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76 results for “Genome-wide selection”
Data from: Genome-wide selection components analysis in a fish with male pregnancy
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Genome-wide selection signatures reveal widespread synergistic effects of two different stressors in Drosophila melanogaster: scripts and files
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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>
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>
Elevated temperature increases genome-wide selection on de novo mutations
<p>Adaptation in new environments depends on the amount of genetic variation available for evolution, and the efficacy by which natural selection discriminates among this variation. However, whether some ecological factors reveal more genetic variation, or impose stronger selection pressures than others, is typically not known. Here, we apply enzyme kinetic theory to show that rising global temperatures are predicted to intensify natural selection throughout the genome by increasing the effects of DNA sequence variation on protein stability. We test this prediction by i) estimating temperature-dependent fitness effects of induced mutations in seed beetles adapted to ancestral or elevated temperature, ii) calculate 100 paired selection estimates on mutations in benign versus stressful environments from unicellular and multicellular organisms. Environmental stress per se did not increase mean selection on de novo mutation, suggesting that the cost of adaptation does not generally increase in new ecological settings to which the organism is maladapted. However, elevated temperature increased the mean strength of selection on genome-wide polymorphism, signified by increases in both mutation load and mutational variance in fitness. These results have important implications for genetic diversity gradients and the rate and repeatability of evolution under climate change.</p>
Data from: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta
Background: Genomic variation is widespread, and both neutral and selective processes can generate similar patterns in the genome. These processes are not mutually exclusive, so it is difficult to infer the evolutionary mechanisms that govern population and species divergence. Boechera stricta,is a perennial relative of Arabidopsis thaliana native to largely undisturbed habitats with two geographic and ecologically divergence subspecies. Here we delineate the evolutionary processes driving genetic diversity and population differentiation in this species. Results: Using whole genome re-sequencing data from 517 Boechera stricta accessions, we identify four genetic groups that diverged around 30 - 180 thousand years ago, with long-term small effective population sizes and recent population expansion after the Last Glacial Maximum. We find three genomic regions with elevated nucleotide diversity, totaling about 10% of the genome. These three regions of elevated nucleotide diversity show excess of intermediate-frequency alleles, higher absolute divergence (dXY) and lower relative divergence (FST) than genomic background, and significant enrichment in immune-related genes, reflecting long-term balancing selection. Scattered across the genome we also find regions with both high FST and DXY among groups, termed FST-islands. Population genetic signatures indicate that FST-islands with elevated divergence, which have experienced directional selection, are derived from divergent sorting of ancient polymorphisms. Conclusions: Our results suggest that long-term balancing selection on disease resistance genes may have maintained ancestral haplotypes across different geographical lineages, and unequal sorting of balanced polymorphisms may have generated genomic regions with elevated divergence. This study highlights the importance of ancestral balanced polymorphisms as crucial components of genome-wide variation.
Natural selection drives genome-wide evolution via chance genetic associations
<p>Understanding selection's impact on the genome is a major theme in biology. Functionally-neutral genetic regions can be affected indirectly by natural selection, via their statistical association with genes under direct selection. The genomic extent of such indirect selection, particularly across loci not physically linked to those under direct selection, remains poorly understood, as does the time scale at which indirect selection occurs. Here we use field experiments and genomic data in stick insects, deer mice and stickleback fish to show that widespread statistical associations with genes known to affect fitness cause many genetic loci across the genome to be impacted indirectly by selection. This includes regions physically distant from those directly under selection. Then, focusing on the stick insect system, we show that statistical associations between SNPs and other unknown, causal variants result in additional indirect selection in general and specifically within genomic regions of physically linked loci. This widespread indirect selection necessarily makes aspects of evolution more predictable. Thus, natural selection combines with chance genetic associations to affect genome-wide evolution across linked and unlinked loci and even in modest-sized populations. This process has implications for the application of evolutionary principles in basic and applied science.</p>
Genomic evidence that a sexually selected trait captures genome-wide variation and facilitates the purging of genetic load
<p><span>The evolution of costly traits like deer antlers and peacock trains, which drove the formation of Darwinian sexual selection theory, has been hypothesised to both reflect and affect patterns of genetic variance across the genome, but direct tests are missing. Here, we used an evolve and re-sequence approach to reveal patterns of genome-wide diversity associated with the expression of a sexually-selected weapon that is dimorphic among males of the bulb mite,</span> <em>Rhizoglyphus robini</em><span>. Populations selected for the weapon </span>showed reduced genome-wide diversity compared to populations selected against the weapon, particularly in terms of the number of segregating non-synonymous positions, indicating enhanced purifying selection. <span>This increased purifying selection reduced inbreeding depression, but outbred female fitness did not improve, possibly because any benefits were offset by increased sexual antagonism. </span>The majority of single nucleotide polymorphisms (SNPs) that consistently diverged in response to selection were initially rare and overrepresented in exons, and enriched in regions under balancing or relaxed selection, suggesting they are likely moderately deleterious variants. These diverged SNPs were scattered across the genome, <span>further demonstrating that selection for or against the weapon and the associated changes to the mating system can both capture and influence genome-wide variation. </span></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>
Natural selection shapes variation in genome-wide recombination rate in Drosophila pseudoobscura
<p>While recombination is widely recognized to be a key modulator of numerous evolutionary phenomena, we have a poor understanding of how recombination rate itself varies and evolves within a species. Here, we performed a comprehensive study of recombination rate (rate of meiotic crossing over) in two natural populations of <i>Drosophila pseudoobscura</i> from Utah and Arizona, USA. We used an amplicon sequencing approach to obtain high-quality genotypes in approximately 8000 individual backcrossed offspring (17 mapping populations with roughly 530 individuals each), for which we then quantified crossovers. Interestingly, variation in recombination rate within and between populations largely manifested as differences in genome-wide recombination rate rather than remodeling of the local recombination landscape. Comparing populations, we discovered individuals from the Utah population displayed on average 8% higher crossover rates than the Arizona population, a statistically significant difference. Using a Q<sub>ST</sub>-F<sub>ST</sub> analysis, we found that this difference in crossover rate was dramatically higher than expected under neutrality, indicating that this difference may have been driven by natural selection. Finally, using a combination of short and long read whole-genome sequencing, we found no significant association between crossover rate and structural variation at the 200-400kb scale. Our results demonstrate that (1) there is abundant variation in genome-wide crossover rate in natural populations, (2) at the 200-400kb scale, recombination rate appears to vary largely genome wide, rather than in specific intervals and (3) interpopulation differences in recombination rate may be the result of local adaptation.</p>
Elevated temperature increases genome-wide selection on de novo mutations
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Data from: Ancient polymorphisms contribute to genome-wide variation by long-term balancing selection and divergent sorting in Boechera stricta
Open the record for dataset details and reuse information.
Natural selection shapes variation in genome-wide recombination rate in Drosophila pseudoobscura
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Natural selection drives genome-wide evolution via chance genetic associations
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Genomic evidence that a sexually selected trait captures genome-wide variation and facilitates the purging of genetic load
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Data from: Genome-wide scans reveal selection signatures and cross-population variation in South African and European beef cattle breeds
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Data from: Vive la résistance: genome-wide selection against introduced alleles in invasive hybrid zones
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Data from: Genome-wide analyses suggest parallel selection for universal traits may eclipse local environmental selection in a highly mobile carnivore
Ecological and environmental heterogeneity can produce genetic differentiation in highly mobile species. Accordingly, local adaptation may be expected across comparatively short distances in the presence of marked environmental gradients. Within the European continent, wolves (Canis lupus) exhibit distinct north–south population differentiation. We investigated more than 67-K single nucleotide polymorphism (SNP) loci for signatures of local adaptation in 59 unrelated wolves from four previously identified population clusters (northcentral Europe n = 32, Carpathian Mountains n = 7, Dinaric-Balkan n = 9, Ukrainian Steppe n = 11). Our analyses combined identification of outlier loci with findings from genome-wide association study of individual genomic profiles and 12 environmental variables. We identified 353 candidate SNP loci. We examined the SNP position and neighboring megabase (1 Mb, one million bases) regions in the dog (C. lupus familiaris) genome for genes potentially under selection, including homologue genes in other vertebrates. These regions included functional genes for, for example, temperature regulation that may indicate local adaptation and genes controlling for functions universally important for wolves, including olfaction, hearing, vision, and cognitive functions. We also observed strong outliers not associated with any of the investigated variables, which could suggest selective pressures associated with other unmeasured environmental variables and/or demographic factors. These patterns are further supported by the examination of spatial distributions of the SNPs associated with universally important traits, which typically show marked differences in allele frequencies among population clusters. Accordingly, parallel selection for features important to all wolves may eclipse local environmental selection and implies long-term separation among population clusters.
Data from: Genome-wide association mapping of phenotypic traits subject to a range of intensities of natural selection in Timema cristinae
The genetic architecture of adaptive traits can reflect the evolutionary history of populations and also shape divergence among populations. Despite this central role in evolution, relatively little is known regarding the genetic architecture of adaptive traits in nature, particularly for traits subject to known selection intensities. Here we quantitatively describe the genetic architecture of traits that are subject to known intensities of differential selection between host plant species in Timema cristinae stick insects. Specifically, we used phenotypic measurements of 10 traits and 211,004 single-nucleotide polymorphisms (SNPs) to conduct multilocus genome-wide association mapping. We identified a modest number of SNPs that were associated with traits and sometimes explained a large proportion of trait variation. These SNPs varied in their strength of association with traits, and both major and minor effect loci were discovered. However, we found no relationship between variation in levels of divergence among traits in nature and variation in parameters describing the genetic architecture of those same traits. Our results provide a first step toward identifying loci underlying adaptation in T. cristinae. Future studies will examine the genomic location, population differentiation, and response to selection of the trait-associated SNPs described here.
Data from: Genome-wide differentiation in closely related populations: the roles of selection and geographic isolation
Population divergence in geographic isolation is due to a combination of factors. Natural and sexual selection may be important in shaping patterns of population differentiation, a pattern referred to as 'isolation by adaptation' (IBA). IBA can be complementary to the well-known pattern of 'isolation by distance' (IBD), in which the divergence of closely related populations (via any evolutionary process) is associated with geographic isolation. The barn swallow Hirundo rustica complex comprises six closely related subspecies, where divergent sexual selection is associated with phenotypic differentiation among allopatric populations. To investigate the relative contributions of selection and geographic distance to genome-wide differentiation, we compared genotypic and phenotypic variation from 350 barn swallows sampled across eight populations (28 pairwise comparisons) from four different subspecies. We report a draft whole-genome sequence for H. rustica, to which we aligned a set of 9493 single nucleotide polymorphisms (SNPs). Using statistical approaches to control for spatial autocorrelation of phenotypic variables and geographic distance, we find that divergence in traits related to migratory behaviour and sexual signalling, as well as geographic distance, together explain over 70% of genome-wide divergence among populations. Controlling for IBD, we find 42% of genomewide divergence is attributable to IBA through pairwise differences in traits related to migratory behaviour and sexual signalling alone. By (i) combining these results with prior studies of how selection shapes morphological differentiation and (ii) accounting for spatial autocorrelation, we infer that morphological adaptation plays a large role in shaping population-level differentiation in this group of closely related populations.
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