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40 results for “locus selection”
Figures S1-S7. SMR-HEIDI analysis results for 8q24.21 locus between BP and selected phenotypes.
<p><strong>Supplementary Figures S1-S7. </strong><strong>SMR-HEIDI analysis results for rs6651255 between BP and selected phenotypes.</strong></p> <p>This project contains the following figures:</p> <ul> <li> <p>Figure S1. SMR-HEIDI analysis results for rs6651255 between BP and LDH.</p> </li> <li> <p>Figure S2. SMR-HEIDI analysis results for rs6651255 between BP and <em>GSDMC</em> expression in skeletal muscle (GTEx v6).</p> </li> <li> <p>Figure S3. SMR-HEIDI analysis results for rs6651255 between BP and <em>FAM49B</em> expression in Brain anterior cingulate cortex BA24 (GTEx v6).</p> </li> <li> <p>Figure S4. SMR-HEIDI analysis results for rs6651255 between BP and <em>FAM49B</em> expression in CD8 cell line (CEDAR).</p> </li> <li> <p>Figure S5. SMR-HEIDI analysis results for rs6651255 between BP and heel bone mineral density (UKBB).</p> </li> <li> <p>Figure S6. SMR-HEIDI analysis results for rs6651255 between BP and disc problem phenotype (UKBB)</p> </li> <li> <p>Figure S7. SMR-HEIDI analysis results for rs6651255 between BP and height (UKBB).</p> </li> </ul> <p> </p> <p><strong>Figures legend:</strong></p> <p>Each figure consists of four parts (1 – top left; 2- top right; 3- bottom left; 4 – bottom right):</p> <ol> <li> <p>Regional association plots for GWAS-1 (in our case BP GWAS) and GWAS-2 (expression or complex trait). Blue triangles represent SNPs used to calculate HEIDI test. Crossed triangle is leading SNP for which SMR test was computed.</p> </li> <li> <p>Z-Z plot (GWAS-1 on y-axis and GWAS-2 on x-axis).</p> </li> <li> <p>Visualization of LD matrix for SNPs used in calculation of HEIDI test.</p> </li> <li> <p>Plot of SMR regression coefficient estimates. The plot visualizes the heterogeneity of SMR coefficient. Blue color represents SNPs used to calculate HEIDI test.</p> </li> </ol>
Balancing selection at a wing pattern locus is associated with major shifts in genome-wide patterns of diversity and gene flow
<p>Selection shapes genetic diversity around target mutations, yet little is known about how selection on specific loci affects the genetic trajectories of populations, including their genome-wide patterns of diversity and demographic responses. Here we study the patterns of genetic variation and geographic structure in a neotropical butterfly, <em>Heliconius numata</em>, and its closely related allies in the so-called melpomene-silvaniform clade. <em>H. numata</em> is known to have evolved an inversion supergene which controls variation in wing patterns involved in mimicry associations with distinct groups of co-mimics. Butterflies show disassortative mate preferences and heterozygote advantage at this locus. We contrasted patterns of genetic diversity and structure 1) among extant polymorphic and monomorphic populations of <em>H. numata</em>, 2) between <em>H. numata</em> and its close relatives, and 3) between ancestral lineages. We show that <em>H. numata</em> populations which carry the inversions as a balanced polymorphism show markedly distinct patterns of diversity compared to all other taxa. They show the highest genetic diversity and effective population size estimates in the entire clade, as well as a low level of geographic structure and isolation by distance across the entire Amazon basin. By contrast, monomorphic populations of <em>H. numata</em> as well as its sister species and their ancestral lineages all show lower effective population sizes and genetic diversity, and higher levels of geographical structure across the continent. One hypothesis is that the large effective population size of polymorphic populations could be caused by the shift to a regime of balancing selection due to the genetic load and disassortative preferences associated with inversions. Testing this hypothesis with forward simulations supported the observation of increased diversity in populations with the supergene. Our results are consistent with the hypothesis that the formation of a supergene triggered a change in gene flow, causing a general increase in genetic diversity and the homogenisation of genomes at the continental scale.</p>
Data from: Pathways underlying selective neuronal vulnerability in Alzheimer's disease: Contrasting the vulnerable locus coeruleus to the resilient substantia nigra
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Data from: Complex selection on a regulator of social cognition: evidence of balancing selection, regulatory interactions and population differentiation in the prairie vole Avpr1a locus
Adaptive variation in social behavior depends upon standing genetic variation, but we know little about how evolutionary forces shape genetic diversity relevant to brain and behavior. In prairie voles (Microtus ochrogaster), variants at the Avpr1a locus predict expression of the vasopressin 1a receptor in the retrosplenial cortex (RSC), a brain region that mediates spatial and contextual memory; cortical V1aR abundance in turn predicts diversity in space-use and sexual fidelity in the field. To examine the potential contributions of adaptive and neutral forces to variation at the Avpr1a locus, we explore sequence diversity at the Avpr1a locus and throughout the genome in two populations of wild prairie voles. First, we refine results demonstrating balancing selection at the locus by comparing the frequency spectrum of variants at the locus to a random sample of the genome. Next, we find that the four SNPs that predict high V1aR expression in the RSC are in stronger linkage disequilibrium than expected by chance despite high recombination among intervening variants, suggesting that epistatic selection maintains their association despite recombination. Analysis of population structure and a haplotype network for two populations revealed that this excessive LD was unlikely to be due to admixture alone. Furthermore, the two populations differed considerably in the region shown to be a regulator of V1aR expression despite the extremely low levels of genome-wide genetic differentiation. Together, our data suggest that complex selection on Avpr1a locus favors specific combinations of regulatory polymorphisms, maintains the resulting alleles at populations-specific frequencies, and may contribute to unique patterns of spatial cognition and sexual fidelity among populations.
Data from: Complex selection on a regulator of social cognition: evidence of balancing selection, regulatory interactions and population differentiation in the prairie vole Avpr1a locus
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Data from: Selection on a single locus drives plumage differentiation in the Rufous-collared Sparrow (Zonotrichia capensis)
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Data from: Multilocus patterns of genetic variation across Cryptosporidium species suggest balancing selection at the gp60 locus
Cryptosporidium is an apicomplexan protozoan that parasites most vertebrates, including humans. Its gp60 gene is functionally involved in its attachement to host's cells and its high level of genetic variation has made it the reference marker for sample typing in epidemiological studies. To understand the origin of such high diversity and to determine the extent to which this classification applies to the rest of the genome, we analysed the patterns of variation at gp60 and nine other nuclear loci in isolates of three Cryptosporidium species. Most loci showed low genetic polymorphism (πS < 1%) and similar levels of between-species divergence. Contrastingly, gp60 exhibited very different features: (i) it was nearly ten times more variable than the other loci, (ii) it displayed a significant excess of polymorphisms relative to between-species differences in a Maximum-likelihood Hudson-Kreitman-Aguadé test (iii) gp60 subtypes turned out to be much older than the species they were found in and (iv) showed a significant excess of polymorphic variants shared across species from random expectations. These observations suggest that this locus evolves under balancing selection, and specifically under negative frequency-dependent selection. Interestingly, genetic variation at the other loci cluster very well within the subtypes defined by gp60, which may provide new tools to understand the genome-wide patterns of genetic variation of the parasite in the wild. These results suggest that gp60 plays an active and essential role in the life cycle of the parasite and that genetic variation at this locus might be essential for the parasite's long-term success.
Data from: Selection at the Esterase-2 locus of Drosophila buzzatii? Perturbation-reperturbation experiments
Apparent selection affecting starch gel electrophoretic alleles at the Esterase-2 locus of Drosophila buzzatii has been detected in laboratory and natural populations. Perturbation-reperturbation of allele frequencies in replicated laboratory populations attempts to test direct selective effects at the locus versus effects of linked loci. Sequential gel electrophoresis has identified more alleles within starch classes, and three of these alleles (within the a, b and c starch alleles) were used in cage population experiments. Allele a/1.00/1.00/1.00 was set up in 10 replicate populations with allele c/1.00/1.00/1.00, and in an independent 10 replicate populations with allele b/0.99/1.01/1.00. For each set, three reperturbations were done. Replicate populations generally showed similar patterns of allele frequency change and clear directionality: effects of selection, not drift. However, four populations deviated from their replicates, indicating dissipation of linkage disequilibrium. Estimates of pre-adult viability in the F2 of pair-wise crosses among 12 sequential gel electrophoretic alleles showed very variable modes of inheritance and relative viability fitnesses. Together with the diversity of patterns of allele frequency change in the cage populations, these results suggest a gene complex, with selection acting on an interacting set of loci which may include Esterase-2.
Data from: Impact of negative frequency-dependent selection on mating pattern and genetic structure: a comparative analysis of the S-locus and nuclear SSR loci in Prunus lannesiana var. speciosa
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Data from: Selection at the Esterase-2 locus of Drosophila buzzatii? Perturbation-reperturbation experiments
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Data from: Detecting genotypic changes associated with selective mortality at sea in Atlantic salmon: polygenic multi-locus analysis surpasses genome scan
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Data from: Signals of heterogeneous selection at an MHC locus in geographically proximate ecotypes of sockeye salmon
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Data from: Multilocus patterns of genetic variation across Cryptosporidium species suggest balancing selection at the gp60 locus
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Data from: Meiotic drive influences the outcome of sexually antagonistic selection at a linked locus
Most meiotic drivers, such as the t-haplotype in Mus and the segregation distorter (SD) in Drosophila, act in a sex-specific manner, gaining a transmission advantage through one sex although suffering only the fitness costs associated with the driver in the other. Their inheritance is thus more likely through one of the two sexes, a property they share with sexually antagonistic alleles. Previous theory has shown that pairs of linked loci segregating for sexually antagonistic alleles are more likely to remain polymorphic and that linkage disequilibrium accrues between them. I probe this similarity between drive and sexual antagonism and examine the evolution of chromosomes experiencing these selection pressures simultaneously. Reminiscent of previous theory, I find that: the opportunity for polymorphism increases for a sexually antagonistic locus that is physically linked to a driving locus; the opportunity for polymorphism at a driving locus also increases when linked to a sexually antagonistic locus; and stable linkage disequilibrium accompanies any polymorphic equilibrium. Additionally, I find that drive at a linked locus favours the fixation of sexually antagonistic alleles that benefit the sex in which drive occurs. Further, I show that under certain conditions reduced recombination between these two loci is selectively favoured. These theoretical results provide clear, testable predictions about the nature of sexually antagonistic variation on driving chromosomes and have implications for the evolution of genomic architecture.
Data from: Inter-locus sexually antagonistic coevolution creates indirect selection for increased recombination
The ubiquity of recombination in nature is a paradox because it breaks up combinations of alleles favored by natural selection. Theoretical work has shown that antagonistic coevolution between hosts and parasites can result in rapid fluctuations in epistasis, which can create a short-term advantage to recombination. Here we show that another kind of antagonistic coevolution, inter-locus sexually antagonistic coevolution (SAC), can also create indirect selection for modifiers that increase the rate of recombination, and that it can lead to very high levels of recombination at equilibrium. Recombination is favored because inter-locus SAC creates heterogeneity in the strength and direction of selection, both within and between generations, which maintains an excess of disadvantageous haplotypes in the population. This result is similar to and consistent with dynamics of fluctuating epistasis produced in models of host-parasite coevolution. However, the conditions under which inter-locus SAC provides an advantage to recombination are more permissive.
Data from: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus
The soybean cyst nematode (SCN) resistance locus Rhg1 is a tandem repeat of a 31.2 kb unit of the soybean genome. Each 31.2-kb unit contains four genes. One allele of Rhg1, Rhg1-b, is responsible for protecting most US soybean production from SCN. Whole-genome sequencing was performed, and PCR assays were developed to investigate allelic variation in sequence and copy number of the Rhg1 locus across a population of soybean germplasm accessions. Four distinct sequences of the 31.2-kb repeat unit were identified, and some Rhg1 alleles carry up to three different types of repeat unit. The total number of copies of the repeat varies from 1 to 10 per haploid genome. Both copy number and sequence of the repeat correlate with the resistance phenotype, and the Rhg1 locus shows strong signatures of selection. Significant linkage disequilibrium in the genome outside the boundaries of the repeat allowed the Rhg1 genotype to be inferred using high-density single nucleotide polymorphism genotyping of 15 996 accessions. Over 860 germplasm accessions were found likely to possess Rhg1 alleles. The regions surrounding the repeat show indications of non-neutral evolution and high genetic variability in populations from different geographic locations, but without evidence of fixation of the resistant genotype. A compelling explanation of these results is that balancing selection is in operation at Rhg1.
Locus Coeruleus firing patterns selectively modulate brain activity and dynamics
<p>This dataset supports the manuscript entitled 'Locus Coeruleus firing patterns selectively modulate brain activity and dynamics' (https://doi.org/10.1101/2022.08.29.505672). Please refer to this manuscript for detailed information. </p> <p>The dataset contains a total of 81 functional (GE-BOLD) and 30 anatomical (T1-weighted) scans of ChR2-expressing C57BL/6-Tg(<em>Dbh</em>-iCre)1Gsc mice in NIFTI format, multiplied by 10. Mice were optogenetically stimulated with blue light in the right Locus Coeruleus in a 3Hz tonic, 5Hz tonic, and 15Hz burst pattern. Sham stimulation entailed red light stimulation at a 5Hz tonic frequency. The 'StimulationProtocol' text file specifies the precise onset (in seconds, minus 10 seconds for dummy scans) and duration (in seconds) of the different optogenetic stimulation protocols during a 1440 seconds functional scan. The 'SubjectDetails' file lists the subject IDs, their gender, their genotype, the stimulation type of functional scans, and their associated anatomical scan.</p>
Data from: Meiotic drive influences the outcome of sexually antagonistic selection at a linked locus
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Data from: Balancing selection maintains sex determining alleles in multiple-locus complementary sex determination
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Data from: Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus
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