A single macrolichen constitutes hundreds of unrecognized species

Lücking, Robert; Dal-Forno, Manuela; Sikaroodi, Masoumeh; Gillevet, Patrick M.; Bungartz, Frank; Moncada, Bibiana; Yánez-Ayabaca, Alba; Chaves, José Luis; Coca, Luis Fernando; Lawrey, James D.

doi:10.1073/pnas.1403517111

Cited by 159 publications

(141 citation statements)

References 42 publications

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“…The best examples for the latter case are to be found in Cladonia (Pino-Bodas et al 2011, b, 2013a, and examples of the former can be found in the Vulpicida juniperus group (Mark et al 2012), the Peltigera polydactylon clade (Magain et al 2012b), or the Tephromela atra group (Muggia et al 2014). By all means, the most emblematic case is the basiolichen Cora pavonia, very much characteristic of montane forests and paramos in Central and South America, which has been shown on molecular basis to contain at least 126 species, over 110 of them being yet undescribed (Lücking et al 2014). …”

Section: Discussionmentioning

confidence: 99%

Dismantling the treasured flagship lichen Sticta fuliginosa (Peltigerales) into four species in Western Europe

Magain

Sérusiaux

2015

Mycol Progress

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In the framework of a worldwide project on the phylogeny of the lichen genus Sticta, dedicated sampling was performed in four regions of Western Europe, roughly along an east-west line between N 48°02′ E 07°01′ and N 52°01′ W 09°30′, ranging from France/Vosges to Ireland/ Kerry. Five clearly distinct ITS haplotypes were detected for isidia-producing species where only two were expected. Subtle anatomical and morphological characters, together with a strongly supported 4-loci molecular phylogeny, permit distinguishing, besides the easily recognized S. canariensis and S. limbata: 1) the two well-known S. fuliginosa and S. sylvatica, whose type collections have been carefully reassessed; the former is widespread in both hemispheres, while the latter is correctly identified only from continental Europe and the Andes in Colombia. The barcode ITS of S. fuliginosa differs by a single substitution from S. limbata (with a single exception), and the 4-loci phylogenetic tree does not resolve them as distinct lineages, most probably highlighting a very recent divergence and incomplete lineage sorting. 2) Three species that were formely included in S. fuliginosa: the resurrected S. ciliata Taylor, belonging to a complex group yet to be disentangled and occurring in the Neotropics, Africa, Macaronesia, and Western Europe, and two species described as new to science, S. fuliginoides, found in continental Europe, the Canary Islands, eastern North America, and Colombia, and S. atlantica only known from Ireland and the Azores archipelago. Molecular inferences demonstrate active divergence and dispersion within S. ciliata that may require recognition of further species. Fresh material can be identified with a morphological and anatomical preliminary key provided here. We propose that the taxonomy of all lichen species be urgently reviewed in the light of molecular data in an evolutionary context, particularly those used as bioindicators of environmental change and woodland management.

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Section: Discussionmentioning

confidence: 99%

Dismantling the treasured flagship lichen Sticta fuliginosa (Peltigerales) into four species in Western Europe

Magain

Sérusiaux

2015

Mycol Progress

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“…Over the last few decades, novel molecular techniques and DNA based sequence data, coupled with phylogenetic analyses, have been used to test traditional taxonomic findings and overcome the difficulties in taxonomic studies (White et al 1990;Liew et al 2000;Hyde et al 2013;Lücking et al 2014). Traditional molecular tools are most appropriate for cultivatable and fast growing species isolated from the environment, but DNA from single spores isolates and fresh specimens can usually also be extracted and sequenced.…”

Section: Introductionmentioning

confidence: 99%

Can we use environmental DNA as holotypes?

et al. 2018

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The advantages and disadvantages of giving a valid name to a sequence of DNA detected from environmental specimens is presently a hot debate amongst the mycological community. The idea of using intracellular DNA (''mgDNA'') from environmental samples as holotypes seems at face value, to be a good idea, considering the expansion of knowledge among these 'dark taxa' or 'dark matter fungi' that it could provide (i.e. sequence based taxa without physical specimens and formal nomenclature). However, the limitations of using mgDNA as holotypes needs careful thought, i.e. can we use a short mgDNA fragment, which may contain a small amount of genetic information, to allow discrimination between species? What is the point and are the potential problems of giving valid scientific names to mgDNA? Numerous mycologists and taxonomists, who have many years of experience working on the taxonomy and phylogeny of different groups of fungi, are concerned about the consequences of providing valid names to mgDNA. There has been much debate, through several publications on the considerable problems of using mgDNA as holotypes. The proponents have tried to debate the virtues of using mgDNA as holotypes. Those against have shown that identification to species using mgDNA does not work in many fungal groups, while those for have shown cases where species can be identified with mgDNA. Different disciplines have different reasons and opinions for using mgDNA as holotypes, however even groups of the same disciplines have dissimilar ideas. In this paper we explore the use of mgDNA as holotypes. We provide evidences and opinions as to the use of mgDNA as holotypes from our own experiences. In no way do we attempt to degrade the study of DNA from environmental samples and the expansion of knowledge in to the dark taxa, but relate the issues to fungal taxonomy. In fact we show the value of using sequence data from these approaches, in dealing with the discovery of already named taxa, taxa numbers and ecological roles. We discuss the advantages and the pitfalls of using mgDNA from environmental samples as holotypes. The impacts of expanding the nomenclatural concept to allow using mgDNA from environmental samples as holotypes are also discussed. We provide evidence from case studies on Botryosphaeria, Colletotrichum, Penicillium and Xylaria. The case studies show that we cannot use mgDNA due to their short fragments and the fact that most ITS sequence data presently result from environmental sequencing. We conclude from the evidence that it is highly undesirable to use mgDNA as holotypes in naming fungal species. If this approach adopted, it would result in numerous problems where species identification cannot be confirmed due to limited sequence data available for the holotypes. We also propose an alternative DNA-based system for naming DNA based species which would provide considerably less problems and should be adopted.

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“…Sampling difficulties occur where other very similar lichen species live mixed or close by, and many saprophytic, endophytic, and parasitic fungi also live intimately admixed with the lichen mycobiont, making the application of Sanger sequencing insufficient in many cases (Flück 2012;Orock et al 2012). A limited number of studies are known to have successfully applied pyrosequencing to recover the identity of a lichen, when Sanger sequencing failed to produce usable results (Hodkinson and Lendemer 2013;Lücking et al 2014a).…”

Section: Introductionmentioning

confidence: 99%

Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation

Mark

Cornejo

Keller

et al. 2016

Genome

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Abstract:Although lichens (lichen-forming fungi) play an important role in the ecological integrity of many vulnerable landscapes, only a minority of lichen-forming fungi have been barcoded out of the currently accepted ϳ18 000 species. Regular Sanger sequencing can be problematic when analyzing lichens since saprophytic, endophytic, and parasitic fungi live intimately admixed, resulting in low-quality sequencing reads. Here, high-throughput, long-read 454 pyrosequencing in a GS FLX+ System was tested to barcode the fungal partner of 100 epiphytic lichen species from Switzerland using fungal-specific primers when amplifying the full internal transcribed spacer region (ITS). The present study shows the potential of DNA barcoding using pyrosequencing, in that the expected lichen fungus was successfully sequenced for all samples except one. Alignment solutions such as BLAST were found to be largely adequate for the generated long reads. In addition, the NCBI nucleotide database-currently the most complete database for lichenforming fungi-can be used as a reference database when identifying common species, since the majority of analyzed lichens were identified correctly to the species or at least to the genus level. However, several issues were encountered, including a high sequencing error rate, multiple ITS versions in a genome (incomplete concerted evolution), and in some samples the presence of mixed lichen-forming fungi (possible lichen chimeras).Key words: 454 pyrosequencing, DNA barcoding, intragenomic variation, internal transcribed spacer, lichenized fungi.Résumé : Bien que les lichens (champignons lichénisés) jouent un rôle important dans l'intégrité écologique du plusieurs environnements vulnérables, seule une minorité de champignons lichénisés ont été examinés au moyen de codes à barres sur un total de ϳ18 000 espèces reconnues. Le séquençage Sanger standard peut s'avérer problématique lorsqu'on analyse les lichens en raison de la présence de champignons saprophytes, endophytes et parasitiques qui y sont intimement associés, ce qui produit des lectures de faible qualité. Dans ce travail, un pyroséquençage 454 à haut débit produisant de longues séquences sur un système GS FLX+ a été testé pour réaliser un codage à barres de la composante fongique de 100 espèces de lichens épiphytes provenant de la Suisse. Des amorces spécifiques des champignons ont été employées pour amplifier l'espaceur interne transcrit (ITS) au complet. Ce travail montre le potentiel des codes à barres réalisés au moyen du pyroséquençage, car les champignons lichénisés attendus ont été séquencés avec succès pour tous les échantillons sauf un. Les outils d'alignement comme BLAST se sont avérés largement adéquats pour l'analyse des longues séquences. De plus, la base de données NCBI -de loin la plus complète pour les champignons lichénisés -peut servir de base de référence pour l'identification des espèces communes, puisque la majorité des lichens analysés ont été correctement identifiés à l'espèce ou à tout le moins au genre. Cependant,...

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A single macrolichen constitutes hundreds of unrecognized species

Cited by 159 publications

References 42 publications

Dismantling the treasured flagship lichen Sticta fuliginosa (Peltigerales) into four species in Western Europe

Dismantling the treasured flagship lichen Sticta fuliginosa (Peltigerales) into four species in Western Europe

Can we use environmental DNA as holotypes?

Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation

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