An Integrative Approach for Understanding Diversity in the Punctelia rudecta Species Complex (Parmeliaceae, Ascomycota)

High species richness in the lichen genus Peltigera (Ascomycota, Lecanoromycetes): 34 species in the dolichorhizoid and scabrosoid clades of section Polydactylon, including 24 new to science

Applying molecular methods to fungi establishing lichenized associations with green algae or cyanobacteria has repeatedly revealed the existence of numerous phylogenetic taxa overlooked by classical taxonomic approaches. Here, we report taxonomical conclusions based on multiple species delimitation and validation analyses performed on an eight-locus dataset that includes world-wide representatives of the dolichorhizoid and scabrosoid clades in section Polydactylon of the genus Peltigera. Following the recommendations resulting from a consensus species delimitation approach and additional species validation analysis (BPP) performed in this study, we present a total of 25 species in the dolichorhizoid clade and nine in the scabrosoid clade, including respectively 18 and six species that are new to science and formally described. Additionally, one combination and three varieties (including two new to science) are proposed in the dolichorhizoid clade. The following 24 new species are described: P. appalachiensis, P. asiatica, P. borealis, P. borinquensis, P. chabanenkoae, P. clathrata, P. elixii, P. esslingeri, P. flabellae, P. gallowayi, P. hawaiiensis, P. holtanhartwigii, P. itatiaiae, P. hokkaidoensis, P. kukwae, P. massonii, P. mikado, P. nigriventris, P. orientalis, P. rangiferina, P. sipmanii, P. stanleyensis, P. vitikainenii and P. willdenowii; the following new varieties are introduced: P. kukwae var. phyllidiata and P. truculenta var. austroscabrosa; and the following new combination is introduced: P. hymenina var. dissecta. Each species from the dolichorhizoid and scabrosoid clades is morphologically and chemically described, illustrated, and characterised with ITS sequences. Identification keys are provided for the main biogeographic regions where species from the two clades occur. Morphological and chemical characters that are commonly used for species identification in the genus Peltigera cannot be applied to unambiguously recognise most molecularly circumscribed species, due to high variation of thalli formed by individuals within a fungal species, including the presence of distinct morphs in some cases, or low interspecific variation in others. The four commonly recognised morphospecies: P. dolichorhiza, P. neopolydactyla, P. pulverulenta and P. scabrosa in the dolichorhizoid and scabrosoid clades represent species complexes spread across multiple and often phylogenetically distantly related lineages. Geographic origin of specimens is often helpful for species recognition; however, ITS sequences are frequently required for a reliable identification. Citation: Magain N, Miadlikowska J, Goffinet B, et al. 2023. High species richness in the lichen genus Peltigera (Ascomycota, Lecanoromycetes): 34 species in the dolichorhizoid and scabrosoid clades of section Polydactylon, including 24 new to science. Persoonia 51: 1-88. doi: 10.3767/persoonia.2023.51.01.

Species assemblages of insular Caribbean Sticta (lichenized Ascomycota: Peltigerales) over ecological and evolutionary time scales

Phylogenetic approaches to macroevolution have provided unique insight into evolutionary relationships, ancestral ranges, and diversification patterns for many taxa. Similar frameworks have also been developed to assess how environmental and/or spatial variables shape species diversity and distribution patterns at different spatial/temporal scales, but studies implementing these are still scarce for many groups, including lichens. Here, we combine phylogeny-based ancestral range reconstruction and diversification analysis with community phylogenetics to reconstruct evolutionary origins and assess patterns of taxonomic and phylogenetic relatedness between island communities of the lichenized fungal genus Sticta in the Caribbean. Sampling was carried out in the Greater Antilles (Cuba, Jamaica, Dominican Republic, and Puerto Rico) and Lesser Antilles (Dominica, Guadeloupe, and Martinique). Data for six molecular loci were obtained for 64 candidate Caribbean species and used to perform both macroevolutionary phylogenetics, which also included worldwide taxa, and phylobetadiversity analyses, which emphasized island-level communities. Our work uncovered high levels of island endemism (∼59%) in Caribbean Sticta. We estimate initial colonization of the region occurred about 19 Mya from a South American ancestor. Reverse migration events by Caribbean lineages to South America were also inferred. We found no evidence for increased diversification rates associated with range expansion into the Caribbean. Taxonomic and phylogenetic turnover between island-level communities was most strongly correlated with environmental variation rather than with geographic distance. We observed less dissimilarity among communities from the Dominican Republic and Jamaica than between these islands and the Lesser Antilles/Puerto Rico. High levels of hidden diversity and endemism in Caribbean Sticta reaffirm that islands are crucial for the maintenance of global biodiversity of lichenized fungi. Altogether, our findings suggest that strong evolutionary links exist between Caribbean and South American biotas but at regional scales, species assemblages exhibit complex taxonomic and phylogenetic relationships that are determined by local environments and shared evolutionary histories.

Betula mcallisteri sp. nov. (sect. Acuminatae, Betulaceae), a new diploid species overlooked in the wild and in cultivation, and its relation to the widespread B. luminifera

Taxa are traditionally identified using morphological proxies for groups of evolutionarily isolated populations. These proxies are common characters deemed by taxonomists as significant. However, there is no general rule on which character or sets of characters are appropriate to circumscribe taxa, leading to discussions and uncertainty. Birch species are notoriously hard to identify due to strong morphological variability and factors such as hybridization and the existence of several ploidy levels. Here, we present evidence for an evolutionarily isolated line of birches from China that are not distinguishable by traditionally assumed taxon recognition proxies, such as fruit or leaf characters. We have discovered that some wild material in China and some cultivated in the Royal Botanic Gardens Edinburgh, formerly recognized as Betula luminifera, differ from other individuals by having a peeling bark and a lack of cambial fragrance. We use restriction site-associated DNA sequencing and flow cytometry to study the evolutionary status of the unidentified Betula samples to assess the extent of hybridization between the unidentified Betula samples and typical B. luminifera in natural populations. Molecular analyses show the unidentified Betula samples as a distinct lineage and reveal very little genetic admixture between the unidentified samples and B. luminifera. This may also be facilitated by the finding that B. luminifera is tetraploid, while the unidentified samples turned out to be diploid. We therefore conclude that the samples represent a yet unrecognized species, which is here described as Betula mcallisteri.

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

We employed a molecular phylogenetic approach using five markers (ITS, nuSSU, nuLSU, TEF1-α, and RPB2) to assess potential cryptic speciation in foliicolous members of Strigula s.lat. (Strigulaceae), including the recently segregated genera Phylloporis, Puiggariella, Raciborskiella, Racoplaca, and Serusiauxiella, from tropical areas in Asia, with selected materials from the Neotropics as reference. On the basis of combined molecular and phenotypic datasets, two new species of Racoplaca and 10 new species of Strigula s.str. are described: Racoplaca macrospora sp. nov., R. maculatoides sp. nov., Strigula guangdongensis sp. nov., S. intermedia sp. nov., S. laevis sp. nov., S. microcarpa sp. nov., S. pseudoantillarum sp. nov., S. pseudosubtilissima sp. nov., S. pycnoradians sp. nov., S. sinoconcreta sp. nov., S. stenoloba sp. nov., and S. subtilissimoides sp. nov. In addition, we propose the new combination Phylloporis palmae comb. nov. (≡ =Manaustrum palmae) and we validate the earlier combination Racoplaca melanobapha comb. nov. (≡ Verrucaria melanobapha; Strigula melanobapha). Our data clearly indicate a considerable degree of cryptic diversification in foliicolous representatives of Strigula s.lat., particularly in the presumably widespread taxa Strigula antillarum, S. concreta, S. nitidula, and S. smaragdula. Given that these phylogenetic revisions are thus far limited to few regions, we predict that our findings only represent the proverbial tip of the iceberg in this group of lichenized fungi.

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

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.

Additions to Italian Pleosporinae, including Italica heraclei sp. nov

Background

In the last few years, many microfungi—including plant-associated species—have been reported from various habitats and substrates in Italy. In this study of pleosporalean fungi, we researched terrestrial habitats in the Provinces of Arezzo (Tuscany region), Forlì-Cesena and Ravenna (Emilia-Romagna region) in Italy.

New information

Our research on Italian pleosporalean fungi resulted in the discovery of a new species, Italicaheraclei (Phaeosphaeriaceae). In addition, we present a new host record for Pseudoophiobolusmathieui (Phaeosphaeriaceae) and the second Italian record of Phomatodesnebulosa (Didymellaceae). Species boundaries were defined, based on morphological study and multi-locus phylogenetic reconstructions using Maximum Likelihood and Bayesian Inference analyses. Our findings expand the knowledge on host and distribution ranges of pleosporalean fungi in Italy.

Phylogenetic revision of South American Teloschistaceae (lichenized Ascomycota, Teloschistales) reveals three new genera and species

Members of the poorly investigated family Teloschistaceae in South America, mostly from Bolivia and Peru, were examined using molecular and morphological data here for the first time. In recent phylogenetic reclassifications of Teloschistaceae, South American representatives were poorly represented but shown to belong to subfamilies Teloschistoideae and Xanthorioideae. In this study, we expanded the sampling of South American taxa and investigated mainly the lobate, sublobate, and squamulose members of Caloplaca s.l., using morphological characters and a molecular phylogeny based on a combined three-locus data set (one mitochondrial and two nuclear loci). Building upon new phylogenies at the family and subfamily levels (Teloschistoideae), we propose here three new genera: Andina, Aridoplaca, and Cinnabaria, with the type species Andina citrinoides, Aridoplaca peltata, and Cinnabaria boliviana. We also propose to reduce Tarasginia to synonymy with Sirenophila and Tayloriellina to synonymy with Villophora and introduce three new combinations: Dufourea ottolangei, D. volkmarwirthii, and Villophora erythrosticta. Scutaria andina is reported as new to Bolivia. A critical revision of the subfamily Brownlielloideae confirmed recent findings that it is an artifactual taxon based on a "chimeric" data set, with the type genus being part of Teloschistoideae.

ASAP: assemble species by automatic partitioning

Here, we describe Assemble Species by Automatic Partitioning (ASAP), a new method to build species partitions from single locus sequence alignments (i.e., barcode data sets). ASAP is efficient enough to split data sets as large 10⁴ sequences into putative species in several minutes. Although grounded in evolutionary theory, ASAP is the implementation of a hierarchical clustering algorithm that only uses pairwise genetic distances, avoiding the computational burden of phylogenetic reconstruction. Importantly, ASAP proposes species partitions ranked by a new scoring system that uses no biological prior insight of intraspecific diversity. ASAP is a stand-alone program that can be used either through a graphical web-interface or that can be downloaded and compiled for local usage. We have assessed its power along with three others programs (ABGD, PTP and GMYC) on 10 real COI barcode data sets representing various degrees of challenge (from small and easy cases to large and complicated data sets). We also used Monte-Carlo simulations of a multispecies coalescent framework to assess the strengths and weaknesses of ASAP and the other programs. Through these analyses, we demonstrate that ASAP has the potential to become a major tool for taxonomists as it proposes rapidly in a full graphical exploratory interface relevant species hypothesis as a first step of the integrative taxonomy process.

Integrative taxonomy confirms three species of Coniocarpon (Arthoniaceae) in Norway

We have studied the highly oceanic genus Coniocarpon in Norway. Our aim has been to delimit species of Coniocarpon in Norway based on an integrative taxonomic approach. The material studied comprises 120 specimens of Coniocarpon, obtained through recent collecting efforts (2017 and 2018) or received from major fungaria in Denmark, Finland, Norway and Sweden, as well as from private collectors. We have assessed (1) species delimitations and relationships based on Bayesian and maximum likelihood phylogenetic analyses of three genetic markers (mtSSU, nucITS and RPB2), (2) morphology and anatomy using standard light microscopy, and (3) secondary lichen chemistry using high-performance thin-layer chromatography. The results show three genetically distinct lineages of Coniocarpon, representing C.cinnabarinum, C.fallax and C.cuspidans comb. nov. The latter was originally described as Arthoniacinnabarinaf.cuspidans and is herein raised to species level. All three species are supported by morphological, anatomical and chemical data.

Fungal species boundaries in the genomics era

Genomic data has opened new possibilities to understand how organisms change over time, and could enable the discovery of previously undescribed species. Although taxonomy used to be based on phenotypes, molecular data has frequently revealed that morphological traits are insufficient to describe biodiversity. Genomics holds the promise of revealing even more genetic discontinuities, but the parameters on how to describe species from genomic data remain unclear. Fungi have been a successful case in which the use of molecular markers has uncovered the existence of genetic boundaries where no crosses are possible. In this minireview, we highlight recent advances, propose a set of standards to use genomic sequences to uncover species boundaries, point out potential pitfalls, and present possible future research directions.

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

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.

Phylogenetic relationships of rock-inhabiting black fungi belonging to the widespread genera Lichenothelia and Saxomyces

Rock-inhabiting fungi (RIF) are adapted to thrive in oligotrophic environments and to survive under conditions of abiotic stress. Under these circumstances, they form biocoenoses with other tolerant organisms, such as lichens, or with less specific phototrophic consortia of aerial algae or cyanobacteria. RIF are phylogenetically diverse, and their plastic morphological characters hamper the straightforward species delimitation of many taxa. Here, we present a phylogenetic study of two RIF genera, Lichenothelia and Saxomyces. Representatives of both genera inhabit rather similar niches on rocks, but their phylogenetic relationships are unknown so far. The cosmopolitan genus Lichenothelia is recognized by characters of fertile ascomata and includes species with different life strategies. In contrast, Saxomyces species were described exclusively by mycelial characters found in cultured isolates from rock samples collected at high alpine elevations. Here, we use an extended taxon sampling of Dothideomycetes to study the phylogenetic relationships of both Lichenothelia and Saxomyces. We consider environmental samples, type species, and cultured isolates of both genera and demonstrate their paraphyly, as well as the occurrence of teleomorphs in Saxomyces. We applied three species delimitation methods to improve species recognition based on molecular data. We show the distinctiveness of the two main lineages of Lichenothelia (Lichenotheliales s. str.) and Saxomyces and discuss differences in species delimitation depending on molecular markers or methods. We revise the taxonomy of the two genera and describe three new taxa, Lichenothelia papilliformis, L. muriformis, and Saxomyces americanus, and the teleomorph of S. penninicus.

Sheep mitochondrial heteroplasmy arises from tandem motifs and unspecific PCR amplification

The mitochondrial DNA control region (D-loop) is a widely used molecular marker in evolutionary and phylogeographic research. However, the occurrence of heteroplasmy of the D-loop region within individuals has rarely been investigated. In this study, a total of 85 Chinese sheep were used to amplify a partial D-loop region, and 15 heteroplasmic animals (17.64%) were identified. A comparative analysis of the PCR amplification and cloning of the D-loop sequences from the heteroplasmic samples revealed most of the sequencing profile from the heteroplasmic regions started at the beginning of a 75-bp random repeat motif. In addition, a total of 22 nonsyngeneic sequences with a D-loop were found in 61 of the clones obtained from the 4 random heteroplasmic and 3 homozygote animals, and their genomic locations were compared for homology. In summary, the D-Loop sequencing profiles appear to be heteroplasmic and could arise from tandem repeat motifs and unspecific replication during PCR amplification; however, they are not likely due to the presence of multiple mitochondrial genomes within an individual.

Species diversity can be overestimated by a fixed empirical threshold: insights from DNA barcoding of the genus Cletus (Hemiptera: Coreidae) and the meta-analysis of COI data from previous phylogeographical studies

The use of genetic distances to identify species within the framework of DNA barcoding has to some extent improved the development of biodiversity studies. However, using a fixed empirical threshold to delimit species may lead to overestimating species diversity. In this study, we use a new data set of COI sequences for 366 specimens within the genus of Cletus as well as conduct an analysis on the same genetic data for collected morphologically defined species from previous phylogeographical studies, to test whether high intraspecific genetic divergences are common with the premises of comprehensive sampling. The results indicate C. graminis Hsiao & Cheng , is the same species with C. punctiger (Dallas, 1852) and should be synonymized and that the distributional record of C. pugnator (Fabricius, 1787) in China is correct. High intraspecific genetic differentiations (0%-4.35%) were found in C. punctiger. Furthermore, as to the mined data, the maximum intraspecific K2P distances of 186 species (48.44% of 384) exceed 3%, and 101 species (26.30%) can be divided into two or more clusters with a threshold of 3% in cluster analysis. If genetic distance is used to delimit species boundaries, the minimum interspecific K2P distance of the congeneric species should be considered rather than only using the fixed empirical value; otherwise, the species richness may be overestimated in some cases.