The subphylum Saccharomycotina is a lineage in the fungal phylum Ascomycota that exhibits levels of genomic diversity similar to those of plants and animals. The Saccharomycotina consist of more than ...1 200 known species currently divided into 16 families, one order, and one class. Species in this subphylum are ecologically and metabolically diverse and include important opportunistic human pathogens, as well as species important in biotechnological applications. Many traits of biotechnological interest are found in closely related species and often restricted to single phylogenetic clades. However, the biotechnological potential of most yeast species remains unexplored. Although the subphylum Saccharomycotina has much higher rates of genome sequence evolution than its sister subphylum, Pezizomycotina , it contains only one class compared to the 16 classes in Pezizomycotina . The third subphylum of Ascomycota , the Taphrinomycotina , consists of six classes and has approximately 10 times fewer species than the Saccharomycotina . These data indicate that the current classification of all these yeasts into a single class and a single order is an underappreciation of their diversity. Our previous genome-scale phylogenetic analyses showed that the Saccharomycotina contains 12 major and robustly supported phylogenetic clades; seven of these are current families ( Lipomycetaceae , Trigonopsidaceae , Alloascoideaceae , Pichiaceae , Phaffomycetaceae , Saccharomycodaceae , and Saccharomycetaceae ), one comprises two current families ( Dipodascaceae and Trichomonascaceae ), one represents the genus Sporopachydermia , and three represent lineages that differ in their translation of the CUG codon (CUG-Ala, CUG-Ser1, and CUG-Ser2). Using these analyses in combination with relative evolutionary divergence and genome content analyses, we propose an updated classification for the Saccharomycotina , including seven classes and 12 orders that can be diagnosed by genome content. This updated classification is consistent with the high levels of genomic diversity within this subphylum and is necessary to make the higher rank classification of the Saccharomycotina more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named.
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•Comparative study of different classical consensus reaching processes applied to large-scale group decision making (LGDM).•Analyze the performance of the models studied by using ...AFRYCA, that is a framework used to simulate different experts behavior patterns during the consensus reaching processes.•New challenges that consensus reaching processes should face to deal with LGDM.
Consensus reaching processes (CRPs) in group decision making (GDM) attempt to reach a mutual agreement among a group of decision makers before making a common decision. Different consensus models have been proposed by different authors in the literature to facilitate CRPs. Classical CRP models focus on achieving an agreement on GDM problems in which few decision makers participate. However, nowadays, societal and technological trends that demand the management of larger scale of decision makers add new requirements to the solution of consensus-based GDM problems. This paper presents a comparative study of different classical CRPs applied to large-scale GDM in order to analyze their performance and find out which are the main challenges that these processes face in large-scale GDM. Such analyses will be developed in a java-based framework (AFRYCA 2.0) simulating different scenarios in large scale GDM.
Variation in synonymous codon usage is abundant across multiple levels of organization: between codons of an amino acid, between genes in a genome, and between genomes of different species. It is now ...well understood that variation in synonymous codon usage is influenced by mutational bias coupled with both natural selection for translational efficiency and genetic drift, but how these processes shape patterns of codon usage bias across entire lineages remains unexplored. To address this question, we used a rich genomic data set of 327 species that covers nearly one third of the known biodiversity of the budding yeast subphylum Saccharomycotina. We found that, while genome-wide relative synonymous codon usage (RSCU) for all codons was highly correlated with the GC content of the third codon position (GC3), the usage of codons for the amino acids proline, arginine, and glycine was inconsistent with the neutral expectation where mutational bias coupled with genetic drift drive codon usage. Examination between genes' effective numbers of codons and their GC3 contents in individual genomes revealed that nearly a quarter of genes (381,174/1,683,203; 23%), as well as most genomes (308/327; 94%), significantly deviate from the neutral expectation. Finally, by evaluating the imprint of translational selection on codon usage, measured as the degree to which genes' adaptiveness to the tRNA pool were correlated with selective pressure, we show that translational selection is widespread in budding yeast genomes (264/327; 81%). These results suggest that the contribution of translational selection and drift to patterns of synonymous codon usage across budding yeasts varies across codons, genes, and genomes; whereas drift is the primary driver of global codon usage across the subphylum, the codon bias of large numbers of genes in the majority of genomes is influenced by translational selection.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Cell-cycle checkpoints and DNA repair processes protect organisms from potentially lethal mutational damage. Compared to other budding yeasts in the subphylum Saccharomycotina, we noticed that a ...lineage in the genus Hanseniaspora exhibited very high evolutionary rates, low Guanine-Cytosine (GC) content, small genome sizes, and lower gene numbers. To better understand Hanseniaspora evolution, we analyzed 25 genomes, including 11 newly sequenced, representing 18/21 known species in the genus. Our phylogenomic analyses identify two Hanseniaspora lineages, a faster-evolving lineage (FEL), which began diversifying approximately 87 million years ago (mya), and a slower-evolving lineage (SEL), which began diversifying approximately 54 mya. Remarkably, both lineages lost genes associated with the cell cycle and genome integrity, but these losses were greater in the FEL. E.g., all species lost the cell-cycle regulator WHIskey 5 (WHI5), and the FEL lost components of the spindle checkpoint pathway (e.g., Mitotic Arrest-Deficient 1 MAD1, Mitotic Arrest-Deficient 2 MAD2) and DNA-damage-checkpoint pathway (e.g., Mitosis Entry Checkpoint 3 MEC3, RADiation sensitive 9 RAD9). Similarly, both lineages lost genes involved in DNA repair pathways, including the DNA glycosylase gene 3-MethylAdenine DNA Glycosylase 1 (MAG1), which is part of the base-excision repair pathway, and the DNA photolyase gene PHotoreactivation Repair deficient 1 (PHR1), which is involved in pyrimidine dimer repair. Strikingly, the FEL lost 33 additional genes, including polymerases (i.e., POLymerase 4 POL4 and POL32) and telomere-associated genes (e.g., Repressor/activator site binding protein-Interacting Factor 1 RIF1, Replication Factor A 3 RFA3, Cell Division Cycle 13 CDC13, Pbp1p Binding Protein PBP2). Echoing these losses, molecular evolutionary analyses reveal that, compared to the SEL, the FEL stem lineage underwent a burst of accelerated evolution, which resulted in greater mutational loads, homopolymer instabilities, and higher fractions of mutations associated with the common endogenously damaged base, 8-oxoguanine. We conclude that Hanseniaspora is an ancient lineage that has diversified and thrived, despite lacking many otherwise highly conserved cell-cycle and genome integrity genes and pathways, and may represent a novel, to our knowledge, system for studying cellular life without them.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Nearly all genetic variants that influence disease risk have human-specific origins; however, the systems they influence have ancient roots that often trace back to evolutionary events long before ...the origin of humans. Here, we review how advances in our understanding of the genetic architectures of diseases, recent human evolution and deep evolutionary history can help explain how and why humans in modern environments become ill. Human populations exhibit differences in the prevalence of many common and rare genetic diseases. These differences are largely the result of the diverse environmental, cultural, demographic and genetic histories of modern human populations. Synthesizing our growing knowledge of evolutionary history with genetic medicine, while accounting for environmental and social factors, will help to achieve the promise of personalized genomics and realize the potential hidden in an individual's DNA sequence to guide clinical decisions. In short, precision medicine is fundamentally evolutionary medicine, and integration of evolutionary perspectives into the clinic will support the realization of its full potential.
Abstract
Motivation
Diverse disciplines in biology process and analyze multiple sequence alignments (MSAs) and phylogenetic trees to evaluate their information content, infer evolutionary events and ...processes and predict gene function. However, automated processing of MSAs and trees remains a challenge due to the lack of a unified toolkit. To fill this gap, we introduce PhyKIT, a toolkit for the UNIX shell environment with 30 functions that process MSAs and trees, including but not limited to estimation of mutation rate, evaluation of sequence composition biases, calculation of the degree of violation of a molecular clock and collapsing bipartitions (internal branches) with low support.
Results
To demonstrate the utility of PhyKIT, we detail three use cases: (1) summarizing information content in MSAs and phylogenetic trees for diagnosing potential biases in sequence or tree data; (2) evaluating gene–gene covariation of evolutionary rates to identify functional relationships, including novel ones, among genes and (3) identify lack of resolution events or polytomies in phylogenetic trees, which are suggestive of rapid radiation events or lack of data. We anticipate PhyKIT will be useful for processing, examining and deriving biological meaning from increasingly large phylogenomic datasets.
Availability and implementation
PhyKIT is freely available on GitHub (https://github.com/JLSteenwyk/PhyKIT), PyPi (https://pypi.org/project/phykit/) and the Anaconda Cloud (https://anaconda.org/JLSteenwyk/phykit) under the MIT license with extensive documentation and user tutorials (https://jlsteenwyk.com/PhyKIT).
Supplementary information
Supplementary data are available at Bioinformatics online.
Bee products, such as honey, are widely consumed as food and consumer interest is currently oriented towards organic foods. Regarding this, the European Commission establishes that the qualification ...of organic honey and other beekeeping products as being from organic production is closely bound with the characteristics of hive treatments as well as the quality of the environment. Agricultural contamination with pesticides is a challenging problem that needs to be fully addressed, in particular in the field of organic production systems. In this study, the occurrence of different classes of contaminants selected as representative of potential contamination sources were investigated in 59 organic honeys: organochlorines, OCs; organophosphates, OPs; polychlorobiphenyls, PCBs and polybromodiphenylethers, PBDEs. A method based on Accelerated Solvent Extraction with “in line” clean-up and GC-MS/MS detection was developed to detect contaminants. Residues of many pesticides were found in most of the samples investigated. The majority of honey samples contained at least one of the pesticides, even if their concentrations were found to be lower than its MRL. Diazinon, Mevinphos, Coumaphos, Chlorpyrifos and Quinoxyfen were the residues frequently detected in samples coming from the apple and citrus orchard areas. Furthermore, the results of the present study show that the presence of the residue in organic honey may also be affected by the geographical area (e.g. the presence of an agricultural system) confirming honey bee and beehive matrices as appropriate sentinels for monitoring contamination in the environment. The optimised method proved to be simple and rapid, requiring small sample sizes and minimising solvent consumption, due to the ASE having an “in line” clean-up step.
•The pesticide contamination of organic honey is strictly related to the contamination source.•The study of contaminants is pivotal for beekeepers to select a production area dedicated to the organic honey production.•Control of residues in foods is essential to assess human exposure to contaminants through the diet.•High frequency of pesticides utilized in apple and citrus orchards were observed in organic honey samples.
This paper presents a high-reliability single-phase transformerless grid-connected inverter that utilizes superjunction MOSFETs to achieve high efficiency for photovoltaic applications. The proposed ...converter utilizes two split ac-coupled inductors that operate separately for positive and negative half grid cycles. This eliminates the shoot-through issue that is encountered by traditional voltage source inverters, leading to enhanced system reliability. Dead time is not required at both the high-frequency pulsewidth modulation switching commutation and the grid zero-crossing instants, improving the quality of the output ac-current and increasing the converter efficiency. The split structure of the proposed inverter does not lead itself to the reverse-recovery issues for the main power switches and as such superjunction MOSFETs can be utilized without any reliability or efficiency penalties. Since MOSFETs are utilized in the proposed converter high efficiency can be achieved even at light load operations achieving a high California energy commission (CEC) or European union efficiency of the converter system. It also has the ability to operate at higher switching frequencies while maintaining high efficiency. The higher operating frequencies with high efficiency enables reduced cooling requirements and results in system cost savings by shrinking passive components. With two additional ac-side switches conducting the currents during the freewheeling phases, the photovoltaic array is decoupled from the grid. This reduces the high-frequency common-mode voltage leading to minimized ground loop leakage current. The operation principle, common-mode characteristic and design considerations of the proposed transformerless inverter are illustrated. The total losses of the power semiconductor devices of several existing transformerless inverters which utilize MOSFETs as main switches are evaluated and compared. The experimental results with a 5 kW prototype circuit show 99.0% CEC efficiency and 99.3% peak efficiency with a 20 kHz switching frequency. The high reliability and efficiency of the proposed converter makes it very attractive for single-phase transformerless photovoltaic inverter applications.
The Leloir galactose utilization or GAL pathway of budding yeasts, including that of the baker’s yeast Saccharomyces cerevisiae and the opportunistic human pathogen Candida albicans, breaks down the ...sugar galactose for energy and biomass production. The GAL pathway has long served as a model system for understanding how eukaryotic metabolic pathways, including their modes of regulation, evolve. More recently, the physical linkage of the structural genes GAL1, GAL7, and GAL10 in diverse budding yeast genomes has been used as a model for understanding the evolution of gene clustering. In this review, we summarize exciting recent work on three different aspects of this iconic pathway’s evolution: gene cluster organization, GAL gene regulation, and the population genetics of the GAL pathway.
The GAL pathway of budding yeasts is a powerful model for inferring the evolutionary principles guiding the evolution of eukaryotic metabolic and genetic pathways.The GAL pathway exhibits substantial variation in its genomic organization across budding yeast species, and a few different mechanisms have driven the evolution of this organization.At least two distinct modes of regulation of the GAL pathway are known in the budding yeast subphylum; there is likely substantial variation between species that use these modes of regulation, and other yet-to-be-discovered modes of regulation likely exist in the subphylum.Population genomic studies have revealed extensive genetic variation, including alternative and highly distinct GAL gene network variants, within budding yeast species, suggesting that yeast populations are subject to varied selection for the utilization of the galactose present in different environments and conditions.
Natural selection shapes the genetic architecture of many human traits. However, the prevalence of different modes of selection on genomic regions associated with variation in traits remains poorly ...understood. To address this, we developed an efficient computational framework to calculate positive and negative enrichment of different evolutionary measures among regions associated with complex traits. We applied the framework to summary statistics from >900 genome-wide association studies (GWASs) and 11 evolutionary measures of sequence constraint, population differentiation, and allele age while accounting for linkage disequilibrium, allele frequency, and other potential confounders. We demonstrate that this framework yields consistent results across GWASs with variable sample sizes, numbers of trait-associated SNPs, and analytical approaches. The resulting evolutionary atlas maps diverse signatures of selection on genomic regions associated with complex human traits on an unprecedented scale. We detected positive enrichment for sequence conservation among trait-associated regions for the majority of traits (>77% of 290 high power GWASs), which included reproductive traits. Many traits also exhibited substantial positive enrichment for population differentiation, especially among hair, skin, and pigmentation traits. In contrast, we detected widespread negative enrichment for signatures of balancing selection (51% of GWASs) and absence of enrichment for evolutionary signals in regions associated with late-onset Alzheimer's disease. These results support a pervasive role for negative selection on regions of the human genome that contribute to variation in complex traits, but also demonstrate that diverse modes of evolution are likely to have shaped trait-associated loci. This atlas of evolutionary signatures across the diversity of available GWASs will enable exploration of the relationship between the genetic architecture and evolutionary processes in the human genome.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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