Three new genera of the Ramalinaceae (lichen-forming Ascomycota) and the phenomenon of presence of ‘extraneous mycobiont DNA’ in lichen associations

Kondratyuk, S. Y.; Lőkös, László; Farkas, Edit; Jang, S.-H.; Liu, Dong; Halda, Josef P.; Persson, Per-Erik; Hansson, Mats; Kärnefelt, Ingvar; Thell, Arne; Hur, Jae‐Seoun

doi:10.1556/034.61.2019.3-4.5

Cited by 11 publications

(13 citation statements)

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“…If there is evidence for a mixup, the safest way to obtain reliable data is repeating the PCR and sequencing steps, rather than trying to make sense of the existing data. Kondratyuk et al (2019) recently reported "extraneous mycobiont DNA", i.e., unexpected sequences corresponding to a particular lichen mycobiont presumably detected in the thallus of other lichens, e.g., of Biatora longispora (Ramalinaceae) in the thallus of Agonimia pacifica (Verrucariaceae). It is unclear whether these are the result of a laboratory mixup or of natural contamination of the underlying lichen thalli.…”

Section: A Quick Primer On Common Molecular Complicationsmentioning

confidence: 99%

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

2021

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

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Section: A Quick Primer On Common Molecular Complicationsmentioning

confidence: 99%

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

2021

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“…These results also appear to be congruent with Reese Naesborg et al . (2007), as well as Kondratyuk et al . (2019); in the latter the relationships between various genus-level clades were also weakly supported.…”

Section: Taxonomymentioning

confidence: 80%

“…However, the species was not included in recent molecular phylogenetic studies of generic delimitation within the broader Ramalinaceae ( e.g ., Kistenich et al 2018). It was included in the phylogenetic studies of Ramalinaceae by Kondratyuk et al . (2019) and transferred to the genus Coppinsidea S.Y.Kondr., E.Farkas and L.L}okös., but much of the underlying data for that study remains unpublished and the analyses were not fully described.…”

Section: Taxonomymentioning

confidence: 99%

Bilimbia fuscoviridis (≡ Bacidia fuscoviridis), another overlooked sorediate crustose lichen widely distributed in temperate eastern North America

Curtis,

Waters,

Lendemer

2023

The Journal of the Torrey Botanical Society

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“…Taxonomic notes: The genus Coppinsidea S. Y. Kondr., Farkas et L. Lőkös as monophyletic branch of the Ramalinaceae proposed to include nine species (Kondratyuk et al 2019b). Coppinsidea vernadskiensis is supposedly the next member of the same branch, while our efforts to get molecular data on this species were so far still unsuccessful.…”

Section: Descriptions Of Taxamentioning

confidence: 99%

New and Noteworthy Lichen-Forming and Lichenicolous Fungi, 12

Kondratyuk

Lőkös

Kärnefelt

et al. 2022

ABot

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Seven species new to science are described, illustrated and compared with closely related taxa. Of them, one species, i.e.: Coppinsidea vernadskiensis S. Y. Kondr., T. O. Kondratiuk et I. Yu. Parnikoza is from the Argentine Islands, Western Maritime Antarctic Peninsula, Jacke lixia hosseussii S. Y. Kondr., L. Lőkös et J.-S. Hur, from South America (Argentina and Uruguay), Loekoeslaszloa reducta Yoshik. Yamam. et S. Y. Kondr. from Eastern Asia (Japan), Orientophila viticola S. Y. Kondr., L. Lőkös et J.-S. Hur from Eastern Asia (South Korea), Ovealmbornia ovei S. Y. Kondr., L. Lőkös, I. Kärnefelt et A. Thell, and Xanthokarrooa elsiae S. Y. Kondr., L. Lőkös, I. Kärnefelt et A. Thell from Africa, as well as Oxneria imshaugii S. Y. Kondr. from North America. The new combination Jackelixia australis (for Xanthoria parietina var. australis Zahlbr.) is proposed. Jackelixia hosseussii is for the first time recorded as host for the lichenicolous fungus Arthonia anjutii S. Y. Kondr. et Alstrup. The latter species is for the first time recorded from South America. Intralichen christiansenii (D. Hawksw.) D. Hawksw. et Cole is for the first time recorded from South Korea.

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Three new genera of the Ramalinaceae (lichen-forming Ascomycota) and the phenomenon of presence of ‘extraneous mycobiont DNA’ in lichen associations

Cited by 11 publications

References 50 publications

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

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

Bilimbia fuscoviridis (≡ Bacidia fuscoviridis), another overlooked sorediate crustose lichen widely distributed in temperate eastern North America

New and Noteworthy Lichen-Forming and Lichenicolous Fungi, 12

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