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Phylogenetic relationships and species concepts in Parmelia s. str. (Parmeliaceae) inferred from nuclear ITS rDNA and -tubulin sequences
Abstract
The phylogenetic relationships of 16 species of Parmelia s. str. are presented based on sequences of nuITS rDNA from 56 specimens, and P-tubulin gene sequences from 29 collections. Parmelia serrana sp. nov. a Mediterranean species morphologically very close to P. saxatilis is described. Parmelia ernstiae is the sister-group to P. saxatilis s. str., and a further undescribed North American species of the P. saxatilis complex may require recognition. The isidiate P. squarrosa is closely allied to the sorediate P. sulcata, which is paraphyletic. Japanese samples of P. cochleata form a monophyletic group but too few collections of these were studied to reach firm conclusions regarding their relationships. An epitype is selected for the lectotype of Lichen saxatilis to unequivocally fix the application of that epithet.
... 40 species (Divakar et al. 2015;Crespo et al. 2020) of foliose lichen species with linear, simple to branched pseudocyphellae on the upper cortex, atranorin in the upper cortex, frequent production of vegetative propagules, and simple to branched rhizines on the lower surface of thalli (Hale 1987). Knowledge of individual taxa of Parmelia varies, and there are well-studied species requiring further research (Molina et al. 2004(Molina et al. , 2017Thell et al. 2008). These differences are related to species distributions, with common members of the genus more often the subject of various studies (e.g. ...
... These differences are related to species distributions, with common members of the genus more often the subject of various studies (e.g. Molina et al. 2004Molina et al. , 2011aMolina et al. , b, 2017Ossowska et al. 2018;Corsie et al. 2019;Tsurykau et al. 2019;Mark et al. 2020;Castellani et al. 2021;Moya et al. 2021). Such an example is P. sulcata Taylor, which was previously thought to be one of the most common members of the genus (Hale 1987;Hawksworth et al. 2008;Thell et al. 2011). ...
... In recent years many new Parmelia species have been described, mostly based on DNA sequences, however very often these species have well-defined diagnostic characters, which facilitate their identification even without molecular studies (e.g. Feurer & Thell 2002;Molina et al. 2004Molina et al. , 2011aMolina et al. , b, 2017Crespo et al. 2020). This is particularly important in the context of determining their geographical distributions. ...
The first record of Parmelia asiatica from North America is presented. The species differs from other sorediate Parmelia taxa in having narrow, sublinear lobes with circular or semicircular, terminal or marginal soralia. New records and earlier data together suggest that P. asiatica may be a more common taxon in the Northern Hemisphere than previously reported. Additionally, the first record of P. barrenoae from Canada and the central states of the USA is presented. Notes on similar sorediate species of the genus Parmelia are provided with information about secondary chemistry checked by thin-layer chromatography methods in solvents A and C.
... The application of phylogenetic analysis based on molecular (DNA) characters to delimit species allows us to determine a posteriori which types of phenotypic characters are good predictors of phylogenetic species and demonstrate how these characters evolve in this family and in lichenized fungi in general. These molecular data have led to the recognition of morphologically cryptic species, such as Parmelia serrana (Molina et al. 2004), P. barrenoae (Divakar et al. 2005a), P. encryptata (Molina et al. 2011a) and Melanelixia californica , and conversely also to the union of species traditionally regarded as morphologically distinct (see e.g. Boluda et al. 2019). ...
... Previous studies have shown that phylogenetic analyses alone are insufficient to explain phylogenetic relationships within Parmeliaceae. For example, based only on maximum parsimony and Bayesian analyses the sorediate P. sulcata was shown to belong to the same clade as the isidiate P. squarrosa (Molina et al. 2004), leaving the authors unable to reach any conclusion regarding species boundaries. Similarly, phylogenetic analyses were insufficient to resolve genetic variability among Parmelia saxatilis specimens; whereas samples from distant geographical regions formed a monophyletic group, samples from neighbouring localities were separated (Crespo et al. 2002;Molina et al. 2011bMolina et al. , 2017. ...
... Results indicated that all samples morphologically referred to U. antarctica and U. kappenii form a monophyletic group and they proposed placing U. kappenii into synonymy with U. antarctica (Ott et al. 2004). In Parmelia, Molina et al. (2011b) rejected the previous hypothesis that P. sulcata and P. squarrosa form a monophyletic group (Molina et al. 2004) and based on phylogenetic analyses and species delimitation approaches confirmed that P. sulcata is not conspecific with P. squarrosa. In addition, P. squarrosa is a reproductively isolated lineage and genetic distances clearly separate this from other Parmelia species . ...
The widespread species Parmotrema crinitum (Ach.) M. Choisy and Parmotrema perlatum (Huds.) M. Choisy are mainly distinguished by their reproductive strategies. While P. crinitum propagates by isidia, P. perlatum produces soredia. In this study, we aim to evaluate the phylogenetic relationship between both species and to critically examine their species boundaries. To this purpose, 46 samples belonging to P. crinitum and P. perlatum were used in our analysis, including 22 for which we studied the morphology and chemistry, before extracting their DNA. We used 35 sequences of the internal transcribed spacer region of nuclear ribosomal DNA (ITS) of Parmotrema perlatum from Europe and Africa (20 of which were newly generated), and 11 of Parmotrema crinitum from Europe, North America and North Africa (two newly generated). Additionally, 28 sequences of several species from Parmotrema were included in the ITS dataset. The ITS data matrix was analyzed using different approaches, such as traditional phylogeny (maximum likelihood and Bayesian analyses), genetic distances, automatic barcode gap discovery (ABGD) and the coalescent-based method poisson tree processes (PTP), in order to test congruence among results. Our results indicate that all samples referred to P. crinitum and P. perlatum nested in a well-supported monophyletic clade, but phylogenetic relationships among them remain unresolved. Delimitations inferred from PTP, ABGD and genetic distance analyses were comparable and suggested that P. crinitum and P. perlatum belong to the same lineage. Interestingly, two samples of P. perlatum separate in a different monophyletic clade, which is supported as a different lineage by all the analyses.
... The application of phylogenetic analysis based on molecular (DNA) characters to delimit species allows us to determine a posteriori which types of phenotypic characters are good predictors of phylogenetic species and demonstrate how these characters evolve in this family and in lichenized fungi in general. These molecular data have led to the recognition of morphologically cryptic species, such as Parmelia serrana (Molina et al. 2004), P. barrenoae (Divakar et al. 2005a), P. encryptata (Molina et al. 2011a) and Melanelixia californica , and conversely also to the union of species traditionally regarded as morphologically distinct (see e.g. Boluda et al. 2019). ...
... Previous studies have shown that phylogenetic analyses alone are insufficient to explain phylogenetic relationships within Parmeliaceae. For example, based only on maximum parsimony and Bayesian analyses the sorediate P. sulcata was shown to belong to the same clade as the isidiate P. squarrosa (Molina et al. 2004), leaving the authors unable to reach any conclusion regarding species boundaries. Similarly, phylogenetic analyses were insufficient to resolve genetic variability among Parmelia saxatilis specimens; whereas samples from distant geographical regions formed a monophyletic group, samples from neighbouring localities were separated (Crespo et al. 2002;Molina et al. 2011bMolina et al. , 2017. ...
... Results indicated that all samples morphologically referred to U. antarctica and U. kappenii form a monophyletic group and they proposed placing U. kappenii into synonymy with U. antarctica (Ott et al. 2004). In Parmelia, Molina et al. (2011b) rejected the previous hypothesis that P. sulcata and P. squarrosa form a monophyletic group (Molina et al. 2004) and based on phylogenetic analyses and species delimitation approaches confirmed that P. sulcata is not conspecific with P. squarrosa. In addition, P. squarrosa is a reproductively isolated lineage and genetic distances clearly separate this from other Parmelia species . ...
The widespread species Parmotrema crinitum (Ach.) M. Choisy and Parmotrema perlatum (Huds.) M. Choisy are mainly distinguished by their reproductive strategies. While P. crinitum propagates by isidia, P. perlatum produces soredia. In this study, we aim to evaluate the phylogenetic relationship between both species and to critically examine their species boundaries. To this purpose, 46 samples belonging to P. crinitum and P. perlatum were used in our analysis, including 22 for which we studied the morphology and chemistry, before extracting their DNA. We used 35 sequences of the internal transcribed spacer region of nuclear ribosomal DNA (ITS) of Parmotrema perlatum from Europe and Africa (20 of which were newly generated), and 11 of Parmotrema crinitum from Europe, North America and North Africa (two newly generated). Additionally, 28 sequences of several species from Parmotrema were included in the ITS dataset. The ITS data matrix was analyzed using different approaches, such as traditional phylogeny (maximum likelihood and Bayesian analyses), genetic distances, automatic barcode gap discovery (ABGD) and the coalescent-based method poisson tree processes (PTP), in order to test congruence among results. Our results indicate that all samples referred to P. crinitum and P. perlatum nested in a well-supported monophyletic clade, but phylogenetic relationships among them remain unresolved. Delimitations inferred from PTP, ABGD and genetic distance analyses were comparable and suggested that P. crinitum and P. perlatum belong to the same lineage. Interestingly, two samples of P. perlatum separate in a different monophyletic clade, which is supported as a different lineage by all the analyses.
... Castellani et al., 2021;Corsie et al., 2019;Haugan & Timdal, 2019;Ossowska et al., 2018Ossowska et al., , 2019Tsurykau et al., 2019). For example, the presence of pruina has been reported as a diagnostic feature in isidiate Parmelia species Molina et al., 2004), but it has no diagnostic value as sampled studies show that individual specimens can vary in the pruinosity degree (Corsie et al., 2019;Ossowska et al., 2018). In the group of Parmelia species without vegetative propagule, the presence of lobaric acid was reported as a diagnostic (Hale, 1987;ell et al., 2008), however, it has been shown that this secondary metabolite can be present or absent in different specimens of the same species (Ossowska et al., 2019). ...
... Parmelia ernstiae was previously separated from other isidiate species mainly on the basis of the presence of pruina, placement of isidia and the production of fatty acids and lobaric acid Molina et al., 2004;Ossowska, 2021;Ossowska et al., 2018 correct differentiation, therefore, requires the use of a combination of molecular and phenotypic characters. Variation in morphological characters was also observed in specimens from Madeira. ...
The first records of Parmelia ernstiae from Madeira, as well as the new localities of P. encryptata from Poland and P. sulcata from Chile, are presented. All records are confirmed by molecular data, BLAST search, and haplotype network analysis of the nucITS rDNA sequences. The discussion on the morphology and secondary chemistry of all three species is provided with notes on their distribution and similar taxa. Parmelia encryptata is a rarely reported cryptic species that is morphologically indistinguishable from P. sulcata , and its identification requires molecular data. New localities of P. encryptata from northern Poland suggest that the taxon may be widespread in the country and not confined to large forests but also present in open areas on free-standing trees. Moreover, a new nucITS rDNA haplotype of the species is reported. Parmelia ernstiae is a near-cryptic species, morphologically and chemically very similar to P. saxatilis and P. serrana . Two specimens of the species from Madeira have sublinear lobes with marginal and laminal isidia, unlike most specimens of P. ernstiae, having short, broad lobes with laminal isidia, and thus are morphologically closer to P. saxatilis in lobe shape and to P. serrana in placement of isidia. However, the BLAST search and haplotype analysis of nucITS rDNA sequences placed these specimens in P. ernstiae . Parmelia sulcata , a common species in the Northern Hemisphere, is rare elsewhere, and only two records confirmed by molecular data were known from South America. The nucITS rDNA haplotype of two new and two previous records of the species represent the most common haplotype of the species known from the Northern Hemisphere.
... This species has been the subject of much recent taxonomic work, including splitting off the segregate species Parmelia ernstiae, P. serrana, P. mayi and P. rojoi (Feuerer and Thell 2002, Molina et al. 2004, Molina et al. 2011, Crespo et al. 2020, and investigations into the diversity in the genus (Divakar et al. 2016). None of these segregate species can be diagnosed confidently using morphology only (Corsie et al. 2019). ...
... Parmelia saxatilis is one of the most common lichens in temperate and boreal habitats, and occurs in a wide range of settings (Molina et al. 2004). Even with the recently-recognized segregate species, recent molecular work has shown that P. saxatilis in the strict sense is found from pole to pole (Crespo et al. 2002(Crespo et al. , 2020. ...
... Over the last two decades' molecular investigations focusing on PSAXgp and PSULgp from the Iberian Peninsula have been carried out. These studies allowed us to described Parmelia serrana (Molina et al., 2004) and Parmelia encryptata (Molina et al., 2011a). Also, Divakar et al. (2005) detected additional Parmelia barrenoae species in the PSULgp from the Iberian Peninsula, North America and Africa. ...
The worldwide, ecologically relevant lichen-forming genus Parmelia currently includes 41 accepted species, of which the Parmelia sulcata group (PSULgp) and the Parmelia saxatilis group (PSAXgp) have received considerable attention over recent decades; however, phycobiont diversity is poorly known in Parmelia s. lat. Here, we studied the diversity of Trebouxia microalgae associated with 159 thalli collected from 30 locations, including nine Parmelia spp.: P. barrenoae, P. encryptata, P. ernstiae, P. mayi, P. omphalodes, P. saxatilis, P. serrana, P. submontana, and P. sulcata. The mycobionts were studied by carrying out phylogenetic analyses of the nrITS. Microalgae genetic diversity was examined by using both nrITS and LSU rDNA markers. To evaluate putative species boundaries, three DNA species delimitation analyses were performed on Trebouxia and Parmelia. All analyses clustered the mycobionts into two main groups: PSULgp and PSAXgp. Species delimitation identified 13 fungal and 15 algal species-level lineages. To identify patterns in specificity and selectivity, the diversity and abundance of the phycobionts were identified for each Parmelia species. High specificity of each Parmelia group for a given Trebouxia clade was observed; PSULgp associated only with clade I and PSAXgp with clade S. However, the degree of specificity is different within each group, since the PSAXgp mycobionts were less specific and associated with 12 Trebouxia spp., meanwhile those of PSULgp interacted only with three Trebouxia spp. Variation-partitioning analyses were conducted to detect the relative contributions of climate, geography, and symbiotic partner to phycobiont and mycobiont distribution patterns. Both analyses explained unexpectedly high portions of variability (99 and 98%) and revealed strong correlations between the fungal and algal diversity. Network analysis discriminated seven ecological clusters. Even though climatic conditions explained the largest proportion of the variation among these clusters, they seemed to show indifference relative to climatic parameters. However, the cluster formed by P. saxatilis A/P. saxatilis B/Trebouxia sp. 2/Trebouxia sp. S02/Trebouxia sp. 3A was identified to prefer cold-temperate as well as humid summer environments.
... Integrative taxonomic studies based on molecular and morphological datasets could serve to re-evaluate earlier classifications and provide more accurate species-level delimitations [11]. Such studies have been performed in many different lichen groups, including Cora [12], Leptogium [13], Lobariella [14], Parmelia [15][16][17], Parmelina [18], Peltigera [19], amplified through polymerase chain reaction (PCR). The nuclear ribosomal RNA gene region, including the internal transcribed spacer (ITS), was amplified using the primer pair ITS5 and ITS4 [53]. ...
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.
... In Europe and adjacent areas, 13 species of Parmelia Ach. have been confirmed based on morphological, chemical and molecular methods (e.g. Feuerer & Thell, 2002;Molina et al., 2004Molina et al., , 2011Divakar et al., 2005;Hawksworth et al., 2008Hawksworth et al., , 2011Thell et al., 2008Thell et al., , 2017Ossowska et al., 2018Ossowska et al., , 2019Corsie et al., 2019;Crespo et al., 2020). The revision of material of two species, Parmelia barrenoae Divakar et al. and P. pinnatifida Kurok., yielded that they have never been reported from some countries in Eurasia, what is supplemented in this paper. ...
The first records of Parmelia barrenoae from Hungary, Slovakia and Sweden and P. pinnatifida from Denmark, Estonia and Turkey are presented.
... Out groups Platismatia glauca, Parmelia laevior and P. signifera were used. These out groups were previously described by Molina et al., (2004). Details of the samples and the GenBank accession numbers are listed in Table 1. ...
Parmelia barrenoae is reported from Turkey and Asia for the first time. Comments on its habitats, substrata, distributional data and macrophoto are provided. In addition, a phylogenetic tree was constructed by comparing the sequence data of the ITS region of closely related species.
Lichens in the genus Platismatia are common, widespread and were some of the first to be studied by Western taxonomists. However, few molecular phylogenetic studies of Platismatia have been published to date. We present an expanded phylogeny of Platismatia inferred from 60 newly generated ITS sequences and 28 existing publicly available sequences. The new phylogeny confirms the delimitation of P. wheeleri as monophyletic and distinct from the widespread P. glauca, the latter of which was recovered as two separate, highly supported clades, that do not appear to differ in phenotype or biogeography. The western North American endemics P. herrei and P. stenophylla were not recovered as reciprocally monophyletic and may be an example of recent speciation similar to that also hypothesized for Alectoria in the same region. Ancestral state reconstructions of reproductive modes (dominant asexual vs. sexual reproduction; asexual propagule type) suggest that sexual species like P. tuckermanii can evolve from primarily asexual ancestors. Evaluation of species distributions suggests that reproductive mode may be related to range size. These data suggest that Platismatia could serve as a model for future studies on reproductive mode, biogeography and speciation in lichens.
Letharia, a genus of lichenized fungi described as a pair of sympatric species, one making abundant sexual structures and the other making few, was investigated as a model system in which to recognize species boundaries. Gene genealogies of 6 and 12 loci were used to estimate the evolutionary history of Letharia, based on the principles of lineage sorting of alleles in divergent lineages after genetic isolation. Instead of a species pair consisting of a putative clonal species derived from a progenitor sexual species, Letharia comprises at least six phylogenetic species. Judging by the presence of perennial apothecia and clonal reproductive structures, one species is exclusively sexual, three species are sexual and isidiate, and two species are sorediate and rarely sexual. Not all of these species would have been detected with a single gene genealogy, demonstrating the need for multiple independent loci in phylogenetic analysis to recognize recent speciation events. The results are concordant with aspects of both biological and phylogenetic species recognition. However, only phylogenetic species recognition can be applied to fungi like Letharia species that are difficult to cultivate and mate in the lab.
ITS, group I intron and partial β-tubulin sequences were used to infer phylogenies of a putative lichen species pair: Physcia aipolia (sexual) and P. caesia (asexual). A jackknife tree obtained from the β-tubulin sequences produced a well-resolved tree, whereas the resolution in the group I intron and in the ITS tree was lower due to homoplasy. The results obtained from the combined group I intron, ITS and β-tubulin data indicate that neither P. caesia nor P. aipolia are monophyletic and suggest that the two taxa are conspecific. Although the combined DNA data suggest the existence of several genetically isolated lineages in the P. aipolia/caesia group, the different lineages were not correlated with any morphological characters. Within one of the lineages, the incongruent placement of one P. aipolia specimen may indicate sexual recombination. A contradictory placement of one P. caesia specimen in different trees suggests that the usually asexual P. caesia is occasionally capable of sexual reproduction. The β-tubulin gene was found to contain enough variation for inferring relationships at the species level. Most of the informative characters were found from intron sequences and third codon positions in the exon regions. All the nucleotide substitutions were synonymous.
Wide chemical variation was shown by Parmelia omphalodes, especially when minor and accessory phenolic compounds were included. -from Author
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
The lichens Usnea florida and U. subfloridana have since long been recognised as distinct species. They show many similarities in morphology, but have different reproductive strategies. Usnea florida is always provided with many apothecia and produces no specialised asexual propagules. Usnea subfloridana has soralia, isidiomorphs and occasionally apothecia. Phylogenetic analyses based on continuous sequences of the ITS and LSU regions of the nuclear ribosomal DNA and the gene coding for β-tubulin, show that specimens of the two species form one monophyletic group of intermixed specimens, and not two groups corresponding to morphology, which would have been expected if two species were at hand. The ‘species pair’ concept in lichenology is discussed. Other Usnea species included in the study are: U. articulata, U. barbata, U. ceratina, U. filipendula, U. hirta, U. rigida and U. wasmuthii.
