Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

IMA Fungus, Journal Year: 2020, Volume and Issue: 11(1)

Published: July 10, 2020

True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of based on global richness estimates, with around 3 million predicted species. Compared to plants animals, have simple body plans often morphologically ecologically obscure structures. This poses challenges for accurate precise identifications. Here we provide a conceptual framework identification fungi, encouraging approach integrative (polyphasic) taxonomy species delimitation, i.e. combination genealogy (phylogeny), phenotype (including autecology), reproductive biology (when feasible). allows objective evaluation diagnostic characters, either phenotypic or molecular both. Verification identifications is crucial but neglected. Because clade-specific evolutionary histories, there currently no single tool although DNA barcoding using internal transcribed spacer (ITS) remains first diagnosis, particularly in metabarcoding studies. Secondary barcodes are increasingly implemented groups where ITS does not sufficient precision. Issues pairwise sequence similarity-based OTU clustering discussed, multiple alignment-based phylogenetic approaches subsequent verification recommended as more alternatives. In approaches, trade-off between speed accuracy precision must be carefully considered. Intragenomic variation other markers should properly documented, phylotype diversity necessarily proxy richness. Important strategies improve are: (1) broadly document intraspecific intragenomic markers; (2) substantially expand repositories, focusing undersampled clades missing taxa; (3) curation labels primary repositories increase number sequences verified material; (4) link data digital information voucher specimens including imagery. parallel, technological improvements genome sequencing offer promising alternatives future. Despite prevalence DNA-based fungal taxonomy, phenotype-based remain an important strategy catalog establish initial hypotheses.

Language: Английский

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Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics

Fungal Diversity, Journal Year: 2021, Volume and Issue: 109(1), P. 99 - 154

Published: July 1, 2021

Abstract Lichens are symbiotic associations resulting from interactions among fungi (primary and secondary mycobionts), algae and/or cyanobacteria photobionts), specific elements of the bacterial microbiome associated with lichen thallus. The question what is a species, both concerning as whole its main fungal component, primary mycobiont, has faced many challenges throughout history reached new dimensions advent molecular phylogenetics phylogenomics. In this paper, we briefly revise definition lichens scientific vernacular naming conventions, concluding that scientific, Latinized name usually invariably refers to whereas encompasses entire lichen. Although same mycobiont may produce different phenotypes when associating photobionts or growing in axenic culture, discrete variation does not warrant application names, but must follow principle "one fungus = one name". Instead, broadly agreed informal designations should be used for such morphologies, chloromorph cyanomorph formed by either green cyanobacteria. taxonomic recognition species lichen-forming other conceptual nomenclatural approaches principles. We identify number current provide recommendations address these. Species delimitation tailored particular concepts instead derived empirical evidence, applying several following principles call LPR approach: lineage (L) coherence vs. divergence (phylogenetic component), phenotype (P) (morphological reproductive (R) compatibility isolation (biological component). hypotheses can established based on L P, then using P (plus R) corroborate them. reliability depends only nature characters also context: closer relationship similarity between higher specimens analyzed reliable delimitations. Alpha taxonomy evidence an evolutionary framework offer alternative practical solutions, long these scientifically defendable. Taxa delimited phylogenetically readily identifiable field, genuinely cryptic, rejected due inaccessibility proper tools. they provisionally treated undifferentiated complexes purposes do require precise determinations. infraspecific (gamma) restricted cases where there biological rationale, i.e . , lineages complex show limited phylogenetic no isolation. Gamma denote phenotypical ecotypes warranting distinction at level. pair concept fungi, which recognizes sexually asexually reproducing morphs underlying species. conclude most hold, actual situation necessarily correlated strategy. data available single multi-marker resolution, recommend maintaining pairs until phylogenomic available. This recommendation example Usnea aurantiacoatra U. antarctica resolved approaches, microsatellites RADseq. Overall, consider advanced dramatically over past three decades, solid framework, still missing taxa. Therefore, while focusing examples will increasingly employed resolve difficult complexes, broad screening barcoding markers aid placing taxa possible into matrix. protocol how assess formally treat novelties. While paper focuses aspects discussed herein apply generally taxonomy. combination Arthonia minor (Lücking) Lücking comb. et stat. nov. (Bas.: cyanea f. Lücking) proposed.

Language: Английский

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RAD sequencing resolved phylogenetic relationships in European shrub willows (Salix L. subg. Chamaetia and subg. Vetrix) and revealed multiple evolution of dwarf shrubs

Ecology and Evolution, Journal Year: 2018, Volume and Issue: 8(16), P. 8243 - 8255

Published: July 22, 2018

The large and diverse genus Salix L. is of particular interest for decades biological research. However, despite the morphological plasticity, reconstruction phylogenetic relationships was so far hampered by lack informative molecular markers. Infrageneric classification based on morphology separates dwarf shrubs (subg. Chamaetia) taller Vetrix), while previous studies placed species these two subgenera just in one largely unresolved clade. Here we want to test utility genomic RAD sequencing markers resolving at different levels divergence Salix. Based a sampling 15 European representing 13 sections subgenera, used five datasets generated ipyrad conduct analyses. Additionally reconstructed evolution growth form analyzed genetic composition whole results showed fully resolved trees both ML BI analysis with high statistical support. Chamaetia Vetrix were recognized as nonmonophyletic, which suggests that they should be merged. Within Vetrix/Chamaetia clade, division into three major subclades could observed. All confirmed monophyletic. our data, arctic-alpine evolved four times independently. structure mainly uniform clusters are congruent sister observed phylogenies. Our study useful tool taxonomic

Language: Английский

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Three challenges to contemporaneous taxonomy from a licheno-mycological perspective

Megataxa, Journal Year: 2020, Volume and Issue: 1(1)

Published: Jan. 31, 2020

This paper discusses three issues that challenge contemporaneous taxonomy, with examples from the fields of mycology and lichenology, formulated as questions: (1) What is importance taxonomy in future science society? (2) An increasing methodological gap alpha taxonomy: or opportunity? (3) The Nagoya Protocol: improvement impediment to taxonomy? society illustrated using example popular field guides digital media, a billion-dollar business, arguing desire name species an intrinsic feature cognitive component nature connectedness humans. While continuous societal support critical mass taxonomists necessary catalogue all on Earth, it shown this finite task, proposal made how remaining 10 million can be catalogued within 40 years by 1,000 well-trained dedicated taxonomists, investment $4 billion, corresponding 0.0001% annual global GDP 0.005% military expenditures. Notorious undercitation actually used taxonomic resources lack coverage impact metrics for monographs other work cannot published indexed journals discussed suggestions are problem remedied. approaches between classic morphological advanced genomic studies, affects particular biodiversity-rich countries amateurs, also regarding proper training apply methods concepts. To counterbalance problem, international collaborations bringing different expertise table undertaking mutual capacitation one successful remedy. Classic still works many groups first approach establish taxon hypotheses, but ultimately each group needs studied array group, including descriptive work. Finally, Convention Biological Diversity (CBD) Protocol has put additional burden basic biodiversity science. Using lichenology Latin America Brazil example, spirit non-monetary benefit-sharing systematics, namely capacitation, joint publications, shared reference collections, been increasingly implemented long before CBD Protocol, does not need “policing”. Indeed, puts heaviest researchers cataloguing biodiversity, whereas intended target those seeking revenue gain nature, protocol may effectively. notion currently freely accessible sequence information (DSI) become subject protocol, even after previous publication, misguided conflicts guidelines ethical scientific conduct. Through its implementation Colombia set welcome precedence exempt systematic research “access genetic resources”, hopefully will follow example.

Language: Английский

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An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

Life, Journal Year: 2020, Volume and Issue: 10(12), P. 356 - 356

Published: Dec. 17, 2020

Fungi are among the most successful eukaryotes on Earth: they have evolved strategies to survive in diverse environments and stressful conditions been selected exploited for multiple aims by humans. The characteristic features intrinsic of required evolutionary changes adaptations at deep molecular levels. Omics approaches, nowadays including genomics, metagenomics, phylogenomics, transcriptomics, metabolomics, proteomics enormously advanced way understand fungal diversity taxonomic levels, under changeable still under-investigated environments. These approaches can be applied both environmental communities individual organisms, either nature or axenic culture led traditional morphology-based systematic increasingly implement molecular-based approaches. advent next-generation sequencing technologies was key boost advances genomics research. Much effort has also directed towards development methodologies optimal genomic DNA protein extraction separation. To date, amount investigations Ascomycetes exceeds those carried out any other group. This is primarily due preponderance their involvement plant animal diseases industrial applications, therefore need biological basis infectious process develop mechanisms biologic control, as well detect proteins with roles stress survival. Here we chose present an overview much comprehensive possible major advances, mainly past decade, fields (including phylogenomics) Ascomycota, focusing particularly reporting opportunistic pathogenic, extremophilic, polyextremotolerant lichenized fungi. We a review mostly used genome methods sequence analyses so far

Language: Английский

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Species boundaries in the messy middle—A genome‐scale validation of species delimitation in a recently diverged lineage of coastal fog desert lichen fungi

Ecology and Evolution, Journal Year: 2021, Volume and Issue: 11(24), P. 18615 - 18632

Published: Dec. 1, 2021

Abstract Species delimitation among closely related species is challenging because traditional phenotype‐based approaches, for example, using morphology, ecological, or chemical characteristics, may not coincide with natural groupings. With the advent of high‐throughput sequencing, it has become increasingly cost‐effective to acquire genome‐scale data which can resolve previously ambiguous boundaries. As availability increased, numerous analyses, such as BPP and SNAPP+Bayes factor (BFD*), have been developed delimit However, even empirical molecular approaches be biased by confounding evolutionary factors, hybridization/introgression incomplete lineage sorting, computational limitations. Here, we investigate boundaries potential micro‐endemism in a lichen‐forming fungi, Niebla Rundel & Bowler, family Ramalinaceae analyzing single‐locus consisting (a) analysis ASAP, (b) maximum likelihood‐based phylogenetic tree inference, (c) models, e.g., SNAPP+BFD, (d) validation genealogical divergence index ( gdi ). We specifically use these methods cross‐validate results between datasets, differently sampled subsets genomic control population‐level genetic divergence. Our models tend support more speciose groupings that were inconsistent taxonomy, supporting hypothesis micro‐endemism, include morphologically cryptic species. did converge on robust, consistent delimitations. While our are somewhat terms boundaries, they provide valuable perspective how nonmodel system. This study thus highlights challenges inherent delimiting species, particularly groups , complex, relatively recent phylogeographic histories.

Language: Английский

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The fruticose genera in the Ramalinaceae (Ascomycota, Lecanoromycetes): their diversity and evolutionary history

MycoKeys, Journal Year: 2020, Volume and Issue: 73, P. 1 - 68

Published: Sept. 11, 2020

We present phylogenetic analyses of the fruticose Ramalinaceae based on extensive collections from many parts world, with a special focus Vizcaíno deserts in north-western Mexico and coastal desert Namibia. generate four-locus DNA sequence dataset for accessions Ramalina two additional loci Niebla Vermilacinia . Four genera are strongly supported: subcosmopolitan , new genus Namibialina endemic to SW Africa, duo formed by New World except sorediate V. zebrina that disjunctly occurs The latter three restricted chaparral where vegetation depends moisture ocean fog. is much more diverse its ecology. show sister diverged each other at c. 48 Myrs, whereas split 30 Myrs. phylogeny remains unresolved their ancestral crustose genera. Species delimitation within rather straightforward. taxonomy fully resolved, youngest clades corticolous taxa, support current taxonomy, including four taxa described here. Secondary metabolite variation generally coincides major which comprised species complexes still relationships. A micro-endemism pattern allopatric suspected both genera, Both saxicolous have chemotypes unique largely deserts. following described: gen. nov. N. melanothrix ( comb. ) as type species, single R. krogiae breviloba lacunosa pustulata reticulata ). combination granulans introduced. Two epithets re-introduced European species: crispans (= peruviana auct. eur.) rosacea bourgeana p.p). lectotype designated procera key presented.

Language: Английский

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Phylogenomics, biogeography, and evolution of the blue‐ or white‐fruited dogwoods (Cornus)—Insights into morphological and ecological niche divergence following intercontinental geographic isolation

Journal of Systematics and Evolution, Journal Year: 2020, Volume and Issue: 58(5), P. 604 - 645

Published: Aug. 27, 2020

Abstract The eastern Asian (EA)–eastern North American (ENA) floristic disjunction represents a major pattern of phytogeography the Northern Hemisphere. Despite 20 years studies dedicated to identification taxa that display this disjunct pattern, its origin and evolution remain an open question, especially regarding post‐isolation evolution. blue‐ or white‐fruited dogwoods (BW) are most species‐rich among four clades Cornus L., consisting ~35 species divided into three subgenera (subg. Yinquania , subg. Mesomora Kraniopsis ). BW group provides excellent example EA–ENA for biogeographic study due diversity distribution centered in Asia America, yet relationships delineation have remained poorly understood. In study, we combined genome‐wide markers from RAD‐seq, morphology, fossils, climate data understand relationships, history, ecological niche morphological Our phylogenomic analyses with RAxML MrBayes recovered strongly supported well‐resolved phylogeny intercontinental EA ENA Eurasia which two newly identified within . These also potential new but failed resolve C. hemsleyi – schindleri complex. effort develop approach reduce computation time, analysis different nodal age settings treePL suggests setting node's minimum constraint lower bound fossil's range obtain similar ages BEAST. Divergence time BEAST dated stem back very Late Cretaceous divergence Paleogene. By integrating fossil total evidence‐based dating was used conjunction time‐slice probabilities dispersal under DEC model ancestral ranges each Miocene: (disjunct 1), western America 2), 3). history supports via Atlantic Land Bridge late Paleogene 1 Bering Miocene disjuncts 2 3. Character mapping stochastic phytools comparison niche, morphospace, rate indicated differential patterns molecules between sisters. Although stasis observed characters, evolutionary changes growth habit some features leaf, flower, fruit morphology occurred one both sister clades. A significant differentiation habitats temperature, precipitation, elevation sisters observed, suggesting role post‐isolation. varied were not always congruent molecules, cases non‐neutral driven by selection. phylogenetic evidence comparisons lineages lend insights formation anomaly ENA, particular support early diversification EA. findings, previous studies, again suggest floras assembly descended Mesophytic Forests evolved “boreotropical flora” through pathways across lineages.

Language: Английский

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DNA Barcoding of Fresh and Historical Collections of Lichen-Forming Basidiomycetes in the Genera Cora and Corella (Agaricales: Hygrophoraceae): A Success Story?

Diversity, Journal Year: 2022, Volume and Issue: 14(4), P. 284 - 284

Published: April 10, 2022

Lichens collected worldwide for centuries have resulted in millions of specimens deposited herbaria that offer the potential to assess species boundaries, phenotypic diversification, ecology, and distribution. The application molecular approaches historical collections has been limited due DNA fragmentation, but high-throughput sequencing offers an opportunity overcome this barrier. Here, we combined a large dataset ITS sequences from recently material collections, obtained through Sanger, 454, or Illumina Sequencing, test performance barcoding two genera lichenized Basidiomycota: Cora Corella. We attempted generate new sequence data 62 fresh (from 2016) 274 (collected between 1888 1998), final 1325 sequences. compared various quantitative delimit (GMYC, bPTP, ASAP, ABGD) tested resolution accuracy fungal marker by comparison with six-marker dataset. Finally, quantitatively phylogenetic delimitation 87 selected formally described. Our HTS approach successfully generated 76% our results show integrative is gold-standard understanding diversity group.

Language: Английский

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Providing Scale to a Known Taxonomic Unknown—At Least a 70-Fold Increase in Species Diversity in a Cosmopolitan Nominal Taxon of Lichen-Forming Fungi

Journal of Fungi, Journal Year: 2022, Volume and Issue: 8(5), P. 490 - 490

Published: May 8, 2022

Robust species delimitations provide a foundation for investigating speciation, phylogeography, and conservation. Here we attempted to elucidate boundaries in the cosmopolitan lichen-forming fungal taxon Lecanora polytropa. This nominal is morphologically variable, with distinct populations occurring on all seven continents. To delimit candidate species, compiled ITS sequence data from worldwide. For subset of samples, also generated alignments 1209 single-copy nuclear genes an alignment spanning most mitochondrial genome assess concordance among ITS, nuclear, inferences. Species partitions were empirically delimited using ASAP bPTP. We inferred phylogeny L. polytropa clade four-marker dataset. revealed up 103 clade, 75 corresponding Inferences phylogenomic generally supported that these represent evolutionarily independent lineages or species. Less than 10% comprised specimens multiple High levels recovered at local scales but limited overlap across regions. likely ranks as one largest complexes fungi known date.

Language: Английский

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