36,874 research outputs found
Hypotrachyna cleefii Divakar, A. Crespo, Sipman, Elix, comb. nov.
No full text<i>Hypotrachyna cleefii</i> (Sipman) Divakar, A. Crespo, Sipman, Elix & Lumbsch, <i>comb. nov.</i> MycoBank No.: <p>MB 803583</p> <p> <i>Parmelina cleefii</i> Sipman (1980: 352); <i>Parmelinopsis cleefii</i> (Sipman) V. Marcano & Sipman in Marcano <i>et al</i>. (1996: 214).</p> <p> <i>Hypotrachyna ectypa</i> (Brusse) Divakar, A. Crespo, Sipman, Elix & Lumbsch, <i>comb. nov.</i> MycoBank No.: MB 803584</p> <p> <i>Parmelia ectypa</i> Brusse (1991: 164); <i>Parmelinopsis ectypa</i> (Brusse) DePriest & Hale (1998: 203).</p>Published as part of <i>Divakar, Pradeep K., Crespo, Ana, Núñez-Zapata, Jano, Flakus, Adam, Sipman, Harrie J. M., Elix, John A. & Lumbsch, H. Thorsten, 2013, A molecular perspective on generic concepts in the Hypotrachyna clade (Parmeliaceae, Ascomycota), pp. 21-38 in Phytotaxa 132 (1)</i> on page 33, DOI: 10.11646/phytotaxa.132.1.2, <a href="http://zenodo.org/record/5086040">http://zenodo.org/record/5086040</a>
Formal Development of a Total Order Broadcast for Distributed Transactions using Event-B
No full textAbstract. In a replicated database system, copies of the database are kept across several sites for fault-tolerance and availability. Data access in such systems is usually done within a transactional framework. A read-only transaction accesses data locally and an update transaction modifies the database at all sites. Total order broadcast primitives have been proposed to support transactions and allow fault-tolerant cooperation between the sites in a distributed system. In this paper, we identify and analyze the problem of formation of deadlocks among conflicting update transactions due to race conditions and outline how a system of total order broadcast prevents deadlocks and transaction failures. Later we outline how a refinement based approach with Event-B can be used for formal development of the models of total order broadcast. In this approach we begin with the abstract model of a total order broadcast and verify that the required ordering properties are preserved by the system. total order can correctly be implemented by using a notion of sequence number. This technique requires us to discharge proof obligations due to consistency and refinement checking. To discharge the proof obligations we are required to discover invariants that describes the relationship between the abstract total order and the underlying mechanism.
Formal Specifications and Verification of Message Ordering Properties in a Broadcasting System using Event B
No full textCausal and total order broadcast has been proposed as a mechanism to provide fault tolerance for constructing reliable distributed systems. The use of formal methods to develop a model of a system, specifying critical properties and the verification of them is a way of obtaining better design of dependable services. Event B is a formal technique which provides a framework for developing mathematical models of distributed systems by rigorous description of the problem, gradually introducing solutions in the refinement steps, and verification of solutions by discharge of proof obligations. In this paper, we present a formal development of a system in Event B where processes communicate by broadcast and the messages are delivered following a causal and a total order. We first present separate models of a broadcast system each for a causal order and a total order. Subsequently, we verify that the models of the system preserves the required ordering properties. Further, we develop a model of a system satisfying both causal and a total order on the messages. Later in the refinement, we outline how these ordering properties can correctly be implemented by the vector clocks. In this approach we discover some interesting invariant properties which describes the relationship of abstract causal and total order with the vector clocks and the sequence numbers
Rigorous Design of Fault-Tolerant Transactions for Replicated Database Systems using Event B
No full textSystem availability is improved by the replication of data objects in a distributed database system. However, during updates, the complexity of keeping replicas identical arises due to failures of sites and race conditions among conflicting transactions. Fault tolerance and reliability are key issues to be addressed in the design and architecture of these systems. Event B is a formal technique which provides a framework for developing mathematical models of distributed systems by rigorous description of the problem, gradually introducing solutions in refinement steps, and verification of solutions by discharge of proof obligations. In this paper, we present a formal development of a distributed system using Event B that ensures atomic commitment of distributed transactions consisting of communicating transaction components at participating sites. This formal approach carries the development of the system from an initial abstract specification of transactional updates on a one copy database to a detailed design containing replicated databases in refinement. Through refinement we verify that the design of the replicated database confirms to the one copy database abstraction
Fungal–algal association patterns in lichen symbiosis linked to macroclimate
No full textBoth macroclimate and evolutionary events may influence symbiont association and diversity patterns. Here we assess how climatic factors and evolutionary events shape fungal–algal association patterns in the widely distributed lichen-forming fungal genus Protoparmelia. Multilocus phylogenies of fungal and algal partners were generated using 174 specimens. Coalescent-based species delimitation analysis suggested that 23 fungal hosts are associating with 20 algal species. Principal component analysis (PCA) was performed to infer how fungal–algal association patterns varied with climate. Fungi associated with one to three algal partners whereas algae accepted one to five fungal partners. Both fungi and algae were more specific, associating with fewer partners, in the warmer climates. Interaction with more than one partner was more frequent in cooler climates for both the partners. Cophylogenetic analyses suggest congruent fungal–algal phylogenies. Host switch was a more common event in warm climates, whereas failure of the photobiont to diverge with its fungal host was more frequent in cooler climates. We conclude that both environmental factors and evolutionary events drive fungal and algal evolution in Protoparmelia. The processes leading to phylogenetic congruence of fungi and algae are different in different macrohabitats in our study system. Hence, closely related species inhabiting diverse habitats may follow different evolutionary pathways
Insights into intrathalline genetic diversity of the cosmopolitan lichen symbiotic green alga Trebouxia decolorans Ahmadjian using microsatellite markers
No full textTrebouxia decolorans is a widespread and common symbiotic green alga that is found in association with different species of lichen-forming fungi. By applying T. decolorans-specific microsatellite markers, we investigated the within-thallus diversity of T. decolorans in thalli of Xanthoria parietina and Anaptychia ciliaris. We found several algal strains in most of the thalli of both hosts. High genetic differentiation among thalli suggests that algal diversity is generated de novo via mutation in both fungal hosts. Rarefied allelic richness of the algae was higher in thalli of X. parietina. Our results indicate that in X. parietina intrathalline algal diversity is additionally created by environmental uptake of algae either at the start of the symbiotic association or during the lifetime of the thallus. This study indicates that promiscuous host-symbiont associations in lichen symbioses with Trebouxia spp. may be more common than currently recognized. © 2014 Elsevier Inc
Genome-wide analysis of biosynthetic gene cluster reveals correlated gene loss with absence of usnic acid in lichen-forming fungi
No full textLichen-forming fungi are known to produce a large number of secondary metabolites. Some metabolites are deposited in the cortical layer of the lichen thallus where they exert important ecological functions, such as UV filtering. The fact that closely related lineages of lichen-forming fungi can differ in cortical chemistry suggests that natural product biosynthesis in lichens can evolve independent from phylogenetic constraints. Usnic acid is one of the major cortical pigments in lichens. Here we used a comparative genomic approach on 46 lichen-forming fungal species of the Lecanoromycetes to elucidate the biosynthetic gene content and evolution of the gene cluster putatively responsible for the biosynthesis of usnic acid. Whole-genome sequences were gathered from taxa belonging to different orders and families of Lecanoromycetes, where Parmeliaceae is the most well-represented taxon, and analyzed with a variety of genomic tools. The highest number of biosynthetic gene clusters was found in Evernia prunastri, Pannoparmelia angustata, and Parmotrema austrosinense, respectively, and lowest in Canoparmelia nairobiensis, Bulbothrix sensibilis, and Hypotrachyna scytodes. We found that all studied species producing usnic acid contain the putative usnic acid biosynthetic gene cluster, whereas the cluster was absent in all genomes of species lacking usnic acid. The absence of the gene cluster was supported by an additional unsuccessful search for ß-ketoacylsynthase, the most conserved domain of the gene cluster, in the genomes of species lacking usnic acid. The domain architecture of this PKS cluster-homologous to the already known usnic acid PKS cluster (MPAS) and CYT450 (MPAO)-varies within the studied species, whereas the gene arrangement is highly similar in closely related taxa. We hypothesize that the ancestor of these lichen-forming fungi contained the putative usnic acid producing PKS cluster and that the gene cluster was lost repeatedly during the evolution of these groups. Our study provides insight into the genomic adaptations to the evolutionary success of these lichen-forming fungal species and sets a baseline for further exploration of biosynthetic gene content and its evolutionary significance
Environment and host identity structure communities of green algal symbionts in lichens
No full textAn understanding of how biotic interactions shape species’ distributions is central to predicting host–symbiont responses under climate change. Switches to locally adapted algae have been proposed to be an adaptive strategy of lichen-forming fungi to cope with environmental change. However, it is unclear how lichen photobionts respond to environmental gradients, and whether they play a role in determining the fungal host's upper and lower elevational limits. Deep-coverage Illumina DNA metabarcoding was used to track changes in the community composition of Trebouxia algae associated with two phylogenetically closely related, but ecologically divergent fungal hosts along a steep altitudinal gradient in the Mediterranean region. We detected the presence of multiple Trebouxia species in the majority of thalli. Both altitude and host genetic identity were strong predictors of photobiont community assembly in these two species. The predominantly clonally dispersing fungus showed stronger altitudinal structuring of photobiont communities than the sexually reproducing host. Elevation ranges of the host were not limited by the lack of compatible photobionts. Our study sheds light on the processes guiding the formation and distribution of specific fungal–algal combinations in the lichen symbiosis. The effect of environmental filtering acting on both symbiotic partners appears to shape the distribution of lichens
Characterization of Fungus-Specific Microsatellite Markers in the Lichen-Forming Fungus Parmelina Carporrhizans (Parmeliaceae)
No full textPremise of the study: Microsatellite loci were developed to study the lichen-forming fungus Parmelina (Parmeliaceae) in different habitats of western Europe and the Mediterranean for baseline studies to understand the effects of climate change on its distribution. Methods and Results: We cultured P. carporrhizans from ascospores for genomic sequencing with Illumina HiSeq. We successfully developed 11 polymorphic microsatellite markers and associated primer sets and assessed them with 30 individuals from two of the Canary Islands. The average number of alleles per locus was 8.8. Nei's unbiased gene diversity of these loci ranged from 0.53 to 0.91 in the tested populations. Amplification in two closely related species ( P. tiliacea , P. cryptotiliacea ) yielded only limited success. Conclusions: The new microsatellite markers will allow the study of genetic diversity and population structure in P. carporrhizans . We propose eight markers to combine in two multiplex reactions for further studies on a larger set of populations
Neogene diversification in the temperate lichen-forming fungal genus <i>Parmelia</i> (Parmeliaceae, Ascomycota)
No full textThe lichen-forming genus Parmelia Acharius occurs worldwide but its centre of distribution is in the northern hemisphere and it is widespread in boreal-temperate Eurasia and North America. Recent molecular work on Parmelia has identified phylogenetic relationships within two major groups of the genus: P. saxatilis s. lat. and P. sulcata s. lat. However, little is known about the diversification and historical biogeography of these groups. Here we have used a dataset of two genetic markers and 64 samples to estimate phylogenetic relationships within Parmelia. The dated phylogeny provides evidence for major diversification during the Neogene and Pleistocene. These diversification events are probably correlated with climatic changes during these periods. Evidence of gene flow within species between populations from North America and Europe has been found in three species: P. sulcata Taylor, P. saxatilis (L.) Acharius and P. barrenoae Divakar, M.C. Molina & A. Crespo. Cryptic species recently segregated on the basis of molecular differences (P. encryptata A. Crespo, Divakar & M.C. Molina vs. P. sulcata and P. saxatilis vs. P. mayi Divakar, A. Crespo & M.C. Molina) do not share a common ancestor. Moreover, the P. saxatilis complex is remarkably diverse. Two morphotypes of P. saxatilis s. lat. were shown to represent independent monophyletic lineages. Consequently, two species (P. sulymae Goward, Divakar, & M.C. Molina & A. Crespo and P. imbricaria Goward, Divakar, M.C. Molina & A. Crespo) are newly described here.</p
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