fay
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
- School of Plant Biology, University of Western Australia, Crawley, WA 6009 Australia
| | - Yi-Ching Lee
- Biology Department, National Museum of Natural Science, No 1, Kuan-Chien Rd, 40453 Taichung, Taiwan, Republic of China
| | - Oriane Hidalgo
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
| | - Steven Dodsworth
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB UK
| | - Marinus J. M. Smulders
- Plant Breeding, Wageningen University & Research, P.O. Box 386, NL-6700 AJ Wageningen, The Netherlands
| | - Barbara Gravendeel
- Endless Forms Group, Naturalis Biodiversity Center, Vondellaan 55, 2332 AA Leiden, The Netherlands
- Faculty of Science and Technology, University of Applied Sciences Leiden, Zernikedreef 11, 2333 CK Leiden, The Netherlands
- Institute Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Andrew R. Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS UK
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23
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Fay MF. Orchid conservation: how can we meet the challenges in the twenty-first century? Bot Stud 2018; 59:16. [PMID: 29872972 DOI: 10.1186/s405229-018-0232-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/01/2018] [Indexed: 05/20/2023]
Abstract
With c. 28,000 species, orchids are one of the largest families of flowering plants, and they are also one of the most threatened, in part due to their complex life history strategies. Threats include habitat destruction and climate change, but many orchids are also threatened by unsustainable (often illegal and/or undocumented) harvest for horticulture, food or medicine. The level of these threats now outstrips our abilities to combat them at a species-by-species basis for all species in such a large group as Orchidaceae; if we are to be successful in conserving orchids for the future, we will need to develop approaches that allow us to address the threats on a broader scale to complement focused approaches for the species that are identified as being at the highest risk.
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Affiliation(s)
- Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK.
- School of Biological Sciences, University of Western Australia, Crawley, WA, 6009, Australia.
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24
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Abstract
With c. 28,000 species, orchids are one of the largest families of flowering plants, and they are also one of the most threatened, in part due to their complex life history strategies. Threats include habitat destruction and climate change, but many orchids are also threatened by unsustainable (often illegal and/or undocumented) harvest for horticulture, food or medicine. The level of these threats now outstrips our abilities to combat them at a species-by-species basis for all species in such a large group as Orchidaceae; if we are to be successful in conserving orchids for the future, we will need to develop approaches that allow us to address the threats on a broader scale to complement focused approaches for the species that are identified as being at the highest risk.
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Affiliation(s)
- Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK.
- School of Biological Sciences, University of Western Australia, Crawley, WA, 6009, Australia.
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25
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Head RJ, Fay MF, Cosgrove L, Y C Fung K, Rundle-Thiele D, Martin JH. Persistence of DNA adducts, hypermutation and acquisition of cellular resistance to alkylating agents in glioblastoma. Cancer Biol Ther 2017; 18:917-926. [PMID: 29020502 DOI: 10.1080/15384047.2017.1385680] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Glioblastoma is a lethal form of brain tumour usually treated by surgical resection followed by radiotherapy and an alkylating chemotherapeutic agent. Key to the success of this multimodal approach is maintaining apoptotic sensitivity of tumour cells to the alkylating agent. This initial treatment likely establishes conditions contributing to development of drug resistance as alkylating agents form the O6-methylguanine adduct. This activates the mismatch repair (MMR) process inducing apoptosis and mutagenesis. This review describes key juxtaposed drivers in the balance between alkylation induced mutagenesis and apoptosis. Mutations in MMR genes are the probable drivers for alkylation based drug resistance. Critical to this interaction are the dose-response and temporal interactions between adduct formation and MMR mutations. The precision in dose interval, dose-responses and temporal relationships dictate a role for alkylating agents in either promoting experimental tumour formation or inducing tumour cell death with chemotherapy. Importantly, this resultant loss of chemotherapeutic selective pressure provides opportunity to explore novel therapeutics and appropriate combinations to minimise alkylation based drug resistance and tumour relapse.
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Affiliation(s)
- R J Head
- a University of South Australia , Adelaide , SA , Australia
| | - M F Fay
- b University of Newcastle , Newcastle , NSW , Australia.,c Genesis Cancer Care , NSW , Australia.,d University of Queensland , Brisbane , QLD , Australia
| | - L Cosgrove
- e CSIRO Health & Biosecurity , Adelaide , SA , Australia
| | - K Y C Fung
- f CSIRO Health & Biosecurity , N Ryde , NSW , Australia
| | - D Rundle-Thiele
- g School of Medicine, Flinders University , Bedford Park , SA , Australia
| | - J H Martin
- b University of Newcastle , Newcastle , NSW , Australia.,d University of Queensland , Brisbane , QLD , Australia
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26
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Piñeiro R, Karrman-Bailey F, Cowan RS, Fay MF. Isolation and characterization of microsatellite loci in Sorbus porrigentiformis and cross-amplification in S. aria and S. rupicola (Rosaceae). Appl Plant Sci 2017; 5:apps1600150. [PMID: 28224061 PMCID: PMC5315384 DOI: 10.3732/apps.1600150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 12/31/2016] [Indexed: 05/25/2023]
Abstract
PREMISE OF THE STUDY Southwestern Britain is an emblematic hotspot of polyploid diversity of whitebeams (Sorbus aria agg.; Rosaceae) with ca. 30 polyploid endemic species. The tetraploid S. porrigentiformis is postulated as one of the parents of most of these endemics, along with the sexual diploid S. aria s. str. and the tetraploid S. rupicola. METHODS AND RESULTS We isolated 16 nuclear microsatellite loci from S. porrigentiformis and characterized them on 45 trees representing the three putative parental species. Eleven loci were polymorphic, and eight of them exhibited species-specific alleles. Allele numbers ranged from one to 11, and observed heterozygosity ranged from 0.40 to 1.00. The intraspecific levels of variation were very low, in agreement with the facultative apomictic reproduction hypothesized for this species. CONCLUSIONS The species-specific alleles will be useful for tracing the origin of the narrowly distributed Sorbus taxa. In addition, the assessment of diversity levels will help design a conservation strategy for the polyploid complex.
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Affiliation(s)
- Rosalía Piñeiro
- Jodrell Laboratory, Royal Botanic Gardens, Kew, TW9 3DS Richmond, Surrey, United Kingdom
| | - Freja Karrman-Bailey
- Jodrell Laboratory, Royal Botanic Gardens, Kew, TW9 3DS Richmond, Surrey, United Kingdom
| | - Robyn S. Cowan
- Jodrell Laboratory, Royal Botanic Gardens, Kew, TW9 3DS Richmond, Surrey, United Kingdom
| | - Michael F. Fay
- Jodrell Laboratory, Royal Botanic Gardens, Kew, TW9 3DS Richmond, Surrey, United Kingdom
- School of Plant Biology, University of Western Australia, Crawley, Western Australia 6009, Australia
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27
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Affiliation(s)
- Michael F. Fay
- University of Newcastle; Genesis Cancer Care; Calvary Mater Hospital; Newcastle, New South Wales; University of Queensland, Brisbane, Queensland, Australia
| | - Richard Head
- University of South Australia, Adelaide, South Australia, Australia
| | | | | | | | - Stephen E. Rose
- CSIRO; University of Queensland, Brisbane, Queensland, Australia
| | - Jenny H. Martin
- University of Newcastle; Calvary Mater Hospital, Newcastle, New South Wales; University of Queensland, Brisbane, Queensland, Australia
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Abstract
BACKGROUND Due in great part to their often complex interactions with mycorrhizal fungi, pollinators and host trees, Orchidaceae present particular challenges for conservation. Furthermore, orchids, as potentially the largest family of angiosperms with >26000 species, species complexes and frequent hybrid formation, are complex to catalogue. Following a highlight in 2015, a further seven papers focusing on orchids, their interactions with beneficial organisms, pollinators and mycorrhiza, and other factors relating to their conservation, including threats from human utilization and changing land use, are presented here. CONCLUSIONS The production of an online flora of all known plants and an assessment of the conservation status of all known plant species as far as possible, to guide conservation action are the first two targets of the Global Strategy for Plant Conservation Without knowing how many species there are and how they should be circumscribed, neither of these targets is achievable. Orchids are a fascinating subject for fundamental research with rapid species evolution, specific organ structure and development, but they also suffer from high levels of threat. Effective orchid conservation must take account of the beneficial interactions with fungi and pollinators and the potentially detrimental effects of over-collection and changes in land use.
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Affiliation(s)
- Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK and School of Plant Biology, University of Western Australia, Crawley, WA 6009, Australia
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29
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Perry JR, Laperriere N, O'Callaghan CJ, Brandes AA, Menten J, Phillips C, Fay MF, Nishikawa R, Cairncross JG, Roa W, Osoba D, Sahgal A, Hirte HW, Wick W, Laigle-Donadey F, Franceschi E, Chinot OL, Winch C, Ding K, Mason WP. A phase III randomized controlled trial of short-course radiotherapy with or without concomitant and adjuvant temozolomide in elderly patients with glioblastoma (CCTG CE.6, EORTC 26062-22061, TROG 08.02, NCT00482677). J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.18_suppl.lba2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
LBA2 Background: The EORTC (26981-22981)/NCIC CTG (CE.3) RCT in newly diagnosed glioblastoma (GB) showed increased overall survival (OS) with concomitant and adjuvant temozolomide (TMZ) added to radiotherapy (RT). Pts were 18-71 (median 56) years; however, a trend of decreasing benefit from the addition of TMZ with increasing age was noted. Recent RCTs in elderly GB detected non-inferiority of 40 Gy/15 v 60 Gy/30 RT and superior survival was noted for MGMT-methylated pts treated with TMZ alone. However, whether the addition of TMZ to RT improves survival in elderly pts remained unanswered. Methods: We conducted a global randomized phase III clinical trial for patients ≥ 65 yrs with histologically confirmed newly diagnosed GB, ECOG 0-2, randomized 1:1 to receive 40Gy/15 RT v 40Gy/15 RT with 3 weeks of concomitant TMZ plus monthly adjuvant TMZ until progression or 12 cycles. Stratification was by centre, age (65-70, 71-75, or 76+), ECOG 0,1 vs 2, and biopsy vs resection. Results: 562 pts were randomized, 281 on each arm; median age 73 yrs (range 65-90), male 61%, PS 0/1 77%, resection 68%. RT+TMZ significantly improved OS over RT alone (median 9.3m v 7.6m, HR 0.67, 95%CI 0.56-0.80, p < 0.0001) and significantly improved PFS (median 5.3m v 3.9m, HR 0.50, 95%CI 0.41 – 0.60, p < 0.0001). Tissue from 462 pts was provided and adequate for MGMT analysis in 354 to date. In MGMT methylated patients (n = 165) OS for RT+TMZ v RT was 13.5 m and 7.7m respectively (HR: 0.53 (95% C.I. 0.38, 0.73, p = 0.0001). In MGMT unmethylated patients (n = 189) OS for RT + TMZ v RT was 10.0m vs 7.9m respectively (HR 0.75 (95% C.I. 0.56 – 1.01, p = 0.055). QoL analyses showed no differences in functional domains of QLQC30 and BN20 but were worse in the RT/TMZ arm for nausea, vomiting, and constipation. Systemic therapy after PD was reported in 39% on RT+TMZ v 41% on RT. Conclusions: The addition of concomitant and adjuvant TMZ to hypofractionated RT for elderly pts with GB significantly improves OS and PFS in all patients and is well tolerated. Patients with MGMT methylated tumors benefit the most from the addition of TMZ to RT where median OS is nearly doubled. Clinical trial information: NCT00482677.
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Affiliation(s)
| | | | | | | | - Johan Menten
- Department of Radiotherapy, University Hospitals Leuven and Catholic University of Leuven, Leuven, Belgium
| | | | | | | | | | - Wilson Roa
- Cross Cancer Institute, Edmonton, AB, Canada
| | | | | | | | | | | | - Enrico Franceschi
- Department of Medical Oncology, Bellaria Hospital, Azienda USL - IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Olivier L. Chinot
- Aix-Marseille University, AP-HM, Service de Neuro-Oncologie, CHU Timone, Marseille, France
| | - Chad Winch
- Canadian Cancer Trials Group (CTTG), Kingston, ON, Canada
| | - Keyue Ding
- Canadian Cancer Trials Group, Queen's University, Kingston, ON, Canada
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Perry JR, Laperriere N, O'Callaghan CJ, Brandes AA, Menten J, Phillips C, Fay MF, Nishikawa R, Cairncross JG, Roa W, Osoba D, Sahgal A, Hirte HW, Wick W, Laigle-Donadey F, Franceschi E, Chinot OL, Winch C, Ding K, Mason WP. A phase III randomized controlled trial of short-course radiotherapy with or without concomitant and adjuvant temozolomide in elderly patients with glioblastoma (CCTG CE.6, EORTC 26062-22061, TROG 08.02, NCT00482677). J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.lba2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | | | - Johan Menten
- Department of Radiotherapy, University Hospitals Leuven and Catholic University of Leuven, Leuven, Belgium
| | | | | | | | | | - Wilson Roa
- Cross Cancer Institute, Edmonton, AB, Canada
| | | | | | | | | | | | - Enrico Franceschi
- Department of Medical Oncology, Bellaria Hospital, Azienda USL - IRCCS Institute of Neurological Sciences, Bologna, Italy
| | - Olivier L. Chinot
- Aix-Marseille University, AP-HM, Service de Neuro-Oncologie, CHU Timone, Marseille, France
| | - Chad Winch
- Canadian Cancer Trials Group (CTTG), Kingston, ON, Canada
| | - Keyue Ding
- Canadian Cancer Trials Group, Queen's University, Kingston, ON, Canada
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Cotrim H, Monteiro F, Sousa E, Pinto MJ, Fay MF. Marked hybridization and introgression in Ophrys sect. Pseudophrys in the western Iberian Peninsula. Am J Bot 2016; 103:677-691. [PMID: 27056929 DOI: 10.3732/ajb.1500252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 01/11/2016] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Orchids in the genus Ophrys represent extraordinary cases of tight coevolution between plants and their pollinators, and as a result, they present opportunities for studying hybridization, or a lack thereof, during speciation. However, few studies assess the real effect of hybridization in diversification. The three most representative species of section Pseudophrys in the western Iberian Peninsula-O. dyris, O. fusca, and O. lutea-were chosen to study evolutionary relationships and examine speciation. METHODS Using eight specific nuclear microsatellite loci, 357 individuals from 28 locations were studied; 142 of these samples were also studied with four plastid microsatellite loci. Data were analyzed using Bayesian cluster analysis, a median-joint network, and multivariate analysis. KEY RESULTS Many O. dyris and O. fusca specimens had three or four alleles and were therefore treated as tetraploid. Ophrys dyris is poorly genetically separated from O. fusca, and pure populations are rare. Ophrys fusca and O. lutea are distinct, but hybrids/introgressed individuals were detected in most of the populations and supported by plastid haplotypes. Ophrys fusca is subdivided into three well-delimited genetic lineages with a strict geographic correspondence confirmed by plastid haplotypes. CONCLUSIONS Because postzygotic barriers are weak, leakage in this highly specialized orchid-pollinator system contributes to hybridization and introgression. These leakages may have occurred during periods of past climate change, promoting homogenization and the potential for generations of new biodiversity via production of novel genotypes/phenotypes interacting with pollinators.
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Affiliation(s)
- Helena Cotrim
- Centre for Ecology, Evolution and Environmental Change (CE3C), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal Botanic Garden, National Museum of Natural History and Science, University of Lisbon, 1250-102 Lisbon, Portugal Conservation Science, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, United Kingdom
| | - Filipa Monteiro
- Biosystems and Integrative Sciences Institute (BIOISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Eva Sousa
- Biosystems and Integrative Sciences Institute (BIOISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Manuel J Pinto
- Botanic Garden, National Museum of Natural History and Science, University of Lisbon, 1250-102 Lisbon, Portugal
| | - Michael F Fay
- Conservation Science, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, United Kingdom
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Kelly LJ, Renny‐Byfield S, Pellicer J, Macas J, Novák P, Neumann P, Lysak MA, Day PD, Berger M, Fay MF, Nichols RA, Leitch AR, Leitch IJ. Analysis of the giant genomes of Fritillaria (Liliaceae) indicates that a lack of DNA removal characterizes extreme expansions in genome size. New Phytol 2015; 208:596-607. [PMID: 26061193 PMCID: PMC4744688 DOI: 10.1111/nph.13471] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [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: 03/20/2015] [Accepted: 04/20/2015] [Indexed: 05/18/2023]
Abstract
Plants exhibit an extraordinary range of genome sizes, varying by > 2000-fold between the smallest and largest recorded values. In the absence of polyploidy, changes in the amount of repetitive DNA (transposable elements and tandem repeats) are primarily responsible for genome size differences between species. However, there is ongoing debate regarding the relative importance of amplification of repetitive DNA versus its deletion in governing genome size. Using data from 454 sequencing, we analysed the most repetitive fraction of some of the largest known genomes for diploid plant species, from members of Fritillaria. We revealed that genomic expansion has not resulted from the recent massive amplification of just a handful of repeat families, as shown in species with smaller genomes. Instead, the bulk of these immense genomes is composed of highly heterogeneous, relatively low-abundance repeat-derived DNA, supporting a scenario where amplified repeats continually accumulate due to infrequent DNA removal. Our results indicate that a lack of deletion and low turnover of repetitive DNA are major contributors to the evolution of extremely large genomes and show that their size cannot simply be accounted for by the activity of a small number of high-abundance repeat families.
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Affiliation(s)
- Laura J. Kelly
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonE1 4NSUK
- Jodrell LaboratoryRoyal Botanic GardensKewRichmondTW9 3DSUK
| | - Simon Renny‐Byfield
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonE1 4NSUK
- Department of Plant SciencesUniversity of California DavisDavisCA95616USA
| | - Jaume Pellicer
- Jodrell LaboratoryRoyal Botanic GardensKewRichmondTW9 3DSUK
| | - Jiří Macas
- Biology Centre CASInstitute of Plant Molecular BiologyCZ‐37005České BudějoviceCzech Republic
| | - Petr Novák
- Biology Centre CASInstitute of Plant Molecular BiologyCZ‐37005České BudějoviceCzech Republic
| | - Pavel Neumann
- Biology Centre CASInstitute of Plant Molecular BiologyCZ‐37005České BudějoviceCzech Republic
| | - Martin A. Lysak
- Plant Cytogenomics Research GroupCEITEC – Central European Institute of TechnologyMasaryk UniversityKamenice 5CZ‐62500BrnoCzech Republic
| | - Peter D. Day
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonE1 4NSUK
- Jodrell LaboratoryRoyal Botanic GardensKewRichmondTW9 3DSUK
| | - Madeleine Berger
- Jodrell LaboratoryRoyal Botanic GardensKewRichmondTW9 3DSUK
- School of Biological and Biomedical SciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
- Rothamsted ResearchWest CommonHarpendenHertfordshireAL5 2JQUK
| | - Michael F. Fay
- Jodrell LaboratoryRoyal Botanic GardensKewRichmondTW9 3DSUK
| | - Richard A. Nichols
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonE1 4NSUK
| | - Andrew R. Leitch
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonE1 4NSUK
| | - Ilia J. Leitch
- Jodrell LaboratoryRoyal Botanic GardensKewRichmondTW9 3DSUK
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Abstract
Orchidaceae, one of the largest families of flowering plants, present particular challenges for conservation, due in great part to their often complex interactions with mycorrhizal fungi, pollinators and host trees. In this Highlight, we present seven papers focusing on orchids and their interactions and other factors relating to their conservation.
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Affiliation(s)
- Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK,
| | - Thierry Pailler
- Peuplements Végétaux et Bioagresseurs en Milieu Tropical, CIRAD-Université de La Réunion, 15 Avenue René Cassin BP 7151, 97715 Saint-Denis, La Réunion, France and
| | - Kingsley W Dixon
- Department of Environment and Agriculture, Curtin University, Kent Street, Bentley, Perth, Western Australia, 6102, Australia
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Schneider H, Liu H, Clark J, Hidalgo O, Pellicer J, Zhang S, Kelly LJ, Fay MF, Leitch IJ. Are the genomes of royal ferns really frozen in time? Evidence for coinciding genome stability and limited evolvability in the royal ferns. New Phytol 2015; 207:10-13. [PMID: 25655176 DOI: 10.1111/nph.13330] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Harald Schneider
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Hongmei Liu
- Key Laboratory of Southern Subtropical Plant Diversity, Fairylake Botanical Garden, Shenzhen & The Chinese Academy of Sciences, Shenzhen, 518004, P. R. China
| | - James Clark
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Oriane Hidalgo
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW8 3DS, UK
| | - Jaume Pellicer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW8 3DS, UK
| | - Shouzhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairylake Botanical Garden, Shenzhen & The Chinese Academy of Sciences, Shenzhen, 518004, P. R. China
| | - Laura J Kelly
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Michael F Fay
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW8 3DS, UK
| | - Ilia J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW8 3DS, UK
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Vitales D, García-Fernández A, Pellicer J, Vallès J, Santos-Guerra A, Cowan RS, Fay MF, Hidalgo O, Garnatje T. Key processes for Cheirolophus (Asteraceae) diversification on oceanic islands inferred from AFLP data. PLoS One 2014; 9:e113207. [PMID: 25412495 PMCID: PMC4239036 DOI: 10.1371/journal.pone.0113207] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 10/21/2014] [Indexed: 11/18/2022] Open
Abstract
The radiation of the genus Cheirolophus (Asteraceae) in Macaronesia constitutes a spectacular case of rapid diversification on oceanic islands. Twenty species - nine of them included in the IUCN Red List of Threatened Species - have been described to date inhabiting the Madeiran and Canarian archipelagos. A previous phylogenetic study revealed that the diversification of Cheirolophus in Macaronesia started less than 2 Ma. As a result of such an explosive speciation process, limited phylogenetic resolution was reported, mainly due to the low variability of the employed molecular markers. In the present study, we used highly polymorphic AFLP markers to i) evaluate species' boundaries, ii) infer their evolutionary relationships and iii) investigate the patterns of genetic diversity in relation to the potential processes likely involved in the radiation of Cheirolophus. One hundred and seventy-two individuals representing all Macaronesian Cheirolophus species were analysed using 249 AFLP loci. Our results suggest that geographic isolation played an important role in this radiation process. This was likely driven by the combination of poor gene flow capacity and a good ability for sporadic long-distance colonisations. In addition, we also found some traces of introgression and incipient ecological adaptation, which could have further enhanced the extraordinary diversification of Cheirolophus in Macaronesia. Last, we hypothesize that current threat categories assigned to Macaronesian Cheirolophus species do not reflect their respective evolutionary relevance, so future evaluations of their conservation status should take into account the results presented here.
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Affiliation(s)
- Daniel Vitales
- Laboratori de Botànica – Unitat associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Alfredo García-Fernández
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Barcelona, Catalonia, Spain
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | - Jaume Pellicer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Joan Vallès
- Laboratori de Botànica – Unitat associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | | | - Robyn S. Cowan
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Michael F. Fay
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Oriane Hidalgo
- Laboratori de Botànica – Unitat associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Barcelona, Catalonia, Spain
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Day PD, Berger M, Hill L, Fay MF, Leitch AR, Leitch IJ, Kelly LJ. Evolutionary relationships in the medicinally important genus Fritillaria L. (Liliaceae). Mol Phylogenet Evol 2014; 80:11-9. [PMID: 25124097 DOI: 10.1016/j.ympev.2014.07.024] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [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: 03/22/2014] [Revised: 07/30/2014] [Accepted: 07/31/2014] [Indexed: 10/24/2022]
Abstract
Fritillaria (Liliaceae) is a genus of approximately 140 species of bulbous perennial plants that includes taxa of both horticultural and medicinal importance. As well as being commercially valuable, Fritillaria species have attracted attention because of their exceptionally large genome sizes, with all values recorded to date in excess of 30Gb. Despite such interest in the genus, phylogenetic relationships between the majority of species have remained untested. Here we present the first phylogenetic reconstruction of relationships to encompass most of the currently recognised species diversity in the genus. Three regions of the plastid genome were sequenced in 117 individuals of Fritillaria, representing 92 species (c. 66% of the genus) and in representatives of nine other genera of Liliaceae. Eleven low-copy nuclear gene regions were also screened in selected species for their potential utility. Phylogenetic analysis of a combined plastid dataset using maximum parsimony and Bayesian inference provided support for the monophyly of the majority of currently recognised subgenera. However, subgenus Fritillaria, which is by far the largest of the subgenera and includes the most important species used in traditional Chinese medicine, is found to be polyphyletic. Moreover, several taxa that were represented by multiple individuals show evidence of species non-monophyly. The Japanese endemic subgenus Japonica, which contains the species with the largest recorded genome size for any diploid plant, is resolved as sister to the predominantly Middle Eastern and Central Asian subgenus Rhinopetalum. Whilst relationships between most of the major Fritillaria lineages can now be resolved, our results also highlight the need for data from additional independently evolving loci; an endeavour that may be particularly challenging in light of the huge nuclear genomes found in these plants.
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Affiliation(s)
- Peter D Day
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK.
| | - Madeleine Berger
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Biological and Biomedical Sciences, Durham University, South Road, Durham DH1 3LE, UK.
| | - Laurence Hill
- Petersham Lodge, River Lane, Richmond, Surrey TW10 7AG, UK.
| | - Michael F Fay
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK.
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK.
| | - Ilia J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK.
| | - Laura J Kelly
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK.
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Pinheiro F, Cozzolino S, Draper D, de Barros F, Félix LP, Fay MF, Palma-Silva C. Rock outcrop orchids reveal the genetic connectivity and diversity of inselbergs of northeastern Brazil. BMC Evol Biol 2014; 14:49. [PMID: 24629134 PMCID: PMC4004418 DOI: 10.1186/1471-2148-14-49] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [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: 01/07/2014] [Accepted: 03/07/2014] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Because of their fragmented nature, inselberg species are interesting biological models for studying the genetic consequences of disjoint populations. Inselbergs are commonly compared with oceanic islands, as most of them display a marked ecological isolation from the surrounding area. The isolation of these rock outcrops is reflected in the high number of recorded endemic species and the strong floristic differences between individual inselbergs and adjacent habitats. We examined the genetic connectivity of orchids Epidendrum cinnabarinum and E. secundum adapted to Neotropical inselbergs of northeastern Brazil. Our goals were to identify major genetic divergences or disjunctions across the range of the species and to investigate potential demographic and evolutionary mechanisms leading to lineage divergence in Neotropical mountain ecosystems. RESULTS Based on plastid markers, high genetic differentiation was found for E. cinnabarinum (FST = 0.644) and E. secundum (FST = 0.636). Haplotypes were not geographically structured in either taxon, suggesting that restricted gene flow and genetic drift may be significant factors influencing the diversification of these inselberg populations. Moreover, strong differentiation was found between populations over short spatial scales, indicating substantial periods of isolation among populations. For E. secundum, nuclear markers indicated higher gene flow by pollen than by seeds. CONCLUSIONS The comparative approach adopted in this study contributed to the elucidation of patterns in both species. Our results confirm the ancient and highly isolated nature of inselberg populations. Both species showed similar patterns of genetic diversity and structure, highlighting the importance of seed-restricted gene flow and genetic drift as drivers of plant diversification in terrestrial islands such as inselbergs.
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Affiliation(s)
- Fábio Pinheiro
- Instituto de Botânica, Núcleo de Pesquisa do Orquidário do Estado, Avenida Miguel Estéfano 3687, 04301-012 São Paulo, SP, Brazil.
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Pellicer J, Kelly LJ, Leitch IJ, Zomlefer WB, Fay MF. A universe of dwarfs and giants: genome size and chromosome evolution in the monocot family Melanthiaceae. New Phytol 2014; 201:1484-1497. [PMID: 24299166 DOI: 10.1111/nph.12617] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 10/30/2013] [Indexed: 05/22/2023]
Abstract
• Since the occurrence of giant genomes in angiosperms is restricted to just a few lineages, identifying where shifts towards genome obesity have occurred is essential for understanding the evolutionary mechanisms triggering this process. • Genome sizes were assessed using flow cytometry in 79 species and new chromosome numbers were obtained. Phylogenetically based statistical methods were applied to infer ancestral character reconstructions of chromosome numbers and nuclear DNA contents. • Melanthiaceae are the most diverse family in terms of genome size, with C-values ranging more than 230-fold. Our data confirmed that giant genomes are restricted to tribe Parideae, with most extant species in the family characterized by small genomes. Ancestral genome size reconstruction revealed that the most recent common ancestor (MRCA) for the family had a relatively small genome (1C = 5.37 pg). Chromosome losses and polyploidy are recovered as the main evolutionary mechanisms generating chromosome number change. • Genome evolution in Melanthiaceae has been characterized by a trend towards genome size reduction, with just one episode of dramatic DNA accumulation in Parideae. Such extreme contrasting profiles of genome size evolution illustrate the key role of transposable elements and chromosome rearrangements in driving the evolution of plant genomes.
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Affiliation(s)
- Jaume Pellicer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Laura J Kelly
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Ilia J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Wendy B Zomlefer
- Department of Plant Biology, 2502 Plant Sciences, University of Georgia, Athens, GA, 30602-7271, USA
| | - Michael F Fay
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
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White IP, Fay MF, Porter BW, Chinen K. Sem and phylogenetic analysis of naturalized and cultivated <i>Epidendrum</i> in Hawaii. Lankesteriana 2013. [DOI: 10.15517/lank.v0i0.11548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Naturalized populations of Epidendrum L. are found on a rocky hillside in Nuuanu-Pali and Olomana in the Koolau Mountains of Oahu, Hawaii. Scanning electron micrographs were taken to observe polymorphism among the pollinia, petals, leaves, and root tips of two Epidendrum specimens (one naturalized specimen from Nuuanu-Pali and one cultivated specimen in the greenhouse). SEM images of pollen from the naturalized Epidendrum revealed a length of 830.31 μm and a width of 462.58 μm. Pollen length from the cultivated cultivar, by comparison, was 724.60 μm and the width 276.17 μm. Differing cell structures on the lower surface of the petals were also observed. Polyhedral concave cells with numerous fossae (pits) were seen on the naturalized cultivar and elongated flattened cells on the cultivated one. Transections of the leaf of the naturalized specimen were much thinner (546.33 μm) compared to the thickness of the cultivated cultivar leaf (1505.83 μm), which contained more spongy parenchyma cells. A thinner root tip (1094.19 μm) was seen in the naturalized cultivar, as opposed to 1636.34 μm in the cultivated specimen. To compare relationships between these two specimens along with ten other unknown Epidendrum cultivars, we sequenced the plastid trnL-F gene region and conducted parsimony analysis among the naturalized Epidendrum from Nuuanu-Pali At least six changes separated these specimens into two clades. Shorter and longer plastid simple sequence repeats (cpSSR) from the rps16-trnK region support separation of the five Epidendrum genotypes evaluated into these two groups, including a naturalized Epidendrum from Olomana.
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Pinheiro F, Cozzolino S, de Barros F, Gouveia TMZM, Suzuki RM, Fay MF, Palma-Silva C. Phylogeographic structure and outbreeding depression reveal early stages of reproductive isolation in the neotropical orchid Epidendrum denticulatum. Evolution 2013; 67:2024-39. [PMID: 23815657 DOI: 10.1111/evo.12085] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 01/31/2013] [Indexed: 11/27/2022]
Abstract
Phylogeographic studies provide an important framework for investigating the mechanisms operating during the earliest stages of speciation, as reproductive barriers can be examined among divergent lineages in a geographic context. We investigated the evolution of early stages of intrinsic postmating isolation among different populations and lineages of Epidendrum denticulatum, a Neotropical orchid distributed across different biomes in South America. We estimated genetic diversity and structure for both nuclear and plastid markers, using a haplotype network, differentiation tests, Bayesian assignment analysis, and divergence time estimates of the main lineages. Reproductive barriers among divergent lineages were examined by analyzing seed viability following reciprocal crossing experiments. Strong plastid phylogeographic structure was found, indicating that E. denticulatum was restricted to multiple refuges during South American forest expansion events. In contrast, significant phylogeographic structure was not found for nuclear markers, suggesting higher gene flow by pollen than by seeds. Large asymmetries in seed set were observed among different plastid genetic groups, suggesting the presence of polymorphic genic incompatibilities associated with cytonuclear interactions. Our results confirm the importance of phylogeographic studies associated with reproductive isolation experiments and suggest an important role for outbreeding depression during the early stages of lineage diversification.
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Goergen SK, Pool FJ, Turner TJ, Grimm JE, Appleyard MN, Crock C, Fahey MC, Fay MF, Ferris NJ, Liew SM, Perry RD, Revell A, Russell GM, Wang SCSC, Wriedt C. Evidence-based guideline for the written radiology report: methods, recommendations and implementation challenges. J Med Imaging Radiat Oncol 2012; 57:1-7. [PMID: 23374546 DOI: 10.1111/1754-9485.12014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 08/28/2012] [Indexed: 11/26/2022]
Abstract
The written radiology report is the dominant method by which radiologists communicate the results of diagnostic and interventional imaging procedures. It has an important impact on decisions about further investigation and management. Its form and content can be influential in reducing harm to patients and mitigating risk for practitioners but varies markedly with little standardisation in practice. Until now, the Royal Australian and New Zealand College of Radiologists has not had a guideline for the written report. International guidelines on this subject are not evidence based and lack description of development methods. The current guideline seeks to improve the quality of the written report by providing evidence-based recommendations for good practice. The following attributes of the report are addressed by recommendations: Content Clinical information available to the radiologist at the time the report was created Technical details of the procedure Examination quality and limitations Findings (both normal and abnormal) Comparison with previous studies Pathophysiological diagnosis Differential diagnoses Clinical correlation and/or answer to the clinical question Recommendations, particularly for further imaging and other investigations Conclusion/opinion/impression Format Length Format Language Confidence and certainty Clarity Readability Accuracy Communication of discrepancies between an original verbal or written report and the final report Proofreading/editing of own and trainee reports.
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Affiliation(s)
- Stacy K Goergen
- Department of Diagnostic Imaging, Southern Health, Monash University, Sydney, Australia.
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Pellicer J, Clermont S, Houston L, Rich TCG, Fay MF. Cytotype diversity in the Sorbus complex (Rosaceae) in Britain: sorting out the puzzle. Ann Bot 2012; 110:1185-93. [PMID: 22922587 PMCID: PMC3478048 DOI: 10.1093/aob/mcs185] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [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: 04/18/2012] [Accepted: 07/09/2012] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Large-scale ploidy surveys using flow cytometry have become an essential tool to study plant genome dynamics and to gain insight into the mechanisms and genetic barriers framing ploidy diversity. As an ideal complement to traditional techniques such as chromosome counting, the analysis of cytotype diversity in plant systems such as Sorbus provides primary investigation into the potential patterns and evolutionary implications of hybrid speciation. METHODS Ploidy was assessed by means of relative nuclear DNA content using propidium iodide flow cytometry in 474 Sorbus samples collected from 65 populations in southern Wales and South-West England. Statistical tests were applied to evaluate the utility of this technique to confidently discriminate ploidy in the genus. KEY RESULTS Flow cytometric profiles revealed the presence of four cytotypes (2x, 3x, 4x and 5x), confirming in many cases chromosome counts previously reported and demonstrating cytotype heterogeneity within specific Sorbus aggregates. Diploid cytotypes were restricted to the potential parental species and homoploid hybrids. Most of the samples processed were polyploid. The occurrence of the pentaploid cytotype had previously only been reported from a single specimen; it is now confirmed for two taxa occurring at different sites. CONCLUSIONS Flow cytometry results obtained have proved useful in shedding light on the taxonomy of several controversial taxa and in confirming the presence of cytoypes which occur at very low frequencies. Notably, the coexistence of several cytotypes in Sorbus populations has probably been facilitated by the overlapping distribution of many of the species studied, which might also explain the high incidence of potential hybrid apomictic polyploids. These results will provide a solid baseline for molecular research aiming to better understand the genetic pathways controlling the formation and establishment of polyploid Sorbus.
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Affiliation(s)
- Jaume Pellicer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, UK.
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Versieux LM, Barbará T, Wanderley MDGL, Calvente A, Fay MF, Lexer C. Molecular phylogenetics of the Brazilian giant bromeliads (Alcantarea, Bromeliaceae): implications for morphological evolution and biogeography. Mol Phylogenet Evol 2012; 64:177-89. [DOI: 10.1016/j.ympev.2012.03.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Revised: 03/04/2012] [Accepted: 03/23/2012] [Indexed: 11/16/2022]
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Perry JR, O'Callaghan CJ, Ding K, Roa W, Mason WP, Cairncross JG, Brandes AA, Menten J, Phillips C, Fay MF, Nishikawa R, Winch C, Laperriere N. A phase III randomized controlled trial of short-course radiotherapy with or without concomitant and adjuvant temozolomide in elderly patients with glioblastoma (NCIC CTG CE.6, EORTC 26062-22061, TROG 08.02, NCT00482677). J Clin Oncol 2012. [DOI: 10.1200/jco.2012.30.15_suppl.tps2104] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
TPS2104 Background: The EORTC (26981-22981)/NCIC CTG (CE.3) RCT in newly diagnosed GBM found improved survival with concomitant and adjuvant temozolomide (TMZ) added to radiotherapy (RT). Study pts were 18-71 (median 56) years; however a sub-group analysis noted a trend of decreasing benefit from the addition of TMZ with increasing age, such that for age 65-71, the hazard ratio of 0.8 did not reach statistical significance (p=0.340). Recent RCTs in elderly GBM found improved survival with RT compared to supportive care alone and detected non-inferiority of 40 Gy/15 vs. a 60 Gy/30 RT regimen. Based upon these results short-course hypofractionated RT is often recommended for elderly pts. However, whether the addition of TMZ to RT confers a survival advantage in elderly pts remains unanswered. Methods: Patients ≥65 yrs of age with histologically confirmed newly diagnosed glioblastoma, ECOG 0-2, are randomized 1:1 to receive 40Gy/15 RT vs. 40Gy/15 RT with 3 weeks of concomitant temozolomide plus monthly adjuvant TMZ until progression or 12 cycles. Stratification is by centre, age (65-70, 71-75, or 76+), ECOG 0,1 vs 2, and biopsy vs resection. For 90% power to detect a 25% reduction in the primary outcome of overall survival (increased MST from 6 to 8 months) between arms, using a two-sided 5% alpha, a minimum of 520 deaths must be observed prior to analysis; total sample size is 560 patients. The trial is open in Canada (NCIC CTG), Europe (EORTC), Australia and New Zealand (TROG), and Japan. As of Jan 25, 2012, 361 (65%) of the target 560 pts were randomized (147 Canada, 144 Europe, 64 Australasia, 6 Japan). Median age of randomized patients is 73 (65-88) years. A planned futility analysis after 120 events by the independent DSMB resulted in a recommendation that the trial continue.Accrual is expected to be complete in 2013. A comprehensive molecular companion analysis, including MGMT promoter methylation, is planned.
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Affiliation(s)
| | | | - Keyue Ding
- NCIC Clinical Trials Group, Kingston, ON, Canada
| | - Wilson Roa
- Cross Cancer Institute, Edmonton, AB, Canada
| | - Warren P. Mason
- Princess Margaret Hospital, University of Toronto, Toronto, ON, Canada
| | | | - Alba Ariela Brandes
- Medical Oncology Department, Bellaria-Maggiore Hospital, Azienda USL of Bologna, Bologna, Italy
| | - Johan Menten
- Department of Radiotherapy, University Hospitals Leuven and Catholic University of Leuven, Leuven, Belgium
| | | | | | | | - Chad Winch
- National Cancer Institute of Canada Clinical Trials Group, Kingston, ON, Canada
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Seberg O, Petersen G, Davis JI, Pires JC, Stevenson DW, Chase MW, Fay MF, Devey DS, Jørgensen T, Sytsma KJ, Pillon Y. Phylogeny of the Asparagales based on three plastid and two mitochondrial genes. Am J Bot 2012; 99:875-889. [PMID: 22539521 DOI: 10.3732/ajb.1100468] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY The Asparagales, with ca. 40% of all monocotyledons, include a host of commercially important ornamentals in families such as Orchidaceae, Alliaceae, and Iridaceae, and several important crop species in genera such as Allium, Aloe, Asparagus, Crocus, and Vanilla. Though the order is well defined, the number of recognized families, their circumscription, and relationships are somewhat controversial. METHODS Phylogenetic analyses of Asparagales were based on parsimony and maximum likelihood using nucleotide sequence variation in three plastid genes (matK, ndhF, and rbcL) and two mitochondrial genes (atp1 and cob). Branch support was assessed using both jackknife analysis implementing strict-consensus (SC) and bootstrap analysis implementing frequency-within-replicates (FWR). The contribution of edited sites in the mitochondrial genes to topology and branch support was investigated. KEY RESULTS The topologies recovered largely agree with previous results, though some clades remain poorly resolved (e.g., Ruscaceae). When the edited sites were included in the analysis, the plastid and mitochondrial genes were highly incongruent. However, when the edited sites were removed, the two partitions became congruent. CONCLUSIONS Some deeper nodes in the Asparagales tree remain poorly resolved or unresolved as do the relationships of certain monogeneric families (e.g., Aphyllanthaceae, Ixioliriaceae, Doryanthaceae), whereas support for many families increases. However, the increased support is dominated by plastid data, and the potential influence of mitochondrial and biparentially inherited single or low-copy nuclear genes should be investigated.
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Affiliation(s)
- Ole Seberg
- Botanical Garden, Natural History Museum of Denmark, Sølvgade 83, Copenhagen K, Denmark.
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Zarrei M, Wilkin P, Ingrouille MJ, Leitch IJ, Buerki S, Fay MF, Chase MW. Speciation and evolution in the Gagea reticulata species complex (Tulipeae; Liliaceae). Mol Phylogenet Evol 2012; 62:624-39. [DOI: 10.1016/j.ympev.2011.11.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 10/29/2011] [Accepted: 11/04/2011] [Indexed: 10/15/2022]
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Paun O, Forest F, Fay MF, Chase MW. Parental divergence and hybrid speciation in angiosperms revisited. Taxon 2011; 60:1241-1244. [PMID: 23526840 PMCID: PMC3605764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Affiliation(s)
- Ovidiu Paun
- Department of Systematic and Evolutionary Botany, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Félix Forest
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, United Kingdom
| | - Michael F. Fay
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, United Kingdom
| | - Mark W. Chase
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, United Kingdom
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