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46 results for “selective sweeps”
BIR-MicroED: selected area electron diffraction datasets from tilting microcrystals, with multiple sweeps of data collected on each crystal (Co(II) meso-tetraphenyl porphyrin) at 200 keV
<div> <p>This deposition contains a series zip files each containing electron diffraction datasets in .mrc file format. Each folder collects data acquired from crystals of a particular compound under the same conditions (electron energy, temperature). For each crystal, multiple subsequent sweeps (passes) at the same incident flux covering the same angular range are given. Zip files are named according to the format: <em>"CompoundName</em>_multipass_<em>RotationSpeed</em>_<em>FrameRate</em>_<em>SpotSize</em>_tiltseries_<em>Temperature</em>.zip"</p> <p>Where spot size 11 = 0.01 electrons per square Angstrom per second incident flux, and spot size 10 = 0.03 electrons per square Angstrom per second incident flux</p> <p>Diffraction datasets within each folder are named according to the format: <em>"CompoundName</em>_tiltseries_<em>AcceleratingVoltage</em>_<em>Temperature_IncidentFlux</em>_crystal#sweep#.mrc"</p> <p>Where crystal1sweep1 and crystal1sweep2 indicate the first and second sweep of data acquired on the same crystal, respectively.</p> </div>
BIR-MicroED: selected area electron diffraction datasets from tilting microcrystals, with multiple sweeps of data collected on each crystal (Zn(II)-histidine) at 200 keV
<p>This deposition contains a series zip files each containing electron diffraction datasets in .mrc file format. Each folder collects data acquired from crystals of a particular compound under the same conditions (electron energy, temperature). For each crystal, multiple subsequent sweeps (passes) at the same incident flux covering the same angular range are given. Zip files are named according to the format: <em>"CompoundName</em>_multipass_<em>RotationSpeed</em>_<em>FrameRate</em>_<em>SpotSize</em>_tiltseries_<em>Temperature</em>.zip"</p> <p>Where spot size 11 = 0.01 electrons per square Angstrom per second incident flux, and spot size 10 = 0.03 electrons per square Angstrom per second incident flux</p> <p>Diffraction datasets within each folder are named according to the format: <em>"CompoundName</em>_tiltseries_<em>AcceleratingVoltage</em>_<em>Temperature_IncidentFlux</em>_crystal#sweep#.mrc"</p> <p>Where crystal1sweep1 and crystal1sweep2 indicate the first and second sweep of data acquired on the same crystal, respectively.</p>
BIR-MicroED: selected area electron diffraction datasets from tilting microcrystals, with multiple sweeps of data collected on each crystal (biotin, Zn(II)-methionine) at 200 keV
<p>This deposition contains a series zip files each containing electron diffraction datasets in .mrc file format. Each folder collects data acquired from crystals of a particular compound under the same conditions (electron energy, temperature). For each crystal, multiple subsequent sweeps (passes) at the same incident flux covering the same angular range are given. Zip files are named according to the format: <em>"CompoundName</em>_multipass_<em>RotationSpeed</em>_<em>FrameRate</em>_<em>SpotSize</em>_tiltseries_<em>Temperature</em>.zip"</p> <p>Where spot size 11 = 0.01 electrons per square Angstrom per second incident flux, and spot size 10 = 0.03 electrons per square Angstrom per second incident flux</p> <p>Diffraction datasets within each folder are named according to the format: <em>"CompoundName</em>_tiltseries_<em>AcceleratingVoltage</em>_<em>Temperature_IncidentFlux</em>_crystal#sweep#.mrc"</p> <p>Where crystal1sweep1 and crystal1sweep2 indicate the first and second sweep of data acquired on the same crystal, respectively.</p>
Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement
<p><strong>Background</strong></p> <p>During domestication and subsequent improvement, plants were subjected to intensive positive selection for desirable traits. Identification of selection targets is important with respect to the future targeted broadening of diversity in breeding programmes. Rye (<em>Secale</em> <em>cereale</em> L.) is a cereal that is closely related to wheat, and it is an important crop in Central, Eastern and Northern Europe. The aim of the study was (i) to identify diverse groups of rye accessions based on high-density, genome-wide analysis of genetic diversity within a set of 478 rye accessions, covering a full spectrum of diversity within the genus, from wild accessions to inbred lines used in hybrid breeding, and (ii) to identify selective sweeps in the established groups of cultivated rye germplasm and putative candidate genes targeted by selection. <strong> </strong></p> <p><strong>Results</strong></p> <p>Population structure and genetic diversity analyses based on high-quality SNP (DArTseq) markers revealed the presence of three complexes in the <em>Secale</em> genus: <em>S. sylvestre, S. strictum </em>and<em> S. cereale/vavilovii</em>, a relatively narrow diversity of <em>S. sylvestre</em>, very high diversity of <em>S. strictum</em>, and signatures of strong positive selection in <em>S. vavilovii</em>. Within cultivated ryes, we detected the presence of genetic clusters and the influence of improvement status on the clustering. Rye landraces represent a reservoir of variation for breeding, and especially a distinct group of landraces from Turkey should be of special interest as a source of untapped variation. Selective sweep detection in cultivated accessions identified 133 outlier positions within 13 sweep regions and 170 putative candidate genes related, among others, to response to various environmental stimuli (such as pathogens, drought, cold), plant fertility and reproduction (pollen sperm cell differentiation, pollen maturation, pollen tube growth), and plant growth and biomass production.</p> <p><strong>Conclusions</strong></p> <p>Our study provides valuable information for efficient management of rye germplasm collections, which can help to ensure proper safeguarding of their genetic potential and provides numerous novel candidate genes targeted by selection in cultivated rye for further functional characterisation and allelic diversity studies.</p>
Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement
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Gene-specific selective sweeps are pervasive across human gut microbiomes
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Data from: Prophage maintenance is determined by environment-dependent selective sweeps rather than mutational availability
<p>Prophages, viral sequences integrated into bacterial genomes, can confer fitness benefits and costs. Despite the risk of prophage activation and subsequent bacterial death, active prophages are present in most bacterial genomes. However, our understanding about the selective forces that maintain prophages in bacterial populations is scarce. Combining experimental evolution with stochastic modelling we found that prophage maintenance and loss are primarily determined by environmental conditions that amplify the net fitness effect of the prophage. Whole genome sequencing revealed that prophage loss occurs through environment-specific sequences of selective sweeps, leading to rapid prophage loss when prophages are costly. However, conflicting selection pressures that select against the prophage but for a prophage-encoded accessory gene can prolong prophage maintenance. The extent of prolonged maintenance depends on the sociality of this accessory gene. Selection for non-cooperative genes is more effective for prophage maintenance as cooperative genes allow for protection of phage-free 'cheaters' that may emerge if prophage costs outweigh their benefits. Our mathematical model suggests that environmental variation plays a larger role than mutation rates in determining prophage maintenance. This challenges our understanding of the role of random chance events relative to environmental factors in shaping the evolutionary trajectory of bacterial populations.</p>
Sweepstakes reproductive success via pervasive and recurrent selective sweeps
<p>Highly fecund natural populations characterized by high early mortality abound, yet our knowledge about their recruitment dynamics is somewhat rudimentary. This knowledge gap has implications for our understanding of genetic variation, population connectivity, local adaptation, and the resilience of highly fecund populations. The concept of sweepstakes reproductive success, which posits a considerable variance and skew in individual reproductive output, is key to understanding the distribution of individual reproductive success. However, it still needs to be determined whether highly fecund organisms reproduce through sweepstakes and, if they do, the relative roles of neutral and selective sweepstakes. Here we use coalescent-based statistical analysis of population genomic data to show that selective sweepstakes likely explain recruitment dynamics in the highly fecund Atlantic cod. We show that the Kingman coalescent (modeling no sweepstakes) and the Xi-Beta coalescent (modeling random sweepstakes), including complex demography and background selection, do not provide an adequate fit for the data. The Durrett-Schweinsberg coalescent, in which selective sweepstakes result from recurrent and pervasive selective sweeps of new mutations, offers greater explanatory power. Our results show that models of sweepstakes reproduction and multiple-merger coalescents are relevant and necessary for understanding genetic diversity in highly fecund natural populations. These findings have fundamental implications for understanding the recruitment variation of fish stocks and general evolutionary genomics of high-fecundity organisms.</p>
Sweepstakes reproductive success via pervasive and recurrent selective sweeps
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Candidate selective sweeps in U.S. wheat populations
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Evidence for ancient selective sweeps followed by differentiation among three species of Sphyrapicus sapsuckers
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Data from: Prophage maintenance is determined by environment-dependent selective sweeps rather than mutational availability
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Wang et al Narrow-leafed lupin selective sweep analysis results
<p>Narrow-leafed lupin selective sweep analysis results, supplementary datasets. </p>
Data from: The hitchhiker's guide to Europe: the infection dynamics of an ongoing Wolbachia invasion and mitochondrial selective sweep in Rhagoletis cerasi
Wolbachia is a maternally inherited and ubiquitous endosymbiont of insects. It can hijack host reproduction by manipulations such as cytoplasmic incompatibility (CI) to enhance vertical transmission. Horizontal transmission of Wolbachia can also result in the colonization of new mitochondrial lineages. In this study, we present a 15-year-long survey of Wolbachia in the cherry fruit fly Rhagoletis cerasi across Europe and the spatiotemporal distribution of two prevalent strains, wCer1 and wCer2, and associated mitochondrial haplotypes in Germany. Across most of Europe, populations consisted of either 100% singly (wCer1) infected individuals with haplotype HT1, or 100% doubly (wCer1&2) infected individuals with haplotype HT2, differentiated only by a single nucleotide polymorphism. In central Germany, singly infected populations were surrounded by transitional populations, consisting of both singly and doubly infected individuals, sandwiched between populations fixed for wCer1&2. Populations with fixed infection status showed perfect association of infection and mitochondria, suggesting a recent CI-driven selective sweep of wCer2 linked with HT2. Spatial analysis revealed a range expansion for wCer2 and a large transition zone in which wCer2 splashes appeared to coalesce into doubly infected populations. Unexpectedly, the transition zone contained a large proportion (22%) of wCer1&2 individuals with HT1, suggesting frequent intraspecific horizontal transmission. However, this horizontal transmission did not break the strict association between infection types and haplotypes in populations outside the transition zone, suggesting that this horizontally acquired Wolbachia infection may be transient. Our study provides new insights into the rarely studied Wolbachia invasion dynamics in field populations.
Data from: Recurrent and recent selective sweeps in the piRNA pathway
Uncontrolled transposable element (TE) insertions and excisions can cause chromosome breaks and mutations with dramatic deleterious effects. The PIWI interacting RNA (piRNA) pathway functions as an adaptive TE silencing system during germline development. Several essential piRNA pathway proteins appear to be rapidly evolving, suggesting that TEs and the silencing machinery may be engaged in a classical "evolutionary arms race." Using a variety of molecular evolutionary and population genetic approaches, we find that the piRNA pathway genes rhino, krimper, and aubergine show patterns suggestive of extensive recurrent positive selection across Drosophila species. We speculate that selection on these proteins reflects crucial roles in silencing unfamiliar elements during vertical and horizontal transmission of TEs into naïve populations and species, respectively.
Data from: Soft selective sweeps in fungicide resistance evolution: recurrent mutations without fitness costs in grapevine downy mildew
Adaptation produces hard or soft selective sweeps depending on the supply of adaptive genetic polymorphism. The evolution of pesticide resistance in parasites is a striking example of rapid adaptation that can shed light on selection processes. Plasmopara viticola, which causes grapevine downy mildew, forms large populations, in which resistance has rapidly evolved due to excessive fungicide use. We investigated the pathways by which fungicide resistance has evolved in this plant pathogen, to determine whether hard or soft selective sweeps were involved. An analysis of nucleotide polymorphism in 108 field isolates from the Bordeaux region revealed recurrent mutations of cytb and CesA3 conferring resistance to quinone outside inhibiting (QoI) and carboxylic acid amide (CAA) fungicides, respectively. Higher levels of genetic differentiation were observed for nucleotide positions involved in resistance than for neutral microsatellites, consistent with local adaptation of the pathogen to fungicide treatments. No hitchhiking was found between selected sites and neighbouring polymorphisms in cytb and CesA3, confirming multiple origins of resistance alleles. We assessed resistance costs, by evaluating the fitness of the 108 isolates through measurements of multiple quantitative pathogenicity traits under controlled conditions. No significant differences were found between sensitive and resistant isolates, suggesting that fitness costs may be absent or negligible. Our results indicate that the rapid evolution of fungicide resistance in P. viticola has involved a soft sweep.
Data from: Evaluating the performance of selection scans to detect selective sweeps in domestic dogs
Selective breeding of dogs has resulted in repeated artificial selection on breed-specific morphological phenotypes. A number of quantitative trait loci associated with these phenotypes have been identified in genetic mapping studies. We analyzed the population genomic signatures observed around the causal mutations for 12 of these loci in 25 dog breeds, for which we genotyped 25 individuals in each breed. By measuring the population frequencies of the causal mutations in each breed, we identified those breeds in which specific mutations most likely experienced positive selection. These instances were then used as positive controls for assessing the performance of popular statistics to detect selection from population genomic data. We found that artificial selection during dog domestication has left characteristic signatures in the haplotype and nucleotide polymorphism patterns around selected loci that can be detected in the genotype data from a single population sample. However, the sensitivity and accuracy at which such signatures were detected varied widely between loci, the particular statistic used, and the choice of analysis parameters. We observed examples of both hard and soft selective sweeps and detected strong selective events that removed genetic diversity almost entirely over regions >10 Mbp. Our study demonstrates the power and limitations of selection scans in populations with high levels of linkage disequilibrium due to severe founder effects and recent population bottlenecks.
Data from: Wolbachia-induced meiotic drive and feminization is associated with an independent occurrence of selective mitochondrial sweep in a butterfly
Maternally inherited Wolbachia endosymbionts manipulate arthropod reproduction in various ways. In the butterfly Eurema mandarina, a cytoplasmic incompatibility-inducing Wolbachia strain wCI and the associated mtDNA haplotypes are known to originate from the sister species Eurema hecabe, which offered a good case study for microbe-mediated hybrid introgression. Besides wCI, some females with the Z0 karyotype harbour a distinct Wolbachia strain wFem, which causes all-female production by meiotic drive and feminization. We report that a considerable proportion of E. mandarina females (65.7%) were infected with both wCI and wFem (CF) on Tanegashima Island. While females singly infected with wCI (C) produced offspring at a 1 : 1 sex ratio, CF females produced only females. Although Z-linked sequence polymorphism showed no signs of divergence between C and CF females, mtDNA split into two discrete clades; one consisted of C females and the other CF females, both of which formed a clade with E. hecabe but not with uninfected E. mandarina. This suggests that CF matrilines also, but independently, experienced a selective sweep after hybrid introgression from E. hecabe. Distinct evolutionary forces were suggested to have caused C and CF matrilines to diverge, which would be irreversible because of the particular phenotype of wFem.
Data files for: Hazardous loss of genetic diversity through selective sweeps in asexual populations
<p>With the two-fold cost of sex, derived asexual organisms have an immediate reproductive advantage over their sexual sisters. Yet the "twiggy'' phylogenetic distribution of asexual lineages implies that they go extinct relatively quickly over evolutionary time. Meanwhile, bacteria and archaea have persisted for billions of years without requiring sexual reproduction. A simple explanation for this difference is that prokaryotes have very large population sizes that are not subject to the accumulation of deleterious mutations, but this implies that drift and mutational meltdown dominate derived asexual populations. </p> <p>We explored a different hazard, quantifying the degree to which genetic variation is lost in asexual populations experiencing selective sweeps. Even though large populations generate diversity by mutation during sweeps, we find that populations that are safe from mutational meltdown may still be reduced to dangerous effective population sizes by sweeps. Thus, ironically, adaptation itself reduces further adaptive potential and may predispose asexual populations to extinction. Our data give results for the probability of mutational meltdown across various population sizes, the critical population size required to avoid meltdown, and the effect of selective sweeps on heterozygosity. Analytical predictions are confirmed by simulation.</p> <p>We also derive a simple approximation for the effective population size after a hard sweep, and quantify the impact of recent sweeps on evolutionary rescue. These factors may help to explain the phylogenetic twigginess of asexuals, the maintenance of sex and recombination, and the evolutionary persistence of prokaryotes.</p>
Data from: Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation
Differential gene flow, reductions in diversity following linked selection and/or features of the genome can structure patterns of genomic differentiation during the process of speciation. Possible sources of reproductive isolation are well studied between coastal and inland subspecies groups of Swainson's thrushes, with differences in seasonal migratory behaviour likely playing a key role in reducing hybrid fitness. We assembled and annotated a draft reference genome for this species and generated whole-genome shotgun sequence data for populations adjacent to the hybrid zone between these groups. We documented substantial genomewide heterogeneity in relative estimates of genetic differentiation between the groups. Within population diversity was lower in areas of high relative differentiation, supporting a role for selective sweeps in generating this pattern. Absolute genetic differentiation was reduced in these areas, further suggesting that recurrent selective sweeps in the ancestral population and/or between divergent populations following secondary contact likely occurred. Relative genetic differentiation was also higher near centromeres and on the Z chromosome, suggesting that features of the genome also contribute to genomewide heterogeneity. Genes linked to migratory traits were concentrated in islands of differentiation, supporting previous suggestions that seasonal migration is under divergent selection between Swainson's thrushes. Differences in migratory behaviour likely play a central role in the speciation of many taxa; we developed the infrastructure here to permit future investigations into the role several candidate genes play in reducing gene flow between not only Swainson's thrushes but other species as well.
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