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Ossowska EA, Moncada B, Lücking R, Flakus A, Rodriguez-Flakus P, Olszewska S, Kukwa M. Additional new species and new records of the genus Sticta (lichenised Ascomycota, lobarioid Peltigeraceae) from Bolivia. MycoKeys 2024; 105:21-47. [PMID: 38694266 PMCID: PMC11061559 DOI: 10.3897/mycokeys.105.120810] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 03/20/2024] [Indexed: 05/04/2024] Open
Abstract
Four species of the genus Sticta are described as new from Bolivia, based on morphological examination and phylogenetic analysis of the fungal ITS barcoding marker. Additionally, two species are reported as new to Bolivia (their identification confirmed by molecular data) and one previously reported species is confirmed by molecular data for the first time. Detailed morphological and anatomical descriptions are provided for all new species. Two of the new species, S.isidiolobulata Ossowska, B. Moncada, Lücking & Kukwa and S.madidiensis Ossowska, B. Moncada, Lücking & Kukwa belong to clade I, as defined in previous studies. In contrast, S.montepunkuensis Ossowska, B. Moncada, Lücking & Kukwa and S.macrolobata Ossowska, B. Moncada, Lücking & Kukwa, also described here as new to science, belong to clade III. Stictaisidiolobulata has an irregular to suborbicular thallus of medium size, with isidia developing into spathulate lobules, cyanobacterial photobiont and apothecia with entire to weakly-crenate margins. The large irregular thallus of the cyanobacteria-associated S.macrolobata has broad lobes, apothecia with verrucous to tomentose margins and cyphellae with raised margins, whereas S.madidiensis has a medium-sized, palmate to irregular thallus with a stipe, but without vegetative propagules and apothecia. Stictamontepunkuensis has large and irregular thalli with green algae as photobiont, apothecia with crenate to verrucous margins and urceolate cyphellae with a wide pore and a scabrid basal membrane. Two species, S.beauvoisii Delise and S.riparia Merc.-Díaz are reported as new to Bolivia (the latter also as new to South America) and belong to clade III. Stictatomentosa (Sw.) Ach., species confirmed from Bolivia by molecular data, belongs to clade II. Stictabeauvoisii is characterised by a smooth yellowish-brown upper surface with darker apices and abundant, marginal isidia and a brown lower surface with golden-chocolate brown primary tomentum and sparse, golden-brown rhizines. Stictariparia has a strongly branched thallus, with undulate lobes and abundant, marginal, palmate, grey to dark brown phyllidia and greyish-brown lower surface with the primary tomentum absent towards the margins. Stictatomentosa has palmate, bluish thalli with white cilia and abundant, submarginal apothecia and creamy-white lower surface with a sparse, white primary tomentum.
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Affiliation(s)
- Emilia Anna Ossowska
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, PL-80-308 Gdańsk, PolandUniversity of GdańskGdańskPoland
| | - Bibiana Moncada
- Licenciatura en Biología, Universidad Distrital Francisco José de Caldas, Cra. 4 No. 26D-54, Torre de Laboratorios, Herbario, Bogotá D.C., ColombiaUniversidad Distrital Francisco José de CaldasBogotáColombia
- Research Associate, Science & Education, The Field Museum, 1400 South Lake Shore, Chicago, IL 60605, USAResearch Associate, Science & Education, The Field MuseumChicagoUnited States of America
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, GermanyFreie Universität BerlinBerlinGermany
| | - Robert Lücking
- Research Associate, Science & Education, The Field Museum, 1400 South Lake Shore, Chicago, IL 60605, USAResearch Associate, Science & Education, The Field MuseumChicagoUnited States of America
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, GermanyFreie Universität BerlinBerlinGermany
| | - Adam Flakus
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, PL-31-512 Kraków, PolandW. Szafer Institute of Botany, Polish Academy of SciencesKrakówPoland
| | - Pamela Rodriguez-Flakus
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, PL-31-512 Kraków, PolandW. Szafer Institute of Botany, Polish Academy of SciencesKrakówPoland
| | - Sandra Olszewska
- 10th High School in Gdynia, Władysława IV, PL-81-384 Gdynia, Poland
10th High School in GdyniaGdyniaPoland
| | - Martin Kukwa
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, PL-80-308 Gdańsk, PolandUniversity of GdańskGdańskPoland
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Wilk K, Lücking R. Quantitative integrative taxonomy informs species delimitation in Teloschistaceae (lichenized Ascomycota): the genus Wetmoreana as a case study. IMA Fungus 2024; 15:9. [PMID: 38556886 DOI: 10.1186/s43008-024-00140-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/05/2024] [Indexed: 04/02/2024] Open
Abstract
The genus Wetmoreana was studied using quantitative integrative taxonomy methods to resolve the genus delimitation and explore its taxonomy diversity at the species level. As a result, the genus Fulgogasparrea is synonymized with Wetmoreana, and the latter includes 15 formally described species, one subspecies, and three further, thus far undescribed species: W. appressa, W. awasthii comb. nov., W. bahiensis sp. nov., W. brachyloba comb. nov., W. brouardii, W. chapadensis comb. nov., W. circumlobata sp. nov., W. decipioides, W. intensa comb. nov., W. ochraceofulva comb. nov., W. rubra sp. nov., W. sliwae sp. nov., W. sliwae ssp. subparviloba subsp. nov., W. subnitida comb. nov., W. texana, and W. variegata sp. nov. Eleven of 19 examined taxa are newly placed within this genus or confirmed to belong to it. Two species, W. awasthii and W. intensa, are transferred to Wetmoreana without additional analysis but based on previous studies. The W. brouardii and W. ochraceofulva species complexes are discussed in detail. Additionally, Caloplaca muelleri and C. rubina var. evolutior are transferred to Squamulea, and the latter is elevated to the species rank.
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Affiliation(s)
- Karina Wilk
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512, Kraków, Poland.
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum Berlin, Freie Universität Berlin, Königin-Luise-Strasse 6-8, 14195, Berlin, Germany
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Magain N, Miadlikowska J, Goffinet B, Goward T, Pardo-De la Hoz C, Jüriado I, Simon A, Mercado-Díaz J, Barlow T, Moncada B, Lücking R, Spielmann A, Canez L, Wang L, Nelson P, Wheeler T, Lutzoni F, Sérusiaux E. High species richness in the lichen genus Peltigera ( Ascomycota, Lecanoromycetes): 34 species in the dolichorhizoid and scabrosoid clades of section Polydactylon, including 24 new to science. Persoonia 2023; 51:1-88. [PMID: 38665978 PMCID: PMC11041898 DOI: 10.3767/persoonia.2023.51.01] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 10/10/2022] [Indexed: 04/28/2024]
Abstract
Applying molecular methods to fungi establishing lichenized associations with green algae or cyanobacteria has repeatedly revealed the existence of numerous phylogenetic taxa overlooked by classical taxonomic approaches. Here, we report taxonomical conclusions based on multiple species delimitation and validation analyses performed on an eight-locus dataset that includes world-wide representatives of the dolichorhizoid and scabrosoid clades in section Polydactylon of the genus Peltigera. Following the recommendations resulting from a consensus species delimitation approach and additional species validation analysis (BPP) performed in this study, we present a total of 25 species in the dolichorhizoid clade and nine in the scabrosoid clade, including respectively 18 and six species that are new to science and formally described. Additionally, one combination and three varieties (including two new to science) are proposed in the dolichorhizoid clade. The following 24 new species are described: P. appalachiensis, P. asiatica, P. borealis, P. borinquensis, P. chabanenkoae, P. clathrata, P. elixii, P. esslingeri, P. flabellae, P. gallowayi, P. hawaiiensis, P. holtanhartwigii, P. itatiaiae, P. hokkaidoensis, P. kukwae, P. massonii, P. mikado, P. nigriventris, P. orientalis, P. rangiferina, P. sipmanii, P. stanleyensis, P. vitikainenii and P. willdenowii; the following new varieties are introduced: P. kukwae var. phyllidiata and P. truculenta var. austroscabrosa; and the following new combination is introduced: P. hymenina var. dissecta. Each species from the dolichorhizoid and scabrosoid clades is morphologically and chemically described, illustrated, and characterised with ITS sequences. Identification keys are provided for the main biogeographic regions where species from the two clades occur. Morphological and chemical characters that are commonly used for species identification in the genus Peltigera cannot be applied to unambiguously recognise most molecularly circumscribed species, due to high variation of thalli formed by individuals within a fungal species, including the presence of distinct morphs in some cases, or low interspecific variation in others. The four commonly recognised morphospecies: P. dolichorhiza, P. neopolydactyla, P. pulverulenta and P. scabrosa in the dolichorhizoid and scabrosoid clades represent species complexes spread across multiple and often phylogenetically distantly related lineages. Geographic origin of specimens is often helpful for species recognition; however, ITS sequences are frequently required for a reliable identification. Citation: Magain N, Miadlikowska J, Goffinet B, et al. 2023. High species richness in the lichen genus Peltigera (Ascomycota, Lecanoromycetes): 34 species in the dolichorhizoid and scabrosoid clades of section Polydactylon, including 24 new to science. Persoonia 51: 1-88. doi: 10.3767/persoonia.2023.51.01.
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Affiliation(s)
- N. Magain
- Evolution and Conservation Biology, InBioS Research Center, University of Liège, Sart Tilman B22, Quartier vallée 1, Chemin de la vallée 4, B-4000 Liège, Belgium
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708 USA
| | - J. Miadlikowska
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708 USA
| | - B. Goffinet
- Ecology and Evolutionary Biology, Unit 3043, University of Connecticut, 75 North Eagleville road, Storrs CT, 06269-3043 USA
| | - T. Goward
- Beaty Biodiversity Museum, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - C.J. Pardo-De la Hoz
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708 USA
| | - I. Jüriado
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu 50409, Estonia; Institute of Agricultural & Environmental Sciences, Estonian University of Life Sciences, Fr. R. Kreutzwaldi 5, Tartu 51006, Estonia
| | - A. Simon
- Evolution and Conservation Biology, InBioS Research Center, University of Liège, Sart Tilman B22, Quartier vallée 1, Chemin de la vallée 4, B-4000 Liège, Belgium
- Ecology and Evolutionary Biology, Unit 3043, University of Connecticut, 75 North Eagleville road, Storrs CT, 06269-3043 USA
| | - J.A. Mercado-Díaz
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois, 60605 USA
| | - T. Barlow
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708 USA
| | - B. Moncada
- Licenciatura en Biología, Universidad Distrital Francisco José de Caldas, Cra. 4 No. 26B-54, Torre de Laboratorios, Herbario, Bogotá, Colombia; current address: Botanischer Garten, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, Germany
| | - R. Lücking
- Botanischer Garten, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, Germany
| | - A. Spielmann
- Laboratòrio de Botanica / Liquenologia, Instituto de Biociencias, Universidade Federal de Mato Grosso do Sul, Campo Grande – MS, Brazil
| | - L. Canez
- Laboratòrio de Botanica / Liquenologia, Instituto de Biociencias, Universidade Federal de Mato Grosso do Sul, Campo Grande – MS, Brazil
| | - L.S. Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, CAS, Kunming 650201, China
| | - P. Nelson
- Natural and Behavioral Sciences Division, University of Maine – Fort Kent, Fort Kent, ME, USA
| | - T. Wheeler
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - F. Lutzoni
- Department of Biology, Duke University, Box 90338, Durham, North Carolina, 27708 USA
| | - E. Sérusiaux
- Evolution and Conservation Biology, InBioS Research Center, University of Liège, Sart Tilman B22, Quartier vallée 1, Chemin de la vallée 4, B-4000 Liège, Belgium
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Mercado-Díaz JA, Lücking R, Moncada B, C St E Campbell K, Delnatte C, Familia L, Falcón-Hidalgo B, Motito-Marín A, Rivera-Queralta Y, Widhelm TJ, Thorsten Lumbsch H. Species assemblages of insular Caribbean Sticta (lichenized Ascomycota: Peltigerales) over ecological and evolutionary time scales. Mol Phylogenet Evol 2023:107830. [PMID: 37247703 DOI: 10.1016/j.ympev.2023.107830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 01/28/2023] [Accepted: 05/26/2023] [Indexed: 05/31/2023]
Abstract
Phylogenetic approaches to macroevolution have provided unique insight into evolutionary relationships, ancestral ranges, and diversification patterns for many taxa. Similar frameworks have also been developed to assess how environmental and/or spatial variables shape species diversity and distribution patterns at different spatial/temporal scales, but studies implementing these are still scarce for many groups, including lichens. Here, we combine phylogeny-based ancestral range reconstruction and diversification analysis with community phylogenetics to reconstruct evolutionary origins and assess patterns of taxonomic and phylogenetic relatedness between island communities of the lichenized fungal genus Sticta in the Caribbean. Sampling was carried out in the Greater Antilles (Cuba, Jamaica, Dominican Republic, and Puerto Rico) and Lesser Antilles (Dominica, Guadeloupe, and Martinique). Data for six molecular loci were obtained for 64 candidate Caribbean species and used to perform both macroevolutionary phylogenetics, which also included worldwide taxa, and phylobetadiversity analyses, which emphasized island-level communities. Our work uncovered high levels of island endemism (∼59%) in Caribbean Sticta. We estimate initial colonization of the region occurred about 19 Mya from a South American ancestor. Reverse migration events by Caribbean lineages to South America were also inferred. We found no evidence for increased diversification rates associated with range expansion into the Caribbean. Taxonomic and phylogenetic turnover between island-level communities was most strongly correlated with environmental variation rather than with geographic distance. We observed less dissimilarity among communities from the Dominican Republic and Jamaica than between these islands and the Lesser Antilles/Puerto Rico. High levels of hidden diversity and endemism in Caribbean Sticta reaffirm that islands are crucial for the maintenance of global biodiversity of lichenized fungi. Altogether, our findings suggest that strong evolutionary links exist between Caribbean and South American biotas but at regional scales, species assemblages exhibit complex taxonomic and phylogenetic relationships that are determined by local environments and shared evolutionary histories.
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Affiliation(s)
- Joel A Mercado-Díaz
- Committee on Evolutionary Biology, University of Chicago 1025 E. 57th Street, Chicago, Illinois 60637, U.S.A; Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605, U.S.A.
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Königin-Luise-Straße 6-8, 14195 Berlin, Germany.
| | - Bibiana Moncada
- Licenciatura en Biología, Universidad Distrital Francisco José de Caldas, Cra. 4 No. 26B-54, Torre de Laboratorios, Herbario, Bogotá, Colombia.
| | - Keron C St E Campbell
- Natural History Museum of Jamaica, Institute of Jamaica, 10-16 East Street, Kingston, Jamaica.
| | - Cesar Delnatte
- Biotope Amazonie, 3 rue Mezin Gildon, F-97354 Rémire-Montjoly, Guyane française.
| | - Lemuel Familia
- Departamento de Vida Silvestre, Ministerio de Medio Ambiente y Recursos Naturales, Avenida Cayetano Germosén esq. Avenida Gregorio Luperón, Ensanche El Pedregal, Santo Domingo, República Dominicana.
| | - Banessa Falcón-Hidalgo
- Jardín Botánico Nacional, Universidad de La Habana, Carretera "El Rocío" km 3.5, Calabazar, Boyeros, La Habana, Cuba.
| | - Angel Motito-Marín
- Departamento de Biología Vegetal, Centro Oriental de Ecosistemas y Biodiversidad (BioEco), Código Postal 90100, José A. Saco 601, Esquina Barnada, Santiago de Cuba, Cuba.
| | - Yoira Rivera-Queralta
- Departamento de Biología Vegetal, Centro Oriental de Ecosistemas y Biodiversidad (BioEco), Código Postal 90100, José A. Saco 601, Esquina Barnada, Santiago de Cuba, Cuba.
| | - Todd J Widhelm
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605, U.S.A.
| | - H Thorsten Lumbsch
- Science & Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605, U.S.A.
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dos Santos LA, Aptroot A, Lücking R, Cáceres MEDS. Lecanora s.lat. (Ascomycota, Lecanoraceae) in Brazil: DNA Barcoding Coupled with Phenotype Characters Reveals Numerous Novel Species. J Fungi (Basel) 2023; 9:jof9040415. [PMID: 37108870 PMCID: PMC10141014 DOI: 10.3390/jof9040415] [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: 02/26/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
We sequenced over 200 recent specimens of Lecanora s.lat. from Brazil, delimiting 28 species in our material. Many seem to represent undescribed species, some of which being morphologically and chemically similar to each other or to already described species. Here, we present a phylogenetic analysis based on ITS, including our specimens and GenBank data. We describe nine new species. The purpose of the paper is to illustrate the diversity of the genus in Brazil, not to focus on segregate genera. However, we found that all Vainionora species cluster together and these will be treated separately. Other Lecanora species with dark hypothecium clustered in several different clades. Species with the morphology of Lecanora caesiorubella, in which currently several subspecies with different chemistry and distribution are recognized, fall apart in different, distantly related clades, so they cannot be regarded as subspecies but should be recognized at species level. A key is given for the Lecanora species from Brazil.
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Affiliation(s)
- Lidiane Alves dos Santos
- Programa de Pós-Graduação em Biologia de Fungos, Departamento de Micologia, Universidade Federal de Pernambuco, Campus Universitário, Recife 50670-901, PE, Brazil;
| | - André Aptroot
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Avenida Costa e Silva, s/n Bairro Universitário, Campo Grande 79070-900, MS, Brazil
- Correspondence:
| | - Robert Lücking
- Botanischer Garten, Freie Universität Berlin, Königin-Luise-Str. 6–8, 14195 Berlin, Germany;
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de Mestier A, Mulcahy D, Harris DJ, Korotkova N, Long S, Häffner E, Paton A, Schiller E, Leliaert F, Mackenzie-Dodds J, Fulcher T, Stahls G, von Rintelen T, Martín MP, Lücking R, Williams C, Lyal C, Güntsch A, Aronsson H, Castelin M, Pielach A, Poczai P, Ruiz-León Y, Sanmartin Bastida I, Thines M, Droege G. Policies Handbook on Using Molecular Collections. RIO 2023. [DOI: 10.3897/rio.9.e102908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
Abstract
The access to molecular collections worldwide greatly improves the quality of scientific research by making a growing number of data available for investigation. The efforts on digitisation also aim at facilitating the exchange of material between institutions and researchers that must follow regulations in place and respect best practice. The handbook presented here proposes a workflow to follow to safely exchange materials, in accordance with international laws and legislation. We make numerous recommendations here to help the institutions and researchers to navigate the legal and administrative procedures, in order to manage molecular collections in the best way possible.
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dos Santos LA, Aptroot A, de Souza MF, Lücking R, Guzmán-Guillermo J, da Silva Cáceres ME. Four New Species of Tephromela M.Choisy (Ascomycota, Tephromelataceae), Three Containing Lichexanthone, from Brazil and Mexico. CRYPTOGAMIE MYCOL 2023. [DOI: 10.5252/cryptogamie-mycologie2023v44a2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Affiliation(s)
- Lidiane Alves dos Santos
- Universidade Federal de Pernambuco, Centro de Biociências, Departamento de Micologia, Avenida Professor Moraes Rego s/n, CEP 50670-420, Recife, Pernambuco (Brazil)
| | - André Aptroot
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Avenida Costa e Silva s/n, Bairro Universitário, CEP 79070-900, Campo Grande, Mato Grosso do Sul (Brazil)
| | - Maria Fernanda de Souza
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Avenida Costa e Silva s/n, Bairro Universitário, CEP 79070-900, Campo Grande, Mato Grosso do Sul (Brazil)
| | - Robert Lücking
- Botanischer Garten, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195 Berlin (Germany)
| | - Jorge Guzmán-Guillermo
- Facultad de Ciencias Biológicas y Agropecuarías, Universidad Veracruzana, Carretera Peñuela-Amatlán Kilómetro 177, 94500 Córdoba, Veracruz (Mexico)
| | - Marcela Eugenia da Silva Cáceres
- Universidade Federal de Sergipe, Departamento de Biociências, Avenida Vereador Olimpio Grande s/n, Bairro Centro, CEP 49500-000, Itabaiana, Sergipe (Brazil)
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de Mestier A, Lücking R, Gutierrez J, Brokamp G, Celis M, Borsch T. Nested singletons in molecular trees: Utility of adding morphological and geographical data from digitized herbarium specimens to test taxon concepts at species level in the case of Casearia (Salicaceae). Ecol Evol 2023; 13:e9736. [PMID: 36694555 PMCID: PMC9843533 DOI: 10.1002/ece3.9736] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/19/2023] Open
Abstract
Using the genus Casearia, we assessed the status of nested singletons: individual specimens corresponding to accepted species but in molecular trees appearing nested within clades of closely related species. Normally, such cases would be left undecided, while on the other hand, timely taxonomic decisions are required. We argue that morphological, chorological, and ecological data can be informative to illuminate patterns of speciation. Their use can provide a first step in testing taxon concepts at species level. We focused on five cases of nested singletons in trees of the genus Casearia. We employed PCA and cluster analysis to assess phenotypic differentiation. Using geocoordinates, we calculated niche space differentiation based on 19 bioclim variables, by means of PCA and niche equivalency and similarity tests and generated dot maps. We found that the singletons were morphologically distinctive in two of the five cases (Casearia selloana and C. manausensis), relatively distinctive in two other cases (C. zizyphoides and C. mariquitensis), and partially overlapping in the last case (C. grandiflora). For two cases (C. mariquitensis and C. selloana), ecological niche space was broadly overlapping, in two cases it was found broadly nested (C. grandiflora and C. zizyphoides), and in one case narrowly nested (C. manausensis), but in no case niche differentiation was observed. Niche overlap, similarity and equivalency showed corresponding patterns. Given these data, one would interpret C. selloana and C. manausensis as presumably well-distinguished taxa, their narrow distribution ranges suggesting recently emerging lineages. The other three cases are not clearcut. Morphological data would suggest particularly C. grandiflora conspecific with C. arborea, but differences in the distribution are intriguing. Our approach would reject the notion of potential synonymy based on nested phylogenetic placement for at least two of the five cases. The other case also shows no complete lack of differentiation which would support synonymy.
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Affiliation(s)
- Astrid de Mestier
- Botanischer GartenFreie Universität BerlinBerlinGermany,Institut für Biologie – Systematische Botanik und PflanzengeographieFreie Universität BerlinBerlinGermany
| | | | - Jorge Gutierrez
- Jardín Botánico Nacional CalabazarUniversidad de La HabanaBoyerosCuba
| | - Grischa Brokamp
- Botanischer GartenFreie Universität BerlinBerlinGermany,Fachbereich Wald und UmweltHochschule für Nachhaltige Entwicklung EberswaldeEberswaldeGermany
| | - Marcela Celis
- Departamento de Química y BiologíaUniversidad del NorteBarranquillaColombia
| | - Thomas Borsch
- Botanischer GartenFreie Universität BerlinBerlinGermany,Institut für Biologie – Systematische Botanik und PflanzengeographieFreie Universität BerlinBerlinGermany
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Yang Q, Wang Y, Lücking R, Lumbsch HT, Du Z, Chen Y, Bai M, Ren D, Wei J, Li H, Wang Y, Wei X. The Jurassic epiphytic macrolichen Daohugouthallus reveals the oldest lichen-plant interaction in a Mesozoic forest ecosystem. iScience 2022; 26:105770. [PMID: 36590161 PMCID: PMC9800524 DOI: 10.1016/j.isci.2022.105770] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 11/03/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Lichens are well known as pioneer organisms or stress-tolerant extremophiles, potentially playing a core role in the early formation of terrestrial ecosystems. Epiphytic macrolichens are known to contribute to the water- and nutrient cycles in forest ecosystem. But due to the scarcity of fossil record, the evolutionary history of epiphytic macrolichens is poorly documented. Based on new fossil of Jurassic Daohugouthallus ciliiferus, we demonstrate the hitherto oldest known macrolichen inhabited a gymnosperm branch. We applied energy dispersive X-ray spectroscopy and geometric morphometric analysis to complementarily verify lichen affinity of D. ciliiferus and quantitatively assess the potential relationships with extant lichenized lineages, providing new approaches for study of this lichen adpression fossil. Considering the results, and the inferred age of D. ciliiferus, a new family, Daohugouthallaceae, is established. This work updates current knowledge to the early evolution of epiphytic macrolichens and reveals more complex lichen-plant interactions in a Jurassic forest ecosystem.
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Affiliation(s)
- Qiuxia Yang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanyan Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Robert Lücking
- Botanischer Garten, Freie Universität Berlin, 14195 Berlin, Germany
| | | | - Zhenyong Du
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yunkang Chen
- School of Agriculture, Ningxia University, Yinchuan 750021, China,College of Plant Protection, Agricultural University of Hebei, Baoding 071001, China
| | - Ming Bai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dong Ren
- College of Life Sciences and Academy for Multidisciplinary Studies, Capital Normal University, Beijing 100048, China
| | - Jiangchun Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hu Li
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China,Corresponding author
| | - Yongjie Wang
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China,Corresponding author
| | - Xinli Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China,Corresponding author
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10
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Díaz-Escandón D, Tagirdzhanova G, Vanderpool D, Allen CCG, Aptroot A, Češka O, Hawksworth DL, Huereca A, Knudsen K, Kocourková J, Lücking R, Resl P, Spribille T. Genome-level analyses resolve an ancient lineage of symbiotic ascomycetes. Curr Biol 2022; 32:5209-5218.e5. [PMID: 36423639 DOI: 10.1016/j.cub.2022.11.014] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/30/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022]
Abstract
Ascomycota account for about two-thirds of named fungal species.1 Over 98% of known Ascomycota belong to the Pezizomycotina, including many economically important species as well as diverse pathogens, decomposers, and mutualistic symbionts.2 Our understanding of Pezizomycotina evolution has until now been based on sampling traditionally well-defined taxonomic classes.3,4,5 However, considerable diversity exists in undersampled and uncultured, putatively early-diverging lineages, and the effect of these on evolutionary models has seldom been tested. We obtained genomes from 30 putative early-diverging lineages not included in recent phylogenomic analyses and analyzed these together with 451 genomes covering all available ascomycete genera. We show that 22 of these lineages, collectively representing over 600 species, trace back to a single origin that diverged from the common ancestor of Eurotiomycetes and Lecanoromycetes over 300 million years BP. The new clade, which we recognize as a more broadly defined Lichinomycetes, includes lichen and insect symbionts, endophytes, and putative mycorrhizae and encompasses a range of morphologies so disparate that they have recently been placed in six different taxonomic classes. To test for shared hidden features within this group, we analyzed genome content and compared gene repertoires to related groups in Ascomycota. Regardless of their lifestyle, Lichinomycetes have smaller genomes than most filamentous Ascomycota, with reduced arsenals of carbohydrate-degrading enzymes and secondary metabolite gene clusters. Our expanded genome sample resolves the relationships of numerous "orphan" ascomycetes and establishes the independent evolutionary origins of multiple mutualistic lifestyles within a single, morphologically hyperdiverse clade of fungi.
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Affiliation(s)
- David Díaz-Escandón
- Department of Biological Sciences CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Gulnara Tagirdzhanova
- Department of Biological Sciences CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Dan Vanderpool
- National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, 800 E Beckwith, Missoula, MT 59812, USA
| | - Carmen C G Allen
- Department of Biological Sciences CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - André Aptroot
- Laboratório de Botânica / Liquenologia, Instituto de Biociências Universidade Federal de Mato Grosso do Sul, Avenida Costa e Silva s/n Bairro Universitário, Campo Grande, Mato Grosso do Sul CEP 79070-900, Brazil
| | | | - David L Hawksworth
- Comparative Fungal Biology, Royal Botanic Gardens, Kew, Surrey TW9 3DS, UK; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Jilin Agricultural University, Changchun, Jilin Province 130118, China
| | - Alejandro Huereca
- Department of Biological Sciences CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Kerry Knudsen
- Czech University of Life Sciences, Faculty of Environmental Sciences, Department of Ecology, Kamýcká 129, Praha-Suchdol 165 00, Czech Republic
| | - Jana Kocourková
- Czech University of Life Sciences, Faculty of Environmental Sciences, Department of Ecology, Kamýcká 129, Praha-Suchdol 165 00, Czech Republic
| | - Robert Lücking
- Botanischer Garten, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195 Berlin, Germany
| | - Philipp Resl
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Toby Spribille
- Department of Biological Sciences CW405, University of Alberta, Edmonton, AB T6G 2R3, Canada.
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11
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Phraphuchamnong P, Nelsen MP, Distefano I, Mercado-Diaz JA, Parnmen S, Rangsiruji A, Buaruang K, Lücking R, Lumbsch HT. A new species of Megalaria (Ramalinaceae, Ascomycota) from Thailand, and recognition of subgenus Catillochroma. MycoKeys 2022; 93:149-163. [PMID: 36761912 PMCID: PMC9836422 DOI: 10.3897/mycokeys.93.90962] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022] Open
Abstract
Tropical regions harbor a substantial diversity of lichenized fungi, but face numerous threats to their persistence, often even before previously unknown species have been described and their evolutionary relationships have been elucidated. Megalaria (Ramalinaceae) is a lichen-forming genus of fungi that produces crustose thalli, and includes a number of lineages occupying tropical rain forests; however, taxonomic and phylogenetic work on this clade is limited. Here we leverage both morphological and sequence data to describe a new species from the tropics, M.pachaylenophila. This taxon forms a crustose thallus, lacks secondary metabolites, and occurs in mangrove forests of Thailand. We supplemented molecular data from this species with data from other species, including two genera related to and occasionally included in Megalaria, namely Catillochroma and Lopezaria. Our analyses revealed Catillochroma species form a monophyletic group embedded within Megalaria, and we therefore recognize this clade at the subgeneric level. Since we only included the type species of Lopezaria in this study, we refrain from proposing a taxonomic conclusion for that clade at the moment. Several taxonomic combinations are made to reflect phylogenetic evidence supporting the inclusion of these species in Megalaria.
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Affiliation(s)
- Phimpisa Phraphuchamnong
- Lichen Research Unit, Department of Biology, Faculty of Science, Ramkhamhaeng University, Ramkhamhaeng, Bangkok, 10240 ThailandRamkhamhaeng UniversityBangkokThailand
| | - Matthew P. Nelsen
- Negaunee Integrative Research Center and Grainger Bioinformatics Center, Field Museum of Natural History, 1400 S. DuSable Lake Shore Drive, Chicago, IL, 60605, USAField Museum of Natural HistoryChicagoUnited States of America
| | - Isabel Distefano
- Negaunee Integrative Research Center and Grainger Bioinformatics Center, Field Museum of Natural History, 1400 S. DuSable Lake Shore Drive, Chicago, IL, 60605, USAField Museum of Natural HistoryChicagoUnited States of America
| | - Joel A. Mercado-Diaz
- Negaunee Integrative Research Center and Grainger Bioinformatics Center, Field Museum of Natural History, 1400 S. DuSable Lake Shore Drive, Chicago, IL, 60605, USAField Museum of Natural HistoryChicagoUnited States of America,Committee on Evolutionary Biology, University of Chicago, 1025 E. 57th Street, Chicago, IL 60637, USAUniversity of ChicagoChicagoUnited States of America
| | - Sittiporn Parnmen
- Toxicology Center, National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Tivanon Rd., Nonthaburi 11000, ThailandToxicology Center, National Institute of Health, Department of Medical Sciences, Ministry of Public HealthNonthaburiThailand
| | - Achariya Rangsiruji
- Department of Biology, Faculty of Science, Srinakharinwirot University, Bangkok, 10110 ThailandSrinakharinwirot UniversityBangkokThailand
| | - Kawinnat Buaruang
- Lichen Research Unit, Department of Biology, Faculty of Science, Ramkhamhaeng University, Ramkhamhaeng, Bangkok, 10240 ThailandRamkhamhaeng UniversityBangkokThailand
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Berlin, GermanyFreie Universität BerlinBerlinGermany
| | - H. Thorsten Lumbsch
- Negaunee Integrative Research Center and Grainger Bioinformatics Center, Field Museum of Natural History, 1400 S. DuSable Lake Shore Drive, Chicago, IL, 60605, USAField Museum of Natural HistoryChicagoUnited States of America
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12
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Thiyagaraja V, Ertz D, Lücking R, Wanasinghe DN, Aptroot A, Cáceres MEDS, Hyde KD, Tapingkae W, Cheewangkoon R. Taxonomic and Phylogenetic Reassessment of Pyrgidium (Mycocaliciales) and Investigation of Ascospore Morphology. J Fungi (Basel) 2022; 8:jof8090966. [PMID: 36135691 PMCID: PMC9500946 DOI: 10.3390/jof8090966] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 12/03/2022] Open
Abstract
Mycocaliciales comprise non-lichenized either saprotrophic or lichenicolous fungi which occur in temperate and tropical regions. The mazaediate, saprotrophic and monospecific genus, Pyrgidium, is currently assigned to this order, yet the phylogenetic placement of the genus has remained uncertain due to the absence of molecular data. In order to investigate the systematic position of Pyrgidium, two specimens collected in Brazil and Thailand, respectively, were used to generate mtSSU, SSU, LSU and ITS sequences. However, given that most other representatives of this order only have LSU and ITS sequences available, the phylogenetic reconstruction was limited to these two markers. The phylogenetic analyses confirmed placement of the genus within Mycocaliciales, the genus possessing a sister group relationship with the lichenicolous genus Sphinctrina. Detailed morphological descriptions and illustrations are provided, including those for type specimens of the various synonyms subsumed under the hitherto only accepted species, Pyrgidium montellicum (Beltr.) Tibell. The ascospore morphology was investigated using compound and scanning electronic microscopy (SEM). Principal component analysis (PCA) was performed for the ascospore size using PC-ORD 7. The molecular data and re-examination of the type specimens support the monospecific nature of this genus.
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Affiliation(s)
- Vinodhini Thiyagaraja
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
- Centre of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Centre for Mountain Futures (CMF), CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia (KLPB), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CIFOR-ICRAF China Program, World Agroforestry Centre, East and Central Asia, 132 Lanhei Road, Kunming 650201, China
| | - Damien Ertz
- Research Department, Meise Botanic Garden, Nieuwelaan 38, BE-1860 Meise, Belgium
- Fédération Wallonie-Bruxelles, Service Général de l’Enseignement Supérieur et de la Recherche Scientifique, Rue A. Lavallée 1, BE-1080 Bruxelles, Belgium
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Str. 6–8, 14195 Berlin, Germany
| | - Dhanushka N. Wanasinghe
- Centre for Mountain Futures (CMF), CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia (KLPB), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CIFOR-ICRAF China Program, World Agroforestry Centre, East and Central Asia, 132 Lanhei Road, Kunming 650201, China
| | - André Aptroot
- Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Avenida Costa e Silva, s/n Bairro Universitário, Campo Grande CEP 79070-900, Brazil
| | | | - Kevin D. Hyde
- Centre of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Centre for Mountain Futures (CMF), CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia (KLPB), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- CIFOR-ICRAF China Program, World Agroforestry Centre, East and Central Asia, 132 Lanhei Road, Kunming 650201, China
| | - Wanaporn Tapingkae
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Ratchadawan Cheewangkoon
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence:
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13
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Ossowska EA, Moncada B, Kukwa M, Flakus A, Rodriguez-Flakus P, Olszewska S, Lücking R. New species of Sticta (lichenised Ascomycota, lobarioid Peltigeraceae) from Bolivia suggest a high level of endemism in the Central Andes. MycoKeys 2022; 92:131-160. [PMID: 36761317 PMCID: PMC9849061 DOI: 10.3897/mycokeys.92.89960] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/11/2022] [Indexed: 11/12/2022] Open
Abstract
Six species of Sticta are described as new to science on the basis of material from Bolivia and supported by phylogenetic analysis of the fungal ITS barcoding marker. The species were resolved in all three of the clades (I, II, III) widespread and common in the Neotropics, as defined in an earlier study on the genus. Comparison with material from neighbouring countries (i.e. Colombia, Ecuador, Peru) suggests that these new species may be potentially endemic to the Bolivian Yungas ecoregion. For each species, a detailed morphological and anatomical description is given. Stictaamboroensis Ossowska, Kukwa, B. Moncada & Lücking is a medium-sized green-algal species with laminal to submarginal apothecia with hirsute margins and with light to dark brown lower tomentum. Stictaaymara Ossowska, Kukwa, B. Moncada, Flakus, Rodriguez-Flakus & Lücking is a comparatively small cyanobacterial taxon with Nostoc as photobiont, laminal, richly branched, aggregate isidia and a golden to chocolate-brown lower tomentum. The medium-sized, cyanobacterial S.bicellulata Ossowska, Kukwa, B. Moncada & Lücking has cyanobacterial photobiont, bicellular ascospores, apothecia with white to golden-brown hairs on the margins, K+ violet apothecial margin (ring around disc) and epihymenium and a white to dark brown lower tomentum. In contrast, the green-algal species, S.carrascoensis Ossowska, Kukwa, B. Moncada & Lücking is characterised by its large size, apothecia with dark brown hairs on the margins and a yellow medulla. The cyanobacterial S.catharinae Ossowska, B. Moncada, Kukwa, Flakus, Rodriguez-Flakus & Lücking forms stipitate thalli with Nostoc as photobiont, abundant, laminal to submarginal apothecia and a golden-brown lower tomentum. Finally, the cyanobacterial S.pseudoimpressula Ossowska, Kukwa, B. Moncada & Lücking produces laminal apothecia with an orange-yellow line of pruina along the margins which reacts K+ carmine-red. In addition to the six new Bolivian taxa, the cyanobacterial S.narinioana B. Moncada, Ossowska & Lücking is described as new from Colombia and it represents the closely-related sister species of the Bolivian S.aymara; it differs from the latter largely in the marginal instead of laminal isidia.
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Affiliation(s)
- Emilia Anna Ossowska
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, PL-80-308 Gdańsk, PolandUniversity of GdańskGdańskPoland
| | - Bibiana Moncada
- Licenciatura en Biología, Universidad Distrital Francisco José de Caldas, Cra. 4 No. 26D-54, Torre de Laboratorios, Herbario, Bogotá D.C., ColombiaUniversidad Distrital Francisco José de CaldasBogotáColombia,Research Associate, Science & Education, The Field Museum, 1400 South Lake Shore, Chicago, IL 60605, USAScience & Education, The Field MuseumChicagoUnited States of America,Botanischer Garten, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, GermanyFreie Universität BerlinBerlinGermany
| | - Martin Kukwa
- Department of Plant Taxonomy and Nature Conservation, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, PL-80-308 Gdańsk, PolandUniversity of GdańskGdańskPoland
| | - Adam Flakus
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, PL-31-512 Kraków, PolandW. Szafer Institute of Botany, Polish Academy of SciencesKrakowPoland
| | - Pamela Rodriguez-Flakus
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, PL-31-512 Kraków, PolandW. Szafer Institute of Botany, Polish Academy of SciencesKrakowPoland
| | - Sandra Olszewska
- 10th High School in Gdynia, Władysława IV, PL-81-384 Gdynia, Poland10th High School in GdyniaGdyniaPoland
| | - Robert Lücking
- Research Associate, Science & Education, The Field Museum, 1400 South Lake Shore, Chicago, IL 60605, USAScience & Education, The Field MuseumChicagoUnited States of America,Botanischer Garten, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, GermanyFreie Universität BerlinBerlinGermany
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14
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Koch NM, Stanton D, Müller SC, Duarte L, Spielmann AA, Lücking R. Nuanced qualitative trait approaches reveal environmental filtering and phylogenetic constraints on lichen communities. Ecosphere 2022. [DOI: 10.1002/ecs2.4042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Natália M. Koch
- Department of Ecology, Evolution and Behavior University of Minnesota Saint Paul Minnesota USA
- Departamento de Ecologia, Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
| | - Daniel Stanton
- Department of Ecology, Evolution and Behavior University of Minnesota Saint Paul Minnesota USA
| | - Sandra C. Müller
- Departamento de Ecologia, Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
| | - Leandro Duarte
- Departamento de Ecologia, Instituto de Biociências Universidade Federal do Rio Grande do Sul Porto Alegre Brazil
| | - Adriano A. Spielmann
- Instituto de Biociências Universidade Federal de Mato Grosso do Sul Campo Grande Brazil
| | - Robert Lücking
- Botanischer Garten Freie Universität Berlin Berlin Germany
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15
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Barreto Xavier-Leite A, da Silva Cáceres ME, Aptroot A, Moncada B, Lücking R, Tomio Goto B. Phylogenetic revision of the lichenized family Gomphillaceae (Ascomycota: Graphidales) suggests post-K-Pg boundary diversification and phylogenetic signal in asexual reproductive structures. Mol Phylogenet Evol 2022; 168:107380. [PMID: 34999241 DOI: 10.1016/j.ympev.2021.107380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 08/26/2021] [Accepted: 11/25/2021] [Indexed: 11/26/2022]
Abstract
We present the first broad molecular-phylogenetic revision of the lichenized family Gomphillaceae, based on 408 newly generated sequences of the mitochondrial SSU rDNA and nuclear LSU rDNA, representing 342 OTUs. The phylogenetic analysis of 20 out of the 28 currently accepted genera resulted in 48 clades. Twelve genera were resolved as monophyletic: Actinoplaca, Arthotheliopsis, Bullatina, Caleniopsis, Corticifraga, Gomphillus, Gyalectidium, Gyalidea, Jamesiella, Rolueckia, Rubrotricha, and Taitaia. Two genera resulted paraphyletic, namely Aulaxina (including Caleniopsis) and Asterothyrium (including Linhartia). Six genera were in part highly polyphyletic: Aderkomyces, Calenia, Echinoplaca, Gyalideopsis, Psorotheciopsis, and Tricharia. While ascoma morphology and anatomy has traditionally been considered as main character complex to distinguish genera, our study supported the notion that the characteristic asexual anamorph of Gomphillaceae, the so-called hyphophores, are diagnostic for most of the newly recognized clades. As a result, we recognize 26 new genus-level clades, three of which have names available (Microxyphiomyces, Psathyromyces, Spinomyces) and 23 that will require formal description as new genera. We also tested monophyly for 53 species-level names for which two or more specimens were sequenced: 27 were supported as monophyletic and representing a single species, 13 as monophyletic but with an internal topology suggesting cryptic speciation, four as paraphyletic, and nine as polyphyletic. These data suggest that species richness in the family is higher than indicated by the number of accepted names (currently 425); they also confirm that recently refined species concepts reflect species richness better than the broad concepts applied in Santesson's monograph. A divergence time analysis revealed that foliicolous Gomphillaceae diversified after the K-Pg-boundary and largely during the Miocene, a notion supported by limited data available for other common foliicolous lineages such as Chroodiscus (Graphidaceae), Pilocarpaceae, and Porinaceae. This contradicts recent studies suggesting that only macrofoliose Lecanoromycetes exhibit increased diversification rates in the Cenozoic.
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Affiliation(s)
- Amanda Barreto Xavier-Leite
- Programa de Pós-Graduação em Sistemática e Evolução, CB, Universidade Federal do Rio Grande do Norte, Campus Universitário, 59072-970, Natal, RN, Brazil.
| | - Marcela E da Silva Cáceres
- Departamento de Biociências, Universidade Federal de Sergipe, CEP: 49500-000, Itabaiana, Sergipe, Brazil.
| | - André Aptroot
- Laboratório de Botânica / Liquenologia, Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, CEP 79070-900, Campo Grande, Mato Grosso do Sul, Brazil.
| | - Bibiana Moncada
- Universidad Distrital Francisco José de Caldas, Licenciatura en Biología, Cra. 4 No. 26B-54, Torre de Laboratorios, Herbario, Bogotá, Colombia.
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Strasse 6-8, 14195 Berlin, Germany.
| | - Bruno Tomio Goto
- Departamento de Botânica e Zoologia, CB, Universidade Federal do Rio Grande do Norte, Campus Universitário, 59072-970, Natal, RN, Brazil.
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16
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Duwe V, Vu L, von Rintelen T, von Raab-Straube E, Schmidt S, Nguyen S, Vu T, Do T, Luu T, Truong V, Di Vincenzo V, Schmidt O, Glöckler F, Jahn R, Lücking R, von Oheimb K, von Oheimb P, Heinze S, Abarca N, Bollendorff S, Borsch T, Buenaventura E, Dang H, Dinh T, Do H, Ehlers S, Freyhof J, Hayden S, Hein P, Hoang T, Hoang D, Hoang S, Kürschner H, Kusber WH, Le H, Le T, Linde M, Mey W, Nguyen H, Nguyen M, Nguyen M, Nguyen D, Nguyen T, Nguyen V, Nguyen D, Ohl M, Parolly G, Pham T, Pham P, Rabe K, Schurian B, Skibbe O, Sulikowska-Drozd A, To Q, Truong T, Zimmermann J, Häuser C. Contributions to the biodiversity of Vietnam – Results of VIETBIO inventory work and field training in Cuc Phuong National Park. Biodivers Data J 2022; 10:e77025. [PMID: 35068979 PMCID: PMC8752577 DOI: 10.3897/bdj.10.e77025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/06/2021] [Indexed: 11/12/2022] Open
Abstract
VIETBIO [Innovative approaches to biodiversity discovery and characterisation in Vietnam] is a bilateral German-Vietnamese research and capacity building project focusing on the development and transfer of new methods and technology towards an integrated biodiversity discovery and monitoring system for Vietnam. Dedicated field training and testing of innovative methodologies were undertaken in Cuc Phuong National Park as part and with support of the project, which led to the new biodiversity data and records made available in this article collection. VIETBIO is a collaboration between the Museum für Naturkunde Berlin – Leibniz Institute for Evolution and Biodiversity Science (MfN), the Botanic Garden and Botanical Museum, Freie Universität Berlin (BGBM) and the Vietnam National Museum of Nature (VNMN), the Institute of Ecology and Biological Resources (IEBR), the Southern Institute of Ecology (SIE), as well as the Institute of Tropical Biology (ITB); all Vietnamese institutions belong to the Vietnam Academy of Science and Technology (VAST). The article collection "VIETBIO" (https://doi.org/10.3897/bdj.coll.63) reports original results of recent biodiversity recording and survey work undertaken in Cuc Phuong National Park, northern Vietnam, under the framework of the VIETBIO project. The collection consist of this “main” cover paper – characterising the study area, the general project approaches and activities, while also giving an extensive overview on previous studies from this area – followed by individual papers for higher taxa as studied during the project. The main purpose is to make primary biodiversity records openly available, including several new and interesting findings for this biodiversity-rich conservation area. All individual data papers with their respective primary records are expected to provide useful baselines for further taxonomic, phylogenetic, ecological and conservation-related studies on the respective taxa and, thus, will be maintained as separate datasets, including separate GUIDs also for further updating.
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17
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Thiyagaraja V, Lücking R, Ertz D, Samarakoon MC, Wanasinghe DN, Karunarathna SC, Cheewangkoon R, Hyde KD. Mendogiadiffusa sp. nov. and an updated key to the species of Mendogia (Myriangiaceae, Dothideomycetes). Biodivers Data J 2021; 9:e67705. [PMID: 34594152 PMCID: PMC8440402 DOI: 10.3897/bdj.9.e67705] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/05/2021] [Indexed: 11/12/2022] Open
Abstract
Background Mendogia belongs to Dothideomycetes and its members are epiphytic on living bamboo culms or palms and distributed in tropical regions. Currently, the genus comprises seven species. Another collection resembling Mendogia was collected from the leaves of Fagales sp. in Thailand. Morphological characteristics and multilocus phylogenetic analyses, using ITS, LSU and SSU sequences, showed that the fungus is new to science, described herein as Mendogiadiffusa. Mendogiadiffusa is characterised by apothecial ascostromata, a carbonised epithecium, dark brown setae on the ascostromatal surface, hyaline paraphysoids, ovoid to clavate asci and oblong to elliptical, muriform ascospores. The fungus has a dark pigmented surface and is occasionally facultatively associated with patches of green algae, but not actually lichenised. Instead, the fungus penetrates the upper leaf surface, forming dark pigmented isodiametric cells below the epidermis. New information Re-examination of specimens of M.chiangraiensis, M.macrostroma and M.yunnanensis revealed the absence of algal associations. The status of Mendogiaphilippinensis (= M.calami) and M.bambusina (= Uleopeltisbambusina) was established, based on morphological comparisons and previous studies. Comprehensive morphological descriptions with phylogenetic analyses support M.diffusa as a novel species in Myriangiaceae. An updated key to the known species of the genus is also provided.
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Affiliation(s)
- Vinodhini Thiyagaraja
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University Chiang Mai 50200 Thailand.,Centre of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand Centre of Excellence in Fungal Research, Mae Fah Luang University Chiang Rai 57100 Thailand.,CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia (KLPB), Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, China CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia (KLPB), Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201 Yunnan China.,World Agro forestry Centre East and Central Asia, Kunming 650201, Yunnan, China World Agro forestry Centre East and Central Asia, Kunming 650201 Yunnan China
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Berlin, Germany Botanischer Garten und Botanisches Museum, Freie Universität Berlin Berlin Germany
| | - Damien Ertz
- Research Department, Meise Botanic Garden, Nieuwelaan 38, BE-1860, Meise, Belgium Research Department, Meise Botanic Garden, Nieuwelaan 38, BE-1860 Meise Belgium.,Fédération Wallonie-Bruxelles, Service Général de l'Enseignement Supérieur et de la Recherche Scientifique, Rue A. Lavallée 1, BE-1080, Bruxelles, Belgium Fédération Wallonie-Bruxelles, Service Général de l'Enseignement Supérieur et de la Recherche Scientifique, Rue A. Lavallée 1, BE-1080 Bruxelles Belgium
| | - Milan C Samarakoon
- Centre of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand Centre of Excellence in Fungal Research, Mae Fah Luang University Chiang Rai 57100 Thailand
| | - Dhanushka N Wanasinghe
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia (KLPB), Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, China CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia (KLPB), Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201 Yunnan China.,World Agro forestry Centre East and Central Asia, Kunming 650201, Yunnan, China World Agro forestry Centre East and Central Asia, Kunming 650201 Yunnan China
| | - Samantha C Karunarathna
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia (KLPB), Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, China CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia (KLPB), Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201 Yunnan China.,World Agro forestry Centre East and Central Asia, Kunming 650201, Yunnan, China World Agro forestry Centre East and Central Asia, Kunming 650201 Yunnan China
| | - Ratchadawan Cheewangkoon
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University Chiang Mai 50200 Thailand.,Innovative Agriculture Research Centre, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand Innovative Agriculture Research Centre, Faculty of Agriculture, Chiang Mai University Chiang Mai 50200 Thailand
| | - Kevin D Hyde
- World Agro forestry Centre East and Central Asia, Kunming 650201, Yunnan, China World Agro forestry Centre East and Central Asia, Kunming 650201 Yunnan China.,Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand Department of Biology, Faculty of Science, Chiang Mai University Chiang Mai 50200 Thailand.,Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University Chiang Mai 50200 Thailand.,CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia (KLPB), Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, Yunnan, China CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia (KLPB), Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201 Yunnan China.,Centre of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand Centre of Excellence in Fungal Research, Mae Fah Luang University Chiang Rai 57100 Thailand
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18
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Lücking R, Leavitt SD, Hawksworth DL. Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics. FUNGAL DIVERS 2021. [DOI: 10.1007/s13225-021-00477-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
AbstractLichens are symbiotic associations resulting from interactions among fungi (primary and secondary mycobionts), algae and/or cyanobacteria (primary and secondary photobionts), and specific elements of the bacterial microbiome associated with the lichen thallus. The question of what is a species, both concerning the lichen as a whole and its main fungal component, the primary mycobiont, has faced many challenges throughout history and has reached new dimensions with the advent of molecular phylogenetics and phylogenomics. In this paper, we briefly revise the definition of lichens and the scientific and vernacular naming conventions, concluding that the scientific, Latinized name usually associated with lichens invariably refers to the primary mycobiont, whereas the vernacular name encompasses the entire lichen. Although the same lichen mycobiont may produce different phenotypes when associating with different photobionts or growing in axenic culture, this discrete variation does not warrant the application of different scientific names, but must follow the principle "one fungus = one name". Instead, broadly agreed informal designations should be used for such discrete morphologies, such as chloromorph and cyanomorph for lichens formed by the same mycobiont but with either green algae or cyanobacteria. The taxonomic recognition of species in lichen-forming fungi is not different from other fungi and conceptual and nomenclatural approaches follow the same principles. We identify a number of current challenges and provide recommendations to address these. Species delimitation in lichen-forming fungi should not be tailored to particular species concepts but instead be derived from empirical evidence, applying one or several of the following principles in what we call the LPR approach: lineage (L) coherence vs. divergence (phylogenetic component), phenotype (P) coherence vs. divergence (morphological component), and/or reproductive (R) compatibility vs. isolation (biological component). Species hypotheses can be established based on either L or P, then using either P or L (plus R) to corroborate them. The reliability of species hypotheses depends not only on the nature and number of characters but also on the context: the closer the relationship and/or similarity between species, the higher the number of characters and/or specimens that should be analyzed to provide reliable delimitations. Alpha taxonomy should follow scientific evidence and an evolutionary framework but should also offer alternative practical solutions, as long as these are scientifically defendable. Taxa that are delimited phylogenetically but not readily identifiable in the field, or are genuinely cryptic, should not be rejected due to the inaccessibility of proper tools. Instead, they can be provisionally treated as undifferentiated complexes for purposes that do not require precise determinations. The application of infraspecific (gamma) taxonomy should be restricted to cases where there is a biological rationale, i.e., lineages of a species complex that show limited phylogenetic divergence but no evidence of reproductive isolation. Gamma taxonomy should not be used to denote discrete phenotypical variation or ecotypes not warranting the distinction at species level. We revise the species pair concept in lichen-forming fungi, which recognizes sexually and asexually reproducing morphs with the same underlying phenotype as different species. We conclude that in most cases this concept does not hold, but the actual situation is complex and not necessarily correlated with reproductive strategy. In cases where no molecular data are available or where single or multi-marker approaches do not provide resolution, we recommend maintaining species pairs until molecular or phylogenomic data are available. This recommendation is based on the example of the species pair Usnea aurantiacoatra vs. U. antarctica, which can only be resolved with phylogenomic approaches, such as microsatellites or RADseq. Overall, we consider that species delimitation in lichen-forming fungi has advanced dramatically over the past three decades, resulting in a solid framework, but that empirical evidence is still missing for many taxa. Therefore, while phylogenomic approaches focusing on particular examples will be increasingly employed to resolve difficult species complexes, broad screening using single barcoding markers will aid in placing as many taxa as possible into a molecular matrix. We provide a practical protocol how to assess and formally treat taxonomic novelties. While this paper focuses on lichen fungi, many of the aspects discussed herein apply generally to fungal taxonomy. The new combination Arthonia minor (Lücking) Lücking comb. et stat. nov. (Bas.: Arthonia cyanea f. minor Lücking) is proposed.
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19
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Aime MC, Miller AN, Aoki T, Bensch K, Cai L, Crous PW, Hawksworth DL, Hyde KD, Kirk PM, Lücking R, May TW, Malosso E, Redhead SA, Rossman AY, Stadler M, Thines M, Yurkov AM, Zhang N, Schoch CL. How to publish a new fungal species, or name, version 3.0. IMA Fungus 2021; 12:11. [PMID: 33934723 PMCID: PMC8091500 DOI: 10.1186/s43008-021-00063-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [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: 12/13/2020] [Accepted: 04/08/2021] [Indexed: 12/19/2022] Open
Abstract
It is now a decade since The International Commission on the Taxonomy of Fungi (ICTF) produced an overview of requirements and best practices for describing a new fungal species. In the meantime the International Code of Nomenclature for algae, fungi, and plants (ICNafp) has changed from its former name (the International Code of Botanical Nomenclature) and introduced new formal requirements for valid publication of species scientific names, including the separation of provisions specific to Fungi and organisms treated as fungi in a new Chapter F. Equally transformative have been changes in the data collection, data dissemination, and analytical tools available to mycologists. This paper provides an updated and expanded discussion of current publication requirements along with best practices for the description of new fungal species and publication of new names and for improving accessibility of their associated metadata that have developed over the last 10 years. Additionally, we provide: (1) model papers for different fungal groups and circumstances; (2) a checklist to simplify meeting (i) the requirements of the ICNafp to ensure the effective, valid and legitimate publication of names of new taxa, and (ii) minimally accepted standards for description; and, (3) templates for preparing standardized species descriptions.
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Affiliation(s)
- M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA.
| | - Andrew N Miller
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, IL, 61820, USA
| | - Takayuki Aoki
- Genetic Resources Center, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Konstanze Bensch
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, NO.1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Pedro W Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT, Utrecht, the Netherlands
| | - David L Hawksworth
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey, TW9 3DS, UK.,Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.,Jilin Agricultural University, Changchun, 130118, Jilin Province, China
| | - Kevin D Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Paul M Kirk
- Biodiversity Informatics & Spatial Analysis, Royal Botanic Garden Kew, Richmond, London, TW9 3AE, UK
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195, Berlin, Germany
| | - Tom W May
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, Victoria, 3004, Australia
| | - Elaine Malosso
- Departamento de Micologia, Centro de Biociências, Universidade Federal de Pernambuco, Recife, PE, 50740-600, Brazil
| | - Scott A Redhead
- Ottawa Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, Ottawa, Ontario, K1A 0C6, Canada
| | - Amy Y Rossman
- Botany and Plant Pathology Department, Oregon State University, Corvallis, OR, 97333, USA
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Marco Thines
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Andrey M Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Ning Zhang
- Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Conrad L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD, 20892, USA
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20
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Affiliation(s)
| | - Leonor Costa Maia
- Center of Biosciences, Department of Mycology Federal University of Pernambuco Recife Pernambuco Brazil
| | | | - Robert Lücking
- Botanic Garden and Botanical Museum Freie Universität Berlin Berlin Germany
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21
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Calbi M, Fajardo‐Gutiérrez F, Posada JM, Lücking R, Brokamp G, Borsch T. Seeing the wood despite the trees: Exploring human disturbance impact on plant diversity, community structure, and standing biomass in fragmented high Andean forests. Ecol Evol 2021; 11:2110-2172. [PMID: 33717446 PMCID: PMC7920791 DOI: 10.1002/ece3.7182] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 10/26/2020] [Accepted: 12/22/2020] [Indexed: 11/16/2022] Open
Abstract
High Andean forests harbor a remarkably high biodiversity and play a key role in providing vital ecosystem services for neighboring cities and settlements. However, they are among the most fragmented and threatened ecosystems in the neotropics. To preserve their unique biodiversity, a deeper understanding of the effects of anthropogenic perturbations on them is urgently needed. Here, we characterized the plant communities of high Andean forest remnants in the hinterland of Bogotá in 32 0.04 ha plots. We assessed the woody vegetation and sampled the understory and epiphytic cover. We gathered data on compositional and structural parameters and compiled a broad array of variables related to anthropogenic disturbance, ranging from local to landscape-wide metrics. We also assessed phylogenetic diversity and functional diversity. We employed nonmetric multidimensional scaling (NMDS) to select meaningful variables in a first step of the analysis. Then, we performed partial redundancy analysis (pRDA) and generalized linear models (GLMs) in order to test how selected environmental and anthropogenic variables are affecting the composition, diversity, and aboveground biomass of these forests. Identified woody vegetation and understory layer communities were characterized by differences in elevation, temperature, and relative humidity, but were also related to different levels of human influence. We found that the increase of human-related disturbance resulted in less phylogenetic diversity and in the phylogenetic clustering of the woody vegetation and in lower aboveground biomass (AGB) values. As to the understory, disturbance was associated with a higher diversity, jointly with a higher phylogenetic dispersion. The most relevant disturbance predictors identified here were as follows: edge effect, proximity of cattle, minimum fragment age, and median patch size. Interestingly, AGB was efficiently predicted by the proportion of late successional species. We therefore recommend the use of AGB and abundance of late successional species as indicators of human disturbance on high Andean forests.
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Affiliation(s)
- Mariasole Calbi
- Botanischer Garten und Botanisches Museum BerlinFreie Universität BerlinBerlinGermany
- Institut für Biologie – Systematische Botanik und PflanzengeographieFreie Universität BerlinBerlinGermany
| | | | - Juan Manuel Posada
- Biology DepartmentFaculty of Natural SciencesUniversidad del RosarioBogotáColombia
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum BerlinFreie Universität BerlinBerlinGermany
| | - Grischa Brokamp
- Botanischer Garten und Botanisches Museum BerlinFreie Universität BerlinBerlinGermany
| | - Thomas Borsch
- Botanischer Garten und Botanisches Museum BerlinFreie Universität BerlinBerlinGermany
- Institut für Biologie – Systematische Botanik und PflanzengeographieFreie Universität BerlinBerlinGermany
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22
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Thiyagaraja V, Lücking R, Ertz D, Karunarathna SC, Wanasinghe DN, Lumyong S, Hyde KD. The Evolution of Life Modes in Stictidaceae, with Three Novel Taxa. J Fungi (Basel) 2021; 7:105. [PMID: 33540644 PMCID: PMC7913076 DOI: 10.3390/jof7020105] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 12/27/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 02/08/2023] Open
Abstract
Ostropales sensu lato is a large group comprising both lichenized and non-lichenized fungi, with several lineages expressing optional lichenization where individuals of the same fungal species exhibit either saprotrophic or lichenized lifestyles depending on the substrate (bark or wood). Greatly variable phenotypic characteristics and large-scale phylogenies have led to frequent changes in the taxonomic circumscription of this order. Ostropales sensu lato is currently split into Graphidales, Gyalectales, Odontotrematales, Ostropales sensu stricto, and Thelenellales. Ostropales sensu stricto is now confined to the family Stictidaceae, which includes a large number of species that are poorly known, since they usually have small fruiting bodies that are rarely collected, and thus, their taxonomy remains partly unresolved. Here, we introduce a new genus Ostropomyces to accommodate a novel lineage related to Ostropa, which is composed of two new species, as well as a new species of Sphaeropezia, S. shangrilaensis. Maximum likelihood and Bayesian inference analyses of mitochondrial small subunit spacers (mtSSU), large subunit nuclear rDNA (LSU), and internal transcribed spacers (ITS) sequence data, together with phenotypic data documented by detailed morphological and anatomical analyses, support the taxonomic affinity of the new taxa in Stictidaceae. Ancestral character state analysis did not resolve the ancestral nutritional status of Stictidaceae with confidence using Bayes traits, but a saprotrophic ancestor was indicated as most likely in a Bayesian binary Markov Chain Monte Carlo sampling (MCMC) approach. Frequent switching in nutritional modes between lineages suggests that lifestyle transition played an important role in the evolution of this family.
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Affiliation(s)
- Vinodhini Thiyagaraja
- Department of Entomology and Plant Pathology, Faculty of Agriculture, Chiang Mai University, Chiang Mai 50200, Thailand;
- Centre of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia (KLPB), Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China; (S.C.K.); (D.N.W.)
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Str. 6-8, 14195 Berlin, Germany;
| | - Damien Ertz
- Research Department, Meise Botanic Garden, Nieuwelaan 38, BE-1860 Meise, Belgium;
- Fédération Wallonie-Bruxelles, Service Général de l’Enseignement Supérieur et de la Recherche Scientifique, Rue A. Lavallée 1, BE-1080 Bruxelles, Belgium
| | - Samantha C. Karunarathna
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia (KLPB), Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China; (S.C.K.); (D.N.W.)
- World Agro forestry Centre East and Central Asia, Kunming 650201, China
| | - Dhanushka N. Wanasinghe
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia (KLPB), Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China; (S.C.K.); (D.N.W.)
- World Agro forestry Centre East and Central Asia, Kunming 650201, China
| | - Saisamorn Lumyong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
- Center of Excellence in Bioresources for Agriculture, Industry and Medicine, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Kevin D. Hyde
- Centre of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia (KLPB), Kunming Institute of Botany, Chinese Academy of Science, Kunming 650201, China; (S.C.K.); (D.N.W.)
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand;
- Innovative Institute of Plant Health, Zhongkai University of Agriculture and Engineering, Haizhu District, Guangzhou 510225, China
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Martínez Colín P, Lücking R, Herrera‐Campos MDLÁ. Diversity begets diversity: Phorophyte and microsite relations of foliicolous lichens in the lowland rain forest at Los Tuxtlas Biosphere Reserve (Veracruz, Mexico). Ecol Res 2021. [DOI: 10.1111/1440-1703.12201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Paola Martínez Colín
- Facultad de Ciencias UNAM Circuito Exterior s/n, Ciudad Universitaria Ciudad de México Mexico
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum Freie Universität Berlin Berlin Germany
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24
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Wilk K, Pabijan M, Saługa M, Gaya E, Lücking R. Phylogenetic revision of South American Teloschistaceae (lichenized Ascomycota, Teloschistales) reveals three new genera and species. Mycologia 2021; 113:278-299. [PMID: 33428561 DOI: 10.1080/00275514.2020.1830672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Members of the poorly investigated family Teloschistaceae in South America, mostly from Bolivia and Peru, were examined using molecular and morphological data here for the first time. In recent phylogenetic reclassifications of Teloschistaceae, South American representatives were poorly represented but shown to belong to subfamilies Teloschistoideae and Xanthorioideae. In this study, we expanded the sampling of South American taxa and investigated mainly the lobate, sublobate, and squamulose members of Caloplaca s.l., using morphological characters and a molecular phylogeny based on a combined three-locus data set (one mitochondrial and two nuclear loci). Building upon new phylogenies at the family and subfamily levels (Teloschistoideae), we propose here three new genera: Andina, Aridoplaca, and Cinnabaria, with the type species Andina citrinoides, Aridoplaca peltata, and Cinnabaria boliviana. We also propose to reduce Tarasginia to synonymy with Sirenophila and Tayloriellina to synonymy with Villophora and introduce three new combinations: Dufourea ottolangei, D. volkmarwirthii, and Villophora erythrosticta. Scutaria andina is reported as new to Bolivia. A critical revision of the subfamily Brownlielloideae confirmed recent findings that it is an artifactual taxon based on a "chimeric" data set, with the type genus being part of Teloschistoideae.
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Affiliation(s)
- Karina Wilk
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
| | - Maciej Pabijan
- Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Kraków, Poland
| | - Marta Saługa
- W. Szafer Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512 Kraków, Poland
| | - Ester Gaya
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Strasse 6-8, 14195 Berlin, Germany
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25
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Hongsanan S, Hyde KD, Phookamsak R, Wanasinghe DN, McKenzie EHC, Sarma VV, Lücking R, Boonmee S, Bhat JD, Liu NG, Tennakoon DS, Pem D, Karunarathna A, Jiang SH, Jones GEB, Phillips AJL, Manawasinghe IS, Tibpromma S, Jayasiri SC, Sandamali D, Jayawardena RS, Wijayawardene NN, Ekanayaka AH, Jeewon R, Lu YZ, Phukhamsakda C, Dissanayake AJ, Zeng XY, Luo ZL, Tian Q, Thambugala KM, Dai D, Samarakoon MC, Chethana KWT, Ertz D, Doilom M, Liu JK(J, Pérez-Ortega S, Suija A, Senwanna C, Wijesinghe SN, Niranjan M, Zhang SN, Ariyawansa HA, Jiang HB, Zhang JF, Norphanphoun C, de Silva NI, Thiyagaraja V, Zhang H, Bezerra JDP, Miranda-González R, Aptroot A, Kashiwadani H, Harishchandra D, Sérusiaux E, Abeywickrama PD, Bao DF, Devadatha B, Wu HX, Moon KH, Gueidan C, Schumm F, Bundhun D, Mapook A, Monkai J, Bhunjun CS, Chomnunti P, Suetrong S, Chaiwan N, Dayarathne MC, Yang J, Rathnayaka AR, Xu JC, Zheng J, Liu G, Feng Y, Xie N. Refined families of Dothideomycetes: orders and families incertae sedis in Dothideomycetes. FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00462-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
AbstractNumerous new taxa and classifications of Dothideomycetes have been published following the last monograph of families of Dothideomycetes in 2013. A recent publication by Honsanan et al. in 2020 expanded information of families in Dothideomycetidae and Pleosporomycetidae with modern classifications. In this paper, we provide a refined updated document on orders and families incertae sedis of Dothideomycetes. Each family is provided with an updated description, notes, including figures to represent the morphology, a list of accepted genera, and economic and ecological significances. We also provide phylogenetic trees for each order. In this study, 31 orders which consist 50 families are assigned as orders incertae sedis in Dothideomycetes, and 41 families are treated as families incertae sedis due to lack of molecular or morphological evidence. The new order, Catinellales, and four new families, Catinellaceae, Morenoinaceae Neobuelliellaceae and Thyrinulaceae are introduced. Seven genera (Neobuelliella, Pseudomicrothyrium, Flagellostrigula, Swinscowia, Macroconstrictolumina, Pseudobogoriella, and Schummia) are introduced. Seven new species (Acrospermum urticae, Bogoriella complexoluminata, Dothiorella ostryae, Dyfrolomyces distoseptatus, Macroconstrictolumina megalateralis, Patellaria microspora, and Pseudomicrothyrium thailandicum) are introduced base on morphology and phylogeny, together with two new records/reports and five new collections from different families. Ninety new combinations are also provided in this paper.
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Thines M, Aoki T, Crous PW, Hyde KD, Lücking R, Malosso E, May TW, Miller AN, Redhead SA, Yurkov AM, Hawksworth DL. Setting scientific names at all taxonomic ranks in italics facilitates their quick recognition in scientific papers. IMA Fungus 2020; 11:25. [PMID: 33292779 PMCID: PMC7670697 DOI: 10.1186/s43008-020-00048-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/27/2020] [Indexed: 11/15/2022] Open
Abstract
It is common practice in scientific journals to print genus and species names in italics. This is not only historical as species names were traditionally derived from Greek or Latin. Importantly, it also facilitates the rapid recognition of genus and species names when skimming through manuscripts. However, names above the genus level are not always italicized, except in some journals which have adopted this practice for all scientific names. Since scientific names treated under the various Codes of nomenclature are without exception treated as Latin, there is no reason why names above genus level should be handled differently, particularly as higher taxon names are becoming increasingly relevant in systematic and evolutionary studies and their italicization would aid the unambiguous recognition of formal scientific names distinguishing them from colloquial names. Several leading mycological and botanical journals have already adopted italics for names of all taxa regardless of rank over recent decades, as is the practice in the International Code of Nomenclature for algae, fungi, and plants, and we hereby recommend that this practice be taken up broadly in scientific journals and textbooks.
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Affiliation(s)
- Marco Thines
- Department of Biological Sciences, Goethe University, Institute of Ecology Evolution and Diversity, Max-von-Laue-Str. 13, 60439 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Takayuki Aoki
- Genetic Resources Center, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Pedro W. Crous
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
| | - Kevin D. Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195 Berlin, Germany
| | - Elaine Malosso
- Departamento de Micologia. Recife, Universidade Federal de Pernambuco, Centro de Biociências, Recife, 50.740-600 Brazil
| | - Tom W. May
- Royal Botanic Gardens Victoria, Melbourne, Victoria 3004 Australia
| | - Andrew N. Miller
- Illinois Natural History Survey, University of Illinois, Champaign, IL 61820 USA
| | - Scott A. Redhead
- Ottawa Research and Development Centre, Science and Technology Branch, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON K1A 0C6 Canada
| | - Andrey M. Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| | - David L. Hawksworth
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey, TW9 3DS UK
- Jilin Agricultural University, Changchun, Jilin Province 130118 People’s Republic of China
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Dal Forno M, Lawrey JD, Sikaroodi M, Gillevet PM, Schuettpelz E, Lücking R. Extensive photobiont sharing in a rapidly radiating cyanolichen clade. Mol Ecol 2020; 30:1755-1776. [PMID: 33080083 DOI: 10.1111/mec.15700] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/24/2020] [Accepted: 10/13/2020] [Indexed: 01/21/2023]
Abstract
Recent studies have uncovered remarkable diversity in Dictyonema s.lat. basidiolichens, here recognized as subtribe Dictyonemateae. This group includes five genera and 148 species, but hundreds more await description. The photobionts of these lichens belong to Rhizonema, a recently resurrected cyanobacterial genus known by a single species. To further investigate photobiont diversity within Dictyonemateae, we generated 765 new cyanobacterial sequences from 635 specimens collected from 18 countries. The ITS barcoding locus supported the recognition of 200 mycobiont (fungal) species among these samples, but the photobiont diversity was comparatively low. Our analyses revealed three main divisions of Rhizonema, with two repeatedly recovered as monophyletic (proposed as new species), and the third mostly paraphyletic. The paraphyletic lineage corresponds to R. interruptum and partnered with mycobionts from all five genera in Dictyonemateae. There was no evidence of photobiont-mycobiont co-speciation, but one of the monophyletic lineages of Rhizonema appears to partner predominantly with one of the two major clades of Cora (mycobiont) with samples collected largely from the northern Andes. Molecular clock estimations indicate the Rhizonema species are much older than the fungal species in the Dictyonemateae, suggesting that these basidiolichens obtained their photobionts from older ascolichen lineages and the photobiont variation in extant lineages of Dictyonemateae is the result of multiple photobiont switches. These results support the hypothesis of lichens representing "fungal farmers," in which diverse mycobiont lineages associate with a substantially lower diversity of photobionts by sharing those photobionts best suited for the lichen symbiosis among multiple and often unrelated mycobiont lineages.
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Affiliation(s)
- Manuela Dal Forno
- Botanical Research Institute of Texas, Fort Worth, TX, USA.,Department of Botany, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - James D Lawrey
- Department of Biology, George Mason University, Fairfax, VA, USA
| | | | | | - Eric Schuettpelz
- Department of Botany, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Robert Lücking
- Botanical Garden and Botanical Museum Berlin, Berlin, Germany.,Research Associate, Science & Education, The Field Museum, Chicago, IL, USA
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28
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Nelsen MP, Lücking R, Boyce CK, Lumbsch HT, Ree RH. The macroevolutionary dynamics of symbiotic and phenotypic diversification in lichens. Proc Natl Acad Sci U S A 2020; 117:21495-21503. [PMID: 32796103 PMCID: PMC7474681 DOI: 10.1073/pnas.2001913117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Symbioses are evolutionarily pervasive and play fundamental roles in structuring ecosystems, yet our understanding of their macroevolutionary origins, persistence, and consequences is incomplete. We traced the macroevolutionary history of symbiotic and phenotypic diversification in an iconic symbiosis, lichens. By inferring the most comprehensive time-scaled phylogeny of lichen-forming fungi (LFF) to date (over 3,300 species), we identified shifts among symbiont classes that broadly coincided with the convergent evolution of phylogenetically or functionally similar associations in diverse lineages (plants, fungi, bacteria). While a relatively recent loss of lichenization in Lecanoromycetes was previously identified, our work instead suggests lichenization was abandoned far earlier, interrupting what had previously been considered a direct switch between trebouxiophycean and trentepohlialean algal symbionts. Consequently, some of the most diverse clades of LFF are instead derived from nonlichenized ancestors and re-evolved lichenization with Trentepohliales algae, a clade that also facilitated lichenization in unrelated lineages of LFF. Furthermore, while symbiont identity and symbiotic phenotype influence the ecology and physiology of lichens, they are not correlated with rates of lineage birth and death, suggesting more complex dynamics underly lichen diversification. Finally, diversification patterns of LFF differed from those of wood-rotting and ectomycorrhizal taxa, likely reflecting contrasts in their fundamental biological properties. Together, our work provides a timeline for the ecological contributions of lichens, and reshapes our understanding of symbiotic persistence in a classic model of symbiosis.
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Affiliation(s)
- Matthew P Nelsen
- Department of Science and Education, Negaunee Integrative Research Center, The Field Museum, Chicago, IL 60605;
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, 14195 Berlin, Germany
| | - C Kevin Boyce
- Department of Geological Sciences, Stanford University, Stanford, CA 94305
| | - H Thorsten Lumbsch
- Department of Science and Education, Negaunee Integrative Research Center, The Field Museum, Chicago, IL 60605
| | - Richard H Ree
- Department of Science and Education, Negaunee Integrative Research Center, The Field Museum, Chicago, IL 60605
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29
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Lücking R, Aime MC, Robbertse B, Miller AN, Ariyawansa HA, Aoki T, Cardinali G, Crous PW, Druzhinina IS, Geiser DM, Hawksworth DL, Hyde KD, Irinyi L, Jeewon R, Johnston PR, Kirk PM, Malosso E, May TW, Meyer W, Öpik M, Robert V, Stadler M, Thines M, Vu D, Yurkov AM, Zhang N, Schoch CL. Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? IMA Fungus 2020; 11:14. [PMID: 32714773 PMCID: PMC7353689 DOI: 10.1186/s43008-020-00033-z] [Citation(s) in RCA: 174] [Impact Index Per Article: 43.5] [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] [Indexed: 01/23/2023] Open
Abstract
True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.
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Affiliation(s)
- Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6–8, 14195 Berlin, Germany
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
| | - M. Catherine Aime
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907 USA
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
| | - Andrew N. Miller
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820-6970 USA
| | - Hiran A. Ariyawansa
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Pathology and Microbiology, College of Bio-Resources and Agriculture, National Taiwan University, Taipe City, Taiwan
| | - Takayuki Aoki
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Agriculture and Food Research Organization, Genetic Resources Center, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Gianluigi Cardinali
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
| | - Pedro W. Crous
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Irina S. Druzhinina
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Microbiology and Applied Genomics Group, Research Area Biochemical Technology, Institute of Chemical, Environmental & Bioscience Engineering (ICEBE), TU Wien, Vienna, Austria
- Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China
| | - David M. Geiser
- Department of Plant Pathology & Environmental Microbiology, The Pennsylvania State University, University Park, PA 16802 USA
| | - David L. Hawksworth
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey, TW9 3DS UK
- Geography and Environment, University of Southampton, Southampton, SO17 1BJ UK
- Jilin Agricultural University, Changchun, 130118 Jilin Province China
| | - Kevin D. Hyde
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Science, Kunming, 650201 Yunnan China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100 Thailand
- World Agroforestry Centre, East and Central Asia, Kunming, 650201 Yunnan China
- Mushroom Research Foundation, 128 M.3 Ban Pa Deng T. Pa Pae, A. Mae Taeng, Chiang Rai, 50150 Thailand
| | - Laszlo Irinyi
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Rajesh Jeewon
- Department of Health Sciences, Faculty of Science, University of Mauritius, Reduit, Mauritius
| | - Peter R. Johnston
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Manaaki Whenua – Landcare Research, Private Bag 92170, Auckland, 1142 New Zealand
| | | | - Elaine Malosso
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Universidade Federal de Pernambuco, Centro de Biociências, Departamento de Micologia, Laboratório de Hifomicetos de Folhedo, Avenida da Engenharia, s/n Cidade Universitária, Recife, PE 50.740-600 Brazil
| | - Tom W. May
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Royal Botanic Gardens Victoria, Birdwood Avenue, Melbourne, Victoria 3004 Australia
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Faculty of Medicine and Health, Sydney Medical School, Westmead Clinical School, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Westmead Hospital (Research and Education Network), Westmead Institute for Medical Research, Sydney, NSW Australia
| | - Maarja Öpik
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- University of Tartu, 40 Lai Street, 51 005 Tartu, Estonia
| | - Vincent Robert
- Department Pharmaceutical Sciences, University of Perugia, Via Borgo 20 Giugno, 74, Perugia, Italy
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Marc Stadler
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department Microbial Drugs, Helmholtz Centre for Infection Research, and German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| | - Marco Thines
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Institute of Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Straße 9, 60439 Frankfurt (Main); Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt (Main), Germany
| | - Duong Vu
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Andrey M. Yurkov
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Ning Zhang
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901 USA
| | - Conrad L. Schoch
- International Commission on the Taxonomy of Fungi, Champaign, IL USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892 USA
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Lindgren H, Moncada B, Lücking R, Magain N, Simon A, Goffinet B, Sérusiaux E, Nelsen MP, Mercado-Díaz JA, Widhelm TJ, Lumbsch HT. Cophylogenetic patterns in algal symbionts correlate with repeated symbiont switches during diversification and geographic expansion of lichen-forming fungi in the genus Sticta (Ascomycota, Peltigeraceae). Mol Phylogenet Evol 2020; 150:106860. [PMID: 32473336 DOI: 10.1016/j.ympev.2020.106860] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/10/2020] [Accepted: 05/21/2020] [Indexed: 12/19/2022]
Abstract
Species in the fungal genus Sticta form symbiotic associations primarily with either green algae or cyanobacteria, but tripartite associations or photosymbiodemes involving both types of photobionts occur in some species. Sticta is known to associate with green algae in the genus Symbiochloris. However, previous studies have shown that algae from other genera, such as Heveochlorella, may also be suitable partners for Sticta. We examined the diversity of green algal partners in the genus Sticta and assessed the patterns of association between the host fungus and its algal symbiont. We used multi-locus sequence data from multiple individuals collected in Australia, Cuba, Madagascar, Mauritius, New Zealand, Reunion and South America to infer phylogenies for fungal and algal partners and performed tests of congruence to assess coevolution between the partners. In addition, event-based methods were implemented to examine which cophylogenetic processes have led to the observed association patterns in Sticta and its green algal symbionts. Our results show that in addition to Symbiochloris, Sticta associates with green algae from the genera Chloroidium, Coccomyxa, Elliptochloris and Heveochlorella, the latter being the most common algal symbiont associated with Sticta in this study. Geography plays a strong role in shaping fungal-algal association patterns in Sticta as mycobionts associate with different algal lineages in different geographic locations. While fungal and algal phylogenies were mostly congruent, event-based methods did not find any evidence for cospeciation between the partners. Instead, the association patterns observed in Sticta and associated algae, were largely explained by other cophylogenetic events such as host-switches, losses of symbiont and failure of the symbiont to diverge with its host. Our results also show that tripartite associations with green algae evolved multiple times in Sticta.
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Affiliation(s)
- Hanna Lindgren
- Science and Education, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605, United States.
| | - Bibiana Moncada
- Licenciatura en Biología, Universidad Distrital Francisco José de Caldas, Cra. 4 No. 26D-54, Torre de Laboratorios, Herbario, Bogotá, Colombia
| | - Robert Lücking
- Botanical Garden and Botanical Museum, Koenigin-Luise-Strasse 6-8, 14195 Berlin, Germany
| | - Nicolas Magain
- Evolution and Conservation Biology, University of Liège, Sart Tilman B22, B-4000 Liège, Belgium; Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | - Antoine Simon
- Evolution and Conservation Biology, University of Liège, Sart Tilman B22, B-4000 Liège, Belgium
| | - Bernard Goffinet
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT 06269-3043, USA
| | - Emmanuël Sérusiaux
- Evolution and Conservation Biology, University of Liège, Sart Tilman B22, B-4000 Liège, Belgium
| | - Matthew P Nelsen
- Science and Education, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605, United States
| | - Joel A Mercado-Díaz
- Science and Education, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605, United States; Committee on Evolutionary Biology, University of Chicago, 1025 E. 57(th) street, Chicago, IL 60637, USA
| | - Todd J Widhelm
- Science and Education, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605, United States
| | - H Thorsten Lumbsch
- Science and Education, The Field Museum, 1400 South Lake Shore Drive, Chicago, IL 60605, United States
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31
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Jiang SH, Hawksworth DL, Lücking R, Wei JC. A new genus and species of foliicolous lichen in a new family of Strigulales ( Ascomycota: Dothideomycetes) reveals remarkable class-level homoplasy. IMA Fungus 2020; 11:1. [PMID: 32617253 PMCID: PMC7325298 DOI: 10.1186/s43008-019-0026-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 08/08/2019] [Accepted: 12/20/2019] [Indexed: 11/23/2022] Open
Abstract
Phylogenetic analysis of some foliicolous lichens collected in Hainan Province, China, revealed a new lineage morphologically similar to Porina but phylogenetically related to Strigulaceae (Dothideomycetes), differing from the latter in ascus type. The monospecific genus Tenuitholiascus gen. nov. is introduced for the single species, T. porinoides sp. nov., which is placed in the new, monogeneric family Tenuitholiascaceae, sister to Strigulaceae in Strigulales. The new taxon closely resembles the genus Porina in external morphology and ascospore type, as well as the thin-walled asci and unbranched paraphyses. Yet, it is entirely unrelated to the latter, which belongs in class Lecanoromycetes in the order Gyalectales.
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Affiliation(s)
- Shu Hua Jiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - David L Hawksworth
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD UK.,Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Surrey, TW9 3DS UK.,Jilin Agricultural University, Changchun, 130118 Jilin Province China
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195 Berlin, Germany
| | - Jiang Chun Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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32
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Nelsen MP, Lücking R, Boyce CK, Lumbsch HT, Ree RH. No support for the emergence of lichens prior to the evolution of vascular plants. Geobiology 2020; 18:3-13. [PMID: 31729136 DOI: 10.1111/gbi.12369] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [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: 06/28/2019] [Revised: 08/28/2019] [Accepted: 10/05/2019] [Indexed: 06/10/2023]
Abstract
The early-successional status of lichens in modern terrestrial ecosystems, together with the role lichen-mediated weathering plays in the carbon cycle, have contributed to the long and widely held assumption that lichens occupied early terrestrial ecosystems prior to the evolution of vascular plants and drove global change during this time. Their poor preservation potential and the classification of ambiguous fossils as lichens or other fungal-algal associations have further reinforced this view. As unambiguous fossil data are lacking to demonstrate the presence of lichens prior to vascular plants, we utilize an alternate approach to assess their historic presence in early terrestrial ecosystems. Here, we analyze new time-calibrated phylogenies of ascomycete fungi and chlorophytan algae, that intensively sample lineages with lichen symbionts. Age estimates for several interacting clades show broad congruence and demonstrate that fungal origins of lichenization postdate the earliest tracheophytes. Coupled with the absence of unambiguous fossil data, our work finds no support for lichens having mediated global change during the Neoproterozoic-early Paleozoic prior to vascular plants. We conclude by discussing our findings in the context of Neoproterozoic-Paleozoic terrestrial ecosystem evolution and the paleoecological context in which vascular plants evolved.
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Affiliation(s)
- Matthew P Nelsen
- Department of Science and Education, The Field Museum, Integrative Research Center, Chicago, IL, USA
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL, USA
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Berlin, Germany
| | - C Kevin Boyce
- Department of Geological Sciences, Stanford University, Stanford, California, USA
| | - H Thorsten Lumbsch
- Department of Science and Education, The Field Museum, Integrative Research Center, Chicago, IL, USA
| | - Richard H Ree
- Department of Science and Education, The Field Museum, Integrative Research Center, Chicago, IL, USA
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Olivier-Jimenez D, Chollet-Krugler M, Rondeau D, Beniddir MA, Ferron S, Delhaye T, Allard PM, Wolfender JL, Sipman HJM, Lücking R, Boustie J, Le Pogam P. A database of high-resolution MS/MS spectra for lichen metabolites. Sci Data 2019; 6:294. [PMID: 31780665 PMCID: PMC6882832 DOI: 10.1038/s41597-019-0305-1] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/31/2019] [Indexed: 11/15/2022] Open
Abstract
While analytical techniques in natural products research massively shifted to liquid chromatography-mass spectrometry, lichen chemistry remains reliant on limited analytical methods, Thin Layer Chromatography being the gold standard. To meet the modern standards of metabolomics within lichenochemistry, we announce the publication of an open access MS/MS library with 250 metabolites, coined LDB for Lichen DataBase, providing a comprehensive coverage of lichen chemodiversity. These were donated by the Berlin Garden and Botanical Museum from the collection of Siegfried Huneck to be analyzed by LC-MS/MS. Spectra at individual collision energies were submitted to MetaboLights (https://www.ebi.ac.uk/metabolights/MTBLS999) while merged spectra were uploaded to the GNPS platform (CCMSLIB00004751209 to CCMSLIB00004751517). Technical validation was achieved by dereplicating three lichen extracts using a Molecular Networking approach, revealing the detection of eleven unique molecules that would have been missed without LDB implementation to the GNPS. From a chemist's viewpoint, this database should help streamlining the isolation of formerly unreported metabolites. From a taxonomist perspective, the LDB offers a versatile tool for the chemical profiling of newly reported species.
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Affiliation(s)
- Damien Olivier-Jimenez
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, Univ Rennes, F-35000, Rennes, France
- CNRS, IETR (Institut d'Électronique et Télécommunications de Rennes)-UMR 6164, Univ Rennes, F-35000, Rennes, France
| | - Marylène Chollet-Krugler
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, Univ Rennes, F-35000, Rennes, France
| | - David Rondeau
- CNRS, IETR (Institut d'Électronique et Télécommunications de Rennes)-UMR 6164, Univ Rennes, F-35000, Rennes, France
- Département de Chimie, Université de Bretagne Occidentale, F-29238, Brest, France
| | - Mehdi A Beniddir
- CNRS, BioCIS (Biomolécules: Conception Isolement et Synthèse)-UMR 8076, Univ Paris-Sud, Université Paris-Saclay, 5, rue J.-B. Clément, F-92290, Châtenay-Malabry, France
| | - Solenn Ferron
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, Univ Rennes, F-35000, Rennes, France
| | - Thomas Delhaye
- CNRS, IETR (Institut d'Électronique et Télécommunications de Rennes)-UMR 6164, Univ Rennes, F-35000, Rennes, France
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, CMU, 1 Rue Michel Servet, 1211, Geneva 4, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, CMU, 1 Rue Michel Servet, 1211, Geneva 4, Switzerland
| | - Harrie J M Sipman
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Strasse 6-8, D-14195, Berlin, Germany
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Strasse 6-8, D-14195, Berlin, Germany
| | - Joël Boustie
- CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, Univ Rennes, F-35000, Rennes, France.
| | - Pierre Le Pogam
- CNRS, BioCIS (Biomolécules: Conception Isolement et Synthèse)-UMR 8076, Univ Paris-Sud, Université Paris-Saclay, 5, rue J.-B. Clément, F-92290, Châtenay-Malabry, France.
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Santos VM, Silva Cáceres ME, Lücking R. Diversity of foliicolous lichens in isolated montane rainforests (Brejos) of northeastern Brazil and their biogeography in a neotropical context. Ecol Res 2019. [DOI: 10.1111/1440-1703.12071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Viviane M. Santos
- Centro de Biociências, Departamento de Micologia Universidade Federal de Pernambuco Recife Brazil
- Departamento de Biociências Universidade Federal de Sergipe Itabaiana Brazil
| | - Marcela E. Silva Cáceres
- Centro de Biociências, Departamento de Micologia Universidade Federal de Pernambuco Recife Brazil
- Departamento de Biociências Universidade Federal de Sergipe Itabaiana Brazil
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum Freie Universität Berlin Berlin Germany
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Soto-Medina E, Lücking R, Silverstone-Sopkin PA, Torres AM. Changes in Functional and Taxonomic Diversity and Composition of Corticolous Lichens in an Altitudinal Gradient in Colombia. CRYPTOGAMIE MYCOL 2019. [DOI: 10.5252/cryptogamie-mycologie2019v40a6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Edier Soto-Medina
- Grupo de ecología y diversidad vegetal, Departamento de Biología, Universidad del Valle, Cali (Colombia)
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Königin-Luise-Straße 6-8, 14195, Berlin (Germany)
| | | | - Alba Marina Torres
- Grupo de ecología y diversidad vegetal, Departamento de Biología, Universidad del Valle, Cali (Colombia)
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Widhelm TJ, Grewe F, Huang JP, Mercado-Díaz JA, Goffinet B, Lücking R, Moncada B, Mason-Gamer R, Lumbsch HT. Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group (Lobariaceae, Ascomycota). Sci Rep 2019; 9:8968. [PMID: 31222061 PMCID: PMC6586878 DOI: 10.1038/s41598-019-45455-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 06/03/2019] [Indexed: 12/19/2022] Open
Abstract
In the age of next-generation sequencing, the number of loci available for phylogenetic analyses has increased by orders of magnitude. But despite this dramatic increase in the amount of data, some phylogenomic studies have revealed rampant gene-tree discordance that can be caused by many historical processes, such as rapid diversification, gene duplication, or reticulate evolution. We used a target enrichment approach to sample 400 single-copy nuclear genes and estimate the phylogenetic relationships of 13 genera in the lichen-forming family Lobariaceae to address the effect of data type (nucleotides and amino acids) and phylogenetic reconstruction method (concatenation and species tree approaches). Furthermore, we examined datasets for evidence of historical processes, such as rapid diversification and reticulate evolution. We found incongruence associated with sequence data types (nucleotide vs. amino acid sequences) and with different methods of phylogenetic reconstruction (species tree vs. concatenation). The resulting phylogenetic trees provided evidence for rapid and reticulate evolution based on extremely short branches in the backbone of the phylogenies. The observed rapid and reticulate diversifications may explain conflicts among gene trees and the challenges to resolving evolutionary relationships. Based on divergence times, the diversification at the backbone occurred near the Cretaceous-Paleogene (K-Pg) boundary (65 Mya) which is consistent with other rapid diversifications in the tree of life. Although some phylogenetic relationships within the Lobariaceae family remain with low support, even with our powerful phylogenomic dataset of up to 376 genes, our use of target-capturing data allowed for the novel exploration of the mechanisms underlying phylogenetic and systematic incongruence.
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Affiliation(s)
- Todd J Widhelm
- Field Museum, Science and Education, Chicago, 60605, USA.
- University of Illinois at Chicago, Biological Sciences, Chicago, 60607, USA.
| | - Felix Grewe
- Field Museum, Grainger Bioinformatics Center, Chicago, 60605, USA
| | - Jen-Pan Huang
- Field Museum, Science and Education, Chicago, 60605, USA
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | | | - Bernard Goffinet
- University of Connecticut, Ecology and Evolutionary Biology, Storrs, 06268, USA
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Herbarium, Berlin, 14195, Germany
| | - Bibiana Moncada
- Universidad Distrital Francisco José de Caldas, Torre de Laboratorios, Herbario, Bogotá, 11021, Colombia
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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] [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: 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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Lücking R, Kirk PM, Hawksworth DL. Sequence-based nomenclature: a reply to Thines et al. and Zamora et al. and provisions for an amended proposal "from the floor" to allow DNA sequences as types of names. IMA Fungus 2018; 9:185-198. [PMID: 30018879 PMCID: PMC6048568 DOI: 10.5598/imafungus.2018.09.01.12] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 06/08/2018] [Indexed: 02/07/2023] Open
Abstract
We reply to two recently published, multi-authored opinion papers by opponents of sequence-based nomenclature, namely Zamora et al. (IMA Fungus9: 167-175,2018) and Thines et al. (IMA Fungus9: 177-183, 2018). While we agree with some of the principal arguments brought forward by these authors, we address misconceptions and demonstrate that some of the presumed evidence presented in these papers has been wrongly interpreted. We disagree that allowing sequences as types would fundamentally alter the nature of types, since a similar nature of abstracted features as type is already allowed in the Code (Art. 40.5), namely an illustration. We also disagree that there is a high risk of introducing artifactual taxa, as this risk can be quantified at well below 5 %, considering the various types of high-throughput sequencing errors. Contrary to apparently widespread misconceptions, sequence-based nomenclature cannot be based on similarity-derived OTUs and their consensus sequences, but must be derived from rigorous, multiple alignment-based phylogenetic methods and quantitative, single-marker species recognition algorithms, using original sequence reads; it is therefore identical in its approach to single-marker studies based on physical types, an approach allowed by the Code. We recognize the limitations of the ITS as a single fungal barcoding marker, but point out that these result in a conservative approach, with "false negatives" surpassing "false positives"; a desirable feature of sequence-based nomenclature. Sequence-based nomenclature does not aim at accurately resolving species, but at naming sequences that represent unknown fungal lineages so that these can serve as a means of communication, so ending the untenable situation of an exponentially growing number of unlabeled fungal sequences that fill online repositories. The risks are outweighed by the gains obtained by a reference library of named sequences spanning the full array of fungal diversity. Finally, we elaborate provisions in addition to our original proposal to amend the Code that would take care of the issues brought forward by opponents to this approach. In particular, taking up the idea of the Candidatus status of invalid, provisional names in prokaryote nomenclature, we propose a compromise that would allow valid publication of voucherless, sequence-based names in a consistent manner, but with the obligate designation as "nom. seq." (nomen sequentiae). Such names would not have priority over specimen- or culture-based names unless either epitypified with a physical type or adopted for protection on the recommendation of a committee of the International Commission on the Taxonomy of Fungi following evaluation based on strict quality control of the underlying studies based on established rules or recommendations.
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Affiliation(s)
- Robert Lücking
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6-8, D-14195 Berlin, Germany
| | - Paul M. Kirk
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Biodiversity Informatics & Spatial Analysis, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
| | - David L. Hawksworth
- Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Jilin Agricultural University, Chanchung, Jilin province, 130118 China
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Widhelm TJ, Bertoletti FR, Asztalos MJ, Mercado-Díaz JA, Huang JP, Moncada B, Lücking R, Magain N, Sérusiaux E, Goffinet B, Crouch N, Mason-Gamer R, Lumbsch HT. Oligocene origin and drivers of diversification in the genus Sticta (Lobariaceae, Ascomycota). Mol Phylogenet Evol 2018; 126:58-73. [PMID: 29656104 DOI: 10.1016/j.ympev.2018.04.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 02/19/2018] [Accepted: 04/05/2018] [Indexed: 11/24/2022]
Abstract
A major challenge to evolutionary biologists is to understand how biodiversity is distributed through space and time and across the tree of life. Diversification of organisms is influenced by many factors that act at different times and geographic locations but it is still not clear which have a significant impact and how drivers interact. To study diversification, we chose the lichen genus Sticta, by sampling through most of the global range and producing a time tree. We estimate that Sticta originated about 30 million years ago, but biogoegraphic analysis was unclear in estimating the origin of the genus. Furthermore, we investigated the effect of dispersal ability finding that Sticta has a high dispersal rate, as collections from Hawaii showed that divergent lineages colonized the islands at least four times. Symbiont interactions were investigated using BiSSE to understand if green-algal or cyanobacterial symbiont interactions influenced diversification, only to find that the positive results were driven almost completely by Type I error. On the other hand, another BiSSE analysis found that an association with Andean tectonic activity increases the speciation rate of species.
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Affiliation(s)
- Todd J Widhelm
- Science & Education, The Field Museum, Chicago, IL, USA; Biological Sciences, Ecology and Evolution, University of Illinois at Chicago, Chicago, IL, USA.
| | | | | | | | - Jen-Pan Huang
- Science & Education, The Field Museum, Chicago, IL, USA
| | - Bibiana Moncada
- Licenciatura en Biología, Universidad Distrital Francisco José de Caldas, Bogotá, Colombia
| | - Robert Lücking
- Kustos Herbarium, Botanischer Garten und Botanisches Museum, Berlin, Germany
| | | | | | - Bernard Goffinet
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Nicholas Crouch
- Biological Sciences, Ecology and Evolution, University of Illinois at Chicago, Chicago, IL, USA
| | - Roberta Mason-Gamer
- Biological Sciences, Ecology and Evolution, University of Illinois at Chicago, Chicago, IL, USA
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Fazio AT, Adler MT, Parnmen S, Lücking R, Maier MS. Production of the bioactive pigment elsinochrome A by a cultured mycobiont strain of the lichen Graphis elongata. Mycol Prog 2018. [DOI: 10.1007/s11557-017-1374-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Soto-Medina EA, Lücking R, Torres AM. Nuevos registros de líquenes (Familia Graphidaceae, biotopos thelotremoides) para Colombia. Biota 2018. [DOI: 10.21068/c2017.v18n02a03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Pereira TA, Passos PDO, Santos LAD, Lücking R, Cáceres MEDS. Going extinct before being discovered? New lichen fungi from a small fragment of the vanishing Atlantic Rainforest in Brazil. Biota Neotrop 2018. [DOI: 10.1590/1676-0611-bn-2017-0445] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract In the frame of an ongoing lichen inventory of Atlantic Rainforest remnants in Northeast Brazil, five new species of Graphidaceae were discovered in a small forest fragment, Mata do Cipó, in Sergipe state, the smallest state of Brazil and among those with the highest deforestation rate in the country. An additional new species had already been collected in Panama before and was now also found in the Mata do Cipó and is described here as well. In total, 40 species of Graphidaceae are reported for this remnant, including a large number of taxa indicative of well-preserved rainforest. The new species are: Fissurina atlantica T.A. Pereira, M. Cáceres & Lücking, sp. nov., Graphis subaltamirensis Passos, M. Cáceres & Lücking, sp. nov., Ocellularia cipoensis L.A. Santos, M. Cáceres & Lücking, sp. nov., O. sosma T.A. Pereira, M. Cáceres & Lücking, sp. nov., O. submordenii Lücking, sp. nov. (also known from Panama), and Pseudochapsa aptrootiana M. Cáceres, T.A. Pereira & Lücking, sp. nov. The findings are discussed in the context of the strong fragmentation of the Atlantic Rainforest, with individual remnants apparently serving as refugia for residual populations of rare species of lichen fungi that were more widely distributed in the past, but currently seem to occur only in isolated fragments.
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Hyde KD, Maharachchikumbura SSN, Hongsanan S, Samarakoon MC, Lücking R, Pem D, Harishchandra D, Jeewon R, Zhao RL, Xu JC, Liu JK, Al-Sadi AM, Bahkali AH, Elgorban AM. The ranking of fungi: a tribute to David L. Hawksworth on his 70th birthday. FUNGAL DIVERS 2017. [DOI: 10.1007/s13225-017-0383-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Affiliation(s)
- Edier Soto Medina
- Grupo de Investigación Ecología y Diversidad Vegetal; Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Calle 13 # 100-00, Universidad del Valle, Cali, Colombia
| | - André Aptroot
- ABL Herbarium, G.v.d.Veenstraat 107, NL-3762 XK Soest, The Netherlands
| | - Robert Lücking
- Botanischer Garten und Botanisches Museum, Königin-Luise-Straße 6-8, 14195 Berlin, Germany; Research Associate, Integrative Research Center, The Field Museum, 1400 South Lake Shore Drive, Chicago, Illinois 60605, USA
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Miller A, Cai L, Crous PW, Beer ZWD, Hawksworth DL, Hyde KD, Kirk PM, Lücking R, Lumbsch HT, May TW, Rossman AY, Seifert KA, Schardl CI, Pfister DH, Rodréguez SAC, Schoch CL, Miller AN, Li CT. Reports. IMA Fungus 2017. [DOI: 10.1007/bf03449429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Lücking R, Moncada B. Dismantling Marchandiomphalina into Agonimia (Verrucariaceae) and Lawreymyces
gen. nov. (Corticiaceae): setting a precedent to the formal recognition of thousands of voucherless fungi based on type sequences. FUNGAL DIVERS 2017. [DOI: 10.1007/s13225-017-0382-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Jia ZF, Lücking R. Resolving the genus Phaeographina Müll. Arg. in China. MycoKeys 2017. [DOI: 10.3897/mycokeys.21.11986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Affiliation(s)
- Martin Grube
- Institute of Botany, Karl-Franzens-University Graz, 8010 Graz, Austria
| | - Robert Lücking
- Department of Botany, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605-2496
| | - Loengrin Umaña-Tenorio
- Laboratorio de Hongos, Instituto Nacional de Biodiversidad (INBio), Apdo. 22-3100, Santo Domingo de Heredia, Costa Rica
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