Evaluation of traditionally circumscribed species in the lichen-forming genus Usnea, section Usnea (Parmeliaceae, Ascomycota) using a six-locus dataset

Mark, Kristiina; Saag, Lauri; Leavitt, Steven D.; Will‐Wolf, Susan; Nelsen, Matthew P.; Tõrra, Tiiu; Saag, Andres; Randlane, Tiina; Lumbsch, H. Thorsten

doi:10.1007/s13127-016-0273-7

Cited by 39 publications

(138 citation statements)

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“…Organisms are always evolving, changing in response to either selective pressures or genetic drift, so that delimiting units to accord species names is not always clear (Naciri & Linder 2015). Several phenomena can hinder species delimitation: phylogenetic/phenotypic mismatches (Articus et al 2002, Mark et al 2016, Pino-Bodas et al 2016), ‘intermediate’ specimens between generally accepted taxa (Seymour et al 2007), hybridization (Konrad et al 2002, Steinová et al 2013), an absence of delimited clades (Jakob & Blattner 2006, Lumley & Sperling 2011), or incomplete lineage sorting (Saag et al 2014, Leavitt et al 2016). Long-term reproductive isolation may produce structured, non-overlapping lineages, whereas an intraspecific phylogeny, as well as a recent or contemporary speciation event, may produce reticulated lineages (Abbott et al 2016).…”

Section: Introductionmentioning

confidence: 99%

“…In some cases, a lack of correlation between genotypes and phenotypes has led to the recognition of cryptic species within morphologically indistinguishable or scarcely indistinguishable morphospecies (Molina et al 2011a, b, Leavitt et al 2012a, b, Singh et al 2015, Boluda et al 2016, Del-Prado et al 2016), and so far, more than 80 cryptic lineages have been detected in Parmeliaceae (Crespo & Lumbsch 2010, Divakar et al 2010). However, in other cases there is a mismatch between lineages revealed by standard DNA-barcoding markers and long-accepted morphospecies (Articus et al 2002, Seymour et al 2007, Velmala et al 2014, Mark et al 2016, Kirika et al 2016a, b, McMullin et al 2016).…”

Section: Introductionmentioning

confidence: 99%

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Evaluating methodologies for species delimitation: the mismatch between phenotypes and genotypes in lichenized fungi (Bryoria sect. Implexae, Parmeliaceae)

et al. 2019

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In many lichen-forming fungi, molecular phylogenetic analyses lead to the discovery of cryptic species within traditional morphospecies. However, in some cases, molecular sequence data also questions the separation of phenotypically characterised species. Here we apply an integrative taxonomy approach – including morphological, chemical, molecular, and distributional characters – to re-assess species boundaries in a traditionally speciose group of hair lichens, Bryoria sect. Implexae. We sampled multilocus sequence and microsatellite data from 142 specimens from a broad intercontinental distribution. Molecular data included DNA sequences of the standard fungal markers ITS, IGS, GAPDH, two newly tested loci (FRBi15 and FRBi16), and SSR frequencies from 18 microsatellite markers. Datasets were analysed with Bayesian and maximum likelihood phylogenetic reconstruction, phenogram reconstruction, STRUCTURE Bayesian clustering, principal coordinate analysis, haplotype network, and several different species delimitation analyses (ABGD, PTP, GMYC, and DISSECT). Additionally, past population demography and divergence times are estimated. The different approaches to species recognition do not support the monophyly of the 11 currently accepted morphospecies, and rather suggest the reduction of these to four phylogenetic species. Moreover, three of these are relatively recent in origin and cryptic, including phenotypically and chemically variable specimens. Issues regarding the integration of an evolutionary perspective into taxonomic conclusions in species complexes, which have undergone recent diversification, are discussed. The four accepted species, all epitypified by sequenced material, are Bryoria fuscescens, B. glabra, B. kockiana, and B. pseudofuscescens. Ten species rank names are reduced to synonymy. In the absence of molecular data, they can be recorded as the B. fuscescens complex. Intraspecific phenotype plasticity and factors affecting the speciation of different morphospecies in this group of Bryoria are outlined.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Evaluating methodologies for species delimitation: the mismatch between phenotypes and genotypes in lichenized fungi (Bryoria sect. Implexae, Parmeliaceae)

et al. 2019

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“…The latter list includes representatives from a closely related species group in the genus Usnea (sect. Usnea; Mark et al 2016), where low genetic variation and possible rapid radiation of species have been characterized (Truong et al 2013;Kraichak et al 2015). However, four other Usnea specimens from this closely related group were also included in our study, where such nucleotide variation was not detected (#91-#92 U. barbata, #94 U. intermedia, and #97 U. substerilis).…”

Section: Reasons For Nucleotide Variationmentioning

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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“…(2018 : 178) use these results as argument for conserved ITS in Daldinia , although in the absence of evidence from other markers we find this is a circular conclusion; also, in other groups of Fungi , analogous variation has been interpreted as intraspecific, e.g. chemical variation in species of Usnea ( Mark et al . 2016 ).…”

Section: Responsesmentioning

confidence: 61%

Sequence-based nomenclature: a reply to Thines et al. and Zamora et al. and provisions for an amended proposal “from the floor” to allow DNA sequences as types of names

2018

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We reply to two recently published, multi-authored opinion papers by opponents of sequence-based nomenclature, namely Zamora et al. (IMA Fungus 9: 167–175,2018) and Thines et al. (IMA Fungus 9: 177–183, 2018). While we agree with some of the principal arguments brought forward by these authors, we address misconceptions and demonstrate that some of the presumed evidence presented in these papers has been wrongly interpreted. We disagree that allowing sequences as types would fundamentally alter the nature of types, since a similar nature of abstracted features as type is already allowed in the Code (Art. 40.5), namely an illustration. We also disagree that there is a high risk of introducing artifactual taxa, as this risk can be quantified at well below 5 %, considering the various types of high-throughput sequencing errors. Contrary to apparently widespread misconceptions, sequence-based nomenclature cannot be based on similarity-derived OTUs and their consensus sequences, but must be derived from rigorous, multiple alignment-based phylogenetic methods and quantitative, single-marker species recognition algorithms, using original sequence reads; it is therefore identical in its approach to single-marker studies based on physical types, an approach allowed by the Code. We recognize the limitations of the ITS as a single fungal barcoding marker, but point out that these result in a conservative approach, with “false negatives” surpassing “false positives”; a desirable feature of sequence-based nomenclature. Sequence-based nomenclature does not aim at accurately resolving species, but at naming sequences that represent unknown fungal lineages so that these can serve as a means of communication, so ending the untenable situation of an exponentially growing number of unlabeled fungal sequences that fill online repositories. The risks are outweighed by the gains obtained by a reference library of named sequences spanning the full array of fungal diversity. Finally, we elaborate provisions in addition to our original proposal to amend the Code that would take care of the issues brought forward by opponents to this approach. In particular, taking up the idea of the Candidatus status of invalid, provisional names in prokaryote nomenclature, we propose a compromise that would allow valid publication of voucherless, sequence-based names in a consistent manner, but with the obligate designation as “nom. seq.” (nomen sequentiae). Such names would not have priority over specimen- or culture-based names unless either epitypified with a physical type or adopted for protection on the recommendation of a committee of the International Commission on the Taxonomy of Fungi following evaluation based on strict quality control of the underlying studies based on established rules or recommendations.

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Evaluation of traditionally circumscribed species in the lichen-forming genus Usnea, section Usnea (Parmeliaceae, Ascomycota) using a six-locus dataset

Cited by 39 publications

References 93 publications

Evaluating methodologies for species delimitation: the mismatch between phenotypes and genotypes in lichenized fungi (Bryoria sect. Implexae, Parmeliaceae)

Evaluating methodologies for species delimitation: the mismatch between phenotypes and genotypes in lichenized fungi (Bryoria sect. Implexae, Parmeliaceae)

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

Sequence-based nomenclature: a reply to Thines et al. and Zamora et al. and provisions for an amended proposal “from the floor” to allow DNA sequences as types of names

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