Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
46
datasets available to search
ShareScore release 0.9.0
Dataset results
46 results for “selective sweeps”
Identifying and classifying shared selective sweeps from multilocus data
Positive selection causes beneficial alleles to rise to high frequency, resulting in a selective sweep of the diversity surrounding the selected sites. Accordingly, the signature of a selective sweep in an ancestral population may still remain in its descendants. Identifying signatures of selection in the ancestor that are shared among its descendants is important to contextualize the timing of a sweep, but few methods exist for this purpose. We introduce the statistic SS-H12, which can identify genomic regions under shared positive selection across populations and is based on the theory of the expected haplotype homozygosity statistic H12, which detects recent hard and soft sweeps from the presence of high-frequency haplotypes. SS-H12 is distinct from comparable statistics because it requires a minimum of only two populations, and properly identifies and differentiates between independent convergent sweeps and true ancestral sweeps, with high power and robustness to a variety of demographic models. Furthermore, we can apply SS-H12 in conjunction with the ratio of statistics we term H2Tot and H1Tot to further classify identified shared sweeps as hard or soft. Finally, we identified both previously-reported and novel shared sweep candidates from human whole-genome sequences. Previously-reported candidates include the well-characterized ancestral sweeps at LCT and SLC24A5 in Indo-Europeans, as well as GPHN worldwide. Novel candidates include an ancestral sweep at RGS18 in sub-Saharan Africans involved in regulating the platelet response and implicated in sudden cardiac death, and a convergent sweep at C2CD5 between European and East Asian populations that may explain their different insulin responses.
Data from: High nucleotide diversity and limited linkage disequilibrium in Helicoverpa armigera facilitates the detection of a selective sweep
Open the record for dataset details and reuse information.
Data from: Evidence for selective sweeps by Wolbachia infections: phylogeny of Altica leaf beetles and their reproductive parasites
Open the record for dataset details and reuse information.
Data from: Recurrent and recent selective sweeps in the piRNA pathway
Open the record for dataset details and reuse information.
Identifying and classifying shared selective sweeps from multilocus data
Open the record for dataset details and reuse information.
Data from: Wolbachia-induced meiotic drive and feminization is associated with an independent occurrence of selective mitochondrial sweep in a butterfly
Open the record for dataset details and reuse information.
Data from: The hitchhiker's guide to Europe: the infection dynamics of an ongoing Wolbachia invasion and mitochondrial selective sweep in Rhagoletis cerasi
Open the record for dataset details and reuse information.
Data from: Evaluating the performance of selection scans to detect selective sweeps in domestic dogs
Open the record for dataset details and reuse information.
Data from: Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation
Open the record for dataset details and reuse information.
Data files for: Hazardous loss of genetic diversity through selective sweeps in asexual populations
Open the record for dataset details and reuse information.
Data from: Soft selective sweeps in fungicide resistance evolution: recurrent mutations without fitness costs in grapevine downy mildew
Open the record for dataset details and reuse information.
Data from: Estimating the parameters of background selection and selective sweeps in Drosophila in the presence of gene conversion
We used whole-genome resequencing data from a population of Drosophila melanogaster to investigate the causes of the negative correlation between the within-population synonymous nucleotide site diversity (πS) of a gene and its degree of divergence from related species at nonsynonymous nucleotide sites (KA). By using the estimated distributions of mutational effects on fitness at nonsynonymous and UTR sites, we predicted the effects of background selection at sites within a gene on πS and found that these could account for only part of the observed correlation between πS and KA. We developed a model of the effects of selective sweeps that included gene conversion as well as crossing over. We used this model to estimate the average strength of selection on positively selected mutations in coding sequences and in UTRs, as well as the proportions of new mutations that are selectively advantageous. Genes with high levels of selective constraint on nonsynonymous sites were found to have lower strengths of positive selection and lower proportions of advantageous mutations than genes with low levels of constraint. Overall, background selection and selective sweeps within a typical gene reduce its synonymous diversity to ∼75% of its value in the absence of selection, with larger reductions for genes with high KA. Gene conversion has a major effect on the estimates of the parameters of positive selection, such that the estimated strength of selection on favorable mutations is greatly reduced if it is ignored.
Data from: Understanding the spectacular failure of DNA barcoding in willows (Salix): Does this result from a trans-specific selective sweep?
Willows (Salix: Salicaceae) form a major ecological component of Holarctic floras, and consequently are an obvious target for a DNA-based identification system. We surveyed two to seven plastid genome regions (~3.8 kb; ~3% of the genome) from 71 Salix species across all five subgenera, to assess their performance as DNA barcode markers. Although Salix has a relatively high level of interspecific hybridization, this may not sufficiently explain the near complete failure of barcoding that we observed: only one species had a unique barcode. We recovered 39 unique haplotypes, from more than 500 specimens, that could be partitioned into six major haplotype groups. A unique variant of group I (haplotype 1*) was shared by 53 species in three of five Salix subgenera. This unusual pattern of haplotype sharing across infrageneric taxa is suggestive of either a massive non-random coalescence failure (incomplete lineage sorting), or of repeated plastid capture events, possibly including a historical selective sweep of haplotype 1* across taxonomic sections. The former is unlikely as molecular dating indicates that haplotype 1* originated recently, and is nested in the oldest major haplotype group in the genus. Further, we detected significant non-neutrality in the frequency spectrum of mutations in group I, but not outside group I, and demonstrated a striking absence of geographic structure to the haplotype distributions in this group. The most likely explanation for the patterns we observed involves recent repeated plastid capture events, aided by widespread hybridization and long-range seed dispersal, but primarily propelled by one or more trans-species selective sweeps.
Data from: Identification of X-linked quantitative trait loci affecting cold tolerance in Drosophila melanogaster and fine-mapping by selective sweep analysis
Drosophila melanogaster is a cosmopolitan species that colonizes a great variety of environments. One trait that shows abundant evidence for naturally segregating genetic variance in different populations of D. melanogaster is cold tolerance. Previous work has found quantitative trait loci (QTL) exclusively on the second and the third chromosomes. To gain insight into the genetic architecture of cold tolerance on the X chromosome and to compare the results with our analyses of selective sweeps, a mapping population was derived from a cross between substitution lines that solely differed in the origin of their X chromosome: one originates from a European inbred line, the other one from an African inbred line. We found a total of six QTL for cold tolerance factors on the X chromosome of D. melanogaster. Although the composite interval mapping revealed slightly different QTL profiles between sexes, a coherent model suggests that most QTL overlapped between sexes and each explained around 5-14% of the genetic variance (which may be slightly overestimated). The allelic effects were largely additive, but we also detected two significant interactions. Taken together, this provides evidence for multiple QTL that are spread along the entire X chromosome and whose effects range from low to intermediate. One detected transgressive QTL influences cold tolerance in different ways for the two sexes. While females benefit from the European allele increasing their cold tolerance, males tend to do better with the African allele. Finally, using selective sweep mapping the candidate gene CG16700 for cold tolerance co-localizing with a QTL was identified.
Data from: Antagonistic versus non-antagonistic models of balancing selection: characterizing the relative timescales and hitchhiking effects of partial selective sweeps
Antagonistically selected alleles-–those with opposing fitness effects between sexes, environments, or fitness components-–represent an important component of additive genetic variance in fitness-related traits, with stably balanced polymorphisms often hypothesized to contribute to observed quantitative genetic variation. Balancing selection hypotheses imply that intermediate-frequency alleles disproportionately contribute to genetic variance of life-history traits and fitness. Such alleles may also associate with population genetic footprints of recent selection, including reduced genetic diversity and inflated linkage disequilibrium at linked, neutral sites. Here, we compare the evolutionary dynamics of different balancing selection models, and characterize the evolutionary timescale and hitchhiking effects of partial selective sweeps generated under antagonistic versus nonantagonistic (e.g., overdominant and frequency-dependent selection) processes. We show that the evolutionary timescales of partial sweeps tend to be much longer, and hitchhiking effects are drastically weaker, under scenarios of antagonistic selection. These results predict an interesting mismatch between molecular population genetic and quantitative genetic patterns of variation. Balanced, antagonistically selected alleles are expected to contribute more to additive genetic variance for fitness than alleles maintained by classic, nonantagonistic mechanisms. Nevertheless, classical mechanisms of balancing selection are much more likely to generate strong population genetic signatures of recent balancing selection.
Data from: A likelihood approach for uncovering selective sweep signatures from haplotype data
<p>Selective sweeps are frequent and varied signatures in the genomes of natural populations, and detecting them is consequently important in understanding mechanisms of adaptation by natural selection. Following a selective sweep, haplotypic diversity surrounding the site under selection decreases, and this deviation from the background pattern of variation can be applied to identify sweeps. Multiple methods exist to locate selective sweeps in the genome from haplotype data, but none leverage the power of a model-based approach to make their inference. Here, we propose a likelihood ratio test statistic <em>T</em> to probe whole genome polymorphism datasets for selective sweep signatures. Our framework uses a simple but powerful model of haplotype frequency spectrum distortion to find sweeps and additionally make an inference on the number of presently sweeping haplotypes in a population. We found that the <em>T</em> statistic is suitable for detecting both hard and soft sweeps across a variety of demographic models, selection strengths, and ages of the beneficial allele. Accordingly, we applied the <em>T</em> statistic to variant calls from European and sub-Saharan African human populations, yielding primarily literature-supported candidates, including <em>LCT, RSPH3</em>, and <em>ZNF211</em> in CEU, <em>SYT1, RGS18</em>, and <em>NNT</em> in YRI, and <em>HLA</em> genes in both populations. We also searched for sweep signatures in <em>Drosophila melanogaster</em>, finding expected candidates at Ace, <em>Uhg1</em>, and <em>Pimet</em>. Finally, we provide open-source software to compute the <em>T</em> statistic and the inferred number of presently sweeping haplotypes from whole-genome data.</p>
Data from: Detecting recent selective sweeps while controlling for mutation rate and background selection
A composite likelihood ratio test implemented in the program SweepFinder is a commonly used method for scanning a genome for recent selective sweeps. SweepFinder uses information on the spatial pattern (along the chromosome) of the site frequency spectrum (SFS) around the selected locus. To avoid confounding effects of background selection and variation in the mutation process along the genome, the method is typically applied only to sites that are variable within species. However, the power to detect and localize selective sweeps can be greatly improved if invariable sites are also included in the analysis. In the spirit of a Hudson-Kreitman-Aguadé test, we suggest adding fixed differences relative to an outgroup to account for variation in mutation rate, thereby facilitating more robust and powerful analyses. We also develop a method for including background selection, modeled as a local reduction in the effective population size. Using simulations we show that these advances lead to a gain in power while maintaining robustness to mutation rate variation. Furthermore, the new method also provides more precise localization of the causative mutation than methods using the spatial pattern of segregating sites alone.
Data from: Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs
Open the record for dataset details and reuse information.
Data from: Detecting recent selective sweeps while controlling for mutation rate and background selection
Open the record for dataset details and reuse information.
Data from: Identification of X-linked quantitative trait loci affecting cold tolerance in Drosophila melanogaster and fine-mapping by selective sweep analysis
Open the record for dataset details and reuse information.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.