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90 results for “Balancing selection”
Heat balance of selected Brayton cycle
<p>The dataset provides the heat balance of the selected Brayton cycle among the 10 cycles considered. Simulations of several cases defined by a different supercritical CO2 cycle type were performed with Ebsilon software in order to assess the net power block efficiency of the cycle and the Levelized Cost of Electricity (LCOE) of the plant. Due to its highest efficiency among the 10 envisaged Brayton cycle options, it is the Partial Cooling with Intercooling and Reheating cycle that is selected.</p> <p>The datasets could help other people design a sCO2 Brayton cycle.</p> <p>For detailed analysis, please refer to Deliverable 1.1 (Process Parameters of Solar sCO2 Brayton Cycle) to be downloaded at: <a href="https://www.compassco2.eu/wp-content/uploads/2021/02/D1.1_Process-parameters-of-solar-sCO2-Brayton-cycle.pdf">https://www.compassco2.eu/wp-content/uploads/2021/02/D1.1_Process-parameters-of-solar-sCO2-Brayton-cycle.pdf</a></p>
Data for: Detecting Long-Term Balancing Selection Using Allele Frequency Correlation
<p>Genome-wide and top 1% scores for 1KG project data output from BetaScan reported in:</p> <p><a href="https://pubmed.ncbi.nlm.nih.gov/28981714/">Detecting Long-Term Balancing Selection Using Allele Frequency Correlation.</a></p> <p>Siewert KM, Voight BF. Mol Biol Evol. 2017 Nov 1;34(11):2996-3005. doi: 10.1093/molbev/msx209.</p> <p>PMID: 28981714</p> <p>Code available at: https://github.com/ksiewert/BetaScan</p>
Data for: BetaScan2: Standardized Statistics to Detect Balancing Selection Utilizing Substitution Data
<p>Genome-wide scan using BetaScan2 in 1KG populations report in:</p> <p><a href="https://pubmed.ncbi.nlm.nih.gov/32011695/">BetaScan2: Standardized Statistics to Detect Balancing Selection Utilizing Substitution Data.</a></p> <p>Siewert KM, Voight BF.Genome Biol Evol. 2020 Feb 1;12(2):3873-3877. doi: 10.1093/gbe/evaa013.</p> <p>PMID: 32011695 </p> <p>Code available at: https://github.com/ksiewert/BetaScan</p>
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: Whole-genome resequencing reveals polygenic signatures of directional and balancing selection on alternative migratory life histories
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Data from: Movement-integrated habitat selection reveals wolves balance ease of travel with human avoidance in a risk-reward trade-off
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The evolutionary advantage of fitness-dependent recombination in diploids: a deterministic mutation–selection–balance model
<p>Recombination's omnipresence in nature is one of the most intriguing problems in evolutionary biology. The question of why recombination exhibits certain general features is no less interesting than that of why it exists at all. One such feature is recombination's fitness dependence (FD). The so far developed population-genetics models have focused on the evolution of FD recombination mainly in haploids, although the empirical evidence for this phenomenon comes mostly from diploids. Using numerical analysis of modifier models for infinite panmictic populations, we show here that FD recombination can be evolutionarily advantageous in diploids subjected to purifying selection. We ascribe this advantage to the differential rate of disruption of lower- vs higher-fitness genotypes, which can be manifested in selected systems with at least three loci. We also show that if the modifier is linked to such selected system, it can additionally benefit from modifying this linkage in a fitness-dependent manner. The revealed evolutionary advantage of FD recombination appeared robust to crossover interference within the selected system, either positive or negative. Remarkably, FD recombination was often favored in situations where any constant non-zero recombination was evolutionarily disfavored, implying a relaxation of the rather strict constraints on major parameters (e.g., selection intensity and epistasis) required for the evolutionary advantage of non-zero recombination formulated by classical models.</p>
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: 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.
Data from: Ecological factors influence balancing selection on leaf chemical profiles of a wildflower
<div> <div> <div> <div> <p>Balancing selection is frequently invoked as a mechanism to maintain variation within and across populations. However, rigorous tests demonstrating balancing selection operating in nature are scarce, particularly on complex traits, which frequently display high levels of variation. Leveraging a focal polymorphism, leaf chemical profile in a perennial wildflower (<em>Boechera stricta</em>, Brassicaceae), we investigated the ecological and genetic mechanisms that may influence the maintenance of variation in this trait. A suite of common garden and greenhouse experiments showed that the alleles underlying variation in chemical profile have contrasting fitness effects across environments, implicating two ecological drivers of selection on chemical profile: herbivory and drought. Phenotype-environment associations and molecular genetic analyses revealed additional evidence of past selection by these drivers. Together, these data are consistent with balancing selection on chemical profile, likely caused by pleiotropic effects of genes that influence secondary chemical biosynthesis on herbivore defense and drought response.</p> </div> </div> </div> </div>
Large-scale fungal strain sequencing unravels the molecular diversity in mating loci maintained by long-term balancing selection
<p><span>Balancing selection, an evolutionary force that retains genetic diversity, has been detected in multiple genes and organisms, such as the sexual mating loci in fungi. However, to quantify the strength of balancing selection and define the mating-related genes require a large number of strains. In tetrapolar basidiomycete fungi, sexual type is determined by two unlinked loci, <em>MATA </em>and <em>MATB</em>. Genes in both loci define mating type identity, control successful mating and completion of the life cycle. These loci are usually highly diverse. Previous studies have speculated, based on culture crosses, that species of the non-model genus <em>Trichaptum </em>(Hymenochaetales, Basidiomycota) possess a tetrapolar mating system, with multiple alleles. Here, we sequenced a hundred and eighty strains of three <em>Trichaptum </em>species. We characterized the chromosomal location of <em>MATA </em>and <em>MATB</em>, the molecular structure of <em>MAT </em>regions and their allelic richness. The sequencing effort was sufficient to molecularly characterize multiple <em>MAT </em>alleles segregating before the speciation event of <em>Trichaptum </em>species. Analyses suggested that long-term balancing selection has generated trans-species polymorphisms. Mating sequences were classified in different allelic classes based on an amino acid identity (AAI) threshold supported by phylogenetics. 17,550 mating types were predicted based on the allelic classes. <em>In vitro </em>crosses allowed us to support the degree of allelic divergence needed for successful mating. Even with the high amount of divergence, key amino acids in functional domains are conserved. We conclude that the genetic diversity of mating loci in <em>Trichaptum </em>is due to long-term balancing selection, with limited recombination and duplication activity. The large number of sequenced strains highlighted the importance of sequencing multiple individuals from different species to detect the mating-related genes, the mechanisms generating diversity and the evolutionary forces maintaining them.</span></p>
Archived data for: Balancing selection, genetic drift, and human mediated-introgression interplay to shape MHC (functional) diversity in Mediterranean brown trout
<p>The extraordinary polymorphism of Major Histocompatibility Complex (MHC) genes is considered a paradigm of pathogen-mediated balancing selection, although empirical evidence is still scarce. Furthermore, the relative contribution of balancing selection to shape MHC population structure and diversity, compared to that of neutral forces, as well as its interaction with other evolutionary processes such as hybridization, remains largely unclear. To investigate these issues, we analysed adaptive (MHC-DAB gene) and neutral (11 microsatellite loci) variation in 156 brown trout (<i>Salmo trutta </i>complex) from six wild populations in central Italy exposed to introgression from domestic hatchery lineages (assessed with the LDH gene). MHC diversity and structuring correlated with those at microsatellites, indicating the substantial role of neutral forces. However, individuals carrying locally rare MHC alleles/supertypes (regardless of the zygosity status and degree of sequence dissimilarity of MHC) were in better body condition (a proxy of individual fitness/parasite load), hence supporting balancing selection under rare allele advantage, but not heterozygote advantage or divergent allele advantage. The association between specific MHC supertypes and body condition confirmed in part this finding. Across populations, MHC allelic richness increased with increasing admixture between native and domestic lineages, indicating introgression as a source of MHC variation. Furthermore, introgression across populations appeared more pronounced for MHC than microsatellites, possibly because initially-rare MHC variants are expected to introgress more readily under rare allele advantage. Providing evidence for the complex interplay among neutral evolutionary forces, balancing selection and human-mediated introgression in shaping the pattern of MHC (functional) variation, our findings contribute to a deeper understanding of the evolution of MHC genes in wild populations exposed to anthropogenic disturbance.</p>
Data for : Social equity shapes zone-selection: Balancing aquatic biodiversity conservation and ecosystem services delivery in the transboundary Danube River Basin
<p>Freshwater biodiversity is declining, despite national and international efforts to manage and protect <a href="https://www.sciencedirect.com/topics/earth-and-planetary-sciences/freshwater-ecosystem">freshwater ecosystems</a>. Ecosystem-based management (EBM) has been proposed as an approach that could more efficiently and adaptively <a href="https://www.sciencedirect.com/topics/earth-and-planetary-sciences/ecological-balance">balance ecological</a> and societal needs. However, this raises the question of how social and ecological objectives can be included in an <a href="https://www.sciencedirect.com/topics/earth-and-planetary-sciences/integrated-management">integrated management</a> plan. Here, we present a generic model-coupling framework tailored to address this question for freshwater ecosystems, using three components: biodiversity, ecosystem services (ESS), and a spatial prioritisation that aims to balance the spatial representation of biodiversity and <a href="https://www.sciencedirect.com/topics/earth-and-planetary-sciences/evolutionarily-stable-strategy">ESS</a> supply and demand. We illustrate this model-coupling approach within the Danube River Basin using the spatially explicit, potential distribution of (i) 85 fish species as a surrogate for biodiversity as modelled using hierarchical Bayesian models, and (ii) four estimated ESS layers produced by the <a href="https://www.sciencedirect.com/topics/earth-and-planetary-sciences/artificial-intelligence">Artificial Intelligence</a> for Ecosystem Services (ARIES) platform (with ESS supply defined as <a href="https://www.sciencedirect.com/topics/earth-and-planetary-sciences/carbon-sequestration">carbon storage</a> and flood regulation, and demand specified as recreation and water use). These are then used for (iii) a joint spatial prioritisation of biodiversity and ESS employing Marxan with Zones, laying out the spatial representation of multiple management zones. Given the transboundary setting of the Danube River Basin, we also run comparative analyses including the country-level <a href="https://www.sciencedirect.com/topics/earth-and-planetary-sciences/purchasing-power-parity">purchasing power parity</a> (PPP)-adjusted gross domestic product (GDP) and each country's percent cover of the total basin area as potential cost factors, illustrating a scheme for balancing the share of establishing specific zones among countries. We demonstrate how emphasizing various biodiversity or ESS targets in an EBM model-coupling framework can be used to cost-effectively test various spatially explicit management options across a multi-national case study. We further discuss possible limitations, future developments, and requirements for effectively managing a balance between biodiversity and ESS supply and demand in freshwater ecosystems.</p>
Temporally-balanced selection during development of larval Pacific oysters (Crassostrea gigas) inherently preserves genetic diversity within offspring
<p>Balancing selection is one of the mechanisms which has been proposed to explain the maintenance of genetic diversity in species across generations. For species with large populations and complex life histories, however, heterogeneous selection pressures may create a scenario in which the net effects of selection are balanced across developmental stages. With replicated cultures and a pooled sequencing approach, we show that genotype-dependent mortality in larvae of the Pacific oyster (Crassostrea gigas) is largely temporally dynamic and inconsistently in favor of a single genotype or allelic variant at each locus. Overall, the patterns of genetic change we observe to be taking place are more complex than what would be expected under classical examples of additive or dominant genetic interactions. They are also not easily explained by our current understanding of the effects of genetic load. Collectively, temporally heterogeneous selection pressures across different larval developmental stages may act to maintain genetic diversity in oysters, while also inherently sheltering genetic load within populations.</p>
Data and scripts from: Balanced polymorphism fuels rapid selection in an invasive crab despite high gene flow and low genetic diversity
<p><em>Carcinus maenas</em> is a globally invasive species which spreads and thrives across a range of temperate environments. In the northwestern Pacific, the species has spread across >12 degrees of latitude in 10 years from a single source, following its introduction <35 years ago. Using six locations spanning >1,500 km, we examined genetic structure and selection to temperature using 9,376 Single Nucleotide Polymorphisms (SNPs) derived from cardiac transcriptome sequencing.</p> <p>Data in this repository includes information on sequenced samples (*.csv, *.txt), a cleaned transcriptome assembly after expression filtering (*.fasta), transcriptome annotation from EnTAP (*.tsv), list of transcripts removed from analysis after mapping (*.txt), high-quality SNPs identified from the transcriptome sequencing with GATK (seven files representing different SNP sets used in the analysis; *.vcf), and four custom scripts used in processing SNP data (*.py and *.R).</p> <p>Raw sequence data is archived in GenBank's SRA. 2015-2016 samples: BioProject ID PRJNA690934 and BioSample IDs SAMN17267686–SAMN17267781. 2011 samples: BioProject ID PRJNA283611 and BioSample IDs SAMN03653390–SAMN03653413.</p>
Balancing Accuracy and Evaluation Overhead in Simulation Point Selection
<p>This is the dataset collected for the paper "Balancing Accuracy and Evaluation Overhead in Simulation Point Selection" published at IISWC 2023. It contains 710850 SimPoint configurations and their statistics collected over 22 SPEC2017 benchmarks.</p>
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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Temporally-balanced selection during development of larval Pacific oysters (Crassostrea gigas) inherently preserves genetic diversity within offspring
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Balancing selection maintains intraspecific diversity in a deep-sea fish
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Data and scripts from: Balanced polymorphism fuels rapid selection in an invasive crab despite high gene flow and low genetic diversity
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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)
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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.