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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The numbers of fungi: is the descriptive curve flattening?

Fungal Diversity, Journal Year: 2020, Volume and Issue: 103(1), P. 219 - 271

Published: July 1, 2020

Language: Английский

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Four priority areas to advance invasion science in the face of rapid environmental change

Environmental Reviews, Journal Year: 2020, Volume and Issue: 29(2), P. 119 - 141

Published: Dec. 7, 2020

Unprecedented rates of introduction and spread non-native species pose burgeoning challenges to biodiversity, natural resource management, regional economies, human health. Current biosecurity efforts are failing keep pace with globalization, revealing critical gaps in our understanding response invasions. Here, we identify four priority areas advance invasion science the face rapid global environmental change. First, should strive develop a more comprehensive framework for predicting how behavior, abundance, interspecific interactions vary relation conditions receiving environments these factors govern ecological impacts invasion. A second is understand potential synergistic effects multiple co-occurring stressors— particularly involving climate change—on establishment impact species. Climate adaptation mitigation strategies will need consider possible consequences promoting species, appropriate management responses be developed. The third address taxonomic impediment. ability detect evaluate risks compromised by growing deficit expertise, which cannot adequately compensated new molecular technologies alone. Management become increasingly challenging unless academia, industry, governments train employ personnel taxonomy systematics. Fourth, recommend that internationally cooperative bridgehead dispersal networks, organisms tend invade regions from locations where they have already established. Cooperation among countries eradicate or control established yield greater benefit than independent attempts individual exclude arriving establishing.

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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Early-diverging fungal phyla: taxonomy, species concept, ecology, distribution, anthropogenic impact, and novel phylogenetic proposals

Fungal Diversity, Journal Year: 2021, Volume and Issue: 109(1), P. 59 - 98

Published: July 1, 2021

Abstract The increasing number of new fungal species described from all over the world along with use genetics to define taxa, has dramatically changed classification system early-diverging fungi past several decades. phyla established for non-Dikarya increased 2 17. However, date, both and phylogeny basal are still unresolved. In this article, we review recent taxonomy re-evaluate relationships among lineages phyla. We also provide information on ecology distribution in Mucoromycota highlight impact chytrids amphibian populations. Species concepts Chytridiomycota , Aphelidiomycota Rozellomycota Neocallimastigomycota discussed paper. To preserve current application genus Nephridiophaga ( : Nephridiophagales ) a type species, blattellae is proposed.

Language: Английский

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Towards a global list of accepted species VI: The Catalogue of Life checklist

Organisms Diversity & Evolution, Journal Year: 2021, Volume and Issue: 21(4), P. 677 - 690

Published: Oct. 11, 2021

Despite the important role that species names play in multiple fields, there is no globally complete list of known and described species. This lack a result simultaneously complexity planetary biodiversity, long history naming publications from all over world, small number taxonomists working on many groups, rapid dynamic change knowledge for few well-studied limited incentives researchers to curate such lists. Recent papers have proposed more formal governance mechanism needed assist with translation taxonomic user communities. The recommendation community groups by maintaining reviewed lists reflect as far possible consensus among practising incorporating new insights understanding these become widely accepted within relevant community. Catalogue Life (COL) most significant international partnership deliver engaging broad network databases contribute expert-curated different groups. COL, which included 1,908,823 May 2021, has great experience developing across been modernising its processes tools since 2017 best practice management large digital information assets. paper explores alignment between current state directions COL initiative improve

Language: Английский

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The 5 ‘D’s of Taxonomy: A User’s Guide

The Quarterly Review of Biology, Journal Year: 2024, Volume and Issue: 99(3), P. 131 - 156

Published: Aug. 16, 2024

Language: Английский

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Towards a global list of accepted species II. Consequences of inadequate taxonomic list governance

Organisms Diversity & Evolution, Journal Year: 2021, Volume and Issue: 21(4), P. 623 - 630

Published: Oct. 14, 2021

Language: Английский

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A checklist of Nylanderia (Hymenoptera: Formicidae: Formicinae) from Hong Kong and Macao SARs, with an illustrated identification key for species in Southeast China and Taiwan

Zootaxa, Journal Year: 2023, Volume and Issue: 5301(5), P. 501 - 539

Published: June 13, 2023

Species of the ant genus Nylanderia constitute some most common ground dwelling Formicinae in tropical and subtropical areas. The includes numerous species introduced into new regions, especially within urban or disturbed environments. Here, we review found Hong Kong Macao, which are both highly urbanized regions critical importance to Southern China's policy-makers non-governmental actors concerned with regional spread non-native species. A total 11 2 morphospecies recorded 6 Macao. We also provide a list records for along taxonomic accounts all recorded. Additionally, present work provides an illustrated identification key occurring Southeast Mainland China Taiwan. briefly discuss possible biogeographical implications our findings, providing additional support exotic status N. bourbonica continental Asia. Lastly, give perspective on ramifications local inaccessibility type specimens current practices.

Language: Английский

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The role of systematics for understanding ecosystem functions: Proceedings of the Zoologica Scripta Symposium, Oslo, Norway, 25 August 2022

Zoologica Scripta, Journal Year: 2023, Volume and Issue: 52(3), P. 187 - 214

Published: March 7, 2023

Abstract On 25 August 2022, the Zoologica Scripta ‐ An International Journal of Systematic Zoology and Norwegian Academy Sciences Letters arranged a symposium entitled ‘The role systematics for understanding ecosystem functions’ in Academy's premises Oslo, Norway. The aimed at offering forum exploring discussing trends future developments field systematics. Eleven international experts contributed expertise on various issues related to global challenges, such as biodiversity assessments, databases, cutting‐edge analysis tools, consequences taxonomic impediment. Here, we compiled multi‐author proceedings paper contributions that are chapters presents content key conclusions majority presentations.

Language: Английский

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