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153 results for “Selective signature”
Data for: Patterns of shared signatures of recent positive selection across human populations
<p>Genome-wide summary stats for modified iHS scan in 1KG as reported in:</p> <p><a href="https://pubmed.ncbi.nlm.nih.gov/29459708/">Patterns of shared signatures of recent positive selection across human populations.</a></p> <p>Johnson KE, Voight BF.Nat Ecol Evol. 2018 Apr;2(4):713-720. doi: 10.1038/s41559-018-0478-6. Epub 2018 Feb 19.</p> <p>PMID: 29459708</p> <p>Code available at: https://github.com/bvoightlab/iHS_calc</p>
Genomic signatures of isolation, hybridization, and selection during speciation of island finches
<p><strong>Data associated</strong> to the study <em>Genomic signatures of isolation, hybridization, and selection during speciation of island finches</em></p> <p><strong>Contents</strong></p> <ul> <li>Table_S9_samples_accession_nos.xlsx: Editable Excel matrix with sample names and accession numbers.</li> <li>RAD_SNPs_stacks_42424_loci.vcf.tar.gz: VCF file (gzip-compressed tarball) containing SNPs in 42,424 loci, based on analyses of restriction site-associated DNA (RAD) sequencing using Stacks.</li> <li>RAD_SNPs_standard_variant_calling.vcf.tar.gz: VCF file (gzip-compressed tarball) containing 131,661 SNPs from standard variant calling pipelines.</li> <li>mitochondrial_markers_full_data.nex: Nexus file containing mitochondrial (mt) sequences used for mt-phylogeny. Partitioned for COX2, tRNA-Lys, ATP8, and ATP6. </li> <li>sequences_nuclear_genotype_with_zebra_finch_TG.tar.gz: Directory (gzip-compressed tarball) containing genotype sequence (heterozygous sites with IUPAC codes) alignments of nuclear markers in nexus files. In addition to the study species, the sequence for zebra finch <em>Taeniopygia guttata</em> is included with sample code TG.</li> <li>sequences_nuclear_phased_and_mitochondrial_haplotypes_matching.tar.gz: Directory (gzip-compressed tarball) containing phased sequence (haplotype) alignments of nuclear markers in nexus files. These include only those individuals that match individuals sequenced for mitochondrial markers (also included here). In case of recombining loci, both the full locus and the largest non-recombining block are represented.</li> <li>sequences_nuclear_phased_haplotypes_all.tar.gz: Directory (gzip-compressed tarball) containing phased sequence (haplotype) alignments of nuclear markers in nexus files. These include all individuals. In case of recombining loci, both the full locus and the largest non-recombining block are represented.</li> <li>microsatellite_dataset.xlsx: Microsatellite datasets for the study species and additional outgroups. <ul> </ul> <p>Sequences and short read datasets available from NCBI; accession numbers in Table S9 (Table_S9_samples_accession_nos.xlsx).</p> </li> </ul> <p> </p> <p><strong>Study summary</strong></p> <p>Sister species occurring sympatrically on islands are rare and offer unique opportunities to understand how speciation can proceed in the face of gene flow. The São Tomé grosbeak is a massive-billed, ‘giant’ finch endemic to the island of São Tomé in the Gulf of Guinea, where it has diverged from its co-occurring sister species the Príncipe seedeater, an average-sized finch that also inhabits two neighbouring islands. Here, we show that the grosbeak carries a large number of unique alleles different from all three Príncipe seedeater populations, but also shares many alleles with the sympatric São Tomé population of the seedeater, a genomic signature signifying divergence in isolation as well as subsequent introgressive hybridization. Furthermore, genomic segments that remain unique to the grosbeak are situated close to genes, including genes that determine bill morphology, suggesting the preservation of adaptive variation through natural selection during divergence with gene flow. This study reveals a complex speciation process whereby genetic drift, introgression, and selection during periods of isolation and secondary contact all have shaped the diverging genomes of these sympatric island endemic finches.</p>
Genome-wide selection signatures reveal widespread synergistic effects of two different stressors in Drosophila melanogaster: scripts and files
<p>Pipeline and analysis scripts as well as final data files</p>
Contrasting genome-wide signatures of selection in two closely related Epichloe plant pathogen species
<p>Deposited here composite plots for each species, each pairwise population combination and each of the seven chromosomes as shown and referred to in the manuscript.</p> <p>The filename contains [species abbrevation]_[chromosome number]_[population 1]_[population 2]. Chromosome-wide SNP data and sweeps identified for the population pair are shown. The top panel shows pairwise FST values, averaged across 5kb windows. Shaded rectangles represent the locations of AT-rich regions. The second panel shows the absolute values of the integrated haplotype score (iHS) calculated at each SNP locus for which the ancestral allele state was known. Scores for pop1 are shown at the top and scores for pop2 are negatively transformed and showed at the bottom. Horizontal dashed lines indicate the 99.9% percentile threshold which was used as a cutoff to identify outlier SNPs and inferred iHS sweeps are shown as shaded rectangles. The third panel shows the cross-population extended haplotype homozygosity (XP-EHH) scores calculated between the two populations. Dashed lines indicate 99.9% percentile threshold which was used as a cutoff to identify outlier SNPs and inferred divergent sweeps are shown as shaded rectangles. Positive and negative XP-EHH values refer to the direction of selection: positive values indicate selection in pop1 negative values indicate selection in pop2. In the bottom panel, composite likelihood ratio (CLR) scores are plotted for pop1 (black) and pop2 (blue), colored dashed lines indicate respective 99.9% threshold and colored rectangles highlight inferred CLR-sweeps.</p>
Integrative QTL mapping and selection signatures in Groningen White Headed cattle inferred from whole-genome sequences
<p>Here, we aimed to identify and characterize genomic regions that differ between Groningen White Headed (GWH) breed and other cattle, and in particular to identify candidate genes associated with coat color and/or eye-protective phenotypes. Firstly, whole genome sequences of 170 animals from eight breeds were used to evaluate the genetic structure of the GWH in relation to other cattle breeds by carrying out principal components and model-based clustering analyses. Secondly, the candidate genomic regions were identified by integrating the findings from: a) a genome-wide association study using GWH, other white headed breeds (Hereford and Simmental), and breeds with a non-white headed phenotype (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel, Dutch Belted, and Holstein Friesian); b) scans for specific signatures of selection in GWH cattle by comparison with four other Dutch traditional breeds (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel and Dutch Belted) and the commercial Holstein Friesian; and c) detection of candidate genes identified via these approaches. The alignment of the filtered reads to the reference genome (ARS-UCD1.2) resulted in a mean depth of coverage of 8.7X. After variant calling, the lowest number of breed-specific variants was detected in Holstein Friesian (148,213), and the largest in Deep Red (558,909). By integrating the results, we identified five genomic regions under selection on BTA4 (70.2–71.3 Mb), BTA5 (10.0–19.7 Mb), BTA20 (10.0–19.9 and 20.0–22.7 Mb), and BTA25 (0.5–9.2 Mb). These regions contain positional and functional candidate genes associated with retinal degeneration (e.g., <em>CWC27</em> and <em>CLUAP1</em>), ultraviole<em>t</em> protection (e.g., <em>ERCC8</em>), and pigmentation (e.g. <em>PDE4D</em>) which are probably associated with the GWH specific pigmentation and/or eye-protective phenotypes, e.g. Ambilateral Circumocular Pigmentation (ACOP). Our results will assist in characterizing the molecular basis of GWH phenotypes and the biological implications of its adaptation.</p>
Data from: Whole-genome resequencing reveals polygenic signatures of directional and balancing selection on alternative migratory life histories
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The role of recombination dynamics in shaping signatures of direct and indirect selection across the Ficedula flycatcher genome
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Data: Genomic signatures of admixture and selection are shared among populations of Zaprionus indianus across the western hemisphere
<p>Introduced species have become an increasingly common component of biological communities around the world. A central goal in invasion biology is therefore to identify the demographic and evolutionary factors that underlie successful introductions. Here we use whole genome sequences, collected from populations in the native and introduced ranges of the African fig fly, <i>Zaprionus indianus</i>, to quantify genetic relationships among them, identify potential sources of the introductions, and test for selection at different spatial scales. We find that geographically widespread populations in the western hemisphere are genetically more similar to each other than to lineages sampled across Africa, and that these populations share a mixture of alleles derived from differentiated African lineages. Using patterns of allele-sharing and demographic modelling we show that <i>Z. indinaus</i> have undergone a single expansion across the western hemisphere with admixture between African lineages predating this expansion. We also find support for selection that is shared across populations in the western hemisphere, and in some cases, with a subset of African populations. This suggests either that parallel selection has acted across a large part of <i>Z. indianus</i>'s introduced range; or, more parsimoniously, that <i>Z. indianus</i> has experienced selection early on during (or prior-to) its expansion into the western hemisphere. We suggest that the range expansion of <i>Z. indianus</i> has been facilitated by admixture and selection, and that management of this invasion could focus on minimizing future admixture by controlling the movement of individuals within this region rather than between the western and eastern hemisphere.</p>
Population Genomics Analysis of 30 Samples from Each of Multiple Populations Reveals Signatures of Selection from Breeding for Rapid Growth and Apical Dominance in Paulownia fortunei
<p><i>Paulownia fortunei</i> is an ecologically and economically valuable tree cultivated for its rapid growth and high-quality timber. To enhance <i>Paulownia</i> germplasm, we have developed the elite variety QingT with patented advantages in growth rate and apical dominance. To illuminate the genetic basis of QingT's superior traits, here we harness comparative population genomics to analyze genomic variation patterns between QingT and common <i>Paulownia</i>. We performed whole-genome re-sequencing of 30 QingT and 30 common samples, detecting 15.6 million SNPs and 2.6 million indels. Phylogeny and population structure analyses robustly partitioned common and QingT into distinct groups which indicate robust genome stabilization. QingT exhibited reduced heterozygosity and linkage disequilibrium decay compared to common <i>Paulownia</i>, reflecting high recombination, indicating hybridizing effects with common white-flowered string is the source of its patented advantages. Genome selection scans uncovered 25 regions of 169 genes with elevated nucleotide diversity, indicating selection sweeps among groups. Functional analysis of sweep genes revealed upregulation of ribosomal, biosynthesis and growth pathways in QingT, implicating enhanced protein production and developmental processes in its rapid growth phenotype. This study's insights comprehensively chart genomic variation during <i>Paulownia</i> breeding, localizing candidate loci governing agronomic traits, and underpinnings of future molecular breeding efforts to boost productivity. </p>
Signatures of natural selection in a foundation tree along Mediterranean climatic gradients
<p>Temperature and precipitation regimes are rapidly changing, resulting in forest dieback and extinction events, particularly in Mediterranean-type climates (MTC). Forest management that enhance forests' resilience is urgently required, however adaptation to climates in heterogeneous landscapes with multiple selection pressures is complex. For widespread trees in MTC we hypothesized that: patterns of local adaptation are associated with climate; precipitation is a stronger factor of adaptation than temperature; functionally related genes show similar signatures of adaptation; and adaptive variants are independently sorting across the landscape. We sampled 28 populations across the geographic distribution of Eucalyptus marginata (jarrah), in South-west Western Australia, and obtained 13,534 independent single nucleotide polymorphic (SNP) markers across the genome. Three genotype-association analyses that employ different ways of correcting population structure were used to identify putatively adapted SNPs associated with independent climate variables. While overall levels of population differentiation were low (<i>F</i><sub>ST</sub> = 0.04), environmental association analyses found a total of 2,336 unique SNPs associated with temperature and precipitation variables, with 1,440 SNPs annotated to genic regions. Considerable allelic turnover was identified for SNPs associated with temperature seasonality and mean precipitation of the warmest quarter, suggesting that both temperature and precipitation are important factors in adaptation. SNPs with similar gene functions had analogous allelic turnover along climate gradients, while SNPs among temperature and precipitation variables had uncorrelated patterns of adaptation. These contrasting patterns provide evidence that there may be standing genomic variation adapted to current climate gradients, providing the basis for adaptive management strategies to bolster forest resilience in the future.</p>
Whole genome resequencing reveals signatures of rapid selection in a virus affected commercial fishery
<p>Infectious diseases are recognised as one of the greatest global threats to biodiversity and ecosystem functioning. Consequently, there is a growing urgency to understand the speed at which adaptive phenotypes can evolve and spread in natural populations to inform future management. Here we provide evidence of rapid genomic changes in wild Australian blacklip abalone (<em>Haliotis rubra</em>) following a major population crash associated with an infectious disease. Genome scans on <em>H. rubra</em> were performed using pooled whole genome re-sequencing data from commercial fishing stocks varying in historical exposure to haliotid herpesvirus-1 (HaHV-1). Approximately 25,000 SNP loci associated with virus exposure were identified, many of which mapped to genes known to contribute to HaHV-1 immunity in the New Zealand pāua (<em>H. iris</em>) and herpesvirus response pathways in haliotids and other animal systems. These findings indicate genetic changes across a single generation in <em>H. rubra </em>fishing stocks decimated by HaHV-1, with stock recovery potentially determined by rapid evolutionary changes leading to virus resistance. This is a novel example of rapid adaptation in natural populations of a non-model marine organism, highlighting the pace at which selection can potentially act to counter disease in wildlife communities.</p>
Multi-element signatures of the selected cobalt-rich metallogenic families. The bold text highlights the most relevant metal occurrences for the selected metallogenic families.
<p>This dataset is table 2 from the article "Predictive assessment of metallogenic signatures using the DataBase Querying (DBQ) method: A European application by Blandine Gourcerol *, Guillaume Bertrand, Laurent Bailly, Pauline Moreau, Isabelle Duhamel-Achin, Maxime Picault, Philippe Négrel</p> <p>DOI : https://doi.org/10.1016/j.gexplo.2022.106966</p>
Data from: Genome-wide scans reveal selection signatures and cross-population variation in South African and European beef cattle breeds
<p>In genetics and evolutionary biology, the concept of selection signatures is used to describe specific patterns in the genome that are associated with the process of natural selection. These selection signatures provide insights into how evolutionary forces have shaped a population over time.In this study, a total of 96 samples were collected in several farms from four different cattle breeds, namely South African indigenous Nguni (n = 28) and Bonsmara (n = 21), Scottish Angus (n = 22), and Swedish Simmental (n = 25). Genotyped samples were subjected to quality control, and a total of 105,675 SNPs from 78 individuals remained for further analysis. Genomic signatures of positive selection within each breed were identified using the Integrated Haplotype Score (iHS) method, and cross-population comparison analysis using cross-population extended haplotype homozygosity ( XP-EHH), relative extended haplotype homozygosity (Rsb), and fixation index (Fst) methods, to assess the genetic differences between breeds. The results from the iHS method revealed selection signatures in two genomic regions for Bonsmara, six for Simmental, four for Nguni, and one for Angus cattle. Ten regions were found to be under selection, with BTA 12 being shared between Nguni and Bonsmara. Comparisons across populations using Rsb, and Fst methods performed better and revealed the most specific genomic regions that varied in selection between breeds. Gene annotation analyses linked candidate genes to several Quantitative Trait Loci (QTL). For example, in Simmental cattle's FAM110B gene was linked to carcass weight and body confirmation score. Bonsmara showed fewer candidate genes, such as CDK8 and FLT1, whereas Angus had none on BTA 18. Nguni identified potential genes such as CRB1, PLAG2GA, and VASH2, with CDK8 shared by Bonsmara and Nguni on BTA 12. Further cross-population studies revealed candidate genes associated with certain traits, genes including as PLCXD3, FAM149B1, and GRIK2 for Bonsmara versus Nguni, and SLIT2 and TSPAN9 for Simmental vs Angus. The study also emphasised gene related to meat quality, reproduction, health, illnesses, fertility, and body conformation score. Gene interaction study with the STRING database revealed a network of 63 candidate genes, demonstrating the structure of genetic connections, some biological processes. The study found that iHS performed well in population analysis with Nguni cattle, having exhibited the highest number of signatures across the genome, and significant signatures were also seen in comparisons between Nguni and Bonsmara using the Fst and Rsb methods. Furthermore, the study discovered that a bigger number of genes were connected with various traits, including sperm count and insemination per conception, sensitivity to bovine respiratory disease, and ease of calving. This genomic analysis underlined the relevance of the genetic relying which distinguishes distinct breeds. This understanding has the potential to significantly enhance selective breeding and increase desirable traits in cattle herds. This genomic analysis underlined the significance of the genetic basis for breed-specific traits. This understanding has the potential to drastically improve selective breeding and increase desirable traits in cattle herds.</p>
Genome-phenotype-environment associations identify signatures of selection in a panmictic population of threespine stickleback
<p>Adaptive genetic divergence occurs when selection imposed by the environment causes the genomic component of the phenotype to differentiate. However, genomic signatures of natural selection are usually identified without information on which trait is responding to selection by which selective agent(s). Here we integrate whole-genome-sequencing with phenomics and measures of putative selective agents to assess the extent of adaptive divergence in threespine stickleback occupying the highly heterogeneous lake Mývatn, NE Iceland. We find negligible genome-wide divergence, yet multiple traits (body size, gill raker structure and defence traits) were divergent along known ecological gradients (temperature, predatory bird densities and water depth). SNP-based heritability of all measured traits was high (h<sup>2</sup> = 0.42 – 0.65), indicating adaptive potential for all traits. Whilst environment-association analyses identified thousands of loci putatively involved in selection, related to genes linked to neuron development and protein phosphorylation, only loci linked to pelvic spine length were concurrently linked to environmental variation (water depth) – supporting the conclusion that divergence in pelvic spine length occurred in face of gene flow. Our results suggest that whilst there is substantial genetic variation in the traits measured, phenotypic divergence of Mývatn stickleback is mostly weakly associated with environmental gradients, potentially as a result of substantial gene flow. Our study illustrates the value of integrative studies that combine genomic assays of multivariate trait variation with landscape genomics.</p>
Data: Genomic signatures of admixture and selection are shared among populations of Zaprionus indianus across the western hemisphere
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Whole genome resequencing reveals signatures of rapid selection in a virus affected commercial fishery
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Signatures of natural selection in a foundation tree along Mediterranean climatic gradients
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Unravelling selection signatures in a single dog breed suggests recent selection for morphological and behavioural traits
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Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality
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Genome-phenotype-environment associations identify signatures of selection in a panmictic population of threespine stickleback
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