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Li R, Wang Z, Xu H, Jiang C, Wang N, Li X, Qiu X, Wang X. Genetic Diversity among Takifugu rubripes and Takifugu obscurus in Different Regions of China Based on Mitochondrial DNA Sequencing Data. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422120079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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González-Burgos E, Fernández-Moriano C, Gómez-Serranillos MP. Current knowledge on Parmelia genus: Ecological interest, phytochemistry, biological activities and therapeutic potential. PHYTOCHEMISTRY 2019; 165:112051. [PMID: 31234093 DOI: 10.1016/j.phytochem.2019.112051] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/03/2019] [Accepted: 06/11/2019] [Indexed: 06/09/2023]
Abstract
Parmelia Acharius is one of the most representative genera within Parmeliaceae family which is the largest and the most widespread family of lichen-forming fungi. Parmelia lichens present a medium to large foliose thallus and they are distributed from the Artic to the Antartic continents, being more concentrated in temperate regions. According to its current description, the genus encompasses up to 41 different species and it is phylogenetically located within the Parmelioid clade (the largest group in the family). Interestingly, some of its species are among the most common epiphytic lichens in Europe such as Parmelia sulcata Taylor and Parmelia saxatilis (L.) Ach. The present work aims at providing a complete overview of the existing knowledge on the genus, from general concepts such as taxonomy and phylogeny, to their ecological relevance and biological interest for pharmaceutical uses. As reported, Parmelia lichens arise as valuable tools for biomonitoring environmental pollution due to their capacity to bioaccumulate metal elements and its response to acid rain. Moreover, they produce a wide array of specialized products/metabolites including depsides, depsidones, triterpenes and dibenzofurans, which have been suggested to exert promising pharmacological activities, mainly antimicrobial, antioxidant and cytotoxic activities. Herein, we discuss past and recent data regarding to the phytochemical characterization of more than 15 species. Even though the knowledge is still scarce in comparsion to other groups of organisms such as higher plants and other non-lichenized fungi. Reviewed works suggest that Parmelia lichens are worthy of further research for determining their actual possibilities as sources of bioactive compounds with potential therapeutic applications.
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Affiliation(s)
- Elena González-Burgos
- Department of Pharmacology, Pharmacognosy and Botany, Faculty of Pharmacy, University Complutense of Madrid, Plaza Ramón y Cajal S/n, 28004, Madrid, Spain
| | - Carlos Fernández-Moriano
- Department of Pharmacology, Pharmacognosy and Botany, Faculty of Pharmacy, University Complutense of Madrid, Plaza Ramón y Cajal S/n, 28004, Madrid, Spain
| | - M Pilar Gómez-Serranillos
- Department of Pharmacology, Pharmacognosy and Botany, Faculty of Pharmacy, University Complutense of Madrid, Plaza Ramón y Cajal S/n, 28004, Madrid, Spain.
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Kitaura MJ, Costa PC, Scur MC, Lorenz A.P. Genetic and morphological variations of the lichenized fungus Steinera intricata (Arctomiaceae, Lecanoromycetes) from southern South America to Antarctic Peninsula. Polar Biol 2019. [DOI: 10.1007/s00300-019-02486-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Wang Y, Wei X, Huang J, Wei J. Modification and functional adaptation of the MBF1 gene family in the lichenized fungus Endocarpon pusillum under environmental stress. Sci Rep 2017; 7:16333. [PMID: 29180801 PMCID: PMC5703946 DOI: 10.1038/s41598-017-16716-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 11/16/2017] [Indexed: 11/09/2022] Open
Abstract
The multiprotein-bridging factor 1 (MBF1) gene family is well known in archaea, non-lichenized fungi, plants, and animals, and contains stress tolerance-related genes. Here, we identified four unique mbf1 genes in the lichenized fungi Endocarpon spp. A phylogenetic analysis based on protein sequences showed the translated MBF1 proteins of the newly isolated mbf1 genes formed a monophyletic clade different from other lichen-forming fungi and Ascomycota groups in general, which may reflect the evolution of the biological functions of MBF1s. In contrast to the lack of function reported in yeast, we determined that lysine114 in the deduced Endocarpon pusillum MBF1 protein (EpMBF1) had a specific function that was triggered by environmental stress. Further, the Endocarpon-specific C-terminus of EpMBF1 was found to participate in stress tolerance. Epmbf1 was induced by a number of abiotic stresses in E. pusillum and transgenic yeast, and its stress-resistant ability was stronger than that of the yeast mbf1. These findings highlight the evolution and function of EpMBF1 and provide new insights into the co-evolution hypothesis of MBF1 and TATA-box-binding proteins.
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Affiliation(s)
- Yanyan Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 10010, China
| | - Xinli Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 10010, China.
| | - Jenpan Huang
- Science & Education, The Field Museum, Chicago, IL, 60605, USA
| | - Jiangchun Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 10010, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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Matteucci E, Occhipinti A, Piervittori R, Maffei ME, Favero-Longo SE. Morphological, Secondary Metabolite and ITS (rDNA) Variability within Usnic Acid-Containing Lichen Thalli ofXanthoparmeliaExplored at the Local Scale of Rock Outcrop in W-Alps. Chem Biodivers 2017; 14. [DOI: 10.1002/cbdv.201600483] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/08/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Enrica Matteucci
- Unità di Lichenologia; Dipartimento di Scienze della Vita e Biologia dei Sistemi; Università degli Studi di Torino; Viale Mattioli 25 10125 Torino Italia
| | - Andrea Occhipinti
- Unità di Fisiologia Vegetale; Dipartimento di Scienze della Vita e Biologia dei Sistemi; Università degli Studi di Torino; Via Quarello 15/A 10135 Torino Italia
| | - Rosanna Piervittori
- Unità di Lichenologia; Dipartimento di Scienze della Vita e Biologia dei Sistemi; Università degli Studi di Torino; Viale Mattioli 25 10125 Torino Italia
| | - Massimo E. Maffei
- Unità di Fisiologia Vegetale; Dipartimento di Scienze della Vita e Biologia dei Sistemi; Università degli Studi di Torino; Via Quarello 15/A 10135 Torino Italia
| | - Sergio E. Favero-Longo
- Unità di Lichenologia; Dipartimento di Scienze della Vita e Biologia dei Sistemi; Università degli Studi di Torino; Viale Mattioli 25 10125 Torino Italia
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Molina MC, Divakar PK, Goward T, Millanes AM, Lumbsch HT, Crespo A. Neogene diversification in the temperate lichen-forming fungal genus Parmelia (Parmeliaceae, Ascomycota). SYST BIODIVERS 2016. [DOI: 10.1080/14772000.2016.1226977] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- M. Carmen Molina
- Departamento de Biología y Geología, Física y Química Inorgánica (Área de Biodiversidad y Conservación), ESCET, Universidad Rey Juan Carlos, Móstoles, 28933 Madrid, Spain
| | - Pradeep K. Divakar
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Trevor Goward
- UBC Herbarium, Beaty Museum, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Ana M. Millanes
- Departamento de Biología y Geología, Física y Química Inorgánica (Área de Biodiversidad y Conservación), ESCET, Universidad Rey Juan Carlos, Móstoles, 28933 Madrid, Spain
| | | | - Ana Crespo
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
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Limitations of Species Delimitation Based on Phylogenetic Analyses: A Case Study in the Hypogymnia hypotrypa Group (Parmeliaceae, Ascomycota). PLoS One 2016; 11:e0163664. [PMID: 27828951 PMCID: PMC5102465 DOI: 10.1371/journal.pone.0163664] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/12/2016] [Indexed: 11/29/2022] Open
Abstract
Delimiting species boundaries among closely related lineages often requires a range of independent data sets and analytical approaches. Similar to other organismal groups, robust species circumscriptions in fungi are increasingly investigated within an empirical framework. Here we attempt to delimit species boundaries in a closely related clade of lichen-forming fungi endemic to Asia, the Hypogymnia hypotrypa group (Parmeliaceae). In the current classification, the Hypogymnia hypotrypa group includes two species: H. hypotrypa and H. flavida, which are separated based on distinctive reproductive modes, the former producing soredia but absent in the latter. We reexamined the relationship between these two species using phenotypic characters and molecular sequence data (ITS, GPD, and MCM7 sequences) to address species boundaries in this group. In addition to morphological investigations, we used Bayesian clustering to identify potential genetic groups in the H. hypotrypa/H. flavida clade. We also used a variety of empirical, sequence-based species delimitation approaches, including: the “Automatic Barcode Gap Discovery” (ABGD), the Poisson tree process model (PTP), the General Mixed Yule Coalescent (GMYC), and the multispecies coalescent approach BPP. Different species delimitation scenarios were compared using Bayes factors delimitation analysis, in addition to comparisons of pairwise genetic distances, pairwise fixation indices (FST). The majority of the species delimitation analyses implemented in this study failed to support H. hypotrypa and H. flavida as distinct lineages, as did the Bayesian clustering analysis. However, strong support for the evolutionary independence of H. hypotrypa and H. flavida was inferred using BPP and further supported by Bayes factor delimitation. In spite of rigorous morphological comparisons and a wide range of sequence-based approaches to delimit species, species boundaries in the H. hypotrypa group remain uncertain. This study reveals the potential limitations of relying on distinct reproductive strategies as diagnostic taxonomic characters for Hypogymnia and also the challenges of using popular sequence-based species delimitation methods in groups with recent diversification histories.
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Lewińska AM, Peuhkuri RH, Rode C, Andersen B, Hoof JB. Rapid detection and identification of Stachybotrys and Chaetomium species using tissue PCR analysis. J Microbiol Methods 2016; 130:115-122. [PMID: 27619348 DOI: 10.1016/j.mimet.2016.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/08/2016] [Accepted: 09/08/2016] [Indexed: 10/21/2022]
Abstract
Indoor fungi are a worldwide problem causing negative health effects for infected building's occupants and even deterioration of building structures. Different fungal species affect buildings and their inhabitants differently. Therefore, rapid and accurate identification of fungi to the species level is essential for health risk assessment and building remediation. This study focuses on molecular identification of two common indoor fungal genera: Stachybotrys and Chaetomium. This study proposes two new DNA barcode candidates for Stachybotrys and Chaetomium: the gene encoding mitogen activated protein kinase (hogA) and the intergenic region between histone 3 and histone 4 (h3-h4) as well as it introduces a rapid - 3.5h - protocol for direct Stachybotrys and Chaetomium species identification, which bypasses culture cultivation, DNA extraction and DNA sequencing.
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Affiliation(s)
- Anna M Lewińska
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark.
| | - Ruut H Peuhkuri
- Danish Building Research Institute, Aalborg University, Copenhagen, SV, Denmark
| | - Carsten Rode
- Department of Civil Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Birgitte Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jakob B Hoof
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark.
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Del-Prado R, Divakar PK, Lumbsch HT, Crespo AM. Hidden Genetic Diversity in an Asexually Reproducing Lichen Forming Fungal Group. PLoS One 2016; 11:e0161031. [PMID: 27513649 PMCID: PMC4981466 DOI: 10.1371/journal.pone.0161031] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/28/2016] [Indexed: 11/19/2022] Open
Abstract
Asexual species with vegetative propagation of both symbiont partners (soredia) in lichens may harbor lower species diversity because they may indeed represent evolutionary dead ends or clones. In this study we aim to critically examine species boundaries in the sorediate lichen forming fungi Parmotrema reticulatum–Parmotrema pseudoreticulatum complex applying coalescent-based approaches and other recently developed DNA-based methods. To this end, we gathered 180 samples from Africa, Asia, Australasia, Europe, North and South America and generated sequences of internal transcribed spacer of nuclear ribosomal DNA (ITS) and DNA replication licensing factor MCM7 (MCM7). The dataset was analysed using different approaches such as traditional phylogeny–maximum likelihood and Bayesian–genetic distances, automatic barcode gap discovery and coalescent-based methods–PTP, GMYC, spedeSTEM and *Beast–in order to test congruence among results. Additionally, the divergence times were also estimated to elucidate diversification events. Delimitations inferred from the different analyses are comparable with only minor differences, and following a conservative approach we propose that the sampled specimens of the P. reticulatum–P. pseudoreticulatum complex belong to at least eight distinct species-level lineages. Seven are currently classified under P. reticulatum and one as P. pseudoreticulatum. In this work we discuss one of only few examples of cryptic species that have so far been found in sorediate reproducing lichen forming fungi. Additionally our estimates suggest a recent origin of the species complex–during the Miocene. Consequently, the wide distribution of several of the cryptic species has to be explained by intercontinental long-distance dispersal events.
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Affiliation(s)
- Ruth Del-Prado
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Madrid, Spain
- * E-mail:
| | - Pradeep Kumar Divakar
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Madrid, Spain
| | - H. Thorsten Lumbsch
- Science and Education, Field Museum, Chicago, Illinois, United States of America
| | - Ana M. Crespo
- Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense, Madrid, Spain
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Structure, Composition, and Function of Biocrust Lichen Communities. BIOLOGICAL SOIL CRUSTS: AN ORGANIZING PRINCIPLE IN DRYLANDS 2016. [DOI: 10.1007/978-3-319-30214-0_7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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11
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Masson D, Divakar PK, Sérusiaux E. Hypotrachyna penduliloba and Remototrachyna pandani, two new species in the hyperdiverse lichen family Parmeliaceae from Réunion in the Mascarene Archipelago. Mycol Prog 2015. [DOI: 10.1007/s11557-015-1039-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Phylogenetic relationships within the snapping shrimp genus Synalpheus (Decapoda: Alpheidae). Mol Phylogenet Evol 2014; 77:116-25. [DOI: 10.1016/j.ympev.2014.03.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Revised: 03/09/2014] [Accepted: 03/11/2014] [Indexed: 11/20/2022]
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Altermann S, Leavitt SD, Goward T, Nelsen MP, Lumbsch HT. How do you solve a problem like Letharia? A new look at cryptic species in lichen-forming fungi using Bayesian clustering and SNPs from multilocus sequence data. PLoS One 2014; 9:e97556. [PMID: 24831224 PMCID: PMC4022584 DOI: 10.1371/journal.pone.0097556] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 04/21/2014] [Indexed: 11/19/2022] Open
Abstract
The inclusion of molecular data is increasingly an integral part of studies assessing species boundaries. Analyses based on predefined groups may obscure patterns of differentiation, and population assignment tests provide an alternative for identifying population structure and barriers to gene flow. In this study, we apply population assignment tests implemented in the programs STRUCTURE and BAPS to single nucleotide polymorphisms from DNA sequence data generated for three previous studies of the lichenized fungal genus Letharia. Previous molecular work employing a gene genealogical approach circumscribed six species-level lineages within the genus, four putative lineages within the nominal taxon L. columbiana (Nutt.) J.W. Thomson and two sorediate lineages. We show that Bayesian clustering implemented in the program STRUCTURE was generally able to recover the same six putative Letharia lineages. Population assignments were largely consistent across a range of scenarios, including: extensive amounts of missing data, the exclusion of SNPs from variable markers, and inferences based on SNPs from as few as three gene regions. While our study provided additional evidence corroborating the six candidate Letharia species, the equivalence of these genetic clusters with species-level lineages is uncertain due, in part, to limited phylogenetic signal. Furthermore, both the BAPS analysis and the ad hoc ΔK statistic from results of the STRUCTURE analysis suggest that population structure can possibly be captured with fewer genetic groups. Our findings also suggest that uneven sampling across taxa may be responsible for the contrasting inferences of population substructure. Our results consistently supported two distinct sorediate groups, ‘L. lupina’ and L. vulpina, and subtle morphological differences support this distinction. Similarly, the putative apotheciate species ‘L. lucida’ was also consistently supported as a distinct genetic cluster. However, additional studies will be required to elucidate the relationships of other L. columbiana s.l. populations with the two sorediate genetic clusters.
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Affiliation(s)
- Susanne Altermann
- Biology Department, Whitman College, Walla Walla, Washington, United States of America
| | - Steven D. Leavitt
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, United States of America
- Science and Education, The Field Museum, Chicago, Illinois, United States of America
- * E-mail:
| | - Trevor Goward
- Beaty Biodiversity Museum, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew P. Nelsen
- Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois, United States of America
- Science and Education, The Field Museum, Chicago, Illinois, United States of America
| | - H. Thorsten Lumbsch
- Science and Education, The Field Museum, Chicago, Illinois, United States of America
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Wang X, Zang R, Yin Z, Kang Z, Huang L. Delimiting cryptic pathogen species causing apple Valsa canker with multilocus data. Ecol Evol 2014; 4:1369-80. [PMID: 24834333 PMCID: PMC4020696 DOI: 10.1002/ece3.1030] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 02/13/2014] [Accepted: 02/18/2014] [Indexed: 11/06/2022] Open
Abstract
Fungal diseases are posing tremendous threats to global economy and food safety. Among them, Valsa canker, caused by fungi of Valsa and their Cytospora anamorphs, has been a serious threat to fruit and forest trees and is one of the most destructive diseases of apple in East Asia, particularly. Accurate and robust delimitation of pathogen species is not only essential for the development of effective disease control programs, but also will advance our understanding of the emergence of plant diseases. However, species delimitation is especially difficult in Valsa because of the high variability of morphological traits and in many cases the lack of the teleomorph. In this study, we delimitated species boundary for pathogens causing apple Valsa canker with a multifaceted approach. Based on three independent loci, the internal transcribed spacer (ITS), β-tubulin (Btu), and translation elongation factor-1 alpha (EF1α), we inferred gene trees with both maximum likelihood and Bayesian methods, estimated species tree with Bayesian multispecies coalescent approaches, and validated species tree with Bayesian species delimitation. Through divergence time estimation and ancestral host reconstruction, we tested the possible underlying mechanisms for fungal speciation and host-range change. Our results proved that two varieties of the former morphological species V. mali represented two distinct species, V. mali and V. pyri, which diverged about 5 million years ago, much later than the divergence of their preferred hosts, excluding a scenario of fungi-host co-speciation. The marked different thermal preferences and contrasting pathogenicity in cross-inoculation suggest ecological divergences between the two species. Apple was the most likely ancestral host for both V. mali and V. pyri. Host-range expansion led to the occurrence of V. pyri on both pear and apple. Our results also represent an example in which ITS data might underestimate species diversity.
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Affiliation(s)
- Xuli Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, 712100, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijing, 100193, China
| | - Rui Zang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, 712100, China
| | - Zhiyuan Yin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, 712100, China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F UniversityYangling, 712100, China
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Fernández JA. Mitochondrial phylogenetics of a rare Mexican endemic: Nelson's woodrat, Neotoma nelsoni(Rodentia: Cricetidae), with comments on its biogeographic history. SOUTHWEST NAT 2014. [DOI: 10.1894/f11-clg-58.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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16
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Pastore AI, Prather CM, Gornish ES, Ryan WH, Ellis RD, Miller TE. Testing the competition–colonization trade-off with a 32-year study of a saxicolous lichen community. Ecology 2014; 95:306-15. [DOI: 10.1890/13-0253.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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17
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Multiple ITS Haplotypes in the Genome of the Lichenized Basidiomycete Cora inversa (Hygrophoraceae): Fact or Artifact? J Mol Evol 2013; 78:148-62. [DOI: 10.1007/s00239-013-9603-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 11/20/2013] [Indexed: 11/25/2022]
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18
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DNA barcoding of brown Parmeliae (Parmeliaceae) species: a molecular approach for accurate specimen identification, emphasizing species in Greenland. ORG DIVERS EVOL 2013. [DOI: 10.1007/s13127-013-0147-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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19
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Truong C, Divakar PK, Yahr R, Crespo A, Clerc P. Testing the use of ITS rDNA and protein-coding genes in the generic and species delimitation of the lichen genus Usnea (Parmeliaceae, Ascomycota). Mol Phylogenet Evol 2013; 68:357-72. [DOI: 10.1016/j.ympev.2013.04.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 02/01/2013] [Accepted: 04/02/2013] [Indexed: 12/31/2022]
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Leavitt S, Fernández-Mendoza F, Pérez-Ortega S, Sohrabi M, Divakar P, Lumbsch T, St. Clair L. DNA barcode identification of lichen-forming fungal species in the Rhizoplaca melanophthalma species-complex (Lecanorales, Lecanoraceae), including five new species. MycoKeys 2013. [DOI: 10.3897/mycokeys.7.4508] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Pino-Bodas R, Ahti T, Stenroos S, Martín MP, Burgaz AR. Multilocus approach to species recognition in the Cladonia humilis complex (Cladoniaceae, Ascomycota). AMERICAN JOURNAL OF BOTANY 2013; 100:664-678. [PMID: 23507737 DOI: 10.3732/ajb.1200162] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
PREMISE OF THE STUDY The members of the Cladonia humilis complex are characterized by a well-developed primary thallus and broadly scyphose podetia. In the present study, this complex was phylogenetically analyzed to test the boundaries between the species and to determine the usefulness of the phenotypic characters to distinguish them. The species C. conista, C. cyathomorpha, C. hammeri, C. humilis, C. kurokawae, C. nashii, C. pulvinella, and C. subconistea were examined. METHODS Four DNA loci were sequenced and analyzed to test the monophyly of the species. For the phylogenetic reconstructions, maximum parsimony, maximum likelihood, and Bayesian methods were employed. The genealogical sorting index was used to quantify the exclusive ancestry of the nonmonophyletic species on the tree. KEY RESULTS The performed phylogenetic analyses showed that the C. humilis complex is not monophyletic. Cladonia nashii is not closely related to the remaining taxa within the complex. Seven monophyletic lineages were identified, most of which comprise specimens belonging to more than one chemotype. Cladonia hammeri and C. pulvinella are conspecific, and this taxon is not present in Europe. CONCLUSIONS This study suggests that morphological characters and secondary metabolites have less taxonomical value than thought in the Cladonia humilis complex. Use of multilocus phylogeny is recommended to delimit species.
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Affiliation(s)
- Raquel Pino-Bodas
- Departamento Biología Vegetal 1, Universidad Complutense de Madrid, Spain.
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Pino-Bodas R, Martín MP, Burgaz AR, Lumbsch HT. Species delimitation in Cladonia (Ascomycota): a challenge to the DNA barcoding philosophy. Mol Ecol Resour 2013; 13:1058-68. [PMID: 23437908 DOI: 10.1111/1755-0998.12086] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Revised: 01/30/2013] [Accepted: 01/31/2013] [Indexed: 01/28/2023]
Abstract
The lichen-forming fungal genus Cladonia is species-rich with approximately 500 described species. The accepted barcode for fungi (ITS rDNA) often fails in identifying Cladonia spp. In order to find other markers that, in combination with the ITS rDNA region can be used for species identification in Cladonia, we studied the loci IGS rDNA, ef1α, rpb2 and cox1. A total of 782 sequences from 36 species have been analyzed. PCR amplification success rate, intraspecific and interspecific genetic distance variation, calculated using the K2P model, and the correct identification percentage (PCI) were taken into account to assess possible barcode regions. The marker showing the least intraspecific genetic distance range was cox1, followed by ITS rDNA and ef1α. Of the five studied markers only cox1 showed a barcoding gap. The rpb2 locus showed the highest PCI values, but it was the most difficult to amplify. The highest correct identification rates using blast method were obtained with rpb2.
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Affiliation(s)
- Raquel Pino-Bodas
- Departamento Biología Vegetal 1, Facultad de Biología, Universidad Complutense de Madrid, E-28040, Madrid, Spain
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Leavitt SD, Esslinger TL, Spribille T, Divakar PK, Thorsten Lumbsch H. Multilocus phylogeny of the lichen-forming fungal genus Melanohalea (Parmeliaceae, Ascomycota): Insights on diversity, distributions, and a comparison of species tree and concatenated topologies. Mol Phylogenet Evol 2013; 66:138-52. [DOI: 10.1016/j.ympev.2012.09.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 08/31/2012] [Accepted: 09/16/2012] [Indexed: 10/27/2022]
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Leavitt SD, Esslinger TL, Divakar PK, Lumbsch HT. Miocene divergence, phenotypically cryptic lineages, and contrasting distribution patterns in common lichen-forming fungi (Ascomycota: Parmeliaceae). Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01978.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Steven D. Leavitt
- Department of Botany; The Field Museum; 1400 S. Lake Shore Drive; Chicago; IL; 60605; USA
| | - Theodore L. Esslinger
- Department of Biological Sciences; North Dakota State University; #2715, PO Box 6050, Stevens Hall; Fargo; ND; 58108-6050; USA
| | - Pradeep K. Divakar
- Departamento de Biología Vegetal II, Facultad de Farmacia; Universidad Complutense de Madrid; Madrid; 28040; Spain
| | - H. Thorsten Lumbsch
- Department of Botany; The Field Museum; 1400 S. Lake Shore Drive; Chicago; IL; 60605; USA
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Leavitt SD, Esslinger TL, Divakar PK, Lumbsch HT. Miocene and Pliocene dominated diversification of the lichen-forming fungal genus Melanohalea (Parmeliaceae, Ascomycota) and Pleistocene population expansions. BMC Evol Biol 2012; 12:176. [PMID: 22963132 PMCID: PMC3499221 DOI: 10.1186/1471-2148-12-176] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 08/30/2012] [Indexed: 01/22/2023] Open
Abstract
Background Factors promoting diversification in lichen symbioses remain largely unexplored. While Pleistocene events have been important for driving diversification and affecting distributions in many groups, recent estimates suggest that major radiations within some genera in the largest clade of macrolichens (Parmeliaceae, Ascomycota) vastly predate the Pleistocene. To better understand the temporal placement and sequence of diversification events in lichens, we estimated divergence times in a common lichen-forming fungal genus, Melanohalea, in the Northern Hemisphere. Divergence times were estimated using both concatenated gene tree and coalescent-based multilocus species tree approaches to assess the temporal context of major radiation events within Melanohalea. In order to complement our understanding of processes impacting genetic differentiation, we also evaluated the effects of Pleistocene glacial cycles on population demographics of distinct Melanohalea lineages, differing in reproductive strategies. Results We found that divergence estimates, from both concatenated gene tree and coalescent-based multilocus species tree approaches, suggest that diversification within Melanohalea occurred predominantly during the Miocene and Pliocene, although estimated of divergence times differed by up to 8.3 million years between the two methods. These results indicate that, in some cases, taxonomically diagnostic characters may be maintained among divergent lineages for millions of years. In other cases, similar phenotypic characters among non-sister taxa, including reproductive strategies, suggest the potential for convergent evolution due to similar selective pressures among distinct lineages. Our analyses provide evidence of population expansions predating the last glacial maximum in the sampled lineages. These results suggest that Pleistocene glaciations were not inherently unfavorable or restrictive for some Melanohalea species, albeit with apparently different demographic histories between sexually and vegetatively reproducing lineages. Conclusions Our results contribute to the understanding of how major changes during the Miocene and Pliocene have been important in promoting diversification within common lichen-forming fungi in the northern Hemisphere. Additionally, we provide evidence that glacial oscillations have influenced current population structure of broadly distributed lichenized fungal species throughout the Holarctic.
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Salgado-Salazar C, Rossman A, Samuels GJ, Capdet M, Chaverri P. Multigene phylogenetic analyses of the Thelonectria coronata and T. veuillotiana species complexes. Mycologia 2012; 104:1325-50. [PMID: 22778168 DOI: 10.3852/12-055] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Thelonectria is a recently established genus of common and ubiquitous fungi on woody hosts, previously placed in the genus Neonectria. Thelonectria coronata and T. veuillotiana occur sympatrically in tropical, subtropical and temperate regions. Previous taxonomic studies including T. coronata and T. veuillotiana suggested these fungi could represent species complexes; however, the morphological features used to define species exhibited few differences useful for testing this hypothesis. To assess the status of T. coronata and T. veuillotiana, phylogenetic analyses of six genomic regions were combined with a morphological examination of specimens. A multi-gene phylogeny reconstructed with maximum parsimony, maximum likelihood and Bayesian approaches identified five phylogenetic groups in T. coronata and six in T. veuillotiana. As is common for cryptic species, unequivocal diagnostic morphological characters could not be identified; however, average values of morphological traits correspond to the phylogenetic groups. An increased number of non-synonymous/synonymous substitutions in the β-tubu-lin gene and a decreased or absent production of conidia were detected within the T. coronata complex, possibly indicating the homothallic nature of these isolates. T. coronata and T. veuillotiana and related species are described and illustrated here; a dichotomous key to all species is provided.
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Affiliation(s)
- Catalina Salgado-Salazar
- University of Maryland, Department of Plant Science and Landscape Architecture, College Park, MD 20742, USA.
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Pérez-Ortega S, Ortiz-Álvarez R, Allan Green T, de los Ríos A. Lichen myco- and photobiont diversity and their relationships at the edge of life (McMurdo Dry Valleys, Antarctica). FEMS Microbiol Ecol 2012; 82:429-48. [DOI: 10.1111/j.1574-6941.2012.01422.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 05/24/2012] [Accepted: 05/25/2012] [Indexed: 11/29/2022] Open
Affiliation(s)
| | | | - T.G. Allan Green
- Departamento de Biología Vegetal II; Facultad de Farmacia; Universidad Complutense de Madrid; Madrid; Spain
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KOBMOO N, MONGKOLSAMRIT S, TASANATHAI K, THANAKITPIPATTANA D, LUANGSA-ARD JJ. Molecular phylogenies reveal host-specific divergence ofOphiocordyceps unilateralis sensu latofollowing its host ants. Mol Ecol 2012; 21:3022-31. [DOI: 10.1111/j.1365-294x.2012.05574.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci U S A 2012; 109:6241-6. [PMID: 22454494 DOI: 10.1073/pnas.1117018109] [Citation(s) in RCA: 2779] [Impact Index Per Article: 231.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
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Abstract
This chapter describes methods currently used for DNA barcoding of fungi, including some comments on the barcoding of aged herbarium material. The collecting procedures are focussed on macro-fungi. The laboratory methods are for medium-throughput DNA barcoding, targeted at the 96-well format, but without the assistance of robotics. In the absence of an approved and standardized DNA barcoding locus for fungi, the chapter outlines the amplification and sequencing of nuclear ribosomal genes, ITS, and LSU D1/D2 which are most widely used for the identification of fungi from diverse environments.
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Affiliation(s)
- Ursula Eberhardt
- CBS-KNAW Fungal Biodiversity Centre, Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands.
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Another example of cryptic diversity in lichen-forming fungi: the new species Parmelia mayi (Ascomycota: Parmeliaceae). ORG DIVERS EVOL 2011. [DOI: 10.1007/s13127-011-0060-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Leavitt SD, Johnson LA, Goward T, St. Clair LL. Species delimitation in taxonomically difficult lichen-forming fungi: An example from morphologically and chemically diverse Xanthoparmelia (Parmeliaceae) in North America. Mol Phylogenet Evol 2011; 60:317-32. [DOI: 10.1016/j.ympev.2011.05.012] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Revised: 05/13/2011] [Accepted: 05/16/2011] [Indexed: 01/03/2023]
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Lumbsch HT, Leavitt SD. Goodbye morphology? A paradigm shift in the delimitation of species in lichenized fungi. FUNGAL DIVERS 2011. [DOI: 10.1007/s13225-011-0123-z] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Kelly LJ, Hollingsworth PM, Coppins BJ, Ellis CJ, Harrold P, Tosh J, Yahr R. DNA barcoding of lichenized fungi demonstrates high identification success in a floristic context. THE NEW PHYTOLOGIST 2011; 191:288-300. [PMID: 21434928 DOI: 10.1111/j.1469-8137.2011.03677.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
• Efforts are currently underway to establish a standard DNA barcode region for fungi; we tested the utility of the internal transcribed spacer (ITS) of nuclear ribosomal DNA for DNA barcoding in lichen-forming fungi by sampling diverse species across eight orders. • Amplification of the ITS region (ITS1-5.8S-ITS2) was conducted for 351 samples, encompassing 107, 55 and 28 species, genera and families, respectively, of lichenized fungi. We assessed the ability of the entire ITS vs the ITS2 alone to discriminate between species in a taxonomic dataset (members of the genus Usnea) and a floristic dataset. • In the floristic dataset, 96.3% of sequenced samples could be assigned to the correct species using ITS or ITS2; a barcode gap for ITS is present in 92.1% of species. Although fewer species have a barcode gap in the taxonomic dataset (73.3% with ITS and 68.8% with ITS2), up to 94.1% of samples were assigned to the correct species using BLAST. • While discrimination between the most closely related species will remain challenging, our results demonstrate the potential to identify a high percentage of specimens to the correct species, and the remainder to the correct genus, when using DNA barcoding in a floristic context.
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Affiliation(s)
- Laura J Kelly
- Science Division, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
- Present address: Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK
| | - Peter M Hollingsworth
- Science Division, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Brian J Coppins
- Science Division, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Christopher J Ellis
- Science Division, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Paul Harrold
- Science Division, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - James Tosh
- Science Division, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Rebecca Yahr
- Science Division, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
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Leavitt SD, Johnson L, St Clair LL. Species delimitation and evolution in morphologically and chemically diverse communities of the lichen-forming genus Xanthoparmelia (Parmeliaceae, Ascomycota) in western North America. AMERICAN JOURNAL OF BOTANY 2011; 98:175-188. [PMID: 21613107 DOI: 10.3732/ajb.1000230] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
PREMISE OF THE STUDY Accurate species delimitation is important for understanding the diversification of biota and has critical implications for ecological and conservation studies. However, a growing body of evidence indicates that morphology-based species circumspection in lichenized fungi misrepresents fungal diversity. The foliose lichen genus Xanthoparmelia includes over 800 species displaying a complex array of morphological and secondary metabolite diversity. METHODS We used a multifaceted approach, applying phylogenetic, population genetic, and genealogical analyses to delimit species in a single well-supported monophyletic clade containing 10 morphologically and chemically diverse Xanthoparmelia species in western North America. Sequence data from four ribosomal and two low-copy, protein-coding markers, along with chemical and morphological data were used to assess species diversity. KEY RESULTS We found that traditionally circumscribed species are not supported by molecular data. Rather, all sampled taxa were better represented by three polymorphic population clusters. Our results suggest that secondary metabolite variation may have limited utility in diagnosing lineages within this group, while identified populations clusters did not reflect major phylogeographic or ecological patterns. CONCLUSIONS In contrast to studies revealing previously undiscovered fungal lineages masked within lichen species circumscribed by traditional morphological and chemical concepts, the present study suggests that species diversity has been overestimated in the species-rich genus Xanthoparmelia.
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Affiliation(s)
- Steven D Leavitt
- Department of Biology and the M. L. Bean Life Science Museum, 401 WIDB, Brigham Young University, Provo, Utah 84602, USA.
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