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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] [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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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] [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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Nascimento ELDL, Maia LC, Cáceres MEDS, Lücking R. Phylogenetic structure of lichen metacommunities in Amazonian and Northeast Brazil. Ecol Res 2021. [DOI: 10.1111/1440-1703.12206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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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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] [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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Gerlach ADCL, Toprak Z, Naciri Y, Caviró EA, da Silveira RMB, Clerc P. New insights into the Usnea cornuta aggregate (Parmeliaceae, lichenized Ascomycota): Molecular analysis reveals high genetic diversity correlated with chemistry. Mol Phylogenet Evol 2019; 131:125-137. [DOI: 10.1016/j.ympev.2018.10.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 09/17/2018] [Accepted: 10/26/2018] [Indexed: 01/01/2023]
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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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Buaruang K, Boonpragob K, Mongkolsuk P, Sangvichien E, Vongshewarat K, Polyiam W, Rangsiruji A, Saipunkaew W, Naksuwankul K, Kalb J, Parnmen S, Kraichak E, Phraphuchamnong P, Meesim S, Luangsuphabool T, Nirongbut P, Poengsungnoen V, Duangphui N, Sodamuk M, Phokaeo S, Molsil M, Aptroot A, Kalb K, Luecking R, Lumbsch T. A new checklist of lichenized fungi occurring in Thailand. MycoKeys 2017. [DOI: 10.3897/mycokeys.23.12666] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Abstract
ABSTRACT
Lichen symbioses comprise a fascinating relationship between algae and fungi. The lichen symbiotic lifestyle evolved early in the evolution of ascomycetes and is also known from a few basidiomycetes. The ascomycete lineages have diversified in the lichenized stage to give rise to a tremendous variety of morphologies. Their thalli are often internally complex and stratified for optimized integration of algal and fungal metabolisms. Thalli are frequently colonized by specific nonlichenized fungi and occasionally also by other lichens. Microscopy has revealed various ways these fungi interact with their hosts. Besides the morphologically recognizable diversity of the lichen mycobionts and lichenicolous (lichen-inhabiting) fungi, many other microorganisms including other fungi and bacterial communities are now detected in lichens by culture-dependent and culture-independent approaches. The application of multi-omics approaches, refined microscopic techniques, and physiological studies has added to our knowledge of lichens, not only about the taxa involved in the lichen interactions, but also about their functions.
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Lumbsch HT, Naksuwankul K, Kraichak E, Parnmen S, Lücking R. Five new species of Graphidaceae (Ascomycota, Ostropales) from Thailand. MycoKeys 2016. [DOI: 10.3897/mycokeys.17.10512] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Alors D, Lumbsch HT, Divakar PK, Leavitt SD, Crespo A. An Integrative Approach for Understanding Diversity in the Punctelia rudecta Species Complex (Parmeliaceae, Ascomycota). PLoS One 2016; 11:e0146537. [PMID: 26863231 PMCID: PMC4749632 DOI: 10.1371/journal.pone.0146537] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 12/18/2015] [Indexed: 11/23/2022] Open
Abstract
High levels of cryptic diversity have been documented in lichenized fungi, especially in Parmeliaceae, and integrating various lines of evidence, including coalescent-based species delimitation approaches, help establish more robust species circumscriptions. In this study, we used an integrative taxonomic approach to delimit species in the lichen-forming fungal genus Punctelia (Parmeliaceae), with a particular focus on the cosmopolitan species P. rudecta. Nuclear, mitochondrial ribosomal DNA and protein-coding DNA sequences were analyzed in phylogenetic and coalescence-based frameworks. Additionally, morphological, ecological and geographical features of the sampled specimens were evaluated. Five major strongly supported monophyletic clades were recognized in the genus Punctelia, and each clade could be characterized by distinct patterns in medullary chemistry. Punctelia rudecta as currently circumscribed was shown to be polyphyletic. A variety of empirical species delimitation methods provide evidence for a minimum of four geographically isolated species within the nominal taxon Punctelia rudecta, including a newly described saxicolous species, P. guanchica, and three corticolous species. In order to facilitate reliable sample identification for biodiversity, conservation, and air quality bio-monitoring research, these three species have been epitypified, in addition to the description of a new species.
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Affiliation(s)
- David Alors
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, Madrid, Spain
| | - H. Thorsten Lumbsch
- Science and Education, Field Museum, Chicago, Illinois, United States of America
| | - Pradeep K. Divakar
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, Madrid, Spain
| | - Steven D. Leavitt
- Science and Education, Field Museum, Chicago, Illinois, United States of America
| | - Ana Crespo
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, Madrid, Spain
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Towards a revised generic classification of lecanoroid lichens (Lecanoraceae, Ascomycota) based on molecular, morphological and chemical evidence. FUNGAL DIVERS 2015. [DOI: 10.1007/s13225-015-0354-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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13
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Zhao X, Zhang LL, Zhao ZT, Wang WC, Leavitt SD, Lumbsch HT. A Molecular Phylogeny of the Lichen Genus Lecidella Focusing on Species from Mainland China. PLoS One 2015; 10:e0139405. [PMID: 26414323 PMCID: PMC4586381 DOI: 10.1371/journal.pone.0139405] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/11/2015] [Indexed: 11/19/2022] Open
Abstract
The phylogeny of Lecidella species is studied, based on a 7-locus data set using ML and Bayesian analyses. Phylogenetic relationships among 43 individuals representing 11 Lecidella species, mainly from mainland China, were included in the analyses and phenotypical characters studied and mapped onto the phylogeny. The Lecidella species fall into three major clades, which are proposed here as three informal groups-Lecidella stigmatea group, L. elaeochroma group and L. enteroleucella group, each of them strongly supported. Our phylogenetic analyses support traditional species delimitation based on morphological and chemical traits in most but not all cases. Individuals considered as belonging to the same species based on phenotypic characters were found to be paraphyletic, indicating that cryptic species might be hidden under these names (e.g. L. carpathica and L. effugiens). Potentially undescribed species were found within the phenotypically circumscribed species L. elaeochroma and L. stigmatea. Additional sampling across a broader taxonomic and geographic scale will be crucial to fully resolving the taxonomy in this cosmopolitan genus.
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Affiliation(s)
- Xin Zhao
- College of Life Sciences, Shandong Normal University, Jinan, 250014, P. R. China
| | - Lu Lu Zhang
- College of Life Sciences, Shandong Normal University, Jinan, 250014, P. R. China
| | - Zun Tian Zhao
- College of Life Sciences, Shandong Normal University, Jinan, 250014, P. R. China
| | - Wei Cheng Wang
- College of Life Sciences, Shandong Normal University, Jinan, 250014, P. R. China
| | - Steven D. Leavitt
- Science & Education, The Field Museum, Chicago, Illinois, United States of America
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, United States of America
| | - Helge Thorsten Lumbsch
- Science & Education, The Field Museum, Chicago, Illinois, United States of America
- * E-mail:
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Kraichak E, Lücking R, Aptroot A, Beck A, Dornes P, John V, Lendemer JC, Nelsen MP, Neuwirth G, Nutakki A, Parnmen S, Sohrabi M, Tønsberg T, Lumbsch HT. Hidden diversity in the morphologically variable script lichen (Graphis scripta) complex (Ascomycota, Ostropales, Graphidaceae). ORG DIVERS EVOL 2015. [DOI: 10.1007/s13127-015-0219-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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A Tale of Two Hyper-diversities: Diversification dynamics of the two largest families of lichenized fungi. Sci Rep 2015; 5:10028. [PMID: 25944223 PMCID: PMC4421861 DOI: 10.1038/srep10028] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 03/26/2015] [Indexed: 11/08/2022] Open
Abstract
Renewed interests in macroevolutionary dynamics have led to the proliferation of studies on diversification processes in large taxonomic groups, such as angiosperms, mammals, and birds. However, such a study has yet to be conducted in lichenized fungi--an extremely successful and diverse group of fungi. Analysing the most comprehensive time-calibrated phylogenies with a new analytical method, we illustrated drastically different diversification dynamics between two hyper-diverse families of lichenized fungi, Graphidaceae and Parmeliaceae, which represent more than a fourth of the total species diversity of lichenized fungi. Despite adopting a similar nutrition mode and having a similar number of species, Graphidaceae exhibited a lower speciation rate, while Parmeliaceae showed a sharp increase in speciation rate that corresponded with the aridification during the Oligocene-Miocene transition, suggesting their adaptive radiation into a novel arid habitat.
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