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

Abstract

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.

Twelve New Species Reveal Cryptic Diversification in Foliicolous Lichens of Strigula s.lat. (Strigulales, Ascomycota)

“…In the hitherto studied species, based on the aforementioned and the present study, the factor of hidden diversity in presumably known species ranges from twofold (e.g., Racoplaca maculata, R. melanobapha; Strigula microspora, S. nitidula) to threefold (e.g., Puiggariella nemathora, R. subtilissima, Strigula concreta) to up to fivefold (S. antillarum, S. smaragdula), for a weighted mean of a threefold increase. These findings align well with Lücking et al [36], who also showed multiplication factors between two and five in studied species complexes. Given that the data on Strigulaceae are mostly from Southeast Asia, even higher multiplication factors (a weighted mean of up to five) could be assumed when expanding such studies to tropical America and Africa.…”

“…Given that R. maculatoides has distinctly shorter (15-25 µm vs. 22.5-27.5 µm long) ascospores and macroconidia with shorter appendages (10-18 µm vs. 17-35 µm), we consider R. macrospora a recently emerging, yet distinct species. Species evolving from paraphyletic residuals are now broadly accepted [36], but an artifactually paraphyletic topology could also result from the most closely related species not having been sequenced yet. Another possible explanation is that R. maculatoides itself represents a species complex.…”

“…However, phylogenetically recognised species may also be morphologically cryptic, for example, in complexes such as Caloplaca crenulatella [28], Cladia aggregata [29], Graphis scripta [30], Melanelixia glabra [31], Parmelina tiliacea [32], Porina epiphylla and P. rufula [33], Punctelia rudecta [34], and Rhizoplaca melanophthalma [35]. Here, we follow Lücking et al [36] in considering species cryptic if there are no clearly discernable phenotypic diagnostic characters and near-cryptic if such characters are subtle and require careful analysis to be properly assessed.…”

Infraspecific variation of some brown Parmeliae (in Poland) – a comparison of ITS rDNA and non-molecular characters

“…Such careful and versatile analysis of distinct phylogenetic lineages may lead to recognising some previously-overlooked characteristics ( Kroken and Taylor 2001 ; del Prado et al 2007 ; Frolov et al 2016 ; Leavitt et al 2016 ; Szczepańska et al 2020 ). In the recent review paper, Lücking et al (2021) proposed a detailed protocol for consistent taxonomy of lichen-forming fungi. The integrative taxonomy employing phylogeny, reproductive biology and phenotype should be used to delimit species ( Lücking et al 2020 ).…”

“…They also noted that description of a new species, based on single-locus phylogenetic analyses, could only be done in exceptional cases. The errors caused by contaminant sequences, laboratory mix-ups and chimeric sequences should be avoided for proper establishment of novel taxa, based on molecular data only ( Lücking et al 2021 ). Therefore, it is crucial to employ unlinked loci from different parts of the genome, even though the ITS rDNA marker is widely used in DNA barcoding of fungal taxa.…”