Low genetic differentiation between apotheciate Usnea florida and sorediate Usnea subfloridana (Parmeliaceae, Ascomycota) based on microsatellite data

Degtjarenko, Polina; Mark, Kristiina; Moisejevs, Rolands; Himelbrant, Dmitry E.; Stepanchikova, Irina S.; Tsurykau, Andrei; Randlane, Tiina; Scheidegger, Christoph

doi:10.1016/j.funbio.2020.07.007

Cited by 5 publications

(4 citation statements)

References 84 publications

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“…Molecular studies on numerous putative species pairs suggest that multiple (semi-)cryptic speciation, as exemplified by the genus Letharia, is the rule rather than the exception: in over 60 examples analyzed, nearly two third (61%) appear to be species complexes, consisting of various lineages reproducing either sexually, asexually, or both (Table 3). Besides Letharia, the best documented case among these is Usnea florida vs. U. subfloridana (Articus et al 2002;Mark et al 2016;Degtjarenko et al 2020;Lücking et al 2020b). In only 11 cases (18%), the separation of an apotheciate and a sorediate or isidiate species was supported, although there were mostly few available data.…”

Section: The Species Pair Concept and Dual Nomenclature In Lichenized Fungimentioning

confidence: 99%

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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: The Species Pair Concept and Dual Nomenclature In Lichenized Fungimentioning

confidence: 99%

“…For exact nomenclature and author citation, see Suppl. File S1 Table 3 (continued) not clearly resolve the two morphs (Degtjarenko et al 2020). The other challenge is the application of formal taxonomic classifications to phylogenetically defined lineages.…”

Section: The Species Pair Concept and Dual Nomenclature In Lichenized Fungimentioning

confidence: 99%

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

2021

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“…To study epiphyte communities and obtain complete species lists during inventories, various complementary methods are used, including surveying fallen twigs and branches (Sarmento Cabral et al, 2015;Gasparyan et al, 2018), using tree pruners (Degtjarenko et al, 2016(Degtjarenko et al, , 2020, and employing rope-based methods (Fanning et al, 2007;Boch et al, 2013;Kiebacher et al, 2016). Canopy crane access has permitted detailed characterization of epiphyte assemblages across forest strata, but these have been limited to only a few locations (Zotz, 2007;Petter et al, 2016) and gondolas can damage the upper or outer canopy.…”

Section: Modes Of Access and Experimental Designmentioning

confidence: 99%

Extending Our Scientific Reach in Arboreal Ecosystems for Research and Management

Cannon¹,

Borchetta²,

Anderson³

et al. 2021

Front. For. Glob. Change

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The arboreal ecosystem is vitally important to global and local biogeochemical processes, the maintenance of biodiversity in natural systems, and human health in urban environments. The ability to collect samples, observations, and data to conduct meaningful scientific research is similarly vital. The primary methods and modes of access remain limited and difficult. In an online survey, canopy researchers (n = 219) reported a range of challenges in obtaining adequate samples, including ∼10% who found it impossible to procure what they needed. Currently, these samples are collected using a combination of four primary methods: (1) sampling from the ground; (2) tree climbing; (3) constructing fixed infrastructure; and (4) using mobile aerial platforms, primarily rotorcraft drones. An important distinction between instantaneous and continuous sampling was identified, allowing more targeted engineering and development strategies. The combination of methods for sampling the arboreal ecosystem provides a range of possibilities and opportunities, particularly in the context of the rapid development of robotics and other engineering advances. In this study, we aim to identify the strategies that would provide the benefits to a broad range of scientists, arborists, and professional climbers and facilitate basic discovery and applied management. Priorities for advancing these efforts are (1) to expand participation, both geographically and professionally; (2) to define 2–3 common needs across the community; (3) to form and motivate focal teams of biologists, tree professionals, and engineers in the development of solutions to these needs; and (4) to establish multidisciplinary communication platforms to share information about innovations and opportunities for studying arboreal ecosystems.

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Section: Modes Of Access and Experimental Designmentioning

confidence: 99%

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Low genetic differentiation between apotheciate Usnea florida and sorediate Usnea subfloridana (Parmeliaceae, Ascomycota) based on microsatellite data

Cited by 5 publications

References 84 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

Extending Our Scientific Reach in Arboreal Ecosystems for Research and Management

Data_Sheet_1.PDF

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