No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
Sinuicella denisonii , a new genus and species in the Peltigeraceae from western North America
Abstract
The new genus Sinuicella , an early successional lichen, was found on bare soil in Oregon, USA. The thallus is minute fruticose, grey to nearly black, branching isotomic dichotomous, branches round, 20–90 μm wide in water mount. The cortex is composed of interlocking cells shaped like jigsaw puzzle pieces. Spores are hyaline, 1-septate, 25–40(–50) × 6.5–9(–11) μm. Maximum likelihood phylogenetic analyses on multilocus data sets, first spanning the entire order Peltigerales and then restricted to Peltigeraceae with extended sampling from Solorina and Peltigera , revealed the placement of Sinuicella outside of currently recognized genera, sister to Peltigera , with high support. Based on the phylogenetic, morphological and ecological distinctness of Sinuicella , we formally introduce a new genus represented by the single species S. denisonii . The cyanobiont of S. denisonii is Nostoc from phylogroup XL, Clade 2, Subclade 3 based on the rbcLX marker.
... The photobiont partner is crucial in the whole symbiosis survival in these conditions since it participates through different mechanisms to mitigate or tolerate different stressors [6,66], which could be aggravated due to climate change [67]. This and other studies [14,37,[68][69][70][71][72] highlight the importance of performing studies in still-understudied areas regarding biodiversity, which can be essential for studying adaptation strategies. Considering the particularity of the climatic factors in the studied environments and their influence in shaping photobiont distributions and their association patterns [23,73,74], the genetic diversity found in this work may not be widely distributed in the whole Andean landscape but is restricted to specific patches. ...
Peltigera lichens can colonize extreme habitats, such as high-elevation ecosystems, but their biodiversity is still largely unknown in these environments, especially in the southern hemi- sphere. We assessed the genetic diversity of mycobionts and cyanobionts of 60 Peltigera lichens collected in three high Andean steppes of southern Chile using LSU, β-tubulin, COR3 and ITS loci for mycobionts, and SSU and rbcLX loci for cyanobionts. We obtained 240 sequences for the different mycobiont markers and 118 for the cyanobiont markers, including the first report of β-tubulin sequences of P. patagonica through modifying a previously designed primer. Phylogenetic analyses, ITS scrutiny and variability of haplotypes were used to compare the sequences with those previously reported. We found seven mycobiont species and eleven cyanobiont haplotypes, including considerable novel symbionts. This was reflected by ~30% of mycobionts and ~20% of cyanobionts haplotypes that yielded less than 99% BLASTn sequence identity, 15 new sequences of the ITS1-HR, and a putative new Peltigera species associated with 3 Nostoc haplotypes not previously reported. Our results suggest that high Andean steppe ecosystems are habitats of unknown or little-explored lichen species and thus valuable environments to enhance our understanding of global Peltigera biodiversity.
This paper provides an updated classification of the Kingdom Fungi (including fossil fungi)
and fungus-like taxa. Five-hundred and twenty-three (535) notes are provided for newly introduced
taxa and for changes that have been made since the previous outline. In the discussion, the latest
taxonomic changes in Basidiomycota are provided and the classification of Mycosphaerellales are
broadly discussed. Genera listed in Mycosphaerellaceae have been confirmed by DNA sequence
analyses, while doubtful genera (DNA sequences being unavailable but traditionally
accommodated in Mycosphaerellaceae) are listed in the discussion. Problematic genera in
Glomeromycota are also discussed based on phylogenetic results.
This paper provides an updated classification of the Kingdom Fungi (including fossil fungi) and fungus-like taxa. Five-hundred and twenty-three (535) notes are provided for newly introduced taxa and for changes that have been made since the previous outline. In the discussion, the latest taxonomic changes in Basidiomycota are provided and the classification of Mycosphaerellales are broadly discussed. Genera listed in Mycosphaerellaceae have been confirmed by DNA sequence analyses, while doubtful genera (DNA sequences being unavailable but traditionally accommodated in Mycosphaerellaceae) are listed in the discussion. Problematic genera in Glomeromycota are also discussed based on phylogenetic results.
Seventeen species of the lichen genus Peltigera, exclusive of the P. canina group, are accepted from Norway. Their morphology, chemistry, ecology, and distribution in Norway are presented, and a key to the species is provided. Peltigera retifoveata is reported as new to Norway and a new species, P. sp. 1, which belongs to the P. aphthosa group, is treated but not formally described.
Different morphotypes of P. aphthosa, P. malacea, and P. neopolydactyla and different chemotypes of P. aphthosa, P. elisabethae, P. horizontalis, P. malacea, P. neopolydactyla, P. scabrosa, and P. sp. 1 are described. Correlations between several morphotypes and chemotypes are shown, but these are not treated as taxonomic units, although they probably are biological species.
Phototype pairs in P. aphthosa, P. britannica, and P. venosa are described, and the close relationship between the two first mentioned and P. malacea is pointed out.
Gregorella humida was found in western Oregon, U.S.A. This is a new genus and species for North America, with both fertile and sterile collections. An ITS sequence demonstrated its affinity with European material. This minute, granular to branched-granular cyanobacterial lichen is a pioneer on recently disturbed soil. The species was previously known from Fennoscandia, the U.K., continental Europe, and Turkey.
The Tree-Based Alignment Selector (T-BAS) toolkit combines phylogenetic-based placement of DNA sequences with alignment and specimen metadata visualization tools in an integrative pipeline for analyzing microbial biodiversity. The release of T-BAS version 2.1 makes available reference phylogenies, supports multilocus sequence placements and permits uploading and downloading trees, alignments, and specimen metadata.
Species circumscription is key to the characterization of patterns of specificity in symbiotic systems at a macroevolutionary scale. Here, a worldwide phylogenetic framework was used to assess the biodiversity and symbiotic patterns of association among partners in trimembered lichens from the genus Peltigera, section Chloropeltigera. We sequenced six loci of the main fungal partner and performed species discovery and validation analyses to establish putative species boundaries. Single locus phylogenies were used to establish the identity of both photobionts, Nostoc (cyanobacterium) and Coccomyxa (green alga). Distribution and specificity patterns were compared to the closely related clade, section Peltidea, which includes mainly Peltigera species with trimembered thalli. For section Chloropeltigera, eight fungal species (including five newly delimited putative species) were found in association with nine Nostoc phylogroups and two Coccomyxa species. In contrast, eight fungal species (including three newly delimited putative species) in section Peltidea were found in association with only four Nostoc phylogroups and the same two Coccomyxa species as for section Chloropeltigera. This difference in cyanobiont biodiversity between these two sections can potentially be explained by a significantly higher frequency of sexual reproductive structures in species from section Chloropeltigera compared to section Peltidea. Therefore, horizontal transmission of the cyanobiont might be more prevalent in Chloropeltigera species, while vertical transmission might be more common in Peltidea species. All Peltigera species in section Chloropeltigera are generalists in their association with Nostoc compared to more specialized Peltigera species in section Peltidea. Constrained distributions of Peltigera species that associate strictly with one species of green algae (Coccomyxa subellipsoidea) indicate that the availability of the green alga and the specificity of the interaction might be important factors limiting geographic ranges of trimembered Peltigera, in addition to constraints imposed by their interaction with Nostoc partners and by climatic factors.
This comprehensive phylogenetic revision of sections Peltigera and Retifoveatae of the cyanolichen genus Peltigera is based on DNA sequences from more than 500 specimens from five continents. We amplified five loci (nrITS, β-tubulin and three intergenic spacers part of colinear orthologous regions [COR]) for the mycobiont, and the rbcLX locus for the cyanobacterial partner Nostoc. Phylogenetic inferences (RAxML, BEAST) and species delimitation methods (bGMYC, bPTP, bPP) suggest the presence of 88 species in section Peltigera, including 50 species new to science, hence uncovering a surprisingly high proportion of previously unnoticed biodiversity. The hypervariable region in ITS1 (ITS1-HR) is a powerful marker to identify species within sections Peltigera and Retifoveatae. Most newly delimited species are restricted to a single biogeographic region, however, up to ten species have a nearly cosmopolitan distribution. The specificity of mycobionts in their association with Nostoc cyanobionts ranges from strict specialists (associate with only one Nostoc phylogroup) to broad generalists (up to eight Nostoc phylogroups uncovered), with widespread species recruiting a broader selection of Nostoc phylogroups than species with limited distributions. In contrast, species from the P. didactyla clade characterized by small thalli and asexual vegetative propagules (soredia) associate with fewer Nostoc phylogroups (i.e., are more specialized) despite their broad distributions, and show significantly higher rates of nucleotide substitutions. © International Association for Plant Taxonomy (IAPT) 2018, all rights reserved.
Patterns of specificity among symbiotic partners are key to a comprehensive understanding of the evolution of symbiotic systems. Specificity of mutualistic partners, within a widespread monophyletic group for which all species are sampled has rarely been explored. Here we assess the level of specificity between the cosmopolitan lichen-forming fungus (mycobiont) from the genus Peltigera, section Polydactylon, and its cyanobacterial partner Nostoc (cyanobiont). The mycobiont and cyanobiont phylogenies are inferred from five nuclear loci and the rbcLX region, respectively. These sequences were obtained from 206 lichen thalli, representing ca. 40 closely related Peltigera species sampled worldwide, doubling the number of known species in this group. We found a broad spectrum of specificity for both partners ranging from strict specialists to generalists. Overall, mycobionts are more specialized than cyanobionts by associating mostly with one or a few Nostoc phylogroups, whereas most cyanobionts associate frequently with several Peltigera species. Specialist mycobionts are older than generalists, supporting the hypothesis that specialization of mycobionts to one or few cyanobionts, is favored through time in geographic areas where species have been established for long periods of time. The relatively recent colonization of a new geographic area (Central and South America) by members of section Polydactylon is associated with a switch to a generalist pattern of association and an increased diversification rate by the fungal partner, suggesting that switches to generalism are rare events that are advantageous in new environments. We detected higher genetic diversity in generalist mycobionts. We also found that Peltigera species specialized on a single Nostoc phylogroup have narrower geographical distributions compared to generalist species.
The present study investigates the photobiont diversity of the boreal felt lichen, Erioderma pedicellatum . Previously sampled genetic data from Newfoundland were reanalyzed and new sequence data (16S rDNA, rbcLX ) of the boreal felt lichen from Alaska (USA), Kamchatka (Russia), and North Trøndelag (Norway) were generated. The highest genetic diversity of the photobiont is found in Alaska and Kamchatka, indicating that these may be the primary sources of the species in the Northern Hemisphere. In Newfoundland, the photobiont of E. pedicellatum was screened on leaves of the symbiotic liverwort Frullania asagrayana and it was found to occur on trees where no other lichens were present, demonstrating that the geographical distribution, and possibly also the ecological requirement of the photobiont of E. pedicellatum , is wider than that of the lichen phenotype. Finally, a postulated association between the occurrence of the vegetatively reproducing Coccocarpia palmicola and the occurrence of the compatible photobiont of E. pedicellatum on the same tree could not be established.
The CIPRES Science Gateway is a community web application that provides public access to a set of parallel tree inference and multiple sequence alignment codes run on large computational resources. These resources are made available at no charge to users by the NSF Extreme Science and Engineering Discovery Environment (XSEDE) project. Here we describe the CIPRES RESTful application programmer interface (CRA), a web service that provides programmatic access to all resources and services currently offered by the CIPRES Science Gateway. Software developers can use the CRA to extend their web or desktop applications to include the ability to run MrBayes, BEAST, RAxML, MAFFT, and other computationally intensive algorithms on XSEDE. The CRA also makes it possible for individuals with modest scripting skills to access the same tools from the command line using curl, or through any scripting language. This report describes the CRA and its use in three web applications (Influenza Research Database – www.fludb.org, Virus Pathogen Resource – www.viprbrc.org, and MorphoBank – www.morphobank.org). The CRA is freely accessible to registered users at https://cipresrest.sdsc.edu/cipresrest/v1; supporting documentation and registration tools are available at https://www.phylo.org/restusers.
Spilonema was originally described to accommodate an unusual group of cyanolichens with thread-like, cushion-forming thalli, and has long been placed in Coccocarpiaceae based on ascomatal development. However, Spilonema is the only genus of Peltigerales to include species lichenized with the cyanobacterial genus Stigonema, and the evolutionary relationships of Spilonema to other genera in the family have yet to be tested using molecular data. We present evidence from combined nuclear 28S, 18S and mitochondrial 12S rDNA to confirm the placement of the core species of Spilonema (S. paradoxum and S. revertens) in Coccocarpiaceae. Our data further show that despite possessing a different genus of photobiont (Scytonema), the north Pacific endemic genus Spilonemella must be included within Spilonema, suggesting that closely related species of the genus have changed photobionts in the course of evolution. However, we recovered Spilonema dendroides, one of the only lichens known to associate with the cyanobacterial genus Hyphomorpha, as only distantly related to the Coccocarpiaceae. The evolutionary relationships of this species are as yet unclear but it may occupy a basal position in the Peltigerales. We create for this species the new genus Erinacellus T. Sprib., Muggia & Tønsberg.
• Premise of this study: Aquatic cyanolichens from the genus Peltigera section Hydrothyriae are subject to anthropogenic threats and, therefore, are considered endangered. In this study we addressed the phylogenetic placement of section Hydrothyriae within Peltigera. We delimited species within the section and identified their symbiotic cyanobacteria.• Methods: Species delimitation and population structure were explored using monophyly as a grouping criterion (RAxML) and Structurama based on three protein-coding genes in combination with two nuclear ribosomal loci. The 16S and rbcLX sequences for the cyanobionts were analyzed in the broad phylogenetic context of free-living and symbiotic cyanobacteria.• Key results: We confirm with high confidence the placement of section Hydrothyriae within the monophyletic genus Peltigera; however, its phylogenetic position within the genus remains unsettled. We recovered three distinct monophyletic groups corresponding to three species: P. hydrothyria, P. gowardii s.s., and P. aquatica Miadl. & Lendemer, the latter being formally introduced here. Each species was associated with an exclusive set of Nostoc haplotypes.• Conclusions: The ITS region alone provides sufficient genetic information to distinguish the three morphologically cryptic species within section Hydrothyriae. Section Hydrothyriae seems to be associated with a monophyletic lineage of Nostoc, that has not been found in symbiotic association with other members of Peltigera. Capsosira lowei should be transferred to the genus Nostoc. Potential threats to P. aquatica should be re-examined based on the recognition of two aquatic species in western North America.
Peltigera (Peltigerineae, lichenized Ascomycota) is one of the most widespread lichen genera incorporating bi- and trimembered associations involving fungi, green algae (cf. Coccomyxa), and cyanobacteria (cf. Nostoc). A wide range of morphological and chemical (secondary compounds) variation at both the intra- and inter- specific levels is present in this genus. Compared to many other genera of macrolichens, its taxonomy, including chemotaxonomy, still remains poorly understood. Existing infrageneric classifications of Peltigera are almost exclusively based on photobiont composition of the thallus. These classifications assumed that bi- and tri- membered taxa were distinct monophyletic entities. The genus Peltigera has never been the focus of a com- prehensive phylogenetic study. The most recent and widely accepted subdivision of the genus into seven groups is based mainly on morphological and chemical characters. Relationships among species of Peltigera are investigated here using chemical, morphological, and large subunit nuclear ribosomal DNA (LSU nrDNA) data. We test the monophyly of these seven morpho-chemical Peltigera groups and propose a classification based on a phylogenetic approach. Data sets of 42 chemical characters (terpenoids), 31 morphological char- acters, and 1135 LSU nrDNA characters for 96 samples representing 38 Peltigera species, eight undescribed putative Peltigera species, and nine species from seven potentially closely related genera from Peltigerineae were subjected to maximum parsimony analyses. Morphological, chemical, and molecular analyses were carried out independently and on a combined data set. Monophyly of Peltigera, including Hydrothyria, was confirmed. The genus Hydrothyria is transferred to Peltigera and a new combination Peltigera hydrothyria Miadlikowska & Lutzoni is proposed. Eight monophyletic sections within the genus Peltigera, with high bootstrap support, are circumscribed: sections Peltigera, Polydactylon Miadlikowska & Lutzoni, Chloropeltigera Gyeln., Peltidea (Ach.) Vain., Horizontales Miadlikowska & Lutzoni, Retifoveatae Miadlikowska & Lutzoni, Phlebia Wallr., and Hydrothyriae Miadlikowska & Lutzoni. Unequivocal morphological and chemical synapomorphies for all sections except section Peltidea are recognized and presented. A key for identification of the sections is provided. In addition, a key based on four main terpenoids for determination of the chemotypes and species within section Polydactylon is included. Five terpenoids (50-54) identified on thin-layer chromatography plates for P. elisabethae and P. horizontalis chemotype I are added to the list of substances found in Peltigera. Five chemotypes, mainly from Poland and Norway, are reported from Peltigera thalli for the first time: P. malacea chemotype V, P. leucophlebia chemotype II, P. hymenina chemotypes II and III, and P. collina chemotype IV. Three main types of vein structure in Peltigera were recognized based on SEM studies.
Understanding the evolutionary history of living organisms is a central problem in biology. Until recently the ability to infer evolutionary relationships was limited by the amount of DNA sequence data available, but new DNA sequencing technologies have largely removed this limitation. As a result, DNA sequence data are readily available or obtainable for a wide spectrum of organisms, thus creating an unprecedented opportunity to explore evolutionary relationships broadly and deeply across the Tree of Life. Unfortunately, the algorithms used to infer evolutionary relationships are NP-hard, so the dramatic increase in available DNA sequence data has created a commensurate increase in the need for access to powerful computational resources. Local laptop or desktop machines are no longer viable for analysis of the larger data sets available today, and progress in the field relies upon access to large, scalable high-performance computing resources. This paper describes development of the CIPRES Science Gateway, a web portal designed to provide researchers with transparent access to the fastest available community codes for inference of phylogenetic relationships, and implementation of these codes on scalable computational resources. Meeting the needs of the community has included developing infrastructure to provide access, working with the community to improve existing community codes, developing infrastructure to insure the portal is scalable to the entire systematics community, and adopting strategies that make the project sustainable by the community. The CIPRES Science Gateway has allowed more than 1800 unique users to run jobs that required 2.5 million Service Units since its release in December 2009. (A Service Unit is a CPU-hour at unit priority).
Heterocystous cyanobacteria form symbiotic associations with a wide range of plant and fungal hosts. We used a molecular phylogenetic approach to investigate the degree of host specialization of cyanobacteria associated with four closely related species of the lichenized fungus Peltigera, and to compare these strains with other symbiotic cyanobacteria. We conducted phylogenetic analyses on 16S, rbcLX, and trnL sequences from cyanobacteria associated with multiple specimens of each lichen species and from symbionts of other fungi and plants, as well as from free-living strains of Nostoc and related genera of cyanobacteria. The genus Nostoc comprises two divergent lineages, but symbiotic strains occur primarily within a single monophyletic lineage that also includes free-living representatives. Cyanobacteria from the same lichen species were often more closely related to strains from other species or to plant symbionts or free-living strains than to each other. These results indicate that host specialization is low for the genus Nostoc, and suggest that opportunities for coevolution with its partners may be rare.
Phylogenetic analyses of non-protein-coding nucleotide sequences such as ribosomal RNA genes, internal transcribed spacers, and introns are often impeded by regions of the alignments that are ambiguously aligned. These regions are characterized by the presence of gaps and their uncertain positions, no matter which optimization criteria are used. This problem is particularly acute in large-scale phylogenetic studies and when aligning highly diverged sequences. Accommodating these regions, where positional homology is likely to be violated, in phylogenetic analyses has been dealt with very differently by molecular systematists and evolutionists, ranging from the total exclusion of these regions to the inclusion of every position regardless of ambiguity in the alignment. We present a new method that allows the inclusion of ambiguously aligned regions without violating homology. In this three-step procedure, first homologous regions of the alignment containing ambiguously aligned sequences are delimited. Second, each ambiguously aligned region is unequivocally coded as a new character, replacing its respective ambiguous region. Third, each of the coded characters is subjected to a specific step matrix to account for the differential number of changes (summing substitutions and indels) needed to transform one sequence to another. The optimal number of steps included in the step matrix is the one derived from the pairwise alignment with the greatest similarity and the least number of steps. In addition to potentially enhancing phylogenetic resolution and support, by integrating previously nonaccessible characters without violating positional homology, this new approach can improve branch length estimations when using parsimony.
Thallus architecture has long been a powerful guide for classifying lichens and has often trumped photobiont association and ascomatal type, but the reliability of these characters to predict phylogenetic affinity has seldom been tested. The cyanolichen genus Polychidium unites species that have strikingly similar gross morphology but consort with different photobiont genera. If Polychidium were found to be monophyletic, photobiont switching among closely related species would be suggested. If, however, species were found to arise in different lineages, a convergent body plan and ascomatal type evolution would be inferred.
We tested the monophyly of Polychidium with a multilocus phylogeny based on nuclear and mitochondrial sequence data from all known Peltigeralean families and reconstructed ancestral states for specific thallus architecture and ascomatal ontogeny types relative to Polychidium and other clades.
We found that Polychidium consists of two species groups that arose independently in different suborders within the Peltigerales, associated with Nostoc and Scytonema photobionts, respectively. We infer from ancestral character state reconstruction that dendroid thallus architecture evolved independently in these two lineages.
The independent development of similar dendroid thallus architecture in different fungal suborders with different photobionts represents a clear and previously overlooked example of convergent evolution in lichens. Our results also suggest a pattern of character state conservation, loss, and reversion in ascomatal ontogeny types, hitherto considered conserved traits useful for higher level ascomycete systematics.
To provide a comprehensive molecular phylogeny for peltigeralean fungi and to establish a classification based on monophyly, phylogenetic analyses were carried out on sequences from the nuclear ribosomal large (LSU) and small (SSU) subunits obtained from 113 individuals that represent virtually all main lineages of ascomycetes. Analyses were also conducted on a subset of 77 individuals in which the ingroup consisted of 59 individuals representing six families, 12 genera, and 54 species potentially part of the Peltigerineae/Peltigerales. Our study revealed that all six families together formed a strongly supported monophyletic group within the Lecanoromycetidae. We propose here a new classification for these lichens consisting of the order Peltigerales and two suborders-Collematineae subordo nov. (Collemataceae, Placynthiaceae, and Pannariaceae) and Peltigerineae (Lobariaceae, Nephromataceae, and Peltigeraceae). To accommodate these new monophyletic groups, we redefined the Lecanorineae, Pertusariales, and Lecanorales sensu Eriksson et al. (Outline of Ascomycota-2003, Myconet 9: 1-103, 2003). Our study confirms the monophyly of the Collemataceae, Lobariaceae, Nephromataceae, and Peltigeraceae, and the genera Nephroma, Sticta, and Peltigera. However, Leptogium, Lobaria, Pseudocyphellaria, and Solorina were found to be nonmonophyletic genera. Reconstruction of ancestral symbiotic states within the Peltigerales, using maximum likelihood (ML) and a Bayesian approach to account for phylogenetic uncertainty, revealed an evolutionary scenario in which bimembered associations with cyanobacteria were ancestral, followed by multiple independent acquisitions of green algae to form tripartite symbioses and rare subsequent losses of the cyanobiont to form bimembered symbioses with green algae.
Likelihood-based methods for placing short read sequences from metagenomic samples into reference phylogenies have been recently introduced. At present, it is unclear how to align those reads with respect to the reference alignment that was deployed to infer the reference phylogeny. Moreover, the adaptability of such alignment methods with respect to the underlying reference alignment strategies/philosophies has not been explored. It has also not been assessed if the reference phylogeny can be deployed in conjunction with the reference alignment to improve alignment accuracy in this context.
We assess different strategies for short read alignment and propose a novel phylogeny-aware alignment procedure. Our alignment method can improve the accuracy of subsequent phylogenetic placement of the reads into a reference phylogeny by up to 5.8 times compared with phylogeny-agnostic methods. It can be deployed to align reads to alignments generated by using fundamentally different alignment strategies (e.g. PRANK(+F) versus MUSCLE).
http://www.exelixis-lab.org/software.html
Phylogenetic diversity of lichen photobionts is low compared to that of fungal counterparts. Most lichen fungi are thought to be associated with just four photobiont genera, among them the cyanobacteria Nostoc and Scytonema, two of the most important nitrogen fixers in humid ecosystems. Although many Nostoc photobionts have been identified using isolated cultures and sequences, the identity of Scytonema photobionts has never been confirmed by culturing or sequencing. We investigated the phylogenetic placement of presumed Scytonema photobionts and unicellular morphotypes previously assigned to Chroococcus, from tropical Dictyonema, Acantholichen, Coccocarpia, and Stereocaulon lichens. While we confirm that filamentous and unicellular photobiont morphotypes belong to a single clade, this clade does not cluster with Scytonema but represents a novel, previously unrecognized, highly diverse, exclusively lichenized lineage, for which the name Rhizonema is available. The phylogenetic structure observed in this novel lineage suggests absence of coevolution with associated mycobionts at the species or clade level. Instead, highly efficient photobiont strains appear to have evolved through photobiont sharing between unrelated, but ecologically similar, coexisting lineages of lichenized fungi ("lichen guilds"), via the selection of particular photobiont strains through and subsequent horizontal transfer among unrelated mycobionts, a phenomenon not unlike crop domestication.
Multiple sequence alignment (MSA) is an important step in comparative sequence analyses. Parallelization is a key technique for reducing the time required for large-scale sequence analyses. The three calculation stages, all-to-all comparison, progressive alignment and iterative refinement, of the MAFFT MSA program were parallelized using the POSIX Threads library. Two natural parallelization strategies (best-first and simple hill-climbing) were implemented for the iterative refinement stage. Based on comparisons of the objective scores and benchmark scores between the two approaches, we selected a simple hill-climbing approach as the default.
Availability: The parallelized version of MAFFT is available at http://mafft.cbrc.jp/alignment/software/. This version currently supports the Linux operating system only.
Contact: kazutaka.katoh@aist.go.jp
Supplementary information: Supplementary data are available at Bioinformatics online.
Despite recent advances achieved by application of high-performance computing methods and novel algorithmic techniques to maximum likelihood (ML)-based inference programs, the major computational bottleneck still consists in the computation of bootstrap support values. Conducting a probably insufficient number of 100 bootstrap (BS) analyses with current ML programs on large datasets-either with respect to the number of taxa or base pairs-can easily require a month of run time. Therefore, we have developed, implemented, and thoroughly tested rapid bootstrap heuristics in RAxML (Randomized Axelerated Maximum Likelihood) that are more than an order of magnitude faster than current algorithms. These new heuristics can contribute to resolving the computational bottleneck and improve current methodology in phylogenetic analyses. Computational experiments to assess the performance and relative accuracy of these heuristics were conducted on 22 diverse DNA and AA (amino acid), single gene as well as multigene, real-world alignments containing 125 up to 7764 sequences. The standard BS (SBS) and rapid BS (RBS) values drawn on the best-scoring ML tree are highly correlated and show almost identical average support values. The weighted RF (Robinson-Foulds) distance between SBS- and RBS-based consensus trees was smaller than 6% in all cases (average 4%). More importantly, RBS inferences are between 8 and 20 times faster (average 14.73) than SBS analyses with RAxML and between 18 and 495 times faster than BS analyses with competing programs, such as PHYML or GARLI. Moreover, this performance improvement increases with alignment size. Finally, we have set up two freely accessible Web servers for this significantly improved version of RAxML that provide access to the 200-CPU cluster of the Vital-IT unit at the Swiss Institute of Bioinformatics and the 128-CPU cluster of the CIPRES project at the San Diego Supercomputer Center. These Web servers offer the possibility to conduct large-scale phylogenetic inferences to a large part of the community that does not have access to, or the expertise to use, high-performance computing resources.
Unlabelled:
RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Gamma yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets > or =4000 taxa it also runs 2-3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively.
Availability:
icwww.epfl.ch/~stamatak
The Lecanoromycetes includes most of the lichen-forming fungal species (> 13500) and is therefore one of the most diverse class of all Fungi in terms of phenotypic complexity. We report phylogenetic relationships within the Lecanoromycetes resulting from Bayesian and maximum likelihood analyses with complementary posterior probabilities and bootstrap support values based on three combined multilocus datasets using a supermatrix approach. Nine of 10 orders and 43 of 64 families currently recognized in Eriksson's classification of the Lecanoromycetes (Outline of Ascomycota--2006 Myconet 12:1-82) were represented in this sampling. Our analyses strongly support the Acarosporomycetidae and Ostropomycetidae as monophyletic, whereas the delimitation of the largest subclass, the Lecanoromycetidae, remains uncertain. Independent of future delimitation of the Lecanoromycetidae, the Rhizocarpaceae and Umbilicariaceae should be elevated to the ordinal level. This study shows that recent classifications include several nonmonophyletic taxa at different ranks that need to be recircumscribed. Our phylogenies confirm that ascus morphology cannot be applied consistently to shape the classification of lichen-forming fungi. The increasing amount of missing data associated with the progressive addition of taxa resulted in some cases in the expected loss of support, but we also observed an improvement in statistical support for many internodes. We conclude that a phylogenetic synthesis for a chosen taxonomic group should include a comprehensive assessment of phylogenetic confidence based on multiple estimates using different methods and on a progressive taxon sampling with an increasing number of taxa, even if it involves an increasing amount of missing data.
The Lecanoromycetes includes most of the lichen-forming fungal species (>13 500) and is therefore one of the most diverse class of all Fungi in terms of phenotypic complexity. We report phylogenetic relationships within the Lecanoromycetes resulting from Bayesian and maximum likelihood analyses with complementary posterior probabilities and bootstrap support values based on three combined multilocus datasets using a supermatrix approach. Nine of 10 orders and 43 of 64 families currently recognized in Eriksson’s classification of the Lecanoromycetes (Outline of Ascomycota—2006 Myconet 12:1–82) were represented in this sampling. Our analyses strongly support the Acarosporomycetidae and Ostropomycetidae as monophyletic, whereas the delimitation of the largest subclass, the Lecanoromycetidae, remains uncertain. Independent of future delimitation of the Lecanoromycetidae, the Rhizocarpaceae and Umbilicariaceae should be elevated to the ordinal level. This study shows that recent classifications include several nonmonophyletic taxa at different ranks that need to be recircumscribed. Our phylogenies confirm that ascus morphology cannot be applied consistently to shape the classification of lichen-forming fungi. The increasing amount of missing data associated with the progressive addition of taxa resulted in some cases in the expected loss of support, but we also observed an improvement in statistical support for many internodes. We conclude that a phylogenetic synthesis for a chosen taxonomic group should include a comprehensive assessment of phylogenetic confidence based on multiple estimates using different methods and on a progressive taxon sampling with an increasing number of taxa, even if it involves an increasing amount of missing data.
Ecological interactions range from purely specialized to extremely generalized in nature. Recent research has showed very high levels of specialization in the cyanolichens involving Peltigera (mycobionts) and their Nostoc photosynthetic partners (cyanobionts). Yet, little is known about the mechanisms contributing to the establishment and maintenance of such high specialization levels. Here, we characterized interactions between Peltigera and Nostoc partners at a global scale, using more than one thousand thalli. We used tools from network theory, community phylogenetics and biogeographical history reconstruction to evaluate how these symbiotic interactions may have evolved. After splitting the interaction matrix into modules of preferentially interacting partners, we evaluated how module membership might have evolved along the mycobionts’ phylogeny. We also teased apart the contributions of geographical overlap vs phylogeny in driving interaction establishment between Peltigera and Nostoc taxa. Module affiliation rarely evolves through the splitting of large ancestral modules. Instead, new modules appear to emerge independently, which is often associated with a fungal speciation event. We also found strong phylogenetic signal in these interactions, which suggests that partner switching is constrained by conserved traits. Therefore, it seems that a high rate of fungal diversification following a switch to a new cyanobiont can lead to the formation of large modules, with cyanobionts associating with multiple closely retated Peltigera species. Finally, when restricting our analyses to Peltigera sister species, the latter differed more through partner acquisition/loss than replacement (i.e., switching). This pattern vanishes as we look at sister species that have diverged longer ago. This suggests that fungal speciation may be accompanied by a stepwise process of (1) novel partner acquisition and (2) loss of the ancestral partner. This could explain the maintenance of high specialization levels in this symbiotic system where the transmission of the cyanobiont to the next generation is assumed to be predominantly horizontal. Synthesis. Overall, our study suggests that oscillation between generalization and ancestral partner loss may maintain high specialization within the lichen genus Peltigera, and that partner selection is not only driven by partners’ geographical overlap, but also by their phylogenetically conserved traits. This article is protected by copyright. All rights reserved.
Synteny can be maintained for certain genomic regions across broad phylogenetic groups. In these homologous genomic regions, sites that are under relaxed purifying selection, such as intergenic regions, could be used broadly as markers for population genetic and phylogenetic studies on species complexes. To explore the potential of this approach, we found 125 Collinear Orthologous Regions (COR) ranging from 1 to > 10 kb across nine genomes representing the Lecanoromycetes and Eurotiomycetes (Pezizomycotina, Ascomycota). Twenty-six of these COR were found in all 24 eurotiomycete genomes surveyed for this study. Given the high abundance and availability of fungal genomes we believe this approach could be adopted for other large groups of fungi outside the Pezizomycotina. As a proof of concept, we selected three Collinear Orthologous Regions (COR1b, COR3, and COR16), based on synteny analyses of several genomes representing three classes of Ascomycota: Eurotiomycetes, Lecanoromycetes, and Lichinomycetes. COR16, for example, was found across these three classes of fungi. Here we compare the resolving power of these three new markers with five loci commonly used in phylogenetic studies of fungi, using section Polydactylon of the cyanolichen-forming genus Peltigera (Lecanoromycetes) - a clade with several challenging species complexes. Sequence data were subjected to three species discovery and two validating methods. COR markers substantially increased phylogenetic resolution and confidence, and highly contributed to species delimitation. The level of phylogenetic signal provided by each of the COR markers was higher than the commonly used fungal barcode ITS. High cryptic diversity was revealed by all methods. As redefined here, most species represent lineages that have relatively narrower, and more homogeneous biogeographical ranges than previously understood. The scabrosoid clade consists of ten species, seven of which are new. For the dolichorhizoid clade, twenty-two new species were discovered for a total of twenty-nine species in this clade.
Ninety years after Zahlbruckner, we present the most recent update to the classification of lichen fungi in the Ascomycota and Basidiomycota to genus level, with species numbers and references to changes compared to the 2010 Outline of Ascomycota and other recent classifications. Updated statistics on global species richness of lichen fungi and species richness at family, order and class level are given. The number of accepted species is 19,387 in 995 genera, 115 families, 39 orders and eight classes. Lichenized Basidiomycota amount to 172 species (0.9% of the total), 15 genera (1.5%), five families (4.3%), five orders (12.8%) and one class (12.5%). The most speciose genera are Xanthoparmelia, Lecanora, Arthonia, Cladonia, Pertusaria, Ocellularia, Graphis, Caloplaca, Usnea and Buellia. The average number of species per genus is 19.5 and 256 genera are monospecific. Using newly defined categories, two genera (Xanthoparmelia, Lecanora) are ultradiverse (more than 500 species), 17 hyperdiverse (201–500 species) and 12 megadiverse (101–200). The largest family is Parmeliaceae, with 2,765 species and 77 genera, followed by Graphidaceae (2,161; 79), Verrucariaceae (943; 43), Ramalinaceae (916; 43) and Lecanoraceae (791; 25). The largest order is Lecanorales, with 6,231 species and 234 genera, followed by Ostropales (3,261; 138), Arthoniales (1,541, 103), Peltigerales (1,301; 67) and Caliciales (1,276; 55). The largest class is Lecanoromycetes, with 15,131 species and 701 genera, followed by Arthoniomycetes (1,541; 103), Eurotiomycetes (1,203; 63), Dothideomycetes (812; 39) and Lichinomycetes (390; 50). A total of 751 out of 995 genera (75%) have molecular data. Fifty-nine genera remain in unresolved positions at the family, order or class level. The phylogenetic position of the 39 orders containing lichenized fungi suggests 20–30 independent lichenization events during the evolution of higher Fungi, 14–23 in the Ascomycota and 6–7 in the Basidiomycota. The following names are validated: Candelariomycetidae Miądl. et al. ex Timdal & M.Westb. subcl. nov., Cystocoleaceae Locq. ex Lücking, B.P.Hodk. & S.D.Leav. fam. nov, Letrouitineae Gaya & Lutzoni subordo nov., Rhizocarpales Miądl. & Lutzoni ordo nov. and Teloschistineae Gaya & Lutzoni subordo nov. Lectotypes are designated for Clathroporinopsis M.Choisy and Protoschistes M.Choisy, making both synonyms of Gyalecta Ach., and Stromatothelium Trevis., making it a synonym of Pyrenula Ach. Members of Cyphobasidiales, which are here interpreted as hyperlichenized fungi, as well as fossil lichen fungi, are added in additional classifications in two appendices.
Motivation:
High-quality phylogenetic placement of sequence data has the potential to greatly accelerate studies of the diversity, systematics, ecology, and functional biology of diverse groups. We developed the Tree-Based Alignment Selector (T-BAS) toolkit to allow evolutionary placement and visualization of diverse DNA sequences representing unknown taxa within a robust phylogenetic context, and to permit the downloading of highly curated, single- and multi-locus alignments for specific clades.
Results:
In its initial form, T-BAS v1.0 uses a core phylogeny of 979 taxa (including 23 outgroup taxa, as well as 61 orders, 175 families, and 496 genera) representing all 13 classes of largest subphylum of Fungi - Pezizomycotina (Ascomycota) - based on sequence alignments for six loci (nr5.8S, nrLSU, nrSSU, mtSSU, RPB1, RPB2). T-BAS v1.0 has three main uses: (1) Users may download alignments and voucher tables for members of the Pezizomycotina directly from the reference tree, facilitating systematics studies of focal clades. (2) Users may upload sequence files with reads representing unknown taxa and place these on the phylogeny using either BLAST or phylogeny-based approaches, and then use the displayed tree to select reference taxa to include when downloading alignments. The placement of unknowns can be performed for large numbers of Sanger sequences obtained from fungal cultures and for alignable, short reads of environmental amplicons. (3) User-customizable metadata can be visualized on the tree.
Availability:
T-BAS Version 1.0 is available online at http://tbas.hpc.ncsu.edu Registration is required to access the CIPRES Science Gateway and NSF XSEDE's large computational resources.
Contact:
icarbon@ncsu.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Phylogenetic analyses of non-protein-coding nucleotide sequences such as ribosomal RNA genes, internal transcribed spacers,
and introns are often impeded by regions of the alignments that are ambiguously aligned. These regions are characterized by
the presence of gaps and their uncertain positions, no matter which optimization criteria are used. This problem is particularly
acute in large-scale phylogenetic studies and when aligning highly diverged sequences. Accommodating these regions, where
positional homology is likely to be violated, in phylogenetic analyses has been dealt with very differently by molecular systematists
and evolutionists, ranging from the total exclusion of these regions to the inclusion of every position regardless of ambiguity
in the alignment. We present a new method that allows the inclusion of ambiguously aligned regions without violating homology.In
this three-step procedure, first homologous regions of the alignment containing ambiguously aligned sequences are delimited.
Second, each ambiguously aligned region is unequivocally coded as a new character, replacing its respective ambiguous region.
Third, each of the coded characters is subjected to a specific step matrix to account for the differential number of changes
(summing substitutions and indels) needed to transform one sequence to another.The optimal number of steps included in the
step matrix is the one derived from the pairwise alignment with the greatest similarity and the least number of steps. In
addition to potentially enhancing phylogenetic resolution and support, by integrating previously nonaccessible characters
without violating positional homology,this new approach can improve branch length estimations when using parsimony.
The term “Lecanorales” must be precisely defined at the outset because of the diverse concepts of this group held by various authors. Nannfeldt (1932) established a broad definition of the group by uniting under the Lecanorales the asco-hymenial discomycetes which are characterized by a perennial ascocarp and an ascus in which the wall stains blue with iodine. As a result, he assigned to this taxon a small number of non-lichen-forming discomycetes, the family Patellariaceae, along with nearly all the discolichens with the exception of the Caliciaceae-like species and some of the paraphysoid graphidiate species. This is nearly the same point of view as that of Dennis (1968). As a result of the work by more recent authors including Richardson (1970), Duncan and James (1970), Luttrell (1973), Poelt (1973), Henssen and Jahns (1974) and Von Arx and Müller (1975), some families or genera have been separated out—generally on the basis of characteristics of the ascus and the ascocarp (e.g., the genera Patellaria Fries and relatives, Baeomyces Persoon and allies and the families Graphidaceae, Lecan-actidaceae, Thelotremataceae and its allies, and Gyalectaceae). These authors differ over only a small number of families. They are in general agreement on a fundamental definition of the order Lecanorales as the ascohymenial discomycetes that have asci of the archaeascé type. This corresponds to the lecanoralean discomycete concept of Chadefaud (1960) with the exclusion of the ascohymenial discomycetes having bitunicate asci.
The Lecanorales are considered to be the typical lichenized discomycetes, including most of the lichen families with fruit bodies in the form of apothecia. All the large foliose lichens and the majority of the large fruticose lichens belong to this group. The order is characterized by an ascohymenial development, inoperculate asci, and the consistency and duration of the hymenium. The fruit bodies are long lived; their hymenium is strongly gelatinized with the paraphyses cemented together by mucilage. Earlier, a unitunicate structure and amyloid reaction of the ascus were mentioned as further important features of the order. However, the restriction of the amyloid reaction to the hymenial gelatin or its complete absence has since become known for many members of the order, and recent electron microscopy studies (Honegger, 1978) have given the final proof for the existence of bitunicate asci in some genera. The last mentioned are bitunicate in the functional sense of Luttrell (1951), with a gliding site between the ascus outer and its expansive inner layer. For the varying use of the term “bitunicate” in the literature, see Honegger (1978).
Along the Oregon coast there are pockets of exceptionally high diversity of rare lichen species. These include a number of extreme disjunct populations, with affinities to the flora of the southern hemi sphere, tropical and subtropical areas, California, northeast Asia, maritime Arctic, eastern North America, and Europe. Only two of these rare species are endemic to the Pacific Northwest. Concentrations of rare lichens tend to occur on peninsulas, headlands, bald mountaintops near the coast, and the extensive dune sheet between Heceta Head and Cape Arago. Many of these species are known in North America only from the immediate coast. The geographic distribution of these populations of rare species and their biogeographic affmities are described. Fourteen species are new records for Oregon. Acarospora subrufula is newly reported for North America. Hypogymnia pulverata is a new record for western North America.
The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 635 newly generated and 3307 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, 'Candelariomycetidae'). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed relatively stable relationships for many families and orders. However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships), potentially including the misplacements of several taxa. Future phylogenetic analyses should include additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part of this study, a new module ("Hypha") of the freely available Mesquite software was developed to compare and display the internodal support values derived from this cumulative supermatrix approach.
Lichens that incorporate cyanobacterial symbionts (cyanolichens) are an ecologically key group of species used as biomonitors at all latitudes. Cyanolichen evolution is however based on intense studies of few keystone species and the bulk of species diversity, especially of small species in cold climates, has yet to be accounted for in phylogenetic studies. We assembled an expanded data set including members of all nine currently accepted Peltigeralean families as well as hitherto undersampled representatives of small, radially symmetrical, placodioid cyanolichen genera from the Northern and Southern Hemispheres. Bayesian and maximum likelihood consensus trees from our multilocus analyses (nuSSU, nuLSU and mtSSU) recovered the genera Koerberia, Vestergrenopsis and Steinera as a new, fully supported, family-level clade within the Peltigerales. This clade is further supported by a posteriori morphological analysis and we describe it here as the new family Koerberiaceae. The recently described and physiognomically similar genus Steineropsis, by contrast, is recovered as sister to Protopannaria in the Pannariaceae (Collematineae). Previous analyses have recovered strong monophyletic groups around Pannariaceae, Lobariaceae and Peltigeraceae. We discuss in detail the phylogenetic relationships of all these taxa, provide a pan-Peltigeralean overview of phenotypic characteristics and illustrate all major ascus apical structures. Our topology provides strong backbone support for the sister relationship of Peltigerineae to Collematineae as well as for most currently recognized families of the Peltigerales. The following new combinations are made: Steinera symptychia (Tuck.) T. Sprib. & Muggia, and Vestergrenopsis sonomensis (Tuck.) T. Sprib. & Muggia.
Bryoria abbreviata, B. oregana and B. subdivergens, all belonging to Bryoria sect. Subdivergentes, form a well-defined group distinct from other species of Bryoria and other genera of lichens, based on cell wall chemistry, cortical anatomy, and general morphology. These three species are recognized here as comprising the new genus Nodobryoria. Bryoria divergescens is excluded from sect. Subdivergentes and the new genus. Details of the ascus structure and dehiscence with reference to the structure and origin of an operculum-like ''inner ascal flap'' are presented.
Two-dimensional thin-layer chromatography is useful for microchemical studies on mixtures difficult to resolve by the standardized one-dimensional thin-layer chromatographic method now commonly used for lichen products. A modified two-dimensional technique uses the large body of standardized RF data already accumulated for these compounds. In addition, correlations of RF values with chemical structures permit tentative identifications of many trace constituents, including new natural products, resolved from microextracts by the two-dimensional method. The standardized two-dimensional procedure also allows more reliable comparisons of chromatograms and the determination of RF classes of components of complex mixtures. The method is illustrated for the orcinol-type depsides of two closely related species, Parmelia loxodes and P. verruculifera.
Because the number of fungal species (mycobionts) exceeds the number of algae and cyanobacteria (photobionts) found in lichens by more than two orders of magnitude, reciprocal one-to-one specificity between one fungal species and one photobiont across their entire distribution is not expected in this symbiotic system, and has not previously been observed. The specificity of the cyanobacterium Nostoc found in lichens was evaluated at a broad geographical scale within one of the main families of lichen-forming fungi (Collemataceae) that associate exclusively with this photobiont. A phylogenetic study was conducted using rbcLXS sequences from Nostoc sampled from 79 thalli (representing 24 species within the Collemataceae), and 163 Nostoc sequences gathered from GenBank. Although most of the lichen-forming fungal species belonging to the Collemataceae exhibited the expected generalist pattern of association with multiple distinct lineages of Nostoc, five independent cases of one-to-one reciprocal specificity at the species level, including two that span intercontinental distributions, were discovered. Each of the five distinct monophyletic Nostoc groups, associated with these five highly specific mycobiont species, represent independent transitions from a generalist state during the evolution of both partners, which might be explained by transitions to asexual fungal reproduction, involving vertical photobiont transmission, and narrowing of ecological niches.
DNA sequence evolution through nucleotide substitution may be assimilated to a stationary Markov process. The fundamental equations of the general model, with 12 independent substitution parameters, are used to obtain a formula which corrects the effect of multiple and parallel substitutions on the measure of evolutionary divergence between two homologous sequences. We show that only reversible models, with six independent parameters, allow the calculation of the substitution rates. Simulation experiments on DNA sequence evolution through nucleotide substitution call into question the effectiveness of the general model (and of any other more detailed description); nevertheless, the general model results are slightly superior to any of its particular cases.
Detailed restriction analyses of many samples often require substantial amounts of time and effort for DNA extraction, restriction digests, Southern blotting, and hybridization. We describe a novel approach that uses the polymerase chain reaction (PCR) for rapid simplified restriction typing and mapping of DNA from many different isolates. DNA fragments up to 2 kilobase pairs in length were efficiently amplified from crude DNA samples of several pathogenic Cryptococcus species, including C. neoformans, C. albidus, C. laurentii, and C. uniguttulatus. Digestion and electrophoresis of the PCR products by using frequent-cutting restriction enzymes produced complex restriction phenotypes (fingerprints) that were often unique for each strain or species. We used the PCR to amplify and analyze restriction pattern variation within three major portions of the ribosomal DNA (rDNA) repeats from these fungi. Detailed mapping of many restriction sites within the rDNA locus was determined by fingerprint analysis of progressively larger PCR fragments sharing a common primer site at one end. As judged by PCR fingerprints, the rDNA of 19 C. neoformans isolates showed no variation for four restriction enzymes that we surveyed. Other Cryptococcus spp. showed varying levels of restriction pattern variation within their rDNAs and were shown to be genetically distinct from C. neoformans. The PCR primers used in this study have also been successfully applied for amplification of rDNAs from other pathogenic and nonpathogenic fungi, including Candida spp., and ought to have wide applicability for clinical detection and other studies.
Lichens and lichenicolous fungi of the Queen Charlotte Islands, British Columbia, Canada. 1. Introduction and new records for B.C., Canada and North America
- I M Brodo
Brodo IM (1995) Lichens and lichenicolous fungi of the Queen Charlotte
Islands, British Columbia, Canada. 1. Introduction and new records for
B.C., Canada and North America. Mycotaxon 56, 135-173.
T-BAS: Tree-Based Alignment Selector toolkit for phylogenetic-based placement, alignment downloads, and metadata visualization: an example with the Pezizomycotina tree of life
- I Carbone
- White
- Jb
- J Miadlikowska
- A E Arnold
- Miller
- Ma
- F Kauff
- U 'ren
- J M May
- F Lutzoni
Carbone I, White JB, Miadlikowska J, Arnold AE, Miller MA, Kauff F,
U'Ren JM, May G and Lutzoni F (2017) T-BAS: Tree-Based Alignment
Selector toolkit for phylogenetic-based placement, alignment downloads,
and metadata visualization: an example with the Pezizomycotina tree of
life. Bioinformatics 33, 1160-1168.
T-BAS version 2.1: Tree-Based Fig. 4. Apothecial details of Sinuicella denisonii (OSC 35280). A, apothecial section in water. B, asci in K followed by IKI. C
- I Carbone
- J B White
- J Miadlikowska
- A E Arnold
- M A Miller
- N Magain
- U 'ren
- J M Lutzoni
Carbone I, White JB, Miadlikowska J, Arnold AE, Miller MA, Magain N,
U'Ren JM and Lutzoni F (2019) T-BAS version 2.1: Tree-Based
Fig. 4. Apothecial details of Sinuicella denisonii (OSC 35280). A, apothecial section in water. B, asci in K followed by IKI. C, ascospores in K. D, proper exciple. Scales:
A = 100 μm;