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Masters LE, Tomaszewska P, Schwarzacher T, Hackel J, Zuntini AR, Heslop-Harrison P, Vorontsova MS. Phylogenomic analysis reveals five independently evolved African forage grass clades in the genus Urochloa. Ann Bot 2024; 133:725-742. [PMID: 38365451 PMCID: PMC11082517 DOI: 10.1093/aob/mcae022] [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: 12/01/2023] [Accepted: 02/21/2024] [Indexed: 02/18/2024]
Abstract
BACKGROUND AND AIMS The grass genus Urochloa (Brachiaria) sensu lato includes forage crops that are important for beef and dairy industries in tropical and sub-tropical Africa, South America and Oceania/Australia. Economically important species include U. brizantha, U. decumbens, U. humidicola, U. mutica, U. arrecta, U. trichopus, U. mosambicensis and Megathyrsus maximus, all native to the African continent. Perennial growth habits, large, fast growing palatable leaves, intra- and interspecific morphological variability, apomictic reproductive systems and frequent polyploidy are widely shared within the genus. The combination of these traits probably favoured the selection for forage domestication and weediness, but trait emergence across Urochloa cannot be modelled, as a robust phylogenetic assessment of the genus has not been conducted. We aim to produce a phylogeny for Urochloa that includes all important forage species, and identify their closest wild relatives (crop wild relatives). Finally, we will use our phylogeny and available trait data to infer the ancestral states of important forage traits across Urochloa s.l. and model the evolution of forage syndromes across the genus. METHODS Using a target enrichment sequencing approach (Angiosperm 353), we inferred a species-level phylogeny for Urochloa s.l., encompassing 54 species (~40 % of the genus) and outgroups. Phylogenies were inferred using a multispecies coalescent model and maximum likelihood method. We determined the phylogenetic placement of agriculturally important species and identified their closest wild relatives, or crop wild relatives, based on well-supported monophyly. Further, we mapped key traits associated with Urochloa forage crops to the species tree and estimated ancestral states for forage traits along branch lengths for continuous traits and at ancestral nodes in discrete traits. KEY RESULTS Agricultural species belong to five independent clades, including U. brizantha and U. decumbens lying in a previously defined species complex. Crop wild relatives were identified for these clades supporting previous sub-generic groupings in Urochloa based on morphology. Using ancestral trait estimation models, we find that five morphological traits that correlate with forage potential (perennial growth habits, culm height, leaf size, a winged rachis and large seeds) independently evolved in forage clades. CONCLUSIONS Urochloa s.l. is a highly diverse genus that contains numerous species with agricultural potential, including crop wild relatives that are currently underexploited. All forage species and their crop wild relatives naturally occur on the African continent and their conservation across their native distributions is essential. Genomic and phenotypic diversity in forage clade species and their wild relatives need to be better assessed both to develop conservation strategies and to exploit the diversity in the genus for improved sustainability in Urochloa cultivar production.
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Affiliation(s)
- Lizo E Masters
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester LE17RH, UK
- Accelerated Taxonomy/Trait Diversity and Function, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Paulina Tomaszewska
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester LE17RH, UK
- Department of Genetics and Cell Physiology, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Trude Schwarzacher
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester LE17RH, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Jan Hackel
- Accelerated Taxonomy/Trait Diversity and Function, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
- Department of Biology, University of Marburg, Karl-von-Frisch-Straße 8, 35043 Marburg, Germany
| | - Alexandre R Zuntini
- Accelerated Taxonomy/Trait Diversity and Function, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Pat Heslop-Harrison
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester LE17RH, UK
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Maria S Vorontsova
- Accelerated Taxonomy/Trait Diversity and Function, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
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Zuntini AR, Carruthers T, Maurin O, Bailey PC, Leempoel K, Brewer GE, Epitawalage N, Françoso E, Gallego-Paramo B, McGinnie C, Negrão R, Roy SR, Simpson L, Toledo Romero E, Barber VMA, Botigué L, Clarkson JJ, Cowan RS, Dodsworth S, Johnson MG, Kim JT, Pokorny L, Wickett NJ, Antar GM, DeBolt L, Gutierrez K, Hendriks KP, Hoewener A, Hu AQ, Joyce EM, Kikuchi IABS, Larridon I, Larson DA, de Lírio EJ, Liu JX, Malakasi P, Przelomska NAS, Shah T, Viruel J, Allnutt TR, Ameka GK, Andrew RL, Appelhans MS, Arista M, Ariza MJ, Arroyo J, Arthan W, Bachelier JB, Bailey CD, Barnes HF, Barrett MD, Barrett RL, Bayer RJ, Bayly MJ, Biffin E, Biggs N, Birch JL, Bogarín D, Borosova R, Bowles AMC, Boyce PC, Bramley GLC, Briggs M, Broadhurst L, Brown GK, Bruhl JJ, Bruneau A, Buerki S, Burns E, Byrne M, Cable S, Calladine A, Callmander MW, Cano Á, Cantrill DJ, Cardinal-McTeague WM, Carlsen MM, Carruthers AJA, de Castro Mateo A, Chase MW, Chatrou LW, Cheek M, Chen S, Christenhusz MJM, Christin PA, Clements MA, Coffey SC, Conran JG, Cornejo X, Couvreur TLP, Cowie ID, Csiba L, Darbyshire I, Davidse G, Davies NMJ, Davis AP, van Dijk KJ, Downie SR, Duretto MF, Duvall MR, Edwards SL, Eggli U, Erkens RHJ, Escudero M, de la Estrella M, Fabriani F, Fay MF, Ferreira PDL, Ficinski SZ, Fowler RM, Frisby S, Fu L, Fulcher T, Galbany-Casals M, Gardner EM, German DA, Giaretta A, Gibernau M, Gillespie LJ, González CC, Goyder DJ, Graham SW, Grall A, Green L, Gunn BF, Gutiérrez DG, Hackel J, Haevermans T, Haigh A, Hall JC, Hall T, Harrison MJ, Hatt SA, Hidalgo O, Hodkinson TR, Holmes GD, Hopkins HCF, Jackson CJ, James SA, Jobson RW, Kadereit G, Kahandawala IM, Kainulainen K, Kato M, Kellogg EA, King GJ, Klejevskaja B, Klitgaard BB, Klopper RR, Knapp S, Koch MA, Leebens-Mack JH, Lens F, Leon CJ, Léveillé-Bourret É, Lewis GP, Li DZ, Li L, Liede-Schumann S, Livshultz T, Lorence D, Lu M, Lu-Irving P, Luber J, Lucas EJ, Luján M, Lum M, Macfarlane TD, Magdalena C, Mansano VF, Masters LE, Mayo SJ, McColl K, McDonnell AJ, McDougall AE, McLay TGB, McPherson H, Meneses RI, Merckx VSFT, Michelangeli FA, Mitchell JD, Monro AK, Moore MJ, Mueller TL, Mummenhoff K, Munzinger J, Muriel P, Murphy DJ, Nargar K, Nauheimer L, Nge FJ, Nyffeler R, Orejuela A, Ortiz EM, Palazzesi L, Peixoto AL, Pell SK, Pellicer J, Penneys DS, Perez-Escobar OA, Persson C, Pignal M, Pillon Y, Pirani JR, Plunkett GM, Powell RF, Prance GT, Puglisi C, Qin M, Rabeler RK, Rees PEJ, Renner M, Roalson EH, Rodda M, Rogers ZS, Rokni S, Rutishauser R, de Salas MF, Schaefer H, Schley RJ, Schmidt-Lebuhn A, Shapcott A, Al-Shehbaz I, Shepherd KA, Simmons MP, Simões AO, Simões ARG, Siros M, Smidt EC, Smith JF, Snow N, Soltis DE, Soltis PS, Soreng RJ, Sothers CA, Starr JR, Stevens PF, Straub SCK, Struwe L, Taylor JM, Telford IRH, Thornhill AH, Tooth I, Trias-Blasi A, Udovicic F, Utteridge TMA, Del Valle JC, Verboom GA, Vonow HP, Vorontsova MS, de Vos JM, Al-Wattar N, Waycott M, Welker CAD, White AJ, Wieringa JJ, Williamson LT, Wilson TC, Wong SY, Woods LA, Woods R, Worboys S, Xanthos M, Yang Y, Zhang YX, Zhou MY, Zmarzty S, Zuloaga FO, Antonelli A, Bellot S, Crayn DM, Grace OM, Kersey PJ, Leitch IJ, Sauquet H, Smith SA, Eiserhardt WL, Forest F, Baker WJ. Phylogenomics and the rise of the angiosperms. Nature 2024:10.1038/s41586-024-07324-0. [PMID: 38658746 DOI: 10.1038/s41586-024-07324-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 03/15/2024] [Indexed: 04/26/2024]
Abstract
Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.
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Affiliation(s)
| | | | | | | | | | | | | | - Elaine Françoso
- Royal Botanic Gardens, Kew, Richmond, UK
- Centre for Ecology, Evolution and Behaviour, Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, London, UK
| | | | | | | | | | - Lalita Simpson
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | | | | | - Laura Botigué
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
| | | | | | - Steven Dodsworth
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | | | - Jan T Kim
- School of Physics, Engineering and Computer Science, University of Hertfordshire, Hatfield, UK
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Biodiversity and Conservation, Real Jardín Botánico (RJB-CSIC), Madrid, Spain
| | - Norman J Wickett
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Guilherme M Antar
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Departamento de Ciências Agrárias e Biológicas, Centro Universitário Norte do Espírito Santo, Universidade Federal do Espírito Santo, São Mateus, Brazil
| | | | | | - Kasper P Hendriks
- Department of Biology, University of Osnabrück, Osnabrück, Germany
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Alina Hoewener
- Plant Biodiversity, Technical University Munich, Freising, Germany
| | - Ai-Qun Hu
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Elizabeth M Joyce
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
- Systematic, Biodiversity and Evolution of Plants, Ludwig Maximilian University of Munich, Munich, Germany
| | - Izai A B S Kikuchi
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Drew A Larson
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Elton John de Lírio
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Jing-Xia Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | | | - Natalia A S Przelomska
- Royal Botanic Gardens, Kew, Richmond, UK
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Toral Shah
- Royal Botanic Gardens, Kew, Richmond, UK
| | | | | | - Gabriel K Ameka
- Department of Plant and Environmental Biology, University of Ghana, Accra, Ghana
| | - Rose L Andrew
- Botany and N.C.W. Beadle Herbarium, University of New England, Armidale, New South Wales, Australia
| | - Marc S Appelhans
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute of Plant Sciences, University of Göttingen, Göttingen, Germany
| | - Montserrat Arista
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - María Jesús Ariza
- General Research Services, Herbario SEV, CITIUS, Universidad de Sevilla, Seville, Spain
| | - Juan Arroyo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | | | | | - C Donovan Bailey
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Helen F Barnes
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | - Matthew D Barrett
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | - Russell L Barrett
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Randall J Bayer
- Department of Biological Sciences, University of Memphis, Memphis, TN, USA
| | - Michael J Bayly
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Ed Biffin
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
| | | | - Joanne L Birch
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Diego Bogarín
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Jardín Botánico Lankester, Universidad de Costa Rica, Cartago, Costa Rica
| | | | | | - Peter C Boyce
- Centro Studi Erbario Tropicale, Dipartimento di Biologia, University of Florence, Florence, Italy
| | | | | | - Linda Broadhurst
- Centre for Australian National Biodiversity Research, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Gillian K Brown
- Queensland Herbarium and Biodiversity Science, Brisbane Botanic Gardens, Toowong, Queensland, Australia
| | - Jeremy J Bruhl
- Botany and N.C.W. Beadle Herbarium, University of New England, Armidale, New South Wales, Australia
| | - Anne Bruneau
- Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques, University of Montreal, Montreal, Quebec, Canada
| | - Sven Buerki
- Department of Biological Sciences, Boise State University, Boise, ID, USA
| | - Edie Burns
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Government of Western Australia, Kensington, Western Australia, Australia
| | | | - Ainsley Calladine
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
| | | | - Ángela Cano
- Cambridge University Botanic Garden, Cambridge, UK
| | | | - Warren M Cardinal-McTeague
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Alejandra de Castro Mateo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Mark W Chase
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | | | | | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, China
| | - Maarten J M Christenhusz
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
- Plant Gateway, Den Haag, The Netherlands
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Mark A Clements
- Centre for Australian National Biodiversity Research, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Skye C Coffey
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Government of Western Australia, Kensington, Western Australia, Australia
| | - John G Conran
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Xavier Cornejo
- Herbario GUAY, Facultad de Ciencias Naturales, Universidad de Guayaquil, Guayaquil, Ecuador
| | | | - Ian D Cowie
- Northern Territory Herbarium Department of Environment Parks & Water Security, Northern Territory Government, Palmerston, Northern Territory, Australia
| | | | | | | | | | | | - Kor-Jent van Dijk
- The University of Adelaide, North Terrace Campus, Adelaide, South Australia, Australia
| | - Stephen R Downie
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Marco F Duretto
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Melvin R Duvall
- Department of Biological Sciences and Institute for the Study of the Environment, Sustainability and Energy, Northern Illinois University, DeKalb, IL, USA
| | | | - Urs Eggli
- Sukkulenten-Sammlung Zürich/ Grün Stadt Zürich, Zürich, Switzerland
| | - Roy H J Erkens
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Maastricht Science Programme, Maastricht University, Maastricht, The Netherlands
- System Earth Science, Maastricht University, Venlo, The Netherlands
| | - Marcial Escudero
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Manuel de la Estrella
- Departamento de Botánica, Ecología y Fisiología Vegetal, Facultad de Ciencias, Universidad de Córdoba, Córdoba, Spain
| | | | | | - Paola de L Ferreira
- Departamento de Biologia, Faculdade de Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
- Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Rachael M Fowler
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Sue Frisby
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Lin Fu
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | | | - Mercè Galbany-Casals
- Systematics and Evolution of Vascular Plants (UAB)-Associated Unit to CSIC by IBB, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Elliot M Gardner
- Department of Biology, Case Western Reserve University, Cleveland, OH, USA
| | | | - Augusto Giaretta
- Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados, Dourados, Brazil
| | - Marc Gibernau
- Laboratoire Sciences Pour l'Environnement, Université de Corse, Ajaccio, France
| | | | - Cynthia C González
- Herbario Trelew, Universidad Nacional de la Patagonia San Juan Bosco, Trelew, Argentina
| | | | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Bee F Gunn
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | - Diego G Gutiérrez
- Museo Argentino de Ciencias Naturales (MACN-CONICET), Buenos Aires, Argentina
| | - Jan Hackel
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Biology, Universität Marburg, Marburg, Germany
| | - Thomas Haevermans
- Institut de Systématique, Evolution, Biodiversité, Muséum National d'Histoire Naturelle, Paris, France
| | - Anna Haigh
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Tony Hall
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Melissa J Harrison
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | | | - Oriane Hidalgo
- Institut Botànic de Barcelona (IBB CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | - Trevor R Hodkinson
- Botany, School of Natural Sciences, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Gareth D Holmes
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | | | | | - Shelley A James
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Government of Western Australia, Kensington, Western Australia, Australia
| | - Richard W Jobson
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Gudrun Kadereit
- Prinzessin Therese von Bayern-Lehrstuhl für Systematik, Biodiversität & Evolution der Pflanzen, Ludwig-Maximilians-Universität München, Botanische Staatssammlung München, Botanischer Garten München-Nymphenburg, Munich, Germany
| | | | | | - Masahiro Kato
- National Museum of Nature and Science, Tsukuba, Japan
| | | | - Graham J King
- Southern Cross University, Lismore, New South Wales, Australia
| | | | | | - Ronell R Klopper
- Foundational Biodiversity Science Division, South African National Biodiversity Institute, Pretoria, South Africa
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | | | - Marcus A Koch
- Centre for Organismal Studies, Biodiversity and Plant Systematics, Heidelberg University, Heidelberg, Germany
| | | | - Frederic Lens
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | | | | | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Lan Li
- CSIRO, Canberra, Australian Capital Territory, Australia
| | | | - Tatyana Livshultz
- Department of Biodiversity, Earth and Environmental Sciences, Drexel University, Philadelphia, PA, USA
- Academy of Natural Science, Drexel University, Philadelphia, PA, USA
| | - David Lorence
- National Tropical Botanical Garden, Kalaheo, HI, USA
| | - Meng Lu
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Patricia Lu-Irving
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Jaquelini Luber
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Mabel Lum
- Bioplatforms Australia Ltd, Sydney, New South Wales, Australia
| | - Terry D Macfarlane
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Government of Western Australia, Kensington, Western Australia, Australia
| | | | - Vidal F Mansano
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Kristina McColl
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Angela J McDonnell
- Department of Biological Sciences, Saint Cloud State University, Saint Cloud, MN, USA
| | - Andrew E McDougall
- The University of Adelaide, North Terrace Campus, Adelaide, South Australia, Australia
| | - Todd G B McLay
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | - Hannah McPherson
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Rosa I Meneses
- Instituto de Arqueología y Antropología, Universidad Católica del Norte, San Pedro de Atacama, Chile
| | | | | | | | | | | | - Taryn L Mueller
- Department of Ecology, Evolution & Behavior, University of Minnesota, St. Paul, MN, USA
| | - Klaus Mummenhoff
- Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Jérôme Munzinger
- AMAP Lab, Université Montpellier, IRD, CIRAD, CNRS INRAE, Montpellier, France
| | - Priscilla Muriel
- Laboratorio de Ecofisiología, Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | - Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
- Centre for Australian National Biodiversity Research, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Lars Nauheimer
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | - Francis J Nge
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
| | - Reto Nyffeler
- Department of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland
| | - Andrés Orejuela
- Royal Botanic Garden Edinburgh, Edinburgh, UK
- Grupo de Investigación en Recursos Naturales Amazónicos, Instituto Tecnológico del Putumayo, Mocoa, Colombia
| | - Edgardo M Ortiz
- Plant Biodiversity, Technical University Munich, Freising, Germany
| | - Luis Palazzesi
- Museo Argentino de Ciencias Naturales (MACN-CONICET), Buenos Aires, Argentina
| | - Ariane Luna Peixoto
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Jaume Pellicer
- Institut Botànic de Barcelona (IBB CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | - Darin S Penneys
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | | | - Claes Persson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Marc Pignal
- Institut de Systématique, Evolution, Biodiversité, Muséum National d'Histoire Naturelle, Paris, France
| | - Yohan Pillon
- LSTM Université Montpellier, CIRADIRD, Montpellier, France
| | - José R Pirani
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | - Carmen Puglisi
- Royal Botanic Gardens, Kew, Richmond, UK
- Missouri Botanical Garden, St. Louis, MO, USA
| | - Ming Qin
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Richard K Rabeler
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Matthew Renner
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Eric H Roalson
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michele Rodda
- National Parks Board, Singapore Botanic Gardens, Singapore, Singapore
| | | | - Saba Rokni
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Rolf Rutishauser
- Department of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland
| | - Miguel F de Salas
- Tasmanian Herbarium, University of Tasmania, Sandy Bay, Tasmania, Australia
| | - Hanno Schaefer
- Plant Biodiversity, Technical University Munich, Freising, Germany
| | | | - Alexander Schmidt-Lebuhn
- Centre for Australian National Biodiversity Research, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Alison Shapcott
- School of Science Technology and Engineering, Center for Bioinnovation, University Sunshine Coast, Sippy Downs, Queensland, Australia
| | | | - Kelly A Shepherd
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Government of Western Australia, Kensington, Western Australia, Australia
| | - Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - André O Simões
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Campinas, Brazil
| | | | - Michelle Siros
- Royal Botanic Gardens, Kew, Richmond, UK
- University of California, San Francisco, San Francisco, CA, USA
| | - Eric C Smidt
- Departamento de Botânica, Universidade Federal do Paraná, Curitiba, Brazil
| | - James F Smith
- Department of Biological Sciences, Boise State University, Boise, ID, USA
| | - Neil Snow
- Pittsburg State University, Pittsburg, KS, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | | | | | - Julian R Starr
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | | | | | | | - Ian R H Telford
- Botany and N.C.W. Beadle Herbarium, University of New England, Armidale, New South Wales, Australia
| | - Andrew H Thornhill
- Botany and N.C.W. Beadle Herbarium, University of New England, Armidale, New South Wales, Australia
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Ifeanna Tooth
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | | | - Frank Udovicic
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | | | - Jose C Del Valle
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - G Anthony Verboom
- Department of Biological Sciences and Bolus Herbarium, University of Cape Town, Cape Town, South Africa
| | - Helen P Vonow
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
| | | | - Jurriaan M de Vos
- Department of Environmental Sciences-Botany, University of Basel, Basel, Switzerland
| | | | - Michelle Waycott
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Cassiano A D Welker
- Instituto de Biologia, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Adam J White
- Australian National Herbarium, Centre for Australian National Biodiversity Research, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | | | - Luis T Williamson
- The University of Adelaide, North Terrace Campus, Adelaide, South Australia, Australia
| | - Trevor C Wilson
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Sin Yeng Wong
- Institute of Biodiversity And Environmental Conservation, Universiti Malaysia Sarawak, Samarahan, Malaysia
| | - Lisa A Woods
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | | | - Stuart Worboys
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | | | - Ya Yang
- University of Minnesota-Twin Cities, St. Paul, MN, USA
| | | | - Meng-Yuan Zhou
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | | | | | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Oxford, Oxford, UK
| | | | - Darren M Crayn
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | - Olwen M Grace
- Royal Botanic Gardens, Kew, Richmond, UK
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | | | | | - Hervé Sauquet
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - William J Baker
- Royal Botanic Gardens, Kew, Richmond, UK.
- Department of Biology, Aarhus University, Aarhus, Denmark.
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3
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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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Hendriks KP, Kiefer C, Al-Shehbaz IA, Bailey CD, Hooft van Huysduynen A, Nikolov LA, Nauheimer L, Zuntini AR, German DA, Franzke A, Koch MA, Lysak MA, Toro-Núñez Ó, Özüdoğru B, Invernón VR, Walden N, Maurin O, Hay NM, Shushkov P, Mandáková T, Schranz ME, Thulin M, Windham MD, Rešetnik I, Španiel S, Ly E, Pires JC, Harkess A, Neuffer B, Vogt R, Bräuchler C, Rainer H, Janssens SB, Schmull M, Forrest A, Guggisberg A, Zmarzty S, Lepschi BJ, Scarlett N, Stauffer FW, Schönberger I, Heenan P, Baker WJ, Forest F, Mummenhoff K, Lens F. Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset. Curr Biol 2023; 33:4052-4068.e6. [PMID: 37659415 DOI: 10.1016/j.cub.2023.08.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/22/2023] [Accepted: 08/08/2023] [Indexed: 09/04/2023]
Abstract
The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data. We found cytonuclear discordance between the two, which is likely a result of rampant hybridization among closely and more distantly related lineages. To evaluate the impact of such hybridization on the nuclear phylogeny reconstruction, we performed five different gene sampling routines, which increasingly removed putatively paralog genes. Our cleaned subset of 297 genes revealed high support for the tribes, whereas support for the main lineages (supertribes) was moderate. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene origin of the family. Finally, our results strongly support a recently published new family classification, dividing the family into two subfamilies (one with five supertribes), together representing 58 tribes. This includes five recently described or re-established tribes, including Arabidopsideae, a monogeneric tribe accommodating Arabidopsis without any close relatives. With a worldwide community of thousands of researchers working on Brassicaceae and its diverse members, our new genus-level family phylogeny will be an indispensable tool for studies on biodiversity and plant biology.
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Affiliation(s)
- Kasper P Hendriks
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany; Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands.
| | - Christiane Kiefer
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | | | - C Donovan Bailey
- Department of Biology, New Mexico State University, PO Box 30001, MSC 3AF, Las Cruces, NM 88003, USA
| | - Alex Hooft van Huysduynen
- Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands; Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Lachezar A Nikolov
- Department of Molecular, Cell and Developmental Biology, University of California, 610 Charles E. Young Dr. S., Los Angeles, CA 90095, USA
| | - Lars Nauheimer
- Australian Tropical Herbarium, James Cook University, PO Box 6811, Cairns, QLD 4870, Australia
| | | | - Dmitry A German
- South-Siberian Botanical Garden, Altai State University, Barnaul, Lesosechnaya Ulitsa, 25, Barnaul, Altai Krai, Russia
| | - Andreas Franzke
- Heidelberg Botanic Garden, Heidelberg University, Im Neuenheimer Feld 361, 69120 Heidelberg, Germany
| | - Marcus A Koch
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Óscar Toro-Núñez
- Departamento de Botánica, Universidad de Concepción, Barrio Universitario, Concepción, Chile
| | - Barış Özüdoğru
- Department of Biology, Hacettepe University, Beytepe, Ankara 06800, Türkiye
| | - Vanessa R Invernón
- Sorbonne Université, Muséum National d'Histoire Naturelle, Institut de Systématique, Évolution, Biodiversité (ISYEB), CP 39, 57 rue Cuvier, 75231 Paris Cedex 05, France
| | - Nora Walden
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Nikolai M Hay
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Philip Shushkov
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, IN 47405, USA
| | - Terezie Mandáková
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Mats Thulin
- Department of Organismal Biology, Uppsala University, Norbyvägen 18, 752 36 Uppsala, Sweden
| | | | - Ivana Rešetnik
- Department of Biology, University of Zagreb, Marulićev trg 20/II, 10000 Zagreb, Croatia
| | - Stanislav Španiel
- Institute of Botany, Slovak Academy of Sciences, Plant Science and Biodiversity Centre, Dúbravská cesta 9, 845 23 Bratislava, Slovakia
| | - Elfy Ly
- Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands; Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - J Chris Pires
- Soil and Crop Sciences, Colorado State University, 307 University Ave., Fort Collins, CO 80523-1170, USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Barbara Neuffer
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Robert Vogt
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195 Berlin, Germany
| | - Christian Bräuchler
- Department of Botany, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Heimo Rainer
- Department of Botany, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Steven B Janssens
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31 - box 2435, 3001 Leuven, Belgium; Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium
| | - Michaela Schmull
- Harvard University Herbaria, 22 Divinity Ave., Cambridge, MA 02138, USA
| | - Alan Forrest
- Centre for Middle Eastern Plants, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Alessia Guggisberg
- ETH Zürich, Institut für Integrative Biologie, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Sue Zmarzty
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Brendan J Lepschi
- Australian National Herbarium, Centre for Australian National Biodiversity Research, Clunies Ross St, Acton, ACT 2601, Australia
| | - Neville Scarlett
- La Trobe University, Plenty Road and Kingsbury Dr., Bundoora, VIC 3086, Australia
| | - Fred W Stauffer
- Conservatory and Botanic Gardens of Geneva, CP 60, Chambésy, 1292 Geneva, Switzerland
| | - Ines Schönberger
- Manaaki Whenua Landcare Research, Allan Herbarium, PO Box 69040, Lincoln, New Zealand
| | - Peter Heenan
- Manaaki Whenua Landcare Research, Allan Herbarium, PO Box 69040, Lincoln, New Zealand
| | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany.
| | - Frederic Lens
- Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands; Institute of Biology Leiden, Plant Sciences, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands.
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5
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Joyce EM, Appelhans MS, Buerki S, Cheek M, de Vos JM, Pirani JR, Zuntini AR, Bachelier JB, Bayly MJ, Callmander MW, Devecchi MF, Pell SK, Groppo M, Lowry PP, Mitchell J, Siniscalchi CM, Munzinger J, Orel HK, Pannell CM, Nauheimer L, Sauquet H, Weeks A, Muellner-Riehl AN, Leitch IJ, Maurin O, Forest F, Nargar K, Thiele KR, Baker WJ, Crayn DM. Phylogenomic analyses of Sapindales support new family relationships, rapid Mid-Cretaceous Hothouse diversification, and heterogeneous histories of gene duplication. Front Plant Sci 2023; 14:1063174. [PMID: 36959945 PMCID: PMC10028101 DOI: 10.3389/fpls.2023.1063174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Sapindales is an angiosperm order of high economic and ecological value comprising nine families, c. 479 genera, and c. 6570 species. However, family and subfamily relationships in Sapindales remain unclear, making reconstruction of the order's spatio-temporal and morphological evolution difficult. In this study, we used Angiosperms353 target capture data to generate the most densely sampled phylogenetic trees of Sapindales to date, with 448 samples and c. 85% of genera represented. The percentage of paralogous loci and allele divergence was characterized across the phylogeny, which was time-calibrated using 29 rigorously assessed fossil calibrations. All families were supported as monophyletic. Two core family clades subdivide the order, the first comprising Kirkiaceae, Burseraceae, and Anacardiaceae, the second comprising Simaroubaceae, Meliaceae, and Rutaceae. Kirkiaceae is sister to Burseraceae and Anacardiaceae, and, contrary to current understanding, Simaroubaceae is sister to Meliaceae and Rutaceae. Sapindaceae is placed with Nitrariaceae and Biebersteiniaceae as sister to the core Sapindales families, but the relationships between these families remain unclear, likely due to their rapid and ancient diversification. Sapindales families emerged in rapid succession, coincident with the climatic change of the Mid-Cretaceous Hothouse event. Subfamily and tribal relationships within the major families need revision, particularly in Sapindaceae, Rutaceae and Meliaceae. Much of the difficulty in reconstructing relationships at this level may be caused by the prevalence of paralogous loci, particularly in Meliaceae and Rutaceae, that are likely indicative of ancient gene duplication events such as hybridization and polyploidization playing a role in the evolutionary history of these families. This study provides key insights into factors that may affect phylogenetic reconstructions in Sapindales across multiple scales, and provides a state-of-the-art phylogenetic framework for further research.
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Affiliation(s)
- Elizabeth M. Joyce
- Systematics, Biodiversity and Evolution of Plants, Ludwig-Maximilians-Universität München, Munich, Germany
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
| | - Marc S. Appelhans
- Department of Systematics, Biodiversity and Evolution of Plants, University of Göttingen, Goettingen, Germany
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Sven Buerki
- Department of Biological Sciences, Boise State University, Boise, ID, United States
| | - Martin Cheek
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Jurriaan M. de Vos
- Department of Environmental Sciences, University Basel, Basel, Switzerland
| | - José R. Pirani
- Departamento de Botaênica, Universidade de Saão Paulo, Herbário SPF, Saão Paulo, Brazil
| | | | | | - Michael J. Bayly
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | | | - Marcelo F. Devecchi
- Departamento de Botaênica, Universidade de Saão Paulo, Herbário SPF, Saão Paulo, Brazil
| | - Susan K. Pell
- United States Botanic Garden, Washington, DC, United States
| | - Milton Groppo
- Departamento de Botaênica, Universidade de Saão Paulo, Herbário SPF, Saão Paulo, Brazil
| | - Porter P. Lowry
- Missouri Botanical Garden, St. Louis, MO, United States
- Institut de Systématique, Évolution, et Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, École Pratique des Hautes Études, Université des Antilles, Paris, France
| | - John Mitchell
- New York Botanical Garden, New York, NY, United States
| | - Carolina M. Siniscalchi
- Department of Biological Sciences, Harned Hall, Mississippi State University, Mississippi State, MS, United States
| | - Jérôme Munzinger
- AMAP, Université Montpellier, Institut de Recherche pour le Développement (IRD), Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Centre National de la Recherche Scientifique (CNRS), Institut national de la recherche agronomique (INRAE), Montpellier, France
| | - Harvey K. Orel
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Caroline M. Pannell
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Biology, Oxford University, Oxford, United Kingdom
- Marine Laboratory, Queen’s University Belfast, Portaferry, United Kingdom
| | - Lars Nauheimer
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
| | - Hervé Sauquet
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia
| | - Andrea Weeks
- Department of Biology, George Mason University, Fairfax, VA, United States
| | - Alexandra N. Muellner-Riehl
- Department of Molecular Evolution and Plant Systematics & Herbarium, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | | | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
- National Research Collections Australia, Commonwealth Industrial and Scientific Research Organization (CSIRO), Canberra, ACT, Australia
| | - Kevin R. Thiele
- School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | | | - Darren M. Crayn
- College of Science and Engineering, James Cook University, Cairns, QLD, Australia
- Australian Tropical Herbarium, James Cook University, Cairns, QLD, Australia
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6
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Haigh AL, Gibernau M, Maurin O, Bailey P, Carlsen MM, Hay A, Leempoel K, McGinnie C, Mayo S, Morris S, Pérez-Escobar OA, Yeng WS, Zuluaga A, Zuntini AR, Baker WJ, Forest F. Target sequence data shed new light on the infrafamilial classification of Araceae. Am J Bot 2023; 110:e16117. [PMID: 36480380 DOI: 10.1002/ajb2.16117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
PREMISE Recent phylogenetic studies of the Araceae have confirmed the position of the duckweeds nested within the aroids, and the monophyly of a clade containing all the unisexual flowered aroids plus the bisexual-flowered Calla palustris. The main objective of the present study was to better resolve the deep phylogenetic relationships among the main lineages within the family, particularly the relationships between the eight currently recognized subfamilies. We also aimed to confirm the phylogenetic position of the enigmatic genus Calla in relation to the long-debated evolutionary transition between bisexual and unisexual flowers in the family. METHODS Nuclear DNA sequence data were generated for 128 species across 111 genera (78%) of Araceae using target sequence capture and the Angiosperms 353 universal probe set. RESULTS The phylogenomic data confirmed the monophyly of the eight Araceae subfamilies, but the phylogenetic position of subfamily Lasioideae remains uncertain. The genus Calla is included in subfamily Aroideae, which has also been expanded to include Zamioculcadoideae. The tribe Aglaonemateae is newly defined to include the genera Aglaonema and Boycea. CONCLUSIONS Our results strongly suggest that new research on African genera (Callopsis, Nephthytis, and Anubias) and Calla will be important for understanding the early evolution of the Aroideae. Also of particular interest are the phylogenetic positions of the isolated genera Montrichardia, Zantedeschia, and Anchomanes, which remain only moderately supported here.
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Affiliation(s)
- Anna L Haigh
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Marc Gibernau
- Laboratory of Sciences for the Environment (UMR 6134), CNRS-University of Corsica, Ajaccio, 20000, France
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Paul Bailey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | | | - Alistair Hay
- Australian Institute of Botanical Science, Royal Botanic Gardens & Domain Trust, Mrs Macquarie's Road, Sydney, 2000, Australia
| | - Kevin Leempoel
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | | | - Simon Mayo
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Sarah Morris
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | | | - Wong Sin Yeng
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak (UNIMAS), 94300, Kota Samarahan, Sarawak, Malaysia
| | - Alejandro Zuluaga
- Departamento de Biología, Universidad del Valle, Calle 13 #100-00, Cali, Colombia
| | | | - William J Baker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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7
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Tang Y, Yin S, Pace MR, Gerolamo CS, Nogueira A, Zuntini AR, Lohmann LG, Plath M, Liesche J. Diameters of phloem sieve elements can predict stem growth rates of woody plants. Tree Physiol 2022; 42:1560-1569. [PMID: 35218199 DOI: 10.1093/treephys/tpac022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Understanding forest dynamics is crucial to addressing climate change and reforestation challenges. Plant anatomy can help predict growth rates of woody plants, contributing key information on forest dynamics. Although features of the water-transport system (xylem) have long been used to predict plant growth, the potential contribution of carbon-transporting tissue (phloem) remains virtually unexplored. Here, we use data from 347 woody plant species to investigate whether species-specific stem diameter growth rates can be predicted by the diameter of both the xylem and phloem conducting cells when corrected for phylogenetic relatedness. We found positive correlations between growth rate, phloem sieve element diameter and xylem vessel diameter in liana species sampled in the field. Moreover, we obtained similar results for data extracted from the Xylem Database, an online repository of functional, anatomical and image data for woody plant species. Information from this database confirmed the correlation of sieve element diameter and growth rate across woody plants of various growth forms. Furthermore, we used data subsets to explore potential influences of biomes, growth forms and botanical family association. Subsequently, we combined anatomical and geoclimatic data to train an artificial neural network to predict growth rates. Our results demonstrate that sugar transport architecture is associated with growth rate to a similar degree as water-transport architecture. Furthermore, our results illustrate the potential value of artificial neural networks for modeling plant growth under future climatic scenarios.
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Affiliation(s)
- Yunjia Tang
- Northwest A&F University, College of Life Sciences, Yangling 712100, China
| | - Shijiao Yin
- Northwest A&F University, College of Life Sciences, Yangling 712100, China
- Biomass Energy Center for Arid Lands, Northwest A & F University, Yangling 712100, China
- State Key Laboratory of Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, China
| | - Marcelo R Pace
- Universidad Nacional Autónoma de México, Instituto de Biología, Departamento de Botánica, Circuito Zona Deportiva s.n., Apartado Postal 70-367, Ciudad Universitaria, Coyoacán, Mexico City 04510, Mexico
| | - Caian S Gerolamo
- Universidade de São Paulo, Instituto de Biociências, Departamento de Botânica, Rua do Matão, 277, Cidade Universitária, São Paulo, SP 05508-090, Brazil
| | - Anselmo Nogueira
- Universidade Federal do ABC, Centro de Ciências Naturais e Humanas (CCNH), Rua Arcturus, 03, São Bernardo do Campo, SP 09606-070, Brazil
| | | | - Lúcia G Lohmann
- Universidade de São Paulo, Instituto de Biociências, Departamento de Botânica, Rua do Matão, 277, Cidade Universitária, São Paulo, SP 05508-090, Brazil
| | - Martin Plath
- Northwest A&F University, College of Animal Science and Technology, Yangling 712100, China
| | - Johannes Liesche
- Northwest A&F University, College of Life Sciences, Yangling 712100, China
- Biomass Energy Center for Arid Lands, Northwest A & F University, Yangling 712100, China
- State Key Laboratory of Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, China
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8
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Simões ARG, Eserman LA, Zuntini AR, Chatrou LW, Utteridge TMA, Maurin O, Rokni S, Roy S, Forest F, Baker WJ, Stefanović S. A Bird's Eye View of the Systematics of Convolvulaceae: Novel Insights From Nuclear Genomic Data. Front Plant Sci 2022; 13:889988. [PMID: 35909765 PMCID: PMC9331175 DOI: 10.3389/fpls.2022.889988] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Convolvulaceae is a family of c. 2,000 species, distributed across 60 currently recognized genera. It includes species of high economic importance, such as the crop sweet potato (Ipomoea batatas L.), the ornamental morning glories (Ipomoea L.), bindweeds (Convolvulus L.), and dodders, the parasitic vines (Cuscuta L.). Earlier phylogenetic studies, based predominantly on chloroplast markers or a single nuclear region, have provided a framework for systematic studies of the family, but uncertainty remains at the level of the relationships among subfamilies, tribes, and genera, hindering evolutionary inferences and taxonomic advances. One of the enduring enigmas has been the relationship of Cuscuta to the rest of Convolvulaceae. Other examples of unresolved issues include the monophyly and relationships within Merremieae, the "bifid-style" clade (Dicranostyloideae), as well as the relative positions of Erycibe Roxb. and Cardiochlamyeae. In this study, we explore a large dataset of nuclear genes generated using Angiosperms353 kit, as a contribution to resolving some of these remaining phylogenetic uncertainties within Convolvulaceae. For the first time, a strongly supported backbone of the family is provided. Cuscuta is confirmed to belong within family Convolvulaceae. "Merremieae," in their former tribal circumscription, are recovered as non-monophyletic, with the unexpected placement of Distimake Raf. as sister to the clade that contains Ipomoeeae and Decalobanthus Ooststr., and Convolvuleae nested within the remaining "Merremieae." The monophyly of Dicranostyloideae, including Jacquemontia Choisy, is strongly supported, albeit novel relationships between genera are hypothesized, challenging the current tribal delimitation. The exact placements of Erycibe and Cuscuta remain uncertain, requiring further investigation. Our study explores the benefits and limitations of increasing sequence data in resolving higher-level relationships within Convolvulaceae, and highlights the need for expanded taxonomic sampling, to facilitate a much-needed revised classification of the family.
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Affiliation(s)
| | - Lauren A. Eserman
- Conservation & Research Department, Atlanta Botanical Garden, Atlanta, GA, United States
| | | | - Lars W. Chatrou
- Systematic and Evolutionary Botany Lab, University of Ghent, Ghent, Belgium
| | | | | | - Saba Rokni
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Shyamali Roy
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Saša Stefanović
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
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Fonseca LHM, Nazareno AG, Thode VA, Zuntini AR, Lohmann LG. Putting small and big pieces together: a genome assembly approach reveals the largest Lamiid plastome in a woody vine. PeerJ 2022; 10:e13207. [PMID: 35415013 PMCID: PMC8995027 DOI: 10.7717/peerj.13207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 03/10/2022] [Indexed: 01/12/2023] Open
Abstract
The plastid genome of flowering plants generally shows conserved structural organization, gene arrangement, and gene content. While structural reorganizations are uncommon, examples have been documented in the literature during the past years. Here we assembled the entire plastome of Bignonia magnifica and compared its structure and gene content with nine other Lamiid plastomes. The plastome of B. magnifica is composed of 183,052 bp and follows the canonical quadripartite structure, synteny, and gene composition of other angiosperms. Exceptionally large inverted repeat (IR) regions are responsible for the uncommon length of the genome. At least four events of IR expansion were observed among the seven Bignoniaceae species compared, suggesting multiple expansions of the IRs over the SC regions in the family. A comparison with 6,231 other complete plastomes of flowering plants available on GenBank revealed that the plastome of B. magnifica is the longest Lamiid plastome described to date. The newly generated plastid genome was used as a source of selected genes. These genes were combined with orthologous regions sampled from other species of Bignoniaceae and all gene alignments concatenated to infer a phylogeny of the family. The tree recovered is consistent with known relationships within the Bignoniaceae.
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Affiliation(s)
- Luiz Henrique M. Fonseca
- Instituto de Biocências, Universidade de São Paulo, São Paulo, Brazil,Department of Biology, Ghent University, Ghent, Flanders, Belgium
| | - Alison G. Nazareno
- Instituto de Biocências, Universidade de São Paulo, São Paulo, Brazil,Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Verônica A. Thode
- Instituto de Biocências, Universidade de São Paulo, São Paulo, Brazil,Departamento de Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Alexandre R. Zuntini
- Instituto de Biocências, Universidade de São Paulo, São Paulo, Brazil,Royal Botanic Gardens, Kew, London, United Kingdom
| | - Lúcia G. Lohmann
- Instituto de Biocências, Universidade de São Paulo, São Paulo, Brazil
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10
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Clarkson JJ, Zuntini AR, Maurin O, Downie SR, Plunkett GM, Nicolas AN, Smith JF, Feist MAE, Gutierrez K, Malakasi P, Bailey P, Brewer GE, Epitawalage N, Zmarzty S, Forest F, Baker WJ. A higher-level nuclear phylogenomic study of the carrot family (Apiaceae). Am J Bot 2021; 108:1252-1269. [PMID: 34287829 DOI: 10.1002/ajb2.1701] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
PREMISE The carrot family (Apiaceae) comprises 466 genera, which include many well-known crops (e.g., aniseed, caraway, carrots, celery, coriander, cumin, dill, fennel, parsley, and parsnips). Higher-level phylogenetic relationships among subfamilies, tribes, and other major clades of Apiaceae are not fully resolved. This study aims to address this important knowledge gap. METHODS Target sequence capture with the universal Angiosperms353 probe set was used to examine phylogenetic relationships in 234 genera of Apiaceae, representing all four currently recognized subfamilies (Apioideae, Azorelloideae, Mackinlayoideae, and Saniculoideae). Recovered nuclear genes were analyzed using both multispecies coalescent and concatenation approaches. RESULTS We recovered hundreds of nuclear genes even from old and poor-quality herbarium specimens. Of particular note, we placed with strong support three incertae sedis genera (Platysace, Klotzchia, and Hermas); all three occupy isolated positions, with Platysace resolved as sister to all remaining Apiaceae. We placed nine genera (Apodicarpum, Bonannia, Grafia, Haplosciadium, Microsciadium, Physotrichia, Ptychotis, Tricholaser, Xatardia) that have never previously been included in any molecular phylogenetic study. CONCLUSIONS We provide support for the maintenance of the four existing subfamilies of Apiaceae, while recognizing that Hermas, Klotzschia, and the Platysace clade may each need to be accommodated in additional subfamilies (pending improved sampling). The placement of the currently apioid genus Phlyctidocarpa can be accommodated by the expansion of subfamily Saniculoideae, although adequate morphological synapomorphies for this grouping are yet to be defined. This is the first phylogenetic study of the Apiaceae using high-throughput sequencing methods and represents an unprecedented evolutionary framework for the group.
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Affiliation(s)
| | | | - Olivier Maurin
- Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AE, UK
| | - Stephen R Downie
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Gregory M Plunkett
- Cullman Program for Molecular Systematics, New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY, 10458, USA
| | | | - James F Smith
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, ID, 83725-1515, USA
| | - Mary Ann E Feist
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, WI, 53706, USA
| | - Karime Gutierrez
- Department of Biology, Smith College, Burton Hall 115, Northampton, MA, 01063, USA
| | | | - Paul Bailey
- Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AE, UK
| | - Grace E Brewer
- Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AE, UK
| | | | - Sue Zmarzty
- Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AE, UK
| | - Félix Forest
- Royal Botanic Gardens Kew, Richmond, Surrey, TW9 3AE, UK
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11
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Antonelli A, Clarkson JJ, Kainulainen K, Maurin O, Brewer GE, Davis AP, Epitawalage N, Goyder DJ, Livshultz T, Persson C, Pokorny L, Straub SCK, Struwe L, Zuntini AR, Forest F, Baker WJ. Settling a family feud: a high-level phylogenomic framework for the Gentianales based on 353 nuclear genes and partial plastomes. Am J Bot 2021; 108:1143-1165. [PMID: 34254285 DOI: 10.1002/ajb2.1697] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Comprising five families that vastly differ in species richness-ranging from Gelsemiaceae with 13 species to the Rubiaceae with 13,775 species-members of the Gentianales are often among the most species-rich and abundant plants in tropical forests. Despite considerable phylogenetic work within particular families and genera, several alternative topologies for family-level relationships within Gentianales have been presented in previous studies. METHODS Here we present a phylogenomic analysis based on nuclear genes targeted by the Angiosperms353 probe set for approximately 150 species, representing all families and approximately 85% of the formally recognized tribes. We were able to retrieve partial plastomes from off-target reads for most taxa and infer phylogenetic trees for comparison with the nuclear-derived trees. RESULTS We recovered high support for over 80% of all nodes. The plastid and nuclear data are largely in agreement, except for some weakly to moderately supported relationships. We discuss the implications of our results for the order's classification, highlighting points of increased support for previously uncertain relationships. Rubiaceae is sister to a clade comprising (Gentianaceae + Gelsemiaceae) + (Apocynaceae + Loganiaceae). CONCLUSIONS The higher-level phylogenetic relationships within Gentianales are confidently resolved. In contrast to recent studies, our results support the division of Rubiaceae into two subfamilies: Cinchonoideae and Rubioideae. We do not formally recognize Coptosapelteae and Luculieae within any particular subfamily but treat them as incertae sedis. Our framework paves the way for further work on the phylogenetics, biogeography, morphological evolution, and macroecology of this important group of flowering plants.
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Affiliation(s)
- Alexandre Antonelli
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 405 30, Sweden
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | | | - Kent Kainulainen
- Gothenburg Botanical Garden, Carl Skottsbergs gata 22 A, Gothenburg, 413 19, Sweden
| | | | | | | | | | | | - Tatyana Livshultz
- Department of Biodiversity Earth and Environmental Sciences and Academy of Natural Sciences, Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA, 19103, USA
| | - Claes Persson
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, 405 30, Sweden
| | | | - Shannon C K Straub
- Department of Biology, Hobart and William Smith Colleges, 300 Pulteney Street, Geneva, NY, 14456, USA
| | - Lena Struwe
- Department of Ecology, Evolution, and Natural Resources & Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, NJ, 08901, USA
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12
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Zuntini AR, Frankel LP, Pokorny L, Forest F, Baker WJ. A comprehensive phylogenomic study of the monocot order Commelinales, with a new classification of Commelinaceae. Am J Bot 2021; 108:1066-1086. [PMID: 34278560 DOI: 10.1002/ajb2.1698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/02/2021] [Indexed: 05/03/2023]
Abstract
PREMISE Resolving relationships within order Commelinales has posed quite a challenge, as reflected in its unstable infra-familial classification. Thus, we investigated (1) relationships across families and genera of Commelinales; (2) phylogenetic placement of never-before sequenced genera; (3) how well off-target plastid data integrate with other plastid-based data sets; and (4) how the novel inferences coincide with the infra-familial classification. METHODS We generated two large data sets (nuclear and plastome) by means of target sequence capture using the Angiosperms353 probe set, with additional sequences mined from publicly available transcriptomes and full plastomes. A third extended-plastid data set was considered, including all species with sequences in public repositories. Species trees were inferred under a multispecies coalescent framework from individual gene trees and also using maximum likelihood analyses from concatenated and partitioned data. RESULTS The nuclear, plastome, and extended-plastid data sets include 52, 53, and 58 genera, respectively, and up to 290 species of Commelinales, representing the most comprehensive molecular sampling for the order to date, which includes seven never-before sequenced genera. CONCLUSIONS We inferred robust phylogenies supporting the monophyly of Commelinales and its five constituent families, and we recovered the clades Pontederiaceae-Haemodoraceae and Hanguanaceae-Commelinaceae, as previously reported. The placement of Philydraceae remains contentious. Relationships within the two largest families, Commelinaceae and Haemodoraceae, are resolved. Based on the latter results, we confirm the subfamilial classification of Haemodoraceae and propose a new classification for Commelinaceae, which includes the synonymization of Tapheocarpa in Commelina.
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Affiliation(s)
| | - Lorna P Frankel
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Faculty of Life and Environmental Sciences, University of Southampton Highfield Campus, Southampton, SO17 1BJ, UK
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Centre for Plant Biotechnology and Genomics (CBGP UPM - INIA), Autopista M-40, Km 38, Pozuelo de Alarcón (Madrid), 28223, Spain
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13
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Maurin O, Anest A, Bellot S, Biffin E, Brewer G, Charles-Dominique T, Cowan RS, Dodsworth S, Epitawalage N, Gallego B, Giaretta A, Goldenberg R, Gonçalves DJP, Graham S, Hoch P, Mazine F, Low YW, McGinnie C, Michelangeli FA, Morris S, Penneys DS, Pérez Escobar OA, Pillon Y, Pokorny L, Shimizu G, Staggemeier VG, Thornhill AH, Tomlinson KW, Turner IM, Vasconcelos T, Wilson PG, Zuntini AR, Baker WJ, Forest F, Lucas E. A nuclear phylogenomic study of the angiosperm order Myrtales, exploring the potential and limitations of the universal Angiosperms353 probe set. Am J Bot 2021; 108:1087-1111. [PMID: 34297852 DOI: 10.1002/ajb2.1699] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 05/29/2021] [Indexed: 06/13/2023]
Abstract
PREMISE To further advance the understanding of the species-rich, economically and ecologically important angiosperm order Myrtales in the rosid clade, comprising nine families, approximately 400 genera and almost 14,000 species occurring on all continents (except Antarctica), we tested the Angiosperms353 probe kit. METHODS We combined high-throughput sequencing and target enrichment with the Angiosperms353 probe kit to evaluate a sample of 485 species across 305 genera (76% of all genera in the order). RESULTS Results provide the most comprehensive phylogenetic hypothesis for the order to date. Relationships at all ranks, such as the relationship of the early-diverging families, often reflect previous studies, but gene conflict is evident, and relationships previously found to be uncertain often remain so. Technical considerations for processing HTS data are also discussed. CONCLUSIONS High-throughput sequencing and the Angiosperms353 probe kit are powerful tools for phylogenomic analysis, but better understanding of the genetic data available is required to identify genes and gene trees that account for likely incomplete lineage sorting and/or hybridization events.
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Affiliation(s)
- Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Artemis Anest
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sidonie Bellot
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Edward Biffin
- School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- State Herbarium of South Australia, PO Box 1047, Adelaide, South Australia, 5001, Australia
| | - Grace Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Tristan Charles-Dominique
- Centre National de la Recherche Scientifique (CNRS), Sorbonne University, 4 Place Jussieu, Paris, 75005, France
| | - Robyn S Cowan
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, University Square, Luton, LU1 3JU, UK
| | | | - Berta Gallego
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Augusto Giaretta
- Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados - UFGD, Dourados, MS, Brazil
| | - Renato Goldenberg
- Departamento de Botânica, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | | | | | - Peter Hoch
- Missouri Botanical Garden, St. Louis, MO, 63110, USA
| | - Fiorella Mazine
- Departamento de Ciências Ambientais, Centro de Ciências e Tecnologias para a Sustentabilidade, Universidade Federal de São Carlos - campus Sorocaba, Sorocaba, SP, 18052-780, Brazil
| | - Yee Wen Low
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, 259569, Singapore
- School of Biological Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | | | - Fabián A Michelangeli
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY, 10458-5126, USA
| | - Sarah Morris
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Darin S Penneys
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, 28403, USA
| | | | - Yohan Pillon
- LSTM, IRD, INRAE, CIRAD, Institut Agro, Univ. Montpellier, Montpellier, France
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Centre for Plant Biotechnology and Genomics (CBGP UPM - INIA), Autopista M-40, Km 38, Pozuelo de Alarcón (Madrid), 28223, Spain
| | - Gustavo Shimizu
- Department of Plant Biology, University of Campinas, Campinas, São Paulo, 13083-970, Brazil
| | - Vanessa G Staggemeier
- Departamento de Ecologia, Centro de Biociências, Universidade Federal do Rio Grande do Norte, Natal, RN, 59078-970, Brazil
| | - Andrew H Thornhill
- School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, South Australia, 5005, Australia
- State Herbarium of South Australia, PO Box 1047, Adelaide, South Australia, 5001, Australia
| | - Kyle W Tomlinson
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, 666303, China
| | - Ian M Turner
- Singapore Botanic Gardens, National Parks Board, 1 Cluny Road, 259569, Singapore
- Singapore Botanical Liaison Officer, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Thais Vasconcelos
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Peter G Wilson
- Royal Botanic Gardens Sydney, Mrs Macquaries Rd, Sydney, NSW, 2000, Australia
| | | | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Eve Lucas
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
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Baker WJ, Bailey P, Barber V, Barker A, Bellot S, Bishop D, Botigué LR, Brewer G, Carruthers T, Clarkson JJ, Cook J, Cowan RS, Dodsworth S, Epitawalage N, Françoso E, Gallego B, Johnson MG, Kim JT, Leempoel K, Maurin O, McGinnie C, Pokorny L, Roy S, Stone M, Toledo E, Wickett NJ, Zuntini AR, Eiserhardt WL, Kersey PJ, Leitch IJ, Forest F. A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life. Syst Biol 2021; 71:301-319. [PMID: 33983440 PMCID: PMC8830076 DOI: 10.1093/sysbio/syab035] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/06/2021] [Accepted: 05/08/2021] [Indexed: 12/22/2022] Open
Abstract
The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this article are to (i) document our methods, (ii) describe our first data release, and (iii) present a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic data set for angiosperms to date, comprising 3099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96\documentclass[12pt]{minimal}
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}{}$\%$\end{document}). A “first pass” angiosperm tree of life was inferred from the data, which totaled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated data set, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as further data become available. This major milestone toward a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardized nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the world’s natural history collections. [Angiosperms; Angiosperms353; genomics; herbariomics; museomics; nuclear phylogenomics; open access; target sequence capture; tree of life.]
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Affiliation(s)
- William J Baker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Paul Bailey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Vanessa Barber
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Abigail Barker
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Sidonie Bellot
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - David Bishop
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Laura R Botigué
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Centre for Research in Agricultural Genomics, Campus UAB, Edifici CRAG, Bellaterra Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Grace Brewer
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Tom Carruthers
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - James J Clarkson
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Jeffrey Cook
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Robyn S Cowan
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Steven Dodsworth
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,School of Life Sciences, University of Bedfordshire, University Square, Luton LU1 3JU, United Kingdom
| | | | - Elaine Françoso
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Berta Gallego
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Jan T Kim
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Department of Computer Science, School of Physics, Engineering and Computer Science, University of Hertfordshire, Hatfield, Hertfordshire, AL10 9AB, United Kingdom
| | - Kevin Leempoel
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | | | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Centre for Plant Biotechnology and Genomics (CBGP) UPM-INIA, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Shyamali Roy
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Malcolm Stone
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Eduardo Toledo
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Norman J Wickett
- Plant Science and Conservation, Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL 60022, USA
| | | | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom.,Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Paul J Kersey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, United Kingdom
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15
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Brewer GE, Clarkson JJ, Maurin O, Zuntini AR, Barber V, Bellot S, Biggs N, Cowan RS, Davies NMJ, Dodsworth S, Edwards SL, Eiserhardt WL, Epitawalage N, Frisby S, Grall A, Kersey PJ, Pokorny L, Leitch IJ, Forest F, Baker WJ. Factors Affecting Targeted Sequencing of 353 Nuclear Genes From Herbarium Specimens Spanning the Diversity of Angiosperms. Front Plant Sci 2019; 10:1102. [PMID: 31620145 PMCID: PMC6759688 DOI: 10.3389/fpls.2019.01102] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/12/2019] [Indexed: 05/03/2023]
Abstract
The world's herbaria collectively house millions of diverse plant specimens, including endangered or extinct species and type specimens. Unlocking genetic data from the typically highly degraded DNA obtained from herbarium specimens was difficult until the arrival of high-throughput sequencing approaches, which can be applied to low quantities of severely fragmented DNA. Target enrichment involves using short molecular probes that hybridise and capture genomic regions of interest for high-throughput sequencing. In this study on herbariomics, we used this targeted sequencing approach and the Angiosperms353 universal probe set to recover up to 351 nuclear genes from 435 herbarium specimens that are up to 204 years old and span the breadth of angiosperm diversity. We show that on average 207 genes were successfully retrieved from herbarium specimens, although the mean number of genes retrieved and target enrichment efficiency is significantly higher for silica gel-dried specimens. Forty-seven target nuclear genes were recovered from a herbarium specimen of the critically endangered St Helena boxwood, Mellissia begoniifolia, collected in 1815. Herbarium specimens yield significantly less high-molecular-weight DNA than silica gel-dried specimens, and genomic DNA quality declines with sample age, which is negatively correlated with target enrichment efficiency. Climate, taxon-specific traits, and collection strategies additionally impact target sequence recovery. We also detected taxonomic bias in targeted sequencing outcomes for the 10 most numerous angiosperm families that were investigated in depth. We recommend that (1) for species distributed in wet tropical climates, silica gel-dried specimens should be used preferentially; (2) for species distributed in seasonally dry tropical climates, herbarium and silica gel-dried specimens yield similar results, and either collection can be used; (3) taxon-specific traits should be explored and established for effective optimisation of taxon-specific studies using herbarium specimens; (4) all herbarium sheets should, in future, be annotated with details of the preservation method used; (5) long-term storage of herbarium specimens should be in stable, low-humidity, and low-temperature environments; and (6) targeted sequencing with universal probes, such as Angiosperms353, should be investigated closely as a new approach for DNA barcoding that will ensure better exploitation of herbarium specimens than traditional Sanger sequencing approaches.
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Affiliation(s)
- Grace E. Brewer
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - James J. Clarkson
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Olivier Maurin
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | | | - Vanessa Barber
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Sidonie Bellot
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Nicola Biggs
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Robyn S. Cowan
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Nina M. J. Davies
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Steven Dodsworth
- School of Life Sciences, University of Bedfordshire, Luton, BedfordshireUnited Kingdom
| | - Sara L. Edwards
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Wolf L. Eiserhardt
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Department of Bioscience, Aarhus University, Ny Munkegade Aarhus C, Denmark
| | | | - Sue Frisby
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Aurélie Grall
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Paul J. Kersey
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Lisa Pokorny
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
- Centre for Plant Biotechnology and Genomics (CBGP, UPM-INIA), Pozuelo de Alarcón, Madrid, Spain
| | - Ilia J. Leitch
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - Félix Forest
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
| | - William J. Baker
- Science Directorate, Royal Botanic Gardens, Kew, Richmond, United Kingdom
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Larridon I, Villaverde T, Zuntini AR, Pokorny L, Brewer GE, Epitawalage N, Fairlie I, Hahn M, Kim J, Maguilla E, Maurin O, Xanthos M, Hipp AL, Forest F, Baker WJ. Tackling Rapid Radiations With Targeted Sequencing. Front Plant Sci 2019; 10:1655. [PMID: 31998342 PMCID: PMC6962237 DOI: 10.3389/fpls.2019.01655] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/22/2019] [Indexed: 05/19/2023]
Abstract
In phylogenetic studies across angiosperms, at various taxonomic levels, polytomies have persisted despite efforts to resolve them by increasing sampling of taxa and loci. The large amount of genomic data now available and statistical tools to analyze them provide unprecedented power for phylogenetic inference. Targeted sequencing has emerged as a strong tool for estimating species trees in the face of rapid radiations, lineage sorting, and introgression. Evolutionary relationships in Cyperaceae have been studied mostly using Sanger sequencing until recently. Despite ample taxon sampling, relationships in many genera remain poorly understood, hampered by diversification rates that outpace mutation rates in the loci used. The C4 Cyperus clade of the genus Cyperus has been particularly difficult to resolve. Previous studies based on a limited set of markers resolved relationships among Cyperus species using the C3 photosynthetic pathway, but not among C4 Cyperus clade taxa. We test the ability of two targeted sequencing kits to resolve relationships in the C4 Cyperus clade, the universal Angiosperms-353 kit and a Cyperaceae-specific kit. Sequences of the targeted loci were recovered from data generated with both kits and used to investigate overlap in data between kits and relative efficiency of the general and custom approaches. The power to resolve shallow-level relationships was tested using a summary species tree method and a concatenated maximum likelihood approach. High resolution and support are obtained using both approaches, but high levels of missing data disproportionately impact the latter. Targeted sequencing provides new insights into the evolution of morphology in the C4 Cyperus clade, demonstrating for example that the former segregate genus Alinula is polyphyletic despite its seeming morphological integrity. An unexpected result is that the Cyperus margaritaceus-Cyperus niveus complex comprises a clade separate from and sister to the core C4 Cyperus clade. Our results demonstrate that data generated with a family-specific kit do not necessarily have more power than those obtained with a universal kit, but that data generated with different targeted sequencing kits can often be merged for downstream analyses. Moreover, our study contributes to the growing consensus that targeted sequencing data are a powerful tool in resolving rapid radiations.
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Affiliation(s)
- Isabel Larridon
- Royal Botanic Gardens, Kew, Surrey, United Kingdom
- Systematic and Evolutionary Botany Lab, Department of Biology, Ghent University, Ghent, Belgium
- *Correspondence: Isabel Larridon, ; Tamara Villaverde,
| | - Tamara Villaverde
- Real Jardín Botánico (RJB-CSIC), Madrid, Spain
- The Morton Arboretum, Lisle, IL, United States
- The Field Museum, Chicago, IL, United States
- *Correspondence: Isabel Larridon, ; Tamara Villaverde,
| | | | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Surrey, United Kingdom
- Real Jardín Botánico (RJB-CSIC), Madrid, Spain
- Centre for Plant Biotechnology and Genomics (CBGP, UPM-INIA), Madrid, Spain
| | | | | | - Isabel Fairlie
- Royal Botanic Gardens, Kew, Surrey, United Kingdom
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | | | - Jan Kim
- Royal Botanic Gardens, Kew, Surrey, United Kingdom
| | - Enrique Maguilla
- The Morton Arboretum, Lisle, IL, United States
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | | | | | - Andrew L. Hipp
- The Morton Arboretum, Lisle, IL, United States
- The Field Museum, Chicago, IL, United States
| | - Félix Forest
- Royal Botanic Gardens, Kew, Surrey, United Kingdom
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17
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Zuntini AR, Taylor CM, Lohmann LG. Problematic specimens turn out to be two undescribed species of Bignonia (Bignoniaceae). PhytoKeys 2015; 56:7-18. [PMID: 26491382 PMCID: PMC4611744 DOI: 10.3897/phytokeys.56.5423] [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] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 07/28/2015] [Indexed: 06/05/2023]
Abstract
Bignonia comprises 29 species of lianas characterized by eight phloem wedges, leaves usually 2-foliolate, mostly simple tendrils and opaque seed wings. The analysis of herbarium specimens in preparation for a taxonomic revision of the genus led to the recognition of two new species: (i) Bignonia cararensis from Costa Rica, characterized by a thyrse with lateral compound dichasia and lack of interpetiolar ridge, and (ii) Bignonia sanctae-crucis from Bolivia and Brazil, distinguishable by its membranous leaflets, membranous calyx and small fruits. We provide detailed descriptions, illustrations, distribution maps, initial conservation status assessments, and comparisons of the newly described taxa with closely related species.
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Affiliation(s)
- Alexandre R. Zuntini
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090, São Paulo, SP, Brazil
| | - Charlotte M. Taylor
- Missouri Botanical Garden, P.O. Box 299, St. Louis, Missouri, 63166-0299, U.S.A
| | - Lúcia G. Lohmann
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090, São Paulo, SP, Brazil
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18
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Zuntini AR, Lohmann LG. Synopsis of Martinella Baill. (Bignonieae, Bignoniaceae), with the description of a new species from the Atlantic Forest of Brazil. PhytoKeys 2014; 37:15-24. [PMID: 24843296 PMCID: PMC4023332 DOI: 10.3897/phytokeys.37.6940] [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] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Accepted: 04/01/2014] [Indexed: 06/03/2023]
Abstract
Martinella has traditionally included two species, Martinella iquitoensis and Martinella obovata, that are characterized by the presence of interpetiolar ridges surrounding the stems and minute prophylls of the axillary buds. A third species, Martinella insignis, is here described as new, illustrated and compared to other species in the genus. Martinella insignis is the first record of the genus in the Atlantic Forest of Brazil, and differs from other species of Martinella by the yellow corolla (vs. red to dark purple) and 5-lobed calices (vs. 2-4-lobed).
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Affiliation(s)
- Alexandre R. Zuntini
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090, São Paulo, SP, Brazil
| | - Lucia G. Lohmann
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, 277, 05508-090, São Paulo, SP, Brazil
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Zuntini AR, Fonseca LHM, Lohmann LG. Primers for phylogeny reconstruction in Bignonieae (Bignoniaceae) using herbarium samples. Appl Plant Sci 2013; 1:apps1300018. [PMID: 25202586 PMCID: PMC4103147 DOI: 10.3732/apps.1300018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 04/23/2013] [Indexed: 05/30/2023]
Abstract
PREMISE OF THE STUDY New primers were developed for Bignonieae to enable phylogenetic studies within this clade using herbarium samples. • METHODS AND RESULTS Internal primers were designed based on available sequences of the plastid ndhF gene and the rpl32-trnL intergenic spacer region, and the nuclear gene PepC. The resulting primers were used to amplify DNA extracted from herbarium materials. High-quality data were obtained from herbarium samples up to 53 yr old. • CONCLUSIONS The standardized methodology allows the inclusion of herbarium materials as alternative sources of DNA for phylogenetic studies in Bignonieae.
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Affiliation(s)
- Alexandre R. Zuntini
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, São Paulo, Brazil
| | - Luiz Henrique M. Fonseca
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, São Paulo, Brazil
| | - Lúcia G. Lohmann
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, São Paulo, Brazil
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