ORIGINAL ARTICLE
 
KEYWORDS
ABSTRACT
We present an exhaustive analysis of the ITS barcoding marker in the genus Usnea s.lat., separated into Dolichousnea, Eumitria, and Usnea including the subgenus Neuropogon, analyzing 1,751 accessions. We found only a few low-quality accessions, whereas information on voucher specimens and accuracy and precision of identifications was of subpar quality for many accessions. We provide an updated voucher table, alignment and phylogenetic tree to facilitate DNA barcoding of Usnea, either locally or through curated databases such as UNITE. Taxonomic and geographic coverage was moderate: while Dolichousnea and subgenus Neuropogon were well-represented among ITS data, sampling for Eumitria and Usnea s.str. was sparse and biased towards certain lineages and geographic regions, such as Antarctica, Europe, and South America. North America, Africa, Asia and Oceania were undersampled. A peculiar situation arose with New Zealand, represented by a large amount of ITS accessions from across both major islands, but most of them left unidentified. The species pair Usnea antarctica vs. U. aurantiacoatra was the most sampled clade, including numerous ITS accessions from taxonomic and ecological studies. However, published analyses of highly resolved microsatellite and RADseq markers showed that ITS was not able to properly resolve the two species present in this complex. While lack of resolution appears to be an issue with ITS in recently evolving species complexes, we did not find evidence for gene duplication (paralogs) or hybridization for this marker. Comparison with other markers demonstrated that particularly IGS and RPB1 are useful to complement ITS-based phylogenies. Both IGS and RPB1 provided better backbone resolution and support than ITS; while IGS also showed better resolution and support at species level, RPB1 was less resolved and delineated for larger species complexes. The nuLSU was of limited use, providing neither resolution nor backbone support. The other three commonly employed protein-coding markers, TUB2, RPB2, and MCM7, showed variable evidence of possible gene duplication and paralog formation, particularly in the MCM7, and these markers should be used with care, especially in multimarker coalescence approaches. A substantial challenge was provided by difficult morphospecies that did not form coherent clades with ITS or other markers, suggesting various levels of cryptic speciation, the most notorious example being the U. cornuta complex. In these cases, the available data suggest that multimarker approaches using ITS, IGS and RPB1 help to assess distinct lineages. Overall, ITS was found to be a good first approximation to assess species delimitation and recognition in Usnea s.lat., as long as the data are carefully analyzed, and reference sequences are critically assessed and not taken at face value. In difficult groups, we recommend IGS as a secondary barcode marker, with the option to employ more resource-intensive approaches, such as RADseq, in species complexes involving so-called species pairs or other cases of disparate morphology not reflected in the ITS or IGS. Attempts should be made to close taxonomic and geographic gaps especially for the latter two markers, in particular in Eumitria and Usnea s.str. and in the highly diverse areas of North America and Central America, Africa, Asia, and Oceania.
 
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CITATIONS (9):
1.
Response to Clerc & Naciri (2021) Usnea dasopoga (Ach.) Nyl. and U. barbata (L.) F. H. Wigg. (Ascomycetes, Parmeliaceae) are two different species: a plea for reliable identifications in molecular studies
Tiina Randlane, Kristiina Mark
The Lichenologist
 
2.
A molecular re-evaluation of Parmelia encryptata with notes on its distribution
Emilia Ossowska, Beata Guzow-Krzemińska, Rafał Szymczyk, Martin Kukwa
The Lichenologist
 
3.
Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics
Robert Lücking, Steven Leavitt, David Hawksworth
Fungal Diversity
 
4.
Phylogenetic revision of the lichenized family Gomphillaceae (Ascomycota: Graphidales) suggests post-K–Pg boundary diversification and phylogenetic signal in asexual reproductive structures
Xavier-Leite Barreto, Silva da, André Aptroot, Bibiana Moncada, Robert Lücking, Goto Tomio
Molecular Phylogenetics and Evolution
 
5.
Policies Handbook on Using Molecular Collections
Mestier de, Daniel Mulcahy, David Harris, Nadja Korotkova, Sarah Long, Eva Häffner, Alan Paton, Edmund Schiller, Frederik Leliaert, Jacqueline Mackenzie-Dodds, Tim Fulcher, Gunilla Stahls, Rintelen von, María Martín, Robert Lücking, China Williams, Christopher Lyal, Anton Güntsch, Heléne Aronsson, Magalie Castelin, Anna Pielach, Peter Poczai, Yolanda Ruiz-León, Bastida Sanmartin, Marco Thines, Gabriele Droege
Research Ideas and Outcomes
 
6.
First record of Usnea stipitata (lichenized Ascomycota, Parmeliaceae) for the African lichenoflora
Ridha Mokni, Philippe Clerc
Herzogia
 
7.
Reference-Based RADseq Unravels the Evolutionary History of Polar Species in ‘the Crux Lichenologorum’ Genus Usnea (Parmeliaceae, Ascomycota)
Ana Otero, Alejandrina Barcenas-Peña, H. Lumbsch, Felix Grewe
Journal of Fungi
 
8.
Survey of Lichenized Fungi DNA Barcodes on King George Island (Antarctica): An Aid to Species Discovery
Torre La, Daniel Ramos, Mayra Mejía, Edgar Neyra, Edwin Loarte, Gisella Orjeda
Journal of Fungi
 
9.
Multi-locus phylogeny of Bryoria reveals recent diversification and unexpected diversity in section Divaricatae
Leena Myllys, Raquel Pino-Bodas, Saara Velmala, Li-Song Wang, Trevor Goward
The Lichenologist
 
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ISSN:2544-7459
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