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Lücking R, Hawksworth DL. Formal description of sequence-based voucherless Fungi: promises and pitfalls, and how to resolve them. IMA Fungus 2018; 9:143-166. [PMID: 30018876 PMCID: PMC6048566 DOI: 10.5598/imafungus.2018.09.01.09] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 05/15/2018] [Indexed: 11/25/2022] Open
Abstract
There is urgent need for a formal nomenclature of sequence-based, voucherless Fungi, given that environmental sequencing has accumulated more than one billion fungal ITS reads in the Sequence Read Archive, about 1,000 times as many as fungal ITS sequences in GenBank. These unnamed Fungi could help to bridge the gap between 115,000 to 140,000 currently accepted and 2.2 to 3.8 million predicted species, a gap that cannot realistically be filled using specimen or culture-based inventories. The Code never aimed at placing restrictions on the nature of characters chosen for taxonomy, and the requirement for physical types is now becoming a constraint on the advancement of science. We elaborate on the promises and pitfalls of sequence-based nomenclature and provide potential solutions to major concerns of the mycological community. Types of sequence-based taxa, which by default lack a physical specimen or culture, could be designated in four alternative ways: (1) the underlying sample ('bag' type), (2) the DNA extract, (3) fluorescent in situ hybridization (FISH), or (4) the type sequence itself. Only (4) would require changes to the Code and the latter would be the most straightforward approach, complying with three of the five principal functions of types better than physical specimens. A fifth way, representation of the sequence in an illustration, has been ruled as unacceptable in the Code. Potential flaws in sequence data are analogous to flaws in physical types, and artifacts are manageable if a stringent analytical approach is applied. Conceptual errors such as homoplasy, intragenomic variation, gene duplication, hybridization, and horizontal gene transfer, apply to all molecular approaches and cannot be used as a specific argument against sequence-based nomenclature. The potential impact of these phenomena is manageable, as phylogenetic species delimitation has worked satisfactorily in Fungi. The most serious shortcoming of sequence-based nomenclature is the likelihood of parallel classifications, either by describing taxa that already have names based on physical types, or by using different markers to delimit species within the same lineage. The probability of inadvertently establishing sequence-based species that have names available is between 20.4 % and 1.5 % depending on the number of globally predicted fungal species. This compares favourably to a historical error rate of about 30 % based on physical types, and this rate could be reduced to practically zero by adding specific provisions to this approach in the Code. To avoid parallel classifications based on different markers, sequence-based nomenclature should be limited to a single marker, preferably the fungal ITS barcoding marker; this is possible since sequence-based nomenclature does not aim at accurate species delimitation but at naming lineages to generate a reference database, independent of whether these lineages represent species, closely related species complexes, or infraspecies. We argue that clustering methods are inappropriate for sequence-based nomenclature; this approach must instead use phylogenetic methods based on multiple alignments, combined with quantitative species recognition methods. We outline strategies to obtain higher-level phylogenies for ITS-based, voucherless species, including phylogenetic binning, 'hijacking' species delimitation methods, and temporal banding. We conclude that voucherless, sequence-based nomenclature is not a threat to specimen and culture-based fungal taxonomy, but a complementary approach capable of substantially closing the gap between known and predicted fungal diversity, an approach that requires careful work and high skill levels.
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Affiliation(s)
- Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Strasse 6–8, 14195 Berlin, Germany
| | - David L. Hawksworth
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; and Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey TW9 3DS, UK; Jilin Agricultural University, Changchun, Jilin Province,130118 China
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2
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Carter BE, Larraín J, Manukjanová A, Shaw B, Shaw AJ, Heinrichs J, de Lange P, Suleiman M, Thouvenot L, von Konrat M. Species delimitation and biogeography of a southern hemisphere liverwort clade, Frullania subgenus Microfrullania (Frullaniaceae, Marchantiophyta). Mol Phylogenet Evol 2016; 107:16-26. [PMID: 27744015 DOI: 10.1016/j.ympev.2016.10.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 09/27/2016] [Accepted: 10/05/2016] [Indexed: 11/30/2022]
Abstract
Frullania subgenus Microfrullania is a clade of ca. 15 liverwort species occurring in Australasia, Malesia, and southern South America. We used combined nuclear and chloroplast sequence data from 265 ingroup accessions to test species circumscriptions and estimate the biogeographic history of the subgenus. With dense infra-specific sampling, we document an important role of long-distance dispersal in establishing phylogeographic patterns of extant species. At deeper time scales, a combination of phylogenetic analyses, divergence time estimation and ancestral range estimation were used to reject vicariance and to document the role of long-distance dispersal in explaining the evolution and biogeography of the clade across the southern Hemisphere. A backbone phylogeny for the subgenus is proposed, providing insight into evolution of morphological patterns and establishing the basis for an improved sectional classification of species within Microfrullania. Several species complexes are identified, the presence of two undescribed but genetically and morphologically distinct species is noted, and previously neglected names are discussed.
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Affiliation(s)
- Benjamin E Carter
- Department of Biology, Duke University, 139 Biological Sciences Building, Box 90338, Durham, NC 27708, USA.
| | - Juan Larraín
- Science & Education, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605-2496, USA
| | - Alžběta Manukjanová
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 31, CZ-370 05 České Budějovice, Czech Republic
| | - Blanka Shaw
- Department of Biology, Duke University, 139 Biological Sciences Building, Box 90338, Durham, NC 27708, USA
| | - A Jonathan Shaw
- Department of Biology, Duke University, 139 Biological Sciences Building, Box 90338, Durham, NC 27708, USA
| | - Jochen Heinrichs
- Department of Biology I and Geobio-Center, Ludwig Maximilian University, Menzinger Str. 67, 80638 Munich, Germany
| | - Peter de Lange
- Science & Policy Group, Department of Conservation, Private Bag 68908, Newton, Auckland 1145, New Zealand
| | - Monica Suleiman
- Institute for Tropical Biology and Conservation, University Malaysia Sabah, Jalan UMS, 88400 Kota Kinabalu, Malaysia
| | | | - Matt von Konrat
- Science & Education, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605-2496, USA
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3
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Söderström L, Hagborg A, von Konrat M, Bartholomew-Began S, Bell D, Briscoe L, Brown E, Cargill DC, Costa DP, Crandall-Stotler BJ, Cooper ED, Dauphin G, Engel JJ, Feldberg K, Glenny D, Gradstein SR, He X, Heinrichs J, Hentschel J, Ilkiu-Borges AL, Katagiri T, Konstantinova NA, Larraín J, Long DG, Nebel M, Pócs T, Puche F, Reiner-Drehwald E, Renner MA, Sass-Gyarmati A, Schäfer-Verwimp A, Moragues JGS, Stotler RE, Sukkharak P, Thiers BM, Uribe J, Váňa J, Villarreal JC, Wigginton M, Zhang L, Zhu RL. World checklist of hornworts and liverworts. PHYTOKEYS 2016; 59:1-828. [PMID: 26929706 PMCID: PMC4758082 DOI: 10.3897/phytokeys.59.6261] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 09/25/2015] [Indexed: 05/19/2023]
Abstract
A working checklist of accepted taxa worldwide is vital in achieving the goal of developing an online flora of all known plants by 2020 as part of the Global Strategy for Plant Conservation. We here present the first-ever worldwide checklist for liverworts (Marchantiophyta) and hornworts (Anthocerotophyta) that includes 7486 species in 398 genera representing 92 families from the two phyla. The checklist has far reaching implications and applications, including providing a valuable tool for taxonomists and systematists, analyzing phytogeographic and diversity patterns, aiding in the assessment of floristic and taxonomic knowledge, and identifying geographical gaps in our understanding of the global liverwort and hornwort flora. The checklist is derived from a working data set centralizing nomenclature, taxonomy and geography on a global scale. Prior to this effort a lack of centralization has been a major impediment for the study and analysis of species richness, conservation and systematic research at both regional and global scales. The success of this checklist, initiated in 2008, has been underpinned by its community approach involving taxonomic specialists working towards a consensus on taxonomy, nomenclature and distribution.
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Affiliation(s)
- Lars Söderström
- Department of Biology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Anders Hagborg
- Department of Science and Education, Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605–2496, United States of America
| | - Matt von Konrat
- Department of Science and Education, Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605–2496, United States of America
| | - Sharon Bartholomew-Began
- Department of Biology, West Chester University, West Chester, PA 19383, United States of America
| | - David Bell
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - Laura Briscoe
- Department of Science and Education, Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605–2496, United States of America
| | - Elizabeth Brown
- Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney NSW2000, Australia
| | - D. Christine Cargill
- Centre for Australian National Biodiversity Research, Australian National Herbarium, GPO Box 1600, Canberra, ACT 2601, Australia
| | - Denise P. Costa
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rua Pacheco Leão 915, 22460-030, Rio de Janeiro, RJ, Brazil
| | - Barbara J. Crandall-Stotler
- Department of Plant Biology, Southern Illinois University, Carbondale, Illinois 62901-6509, United States of America
| | - Endymion D. Cooper
- CMNS-Cell Biology and Molecular Genetics, 2107 Bioscience Research Building, University of Maryland, College Park, MD 20742-4451, United States of America
| | | | - John J. Engel
- Department of Science and Education, Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605–2496, United States of America
| | - Kathrin Feldberg
- Systematic Botany and Mycology, Ludwig Maximilian University of Munich, Menzinger Str. 67, 80638 Munich, Germany
| | - David Glenny
- Allan Herbarium, Landcare Research, P O Box 69-040, Lincoln 7608, New Zealand
| | - S. Robbert Gradstein
- Muséum National d’Histoire Naturelle, Department Systématique et Evolution, C.P. 39, 57 Rue Cuvier, 75231 Paris 05, France
| | - Xiaolan He
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, Helsinki FI-00014, Finland
| | - Jochen Heinrichs
- Systematic Botany and Mycology, Ludwig Maximilian University of Munich, Menzinger Str. 67, 80638 Munich, Germany
| | - Jörn Hentschel
- Department of Systematic Botany with Herbarium Haussknecht and Botanical Garden, Friedrich Schiller University, Fürstengraben 1, 07737 Jena, Germany
| | - Anna Luiza Ilkiu-Borges
- Museu Paraense Emilio Goeldi, Coordenaçao de Botanica, Av. Magalhaes Barata 376, 66040-1 70 Belem, Para, Brazil
| | - Tomoyuki Katagiri
- Department of Biological Science, Graduate School of Science, Hiroshima University, Kagamiyama 1–3–1, Higashihiroshima-shi, Hiroshima 739–8526, Japan
| | | | - Juan Larraín
- Department of Science and Education, Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605–2496, United States of America
| | - David G. Long
- Royal Botanic Garden, Edinburgh EH3 5LR, United Kingdom
| | - Martin Nebel
- Staatliches Museum für Naturkunde Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Tamás Pócs
- Botany Department, Institute of Biology, Eszterházy Károly College, Eger, Pf. 43, H-3301, Hungary
| | - Felisa Puche
- Departamento de Botánica, Facultad de Ciencias Biológicas, Universitat de València. C/ Dr. Moliner 50, E-46100, Burjassot (Valencia), Spain
| | - Elena Reiner-Drehwald
- Albrecht-von-Haller-Institut für Pflanzenwissenschaften, Department of Systematics, Biodiversity and Evolution of Plants, Untere Karspüle 2, 37073 Göttingen, Germany
| | - Matt A.M. Renner
- Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney NSW2000, Australia
| | - Andrea Sass-Gyarmati
- Botany Department, Institute of Biology, Eszterházy Károly College, Eger, Pf. 43, H-3301, Hungary
| | | | - José Gabriel Segarra Moragues
- Centro de Investigaciones sobre Desertificación (CIDE-CSIC-UV-GV), C/ Carretera de Moncada-Náquera Km. 4.5, E-46113, Moncada (Valencia), Spain
| | - Raymond E. Stotler
- Department of Plant Biology, Southern Illinois University, Carbondale, Illinois 62901-6509, United States of America
| | - Phiangphak Sukkharak
- Department of Biology, Faculty of Science, Burapha University, Mueang, 20131 Chonburi, Thailand
| | - Barbara M. Thiers
- William and Lynda Steere Herbarium, The New York, Botanical Garden, Bronx, New York 10458-5126, United States of America
| | - Jaime Uribe
- Instituto de Ciencias Naturales. Universidad Nacional de Colombia. Apartado 7495, Bogotá D.C., Colombia
| | - Jiří Váňa
- Department of Botany, Charles University, Benátská 2, CZ-128 01 Praha 2, Czech Republic
| | - Juan Carlos Villarreal
- Department of Biology, Ludwig-Maximilians-Universität, Menzinger Str. 67, D-80638, München, Germany
| | | | - Li Zhang
- Shenzhen Key Laboratory of Southern Subtropical Plant Diversity, Fairylake Botanical Garden, 160 Xianhu Rd., Liantang, Shenzhen 518004, Guangdong, China
| | - Rui-Liang Zhu
- Department of Biology, School of Life Sciences, East China Normal University, 3663 Zhong Shan North Road, Shanghai 200062, China*
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Larraín J, Carter B, Shaw B, Hentschel J, Strozier LS, Furuki T, Heinrichs J, Crandall-Stotler B, Engel J, von Konrat M. The resurrection of Neohattoria Kamim. (Jubulaceae, Marchantiophyta): a six decade systematic conflict resolved through a molecular perspective. PHYTOKEYS 2015; 50:101-122. [PMID: 26140022 PMCID: PMC4489086 DOI: 10.3897/phytokeys.50.4940] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 04/16/2015] [Indexed: 05/29/2023]
Abstract
The systematic placement of Frullaniaherzogii has been contentious since its description six decades ago. Over the years it has been interpreted as either a member of the genus Frullania or segregated into its own genus, Neohattoria, due to morphological similarities with both Frullania and Jubula. Here we provide molecular evidence that supports the recognition of the genus Neohattoria and its inclusion within the Jubulaceae, together with Jubula and Nipponolejeunea. Jubulaceae are placed sister to Lejeuneaceae rather than to the monogeneric Frullaniaceae.
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Affiliation(s)
- Juan Larraín
- Science & Education, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605-2496, U.S.A
| | - Benjamin Carter
- Department of Biology, Duke University, Durham, NC 27708-0338, U.S.A
| | - Blanka Shaw
- Department of Biology, Duke University, Durham, NC 27708-0338, U.S.A
| | - Jörn Hentschel
- Department of Systematic Botany with Herbarium Haussknecht and Botanical Garden, Friedrich Schiller University, Fürstengraben 1, 07743 Jena, Germany
| | - Lynika S. Strozier
- Science & Education, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605-2496, U.S.A
| | - Tatsuwo Furuki
- Natural History Museum & Institute, 955-2 Aoba-cho, Chuo-ku, Chiba-shi, Chiba 260-8682, Japan
| | - Jochen Heinrichs
- Ludwig-Maximilians-Universität München, Department für Biologie I, Systematische Botanik und Mykologie, GeoBio-Center, Menzinger Straße 67, 80638 München, Germany
| | - Barbara Crandall-Stotler
- Southern Illinois University, Department of Plant Biology, Mail Code 6509, wCarbondale IL 62901-6509, U.S.A
| | - John Engel
- Science & Education, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605-2496, U.S.A
| | - Matt von Konrat
- Science & Education, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605-2496, U.S.A
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Renner MA, Devos N, Patiño J, Brown EA, Orme A, Elgey M, Wilson TC, Gray LJ, von Konrat MJ. Integrative taxonomy resolves the cryptic and pseudo-cryptic Radula buccinifera complex (Porellales, Jungermanniopsida), including two reinstated and five new species. PHYTOKEYS 2013; 27:1-113. [PMID: 24223490 PMCID: PMC3821098 DOI: 10.3897/phytokeys.27.5523] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 08/20/2013] [Indexed: 05/11/2023]
Abstract
Molecular data from three chloroplast markers resolve individuals attributable to Radula buccinifera in six lineages belonging to two subgenera, indicating the species is polyphyletic as currently circumscribed. All lineages are morphologically diagnosable, but one pair exhibits such morphological overlap that they can be considered cryptic. Molecular and morphological data justify the re-instatement of a broadly circumscribed ecologically variable R. strangulata, of R. mittenii, and the description of five new species. Two species Radula mittenii Steph. and R. notabilis sp. nov. are endemic to the Wet Tropics Bioregion of north-east Queensland, suggesting high diversity and high endemism might characterise the bryoflora of this relatively isolated wet-tropical region. Radula demissa sp. nov. is endemic to southern temperate Australasia, and like R. strangulata occurs on both sides of the Tasman Sea. Radula imposita sp. nov. is a twig and leaf epiphyte found in association with waterways in New South Wales and Queensland. Another species, R. pugioniformis sp. nov., has been confused with Radula buccinifera but was not included in the molecular phylogeny. Morphological data suggest it may belong to subg. Odontoradula. Radula buccinifera is endemic to Australia including Western Australia and Tasmania, and to date is known from south of the Clarence River on the north coast of New South Wales. Nested within R. buccinifera is a morphologically distinct plant from Norfolk Island described as R. anisotoma sp. nov. Radula australiana is resolved as monophyletic, sister to a species occurring in east coast Australian rainforests, and nesting among the R. buccinifera lineages with strong support. The molecular phylogeny suggests several long-distance dispersal events may have occurred. These include two east-west dispersal events from New Zealand to Tasmania and south-east Australia in R. strangulata, one east-west dispersal event from Tasmania to Western Australia in R. buccinifera, and at least one west-east dispersal from Australia to New Zealand in R. australiana. Another west-east dispersal event from Australia to Norfolk Island may have led to the budding speciation of R. anisotoma. In contrast, Radula demissa is phylogeographically subdivided into strongly supported clades either side of the Tasman Sea, suggesting long distance dispersal is infrequent in this species.
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Affiliation(s)
- Matt A.M. Renner
- Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney, NSW 2000, Australia
| | - Nicolas Devos
- Department of Biology, Duke University, Box 90388, Durham NC 27708, U.S.A
| | - Jairo Patiño
- Institute of Botany, University of Liège, Liège, Belgium
| | - Elizabeth A. Brown
- Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney, NSW 2000, Australia
| | - Andrew Orme
- Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney, NSW 2000, Australia
| | - Michael Elgey
- Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney, NSW 2000, Australia
| | - Trevor C. Wilson
- Royal Botanic Gardens and Domain Trust, Mrs Macquaries Road, Sydney, NSW 2000, Australia
| | - Lindsey J. Gray
- School of Biological Sciences, The University of Sydney, NSW 2006, Australia
| | - Matt J. von Konrat
- The Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, Illinois, USA
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