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Majority-rule consensus tree with all compatible groups and with average branch lengths, based on a Bayesian posterior tree sample comprising 48,000 trees. A 4×(GTR+I+)+(SYM+I+) likelihood model with interpartition rate heterogeneity was used. Bayesian posterior probabilities are displayed at nodes (in %). The familial classification predicted by this tree is indicated in the right margin.
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Ancestral state reconstructions of morphological or ecological traits on molecular phylogenies are becoming increasingly frequent. They rely on constancy of character state change rates over trees, a correlation between neutral genetic change and phenotypic change, as well as on adequate likelihood models and (for Bayesian methods) prior distributi...
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... sample sizes ranged from several hundreds to tens of thousands for all parameters in all analyses, and arbitrary truncations of posterior distributions were not detected. A majority-rule consensus tree with all compat- ible groups, average branch lengths, and posterior proba- bilities of branches from the Bayesian posterior tree sam- ple (48,000 trees) is provided in Figure 2. In this figure, we also indicate a revised but tentative family classifica- tion that incorporates the newly obtained phylogenetic information by imposing the smallest possible change on the existing classification. ...
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... performed ancestral state reconstruction (Fig. 3, Table 2) of the eight nodes with 95% or better support that unite two or more families, as circumscribed in Fig. 2. In general, maximum parsimony as well as maximum like- lihood reconstructions with a zero likelihood decision threshold, followed by the SIMMAP approach, tend to provide rather "certain" answers in the sense that much of the posterior probability is focused on a single state. Maximum likelihood reconstructions with the decision ...
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... phylogenetic estimates are largely concordant with morphology, although at odds with current classification in some cases (compare Table 1 and the classification suggested in Fig. 2). We chose here an outgroup consisting of three members of Lecideaceae, belonging to the Lecideales in the Lecanoromycetidae ( Miadlikowska et al., 2006). The status of the branch unit- ing Helocarpon, Lecidea atrosanguinea, Lopadium, Halecania, and Catinaria is unclear. These taxa are most likely dis- tantly related and may or may not ...
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... of these taxa in the tree with suspicion, as they constitute two out of three cases in our study for which sequence data was only ob- tained from a single gene. A reasonable working delim- itation of the Lecanorales is the group of taxa united by the most basal ingroup branch receiving 100% posterior SYSTEMATIC BIOLOGY VOL. 57 probability (Fig. 2). A revised taxonomic classification of this order into families being supported (or at least not contradicted) by our phylogenetic estimate is indicated in Fig. 2. All deviations between our suggested classi- fication and the currently most widely used (Eriksson, 2006) represent cases where taxa have been assigned to their current ...
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... A reasonable working delim- itation of the Lecanorales is the group of taxa united by the most basal ingroup branch receiving 100% posterior SYSTEMATIC BIOLOGY VOL. 57 probability (Fig. 2). A revised taxonomic classification of this order into families being supported (or at least not contradicted) by our phylogenetic estimate is indicated in Fig. 2. All deviations between our suggested classi- fication and the currently most widely used (Eriksson, 2006) represent cases where taxa have been assigned to their current place in the system according to their as- cus type. Some families are homogeneous, some het- erogeneous with regard to ascus type. Above the level of family, ascus ...
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... Brigantiaea [Teloschistales: Brigantiaeaceae] has parietin in the apothecia, asci with a distinct K/I+ blue tholus, and paraphyses that are not enlarged at their apices. Ekman et al. (2008), Gilbert & Purvis (2009b), Lücking et al. (2017a), Miądlikowska et al. (2006). ...
Downloads can be obtained from the British Lichen Society website at https://www.britishlichensociety.org.uk/content/lgbi3
... Toninia, widely present in dry and arid regions, is a crucial part of desert lichen ecosystems (Timdal, 1991(Timdal, , 2002. Molecular genetic characteristics (Sun et al., 2019), the asci and paraphyses are the primary factors used in the present delimitation of the genus (Kistenich et al., 2018;Ekman 2001, Ekman et al., 2008. Toninia A. Massal is characterized by a crustose to squamulose and epruinose to densely pruinose thallus; lecideine, epruinose to densely pruinose apothecia; dark brown to colourless hypothecium; usually colourless, grey, green, or brown epihymenium and exciple that changes colour in K and N; clavate, Biatora-type, 8-spored asci; and elliptical to spindleshaped, colourless, 1-8-celled ascospores. ...
Toninia pakistanica sp. nov. is described from Darel Valley, Gilgit Baltistan, Pakistan. Its place within the genus Toninia A. Massal. was validated by a comparative morpho-anatomical investigation and ITS based molecular studies. The taxon is characterized by dark brown lobate squamules, epruinose to weakly pruinose with dark olive to black thallus, densely pruinose upper surface, more thicker epinecral layer 60 μm, 25-45 μm thick grey to blackish grey lower cortex and with the absence of apothecia and secondary metab-olites. Its positioning in a separate branch in the phylogenetic tree also makes it distinct from the other known species. Phylogenetic analysis based on ITS-nrDNA sequencing placed our species relative to Toninia cinereo-virens (Schaer.) A. Massal. Kiliasia nordlandica (Th. Fr.) Kistenich, Timdal, Bendiksby & S. Ekman is included and reported as new record to Pakistan.
... However, according to our observations, species such as L. elaeochroma or L. euphorea show an ascus type similar to the Bacidia-type reported here for Nimisora. Following Ekman et al. (2008), we do not recognize the Biatora-type since the presence of a darker layer surrounding the axial mass is a very variable character, even within species. Finally, Lecidella species often have atranorin as the major substance, usually accompanied by terpenoids and/or xanthones, whereas no TLC-detectable substance is known so far from Nimisora. ...
The new genus Nimisora Pérez-Ort., M. Svenss. & J. C. Zamora is introduced to accommodate a puzzling lecideoid epiphyte common in the central Iberian Peninsula. Nimisora is characterized by the following combination of characters: lecideoid apothecia, excipulum composed of sparingly branched radiating hyphae with narrow lumina, thick walls and swollen terminal cells, the presence of a brown K+ olivaceous green pigment in the epihymenium, an ascus tip similar to the Bacidia -type, and the presence of simple ellipsoid ascospores. Molecular analyses based on nrITS, nrLSU and mtSSU sequences unequivocally place the new genus within the Lecanoraceae ; however, its phylogenetic affinities with other genera of the family remain largely unresolved. Comparisons with the morphologically closest genera are provided. The single species of the genus, Nimisora iberica Pérez-Ort., Turégano, M. Svenss. & J. C. Zamora sp. nov., is also described as new to science.
... There have been relatively few studies on ancestral state reconstructions in fungi to determine character evolution [4,[51][52][53][54]. For more than two decades, character evolution has been highly contentious in lichen systematics [51]. ...
... There have been relatively few studies on ancestral state reconstructions in fungi to determine character evolution [4,[51][52][53][54]. For more than two decades, character evolution has been highly contentious in lichen systematics [51]. Ekman et al. [51] studied the evolution of the ascus in Lecanorales using ancestral state reconstruction. ...
... For more than two decades, character evolution has been highly contentious in lichen systematics [51]. Ekman et al. [51] studied the evolution of the ascus in Lecanorales using ancestral state reconstruction. Slippers et al. [4] performed ancestral state reconstructions for selected characters in Botryosphaeriales, such as ascospore colour, the presence or absence of ascospore septa, conidial colour, the presence or absence of conidial septa and presence or absence of a mucus sheath. ...
Botryosphaeriales (Dothideomycetes, Ascomycota) occur in a wide range of habitats as endo-phytes, saprobes, and pathogens. The order Botryosphaeriales has not been subjected to evaluation since 2019 by Phillips and co-authors using phylogenetic and evolutionary analyses. Subsequently, many studies introduced novel taxa into the order and revised several families separately. In addition , no ancestral character studies have been conducted for this order. Therefore, in this study, we re-evaluated the character evolution and taxonomic placements of Botryosphaeriales species based on ancestral character evolution, divergence time estimation, and phylogenetic relationships, including all the novel taxa that have been introduced so far. Maximum likelihood, maximum parsimony, and Bayesian inference analyses were conducted on a combined LSU and ITS sequence alignment. Ancestral state reconstruction was carried out for conidial colour, septation, and nutritional mode. Divergence times estimates revealed that Botryosphaeriales originated around 109 Mya in the early epoch of the Cretaceous period. All six families in Botryosphaeriales evolved in the late epoch of the Cretaceous period (66-100 Mya), during which Angiosperms also appeared, rapidly diversified and became dominant on land. Families of Botryosphaeriales diversified during the Paleogene and Neogene periods in the Cenozoic era. The order comprises the families Aplosporellaceae, Botryosphaeriaceae, Melanopsaceae, Phyllostictaceae, Planistromellaceae and Saccharataceae. Furthermore, current study assessed two hypotheses; the first one being "All Botryosphaeriales species originated as endophytes and then switched into saprobes when their hosts died or into pathogens when their hosts were under stress"; the second hypothesis states that "There is a link between the conidial colour and nutritional mode in botryosphaerialean taxa". Ancestral state reconstruction and nutritional mode analyses revealed a pathogenic/saprobic nutritional mode as the ancestral character. However, we could not provide strong evidence for the first hypothesis mainly due to the significantly low number of studies reporting the endophytic botryosphaerialean taxa. Results also showed that hyaline and aseptate conidia were ancestral characters in Botryosphaeriales and supported the relationship between conidial pigmentation and the pathogenicity of Botryosphaeriales species.
... Megalaria was initially placed in its own family, Megalariaceae (Hafellner 1984), which was expanded to include the monospecific Tasmidella Kantvilas, Hafellner & Elix (Kantvilas et al. 1999). However, molecular data have since demonstrated the placement of Megalaria in Ramalinaceae (Ekman 2001;Miadlikowska et al. 2006Miadlikowska et al. , 2014Ekman et al. 2008;Kistenich et al. 2018), while Tasmidella was excluded from this family (Kistenich et al. 2018). ...
Tropical regions harbor a substantial diversity of lichenized fungi, but face numerous threats to their persistence, often even before previously unknown species have been described and their evolutionary relationships have been elucidated. Megalaria (Ramalinaceae) is a lichen-forming genus of fungi that produces crustose thalli, and includes a number of lineages occupying tropical rain forests; however, taxonomic and phylogenetic work on this clade is limited. Here we leverage both morphological and sequence data to describe a new species from the tropics, M. pachaylenophila . This taxon forms a crustose thallus, lacks secondary metabolites, and occurs in mangrove forests of Thailand. We supplemented molecular data from this species with data from other species, including two genera related to and occasionally included in Megalaria , namely Catillochroma and Lopezaria . Our analyses revealed Catillochroma species form a monophyletic group embedded within Megalaria , and we therefore recognize this clade at the subgeneric level. Since we only included the type species of Lopezaria in this study, we refrain from proposing a taxonomic conclusion for that clade at the moment. Several taxonomic combinations are made to reflect phylogenetic evidence supporting the inclusion of these species in Megalaria .
... However, the specimen from which the sequences were obtained was actually a species of Micarea, M. oreina Kantvilas & Coppins (Kantvilas and Coppins 2019). Next, in a phylogeny including many different families, Ekman et al. (2008) recovered a specimen identified as Protomicarea limosa (Ach.) Hafellner on a highly supported branch together with Sphaerophorus globosus (Huds.) ...
... J.Steiner, Psora Hoffm.), the Ramalinaceae (Bacidia, Biatora, Bilimbia De Not., Lecania A.Massal. and Ramalina Ach.) and the Sphaerophoraceae (Miadlikowska et al. 2014;Wijayawardene et al. 2018). As BLAST-searches, and earlier phylogenies (Ekman et al. 2008;Ekman and Blaalid 2011) indicated that Gilbertaria could belong to the latter family, we included all genera considered to belong to the Sphaerophoraceae: Austropeltum Henssen, H. Döring & Kantvilas, Bunodophoron A.Massal., Calycidium Stirt., Leifidium Wedin, Neophyllis F.Wilson, and Sphaerophorus Pers. (Prieto et al. 2013; Wedin and D ö r i n g 1 99 9; W edin et a l . 2 000 ; Wedin 200 2; Wijayawardene et al. 2018). ...
Lecideoid lichen-forming fungi are a large, heterogeneous group that includes many species described during the nineteenth century that are of unclear taxonomic status. We revise such a group, the species of which have previously been treated under the much-misunderstood names Catillaria contristans or Toninia squalescens, and use a seven-locus phylogeny to determine its phylogenetic position. We found strong support for a previously unrecognized monophyletic lineage within the Sphaerophoraceae, comprising five phylogenetic species, and describe the new genus Gilbertaria to accommodate them. The new genus is characterized by a crustose growth form, 1-septate ascospores, thick ((1.5-)2-3(-4) μm wide) paraphyses and asci of the Biatora-type. We revise the nomenclature and give new delimitations and descriptions of the Northern Hemisphere species Gilbertaria contristans comb. nov., G. holomeloides comb. nov., G. squalescens comb. nov. and describe the new species G. astrapeana from the Falkland Islands.
... Our data support this prediction and demonstrate the effectiveness of combining AGR with rational mutagenesis to experimentally test this. That said, we fully acknowledge that there are documented limitations with AGR (Thornton 2004;Ekman et al. 2008) not least that the ancestral TRIF sequence presented here is an approximation. To this end, we report high confidence (mean posterior probability per codon ¼ 0.934) in our predicted ancestral sequence, as well as in the identity of the homologous sites under selection. ...
The TIR domain-containing adapter inducing IFN-β (TRIF) protein is an innate immune system protein that mediates the MyD88-independent toll-like receptor response pathway in mice and humans. Previously, we identified positive selection at seven distinct residues in mouse TRIF, as compared with human and other mammalian orthologs, thus predicting protein functional shift in mouse TRIF. We reconstructed TRIF for the most recent common ancestor of mouse and human, and mutated this at the seven sites to their extant mouse/human states. We over expressed these TRIF mutants in immortalized human and mouse cell lines and monitored TRIF-dependent cytokine production and gene expression induction. We show that optimal TRIF function in human and mouse is dependent on the identity of the positively selected sites. These data provide us with molecular data relating observed differences in response between mouse and human MyD88-independent signaling in the innate immune system with protein functional change.
... ex Tuck.) A. Schneid., B. rosella and B. rubella (Hoffm.) A. Massal. (James et al. 2006;Miadlikowska et al. 2006Miadlikowska et al. , 2014Reese Naesborg et al. 2007;Ekman et al. 2008;Kistenich et al. 2018). ...
To clarify deep relationships among species lineages within Bacidia s. str., and to investigate the robustness of the deeper branches, we combined data from three traditionally used RNA-coding genes (nrITS, nrLSU and mtSSU) with two protein-coding genes ( RPB 1 and RPB 2). The multigene phylogeny contained 48 newly generated sequences from the Russian Far East and all Bacidia s. str. sequences from GenBank (131 sequences). We subjected the alignments for the single and concatenated data sets to Bayesian inference (BI) and two maximum likelihood (ML) analyses (RAxML and IQ-TREE). The topologies of phylogenetic trees recovered from BI and ML analyses were highly concordant. The multilocus phylogeny of Bacidia s. str. was congruent with previous results based on nrITS sequences from the Russian Far East but with considerably higher support values for most of the deeper branches. A correlation between the recovered clades and apothecial pigments in the upper part of the hymenium and lateral exciple was observed. Based on morphological and molecular evidence, Bacidia obtecta is described as new to science. It was recovered as the sister lineage of B. elongata . The two species are alike in having up to four enlarged lumina cells along the exciple edge, but B. obtecta differs in the abundant crystals found in the upper hymenium and lateral exciple, and by having spores with fewer septa.
... Assuming microbial functions can be explained based on abundance and type of organisms present in a sample, numerous tools have been developed, using different approaches and reference databases like PICRUSt [35], PICRUSt2, Piphillin, Tax4Fun [36], Tax4Fun2, etc. PIC-RUSt & PICRUSt2 use ancestral state reconstruction to predict gene content of unknown sequence which has been debated [19,37,38], while the accuracy of the direct nearest neighbor matching approach used by Piphillin and Tax4Fun (version 1 & 2) depends on the size of the reference genome database. FAPROTAX, a similar tool like MicFunPred, which predicts phenotypes if all taxa members express it but focus mainly on marine and lake biochemistry [39]. ...
The 16S rRNA gene amplicon sequencing is a popular technique that provides accurate characterization of microbial taxonomic abundances but does not provide any functional information. Several tools are available to predict functional profiles based on 16S rRNA gene sequence data that use different genome databases and approaches. As variable regions of partially-sequenced 16S rRNA gene cannot resolve taxonomy accurately beyond the genus level, these tools may give inflated results. Here, we developed ‘MicFunPred’, which uses a novel approach to derive imputed metagenomes based on a set of core genes only, thereby minimizing false-positive predictions. On simulated datasets, MicFunPred showed the lowest False Positive Rate (FPR) with mean Spearman's correlation of 0.89 (SD = 0.03), while on seven real datasets the mean correlation was 0.75 (SD = 0.08). MicFunPred was found to be faster with low computational requirements and performed better or comparable when compared with other tools.
... The M. prasina group, which includes the type species M. prasina Fr., forms a monophyletic core group in the genus. The group is characterized by a 'micareoid' photobiont (a coccoid green alga with cells of 4-7.5 μm diam.), immarginate small apothecia, a hyaline hypothecium, branched paraphyses, and an ascus of the Micarea type, with a K/I+ blue amyloid tholus and a more lightly staining axial body often with a darkly stained lining (Hafellner 1984;Czarnota 2007;Ekman et al. 2008). Many species develop effuse thalli composed of goniocysts and produce Sedifolia-grey pigment (K+ violet, C+ violet), which is typically present in the epihymenium of the apothecia as well as the pycnidia (Coppins 1983;Czarnota & Guzow-Krzemińska 2010). ...
The genus Micarea was studied for the first time in the Taita Hills, Kenya. Based on new collections and existing data, we reconstructed a phylogeny using ITS, mtSSU and Mcm 7 regions, and generated a total of 27 new sequences. Data were analyzed using maximum likelihood and maximum parsimony methods. Based mainly on new collections, we discovered four undescribed well-supported lineages, characterized by molecular and phenotypic features. These lineages are described here as Micarea pumila , M. stellaris , M. taitensis and M. versicolor . Micarea pumila is characterized by a minutely granular thallus, small cream-white or pale brownish apothecia, small ascospores and the production of prasinic acid. Micarea stellaris has a warted-areolate thallus, cream-white apothecia usually darker at the centre, a hymenium of light grey or brownish pigment that dissolves in K, and intense crystalline granules that appear as a belt-like continuum across the lower hymenium when studied in polarized light. Micarea taitensis is characterized by a warted-areolate thallus and cream-white or yellowish apothecia that sometimes produce the Sedifolia-grey pigment. Micarea versicolor is characterized by a warted-areolate, sometimes partly granular thallus and apothecia varying from cream-white to light grey to blackish in colour. This considerable variation in the coloration of its apothecia is caused by an occasional mixture of the Sedifolia-grey pigment in the epihymenium and another purplish brown pigment in the hymenium. Micarea stellaris , M. taitensis and M. versicolor produce methoxymicareic acid. The main distinguishing characters are presented in a species synopsis. Three of the new species are nested in the M. prasina group, and the fourth one ( M. taitensis ) resolves as a basal taxon to the M. prasina group. The new species inhabit montane cloud forests, which have fragmented dramatically throughout the Eastern Arc Mountains in recent decades.
