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Barcenas-Peña A, Divakar PK, Crespo A, Nuñez-Zapata J, Lumbsch HT, Grewe F. Reference-Based Restriction-Site-Associated DNA Sequencing Data Are Useful for Species Delineation in a Recently Diverged Asexually Reproducing Species Complex (Parmeliaceae, Ascomycota). J Fungi (Basel) 2023; 9:1180. [PMID: 38132781 PMCID: PMC10744373 DOI: 10.3390/jof9121180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/01/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023] Open
Abstract
Cryptic species are common in lichen-forming fungi and have been reported from different genera in the most speciose family, Parmeliaceae. Herein, we address species delimitation in a group of mainly asexually reproducing Parmelina species. The morphologically distinct P. pastillifera was previously found nested within a morphologically circumscribed P. tiliacea based on several loci. However, these studies demonstrated a relatively high genetic diversity within P. tiliacea sensu lato. Here, we revisit the species delimitation in the group by analyzing single-nucleotide polymorphisms (SNPs) through genome-wide assessment using Restriction-Site-Associated sequencing and population genomic methods. Our data support previous studies and provide further insight into the phylogenetic relationships of the four clades found within the complex. Based on the evidence suggesting a lack of gene flow among the clades, we recognize the four clades as distinct species, P. pastillifera and P. tiliacea sensu stricto, and two new species, P. clandestina sp. nov. and P. mediterranea sp. nov.
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Affiliation(s)
- Alejandrina Barcenas-Peña
- The Grainger Bioinformatics Center & Negaunee Integrative Research Center, Collections, Conservation and Research Division, The Field Museum, Chicago, IL 60605, USA; (H.T.L.); (F.G.)
| | - Pradeep K. Divakar
- Department of Pharmacology, Pharmacognosy and Botany (DU Botany), Faculty of Pharmacy, Plaza de Ramón y Cajal s/n, Universidad Complutense, 28040 Madrid, Spain; (P.K.D.); (A.C.); (J.N.-Z.)
| | - Ana Crespo
- Department of Pharmacology, Pharmacognosy and Botany (DU Botany), Faculty of Pharmacy, Plaza de Ramón y Cajal s/n, Universidad Complutense, 28040 Madrid, Spain; (P.K.D.); (A.C.); (J.N.-Z.)
| | - Jano Nuñez-Zapata
- Department of Pharmacology, Pharmacognosy and Botany (DU Botany), Faculty of Pharmacy, Plaza de Ramón y Cajal s/n, Universidad Complutense, 28040 Madrid, Spain; (P.K.D.); (A.C.); (J.N.-Z.)
| | - H. Thorsten Lumbsch
- The Grainger Bioinformatics Center & Negaunee Integrative Research Center, Collections, Conservation and Research Division, The Field Museum, Chicago, IL 60605, USA; (H.T.L.); (F.G.)
| | - Felix Grewe
- The Grainger Bioinformatics Center & Negaunee Integrative Research Center, Collections, Conservation and Research Division, The Field Museum, Chicago, IL 60605, USA; (H.T.L.); (F.G.)
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Gunawardana D, Wanigatunge RP, Wewalwela JJ, Vithanage M, Wijeyaratne C. Sulfur is in the Air: Cyanolichen Marriages and Pollution. Acta Biotheor 2023; 71:14. [PMID: 37148405 DOI: 10.1007/s10441-023-09465-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/15/2023] [Indexed: 05/08/2023]
Abstract
Cyanolichens are symbiotic organisms involving cyanobacteria and fungi (bipartite) or with the addition of an algal partner (tripartite). Cyanolichens are known for their heightened susceptibility to environmental pollution. We focus here on the impacts on cyanolichens due to rising air pollution; we are especially interested in the role of sulfur dioxide on cyanolichen biology. Cyanolichens due to air pollution including sulfur dioxide exposure, show symptomatic changes including degradation of chlorophyll, lipid membrane peroxidation, decrease in ATP production, changes in respiration rate, and alteration of endogenous auxins and ethylene production, although symptoms are known to vary with species and genotype. Sulfur dioxide has been shown to be damaging to photosynthesis but is relatively benign on nitrogen fixation which proposes as a hypothesis that the algal partner may be more in harm's way than the cyanobiont. In fact, the Nostoc cyanobiont of sulfur dioxide-susceptible Lobaria pulmonaria carries a magnified set of sulfur (alkane sulfonate) metabolism genes capable of alkane sulfonate transport and assimilation, which were only unraveled by genome sequencing, a technology unavailable in the 1950-2000 epoch, where most physiology- based studies were performed. There is worldwide a growing corpus of evidence that sulfur has an important role to play in biological symbioses including rhizobia-legumes, mycorrhizae-roots and cyanobacteria-host plants. Furthermore, the fungal and algal partners of L. pulmonaria appear not to have the sulfonate transporter genes again providing the roles of ambient-sulfur (alkanesulfonate metabolism etc.) mediated functions primarily to the cyanobacterial partner. In conclusion, we have addressed here the role of the atmospheric pollutant sulfur dioxide to tripartite cyanolichen viability and suggest that the weaker link is likely to be the photosynthetic algal (chlorophyte) partner and not the nitrogen-fixing cyanobiont.
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Affiliation(s)
- Dilantha Gunawardana
- Research Council, University of Sri Jayewardenepura, Nugegoda, Sri Jayewardenepura Kotte, 10250, Sri Lanka.
| | - Rasika P Wanigatunge
- Department of Plant and Molecular Biology, Faculty of Science, University of Kelaniya, Kelaniya, Sri Lanka
| | - Jayani J Wewalwela
- Department of Agricultural Technology, Faculty of Technology, University of Colombo, Colombo, Sri Lanka
| | - Meththika Vithanage
- Ecosphere Resilience Research Center, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Jayewardenepura Kotte, 10250, Sri Lanka
| | - Chandrani Wijeyaratne
- Department of Botany, University of Sri Jayewardenepura, Nugegoda, Sri Jayewardenepura Kotte, 10250, Sri Lanka
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Yang MX, Werth S, Wang LS, Scheidegger C. Phylogeographic analyses of an epiphytic foliose lichen show multiple dispersal events westward from the Hengduan Mountains of Yunnan into the Himalayas. Ecol Evol 2022; 12:e9308. [PMID: 36177127 PMCID: PMC9475131 DOI: 10.1002/ece3.9308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/09/2022] Open
Abstract
Lobaria pindarensis is an endemic species of the Himalayas and the Hengduan Mountains. Little information is available on the phylogeography genetics and colonization history of this species or how its distribution patterns changed in response to the orographic history of the Himalayas and Hengduan Mountains. Based on samples covering a major part of the species' distribution range, we used 443 newly generated sequences of nine loci for molecular coalescent analyses in order to reconstruct the evolutionary history of L. pindarensis, and to reconstruct the species' ancestral phylogeographic distributions using Bayesian binary MCMC analyses. The results suggest that current populations originated from the Yunnan region of the Hengduan Mountains in the middle Pliocene, and that the Himalayas of Bhutan were colonized by a lineage that diverged from Yunnan ca. 2.72 Ma. The analysis additionally indicates that the Nepal and Xizang areas of the Himalayas were colonized from Yunnan as well, and that there was later a second dispersal event from Yunnan to Bhutan. We conclude that the change in climate and habitat related to the continuous uplift of the Himalayas and the Hengduan Mountains in the late Pliocene and middle Pleistocene influenced the geographic distribution pattern of L. pindarensis.
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Affiliation(s)
- Mei-Xia Yang
- Biodiversity and Conservation Biology Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland.,Institute of Plant Sciences University of Bern Bern Switzerland.,Division of Life Science and Center for Chinese Medicine The Hong Kong University of Science and Technology Hong Kong China
| | - Silke Werth
- Systematics, Biodiversity and Evolution of Plants, Ludwig Maximilian University Munich Munich Germany
| | - Li-Song Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany, Chinese Academy of Sciences Kunming China
| | - Christoph Scheidegger
- Biodiversity and Conservation Biology Swiss Federal Institute for Forest, Snow and Landscape Research WSL Birmensdorf Switzerland
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Shao WH, Cheng JL, Zhang E. Eight in One: Hidden Diversity of the Bagrid Catfish Tachysurus albomarginatus s.l. (Rendhal, 1928) Widespread in Lowlands of South China. Front Genet 2021; 12:713793. [PMID: 34868198 PMCID: PMC8635968 DOI: 10.3389/fgene.2021.713793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 10/19/2021] [Indexed: 11/17/2022] Open
Abstract
There is increasing evidence that species diversity is underestimated in the current taxonomy of widespread freshwater fishes. The bagrid species T. albomarginatus s.l. is mainly distributed in the lowlands of South China, as currently identified. A total of 40 localities (including the type locality), which covers most of its known range, were sampled. Molecular phylogenetic analyses based on concatenated mtDNA and nuclear genes recover nine highly supported lineages clustering into eight geographic populations. The integration of molecular evidence, morphological data, and geographic distribution demonstrates the delineation of T. albomarginatus s.l. as eight putative species. Four species, namely, T. albomarginatus, T. lani, T. analis, and T. zhangfei sp. nov. and the T. similis complex are taxonomically recognized herein. Moreover, T. zhangfei sp. nov. comprises two genetically distinct lineages with no morphological and geographical difference. This study also reveals aspects of estimation of divergence time, distribution, and ecological adaption within the T. albomarginatus group. The unraveling of the hidden species diversity of this lowland bagrid fish highlights the need for not only the molecular scrutiny of widely distributed species of South China but also the adjustment of current biodiversity conservation strategies to protect the largely overlooked diversity of fishes from low-elevation rapids.
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Affiliation(s)
- Wei-Han Shao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jian-Li Cheng
- School of Life Sciences, Jinggangshan University, Ji'an, China
| | - E Zhang
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
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Ikeda MA, Nakamura H, Sawada K. Long-chain alkenes and alkadienes of eight lichen species collected in Japan. PHYTOCHEMISTRY 2021; 189:112823. [PMID: 34098255 DOI: 10.1016/j.phytochem.2021.112823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/12/2021] [Accepted: 05/24/2021] [Indexed: 06/12/2023]
Abstract
The hydrocarbons of eight lichen species isolated in Japan were analyzed, and diverse mono-, di-, and tri-unsaturated alkenes were detected. The positions of the double bonds of C17 alkadienes (heptadecadiene) and C17-C20 alkenes were determined by mass spectrometry of their dimethyl disulfide adducts. We found that the six lichens containing green algal photobionts were distinguished by the presence of 1,8-heptadecadiene, 6,9-heptadecadiene, and 8- and 7-heptadecenes. On the other hand, 1-octadecene, 4-octadecene, and 5-nonadecene were the major alkene components of the two lichens with cyanobacterial photobionts. These alkadienes and alkenes were present in large quantities in the lichen samples. In particular, 1,8-heptadecadiene accounted for more than 90% of the total alkenes in all four lichens containing it. Our results provide new insights into the origin of C17 alkadienes and C17-C20 alkenes in environmental and geological samples, and these alkenes can potentially be applied as lichen biomarkers.
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Affiliation(s)
- Masashi A Ikeda
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, N10W8, Kita-ku, Sapporo, 060-0810, Japan.
| | - Hideto Nakamura
- Department of Geosciences, Graduate School of Science, Osaka City University, Sugimoto 3-3-138, Sumiyoshi-ku, Osaka, 558-8585, Japan
| | - Ken Sawada
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, N10W8, Kita-ku, Sapporo, 060-0810, Japan; Department of Earth and Planetary Sciences, Faculty of Science, Hokkaido University, N10W8, Kita-ku, Sapporo, 060-0810, Japan
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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] [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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Lagostina E, Dal Grande F, Andreev M, Printzen C. The use of microsatellite markers for species delimitation in Antarctic Usnea subgenus Neuropogon. Mycologia 2018; 110:1047-1057. [DOI: 10.1080/00275514.2018.1512304] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Elisa Lagostina
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, D-60325 Frankfurt/Main, Germany
- Fachbereich 15 Biowissenschaften, Biozentrum, Campus Riedberg, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - Mikhail Andreev
- Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popov St. 2, Saint Petersburg 197376, Russia
| | - Christian Printzen
- Department of Botany and Molecular Evolution, Senckenberg Research Institute and Natural History Museum Frankfurt, Senckenberganlage 25, D-60325 Frankfurt/Main, Germany
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Cornejo C, Chabanenko S, Scheidegger C. Are species-pairs diverging lineages? A nine-locus analysis uncovers speciation among species-pairs of the Lobaria meridionalis-group (Ascomycota). Mol Phylogenet Evol 2018; 129:48-59. [PMID: 30036698 DOI: 10.1016/j.ympev.2018.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 03/13/2018] [Accepted: 07/14/2018] [Indexed: 01/17/2023]
Abstract
In spite of considerable effort to verify the theory of species-pairs, uncertainty still exists about the relationship between sexually or vegetatively reproducing populations of morphologically indistinguishable, sympatric lichen species. The current paper studies putative species-pairs within the Asian Lobaria meridionalis-group, using a nine-locus and time calibrated species-tree approach. Analyses demonstrate that pairs of sexually or vegetatively reproducing lineages split into highly supported monophyletic clades-confirming molecularly the species-pair concept for the L. meridionalis-group. In the broader context of evolution and speciation dynamics in lichenized fungi, this paper attempts to synthesize molecular findings from the last two decades to promote a more modern perception of the species-pair concept. Taxonomically, eight species were found to currently conform to the L. meridionalis-group, which differentiated during the Pliocene and Pleistocene. The coincidence of paleoclimatic events with estimated dates of divergence support a bioclimatic hypothesis for the evolution of species in the L. meridionalis-group, which also explains their current eco-geographic distribution patterns. Greater recognition for species with a long and independent evolutionary history, which merit high conservation priority, will be especially critical for preserving geographically restricted endemics from Southeast Asia, where habitat loss is driving rapid declines.
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Affiliation(s)
- Carolina Cornejo
- Swiss Federal Research Institute WSL, Zuercherstrasse 111, 8903 Birmensdorf, Switzerland.
| | - Svetlana Chabanenko
- Sakhalin Branch of the Botanical Garden-Institute FEB RAS, Gorky-street 25, 693023 Yuzhno-Sakhalinsk, Russia.
| | - Christoph Scheidegger
- Swiss Federal Research Institute WSL, Zuercherstrasse 111, 8903 Birmensdorf, Switzerland.
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10
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Meyer JB, Trapiello E, Senn-Irlet B, Sieber TN, Cornejo C, Aghayeva D, González AJ, Prospero S. Phylogenetic and phenotypic characterisation of Sirococcus castaneae comb. nov. (synonym Diplodina castaneae), a fungal endophyte of European chestnut. Fungal Biol 2017; 121:625-637. [PMID: 28705392 DOI: 10.1016/j.funbio.2017.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 03/01/2017] [Accepted: 04/08/2017] [Indexed: 02/04/2023]
Abstract
In this paper we resolve the taxonomic status of the fungus Diplodina castaneae (Ascomycetes, Diaporthales, Gnomoniaceae) which occurs on the European chestnut (Castanea sativa) as endophyte and as the causal agent of Javart disease. Specimens from Switzerland, Spain, and Azerbaijan were sequenced at five nuclear loci (β-tubulin, EF-1α, ITS, LSU, and RPB2). Phylogenies were inferred to place D. castaneae in the Gnomoniaceae family. Moreover, growth rates and morphological characteristics on different agar media were assessed and compared to those of Gnomoniopsis castaneae, which can easily be confused with D. castaneae. Based on morphological and phylogenetic characteristics, we propose to reallocate D. castaneae to the genus Sirococcus, as S. castaneae comb. nov.
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Affiliation(s)
- Joana B Meyer
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH-8903 Birmensdorf, Switzerland.
| | - Estefanía Trapiello
- Servicio Regional de Investigacion y Desarrollo Agroalimentario (SERIDA), Principado de Asturias, 33300 Villaviciosa, Spain; Department of Engineering and Agricultural Sciences, Area of Crop Production, University of León, Avda. Portugal 41, 24071 León, Spain
| | - Beatrice Senn-Irlet
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH-8903 Birmensdorf, Switzerland
| | - Thomas N Sieber
- ETH Zurich, Department of Environmental Systems Science, Forest Pathology and Dendrology, CH-8092 Zurich, Switzerland
| | - Carolina Cornejo
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH-8903 Birmensdorf, Switzerland
| | - Dilzara Aghayeva
- Institute of Botany, Azerbaijan National Academy of Sciences, AZ1000 Baku, Azerbaijan
| | - Ana J González
- Servicio Regional de Investigacion y Desarrollo Agroalimentario (SERIDA), Principado de Asturias, 33300 Villaviciosa, Spain
| | - Simone Prospero
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, CH-8903 Birmensdorf, Switzerland
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11
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Using multi-locus sequence data for addressing species boundaries in commonly accepted lichen-forming fungal species. ORG DIVERS EVOL 2017. [DOI: 10.1007/s13127-016-0320-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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