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376 results for “Adaptive genes”
Adaptive Introgression in Modern Human Circadian Rhythm Genes Datasets
<p><strong>README:</strong></p> <p>Modern human genetic data with evidence of adaptive introgression from Neanderthals or Denisovans within circadian rhythm genes. The data was generated from the phased gnomAD 1KGP + HGDP callset (Koenig <em>et al</em>., 2024) and introgressed segments were identified by SPrime (Browning <em>et al</em>., 2018). Genes of interest were downloaded from the Circadian Genome Database (CGDB) (Li <em>et al</em>., 2017). Additional variants, haplotypes, and genes that have been previously reported to influence circadian rhythm or chronotype that are thought to be derived from Neanderthals and Denisovans were compiled from Dannemann & Kelso (2017), McArthur et al. (2021), Dannemann et al. (2022), and Velazquez-Arcelay et al. (2023).</p> <p><strong>SPrime ND_Match Files</strong></p> <p>Raw SPrime identified files that we used for our entire analysis. These were modified to include the archaic allele, archaic allele frequency, and average introgressed segment allele frequency. Note that these have been lifted over (Hinrichs <em>et</em> <em>al</em>., 2006) from GRCh38 (hg38) to GRCh37 (hg19) coordinates to match the genome builds of the archaic samples used in our study. As such, any manually generated variant IDs (chromosome:position:ReferenceAllele_AlternativeAllele naming convention) may no longer match the position they are currently sitting on as they were generated with hg38 coordinates. However, all of these were subsequently filtered out of our final results and any proper SNP IDs (dbSNP labels) will be accurate.</p> <p><strong>Supplementary Tables</strong></p> <p>All supplementary tables have an associated README as the first sheet that explains in detail the contents.</p> <p><strong>NEXUS Files</strong></p> <p>NEXUS files were used to generate haplotype networks in PopArt (Leigh & Bryant, 2015). There is a larger, master haplotype file and a smaller subset file. The larger file contains 668 haplotypes from all populations generated in the phased gnomAD 1KGP + HGDP callset (Koenig <em>et al</em>., 2024) for the <em>SUSD1 </em>core haplotype. The smaller subset file is the top 50 haplotypes and ties based on frequency, all Oceanic haplotypes with frequencies of at least 2, and the Neanderthal and Denisovan haplotypes for <em>SUSD1</em>. </p> <p><strong>TRAITS file</strong></p> <p>Accompanies the NEXUS files to create pie graphs for the haplotype network and contains frequency counts of number of haplotypes per region.</p>
Data from: Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
Genomic comparisons of closely related species have identified "islands" of locally elevated sequence divergence. Genomic islands may contain functional variants involved in local adaptation or reproductive isolation and may therefore play an important role in the speciation process. However, genomic islands can also arise through evolutionary processes unrelated to speciation, and examination of their properties can illuminate how new species evolve. Here, we performed scans for regions of high relative divergence (FST) in 12 species pairs of Darwin's finches at different genetic distances. In each pair, we identify genomic islands that are, on average, elevated in both relative divergence (FST) and absolute divergence (dXY). This signal indicates that haplotypes within these genomic regions became isolated from each other earlier than the rest of the genome. Interestingly, similar numbers of genomic islands of elevated dXY are observed in sympatric and allopatric species pairs, suggesting that recent gene flow is not a major factor in their formation. We find that two of the most pronounced genomic islands contain the ALX1 and HMGA2 loci, which are associated with variation in beak shape and size, respectively, suggesting that they are involved in ecological adaptation. A subset of genomic island regions, including these loci, appears to represent anciently diverged haplotypes that evolved early during the radiation of Darwin's finches. Comparative genomics data indicate that these loci, and genomic islands in general, have exceptionally low recombination rates, which may play a role in their establishment.
Estimates of molecular convergence reveal genes with intermediate pleiotropy underlying adaptive variation across teleost fish
<p>This dataset comprises raw sequence data, output of analyses, code used to reproduce the study, figures, and supplementary materials.</p> <p>Code and input files are in Datasets.zip</p> <p>Use the README to navigate this folder. </p> <p>Data to reproduce the CSUBST analysis are in the .tar.gz folder.</p> <p> </p> <p>For more information please check: </p> <p>https://github.com/agneeshbarua/Teleost_convergence</p>
Data from: Restriction site-associated DNA sequencing reveals local adaptation despite high levels of gene flow in Sardinella lemuru (Bleeker, 1853) along the northern coast of Mindanao, Philippines
<p>Stock identification and delineation are important in the management and conservation of marine resources. These were highlighted as priority research areas for Bali sardinella (<em>Sardinella lemuru</em>) which is among the most commercially important fishery resources in the Philippines. Previous studies have already assessed the stocks of <em>S. lemuru</em> between Northern Mindanao Region (NMR) and Northern Zamboanga Peninsula (NZP), yielding conflicting results. Phenotypic variation suggests distinct stocks between the two regions, while mitochondrial DNA did not detect evidence of genetic differentiation for this high gene flow species. This paper tested the hypothesis of regional structuring using genome-wide single nucleotide polymorphisms (SNPs) acquired through restriction-site associated DNA sequencing (RADseq). We examined patterns of population genomic structure using a full panel of 3,573 loci, which was then partitioned into a neutral panel of 3,348 loci and an outlier panel of 31 loci. Similar inferences were obtained from the full and neutral panels, which were contrary to the inferences from the outlier panel. While the full and neutral panels suggested a panmictic population (global F<sub>ST</sub> ~ 0, p > 0.05), the outlier panel revealed genetic differentiation between the two regions (global F<sub>ST</sub> = 0.161, p = 0.001; F<sub>CT</sub> = 0.263, p < 0.05). This indicated that while gene flow is apparent, selective forces due to environmental heterogeneity between the two regions play a role in maintaining adaptive variation. Annotation of the outlier loci returned five genes that were mostly involved in organismal development. Meanwhile, three unannotated loci had allele frequencies that correlated with sea surface temperature. Overall, our results provided support for local adaptation despite high levels of gene flow in <em>S. lemuru</em>. Management therefore should not only focus on demographic parameters (e.g., stock size, catch volume), but also consider the preservation of adaptive variation.</p>
Population genomics of a forest fungus reveals high gene flow and climate adaptation signatures
Genome sequencing of spatially distributed individuals sheds light on how evolution structures genetic variation. Populations of <i>Phellopilus nigrolimitatus</i>, a red-listed wood-inhabiting fungus associated with old-growth coniferous forests, have decreased in size over the last century due to a loss of suitable habitats. We assessed the population genetic structure and investigated local adaptation in<i> P. nigrolimitatus</i>, by establishing a reference genome and genotyping 327 individuals sampled from 24 locations in Northern Europe by RAD sequencing. We revealed a shallow population genetic structure, indicating large historical population sizes and high levels of gene flow. Despite this weak sub-structuring, two genetic groups were recognized; a western group distributed mostly in Norway and an eastern group covering most of Finland, Poland and Russia. This sub-structuring may reflect co-immigration with the main host, Norway spruce (<i>Picea abies</i>), into Northern Europe after the last ice age. We found evidence of low levels of genetic diversity in southwestern Finland, which has a long history of intensive forestry and urbanization. Numerous loci were significantly associated with one or more environmental factors, indicating adaptation to specific environments. These loci clustered into two groups with different associations with temperature and precipitation. Overall, our findings indicate that the current population genetic structure of P. nigrolimitatus results from a combination of gene flow, genetic drift and selection. The acquisition of similar knowledge especially over broad geographic scales, linking signatures of adaptive genetic variation to evolutionary processes and environmental variation, for other fungal species will undoubtedly be useful for assessment of the combined effects of habitat fragmentation and climate change on fungi strongly bound to old-growth forests. --
Genome-wide analysis identified candidate variants and genes associated with heat stress adaptation in Egyptian sheep breeds
<p>The current study was conducted from 2009 to 2019 in three hot and dry agroecological zones in Egypt: Western Desert coastal zone, New Valley desert oasis, and hot-dry Upper Egypt. Within these zones, three local sheep breeds were studied: Barki (83 ewes), Wahati (55 ewes) and Saidi (68 ewes). During the study period, the animals exercised under natural heat stress (simulating summer grazing on poor pasture). Meteorological and physiological parameters were measured and recorded. The heat tolerance index of the animals was calculated to identify animals with high and low heat tolerance based on the animals' response to the five main physiological parameters (scale from 0 to 5). DNA samples were extracted for genomic analysis. The genetic diversity measurements showed a significant influence of breed and location on the populations. The influence of breed is more significant than that of location. The inbreeding analysis shows that the desert breeds (Wahati and Barki) have lower values than the urban breed (Saidi). The high rate of sub-clustering indicates the process of sub-population through inbreeding pressure. Wahati and Barki are very distinct breeds with strong identification, while Saidi breed has crosses with other breeds. The most significant SNPs associated with heat tolerance were found in MYO5A, PRKG1, GSTCD, and RTN1 genes (P < 0.0001). MYO5A had an effect of 0.74 on the trait heat tolerance in the studied population. It produces a protein that is widely distributed in the melanin-producing neural crest of the skin. Genetic association between genetic and phenotypic variations showed that OAR1 18300122.1, located in ST3GAL3, had the greatest positive effect on heat tolerance. GWAS analysis identified SNPs associated with heat tolerance in the PLCB1, STEAP3, KSR2, UNC13C , PEBP4, and GPAT2 genes.</p>
Data from: Inversion Invasions: when the genetic basis of local adaptation is concentrated within inversions in the face of gene flow
<p><span></span></p> <p>Across many species where inversions have been implicated in local adaptation, genomes often evolve to contain multiple, large inversions that arise early in divergence. Why this occurs has yet to be resolved. To address this gap, we built forward-time simulations in which inversions have flexible characteristics and can invade a metapopulation undergoing spatially divergent selection for a highly polygenic trait. In our simulations, inversions typically arose early in divergence, captured standing genetic variation upon mutation, and then accumulated many small-effect loci over time. Under special conditions, inversions could also arise late in adaptation and capture locally adapted alleles. Polygenic inversions behaved similarly to a single supergene of large effect and were detectable by genome scans. Our results show that characteristics of adaptive inversions found in empirical studies (e.g., multiple large, old inversions that are FST outliers, sometimes overlapping with other inversions) are consistent with a highly polygenic architecture, and inversions do not need to contain any large-effect genes to play an important role in local adaptation. By combining a population and quantitative genetic framework, our results give a deeper understanding of the specific conditions needed for inversions to be involved in adaptation when the genetic architecture is polygenic.</p>
From common gardens to candidate genes: Exploring local adaptation to climate in red spruce
<p><span>Local adaptation to climate is common in plant species and has been studied in a range of contexts, from improving crop yields to predicting population maladaptation to future conditions. The genomic era has brought new tools to study this process, which was historically explored through common garden experiments. </span></p> <p><span>In this study, we combine genomic methods and common gardens to investigate local adaptation in red spruce and identify environmental gradients and loci involved in climate adaptation. We first use climate transfer functions to estimate the impact of climate change on seedling performance in three common gardens. We then explore the use of multivariate gene-environment association (GEA) methods to identify genes underlying climate adaptation, with particular attention to the implications of conducting genome scans with and without correction for neutral population structure.</span></p> <p><span>This integrative approach uncovered phenotypic evidence of local adaptation to climate and identified a set of putatively adaptive genes, some of which are involved in three main adaptive pathways found in other temperate and boreal coniferous species: drought tolerance, cold hardiness, and phenology. These putatively adaptive genes segregated into two "modules" associated with different environmental gradients.</span></p> <p><span>This study nicely exemplifies the multivariate dimension of adaptation to climate in trees. </span></p>
Fig 1 in Colossoma macropomum (Characiformes: Serrasalmidae) adapted to new climate regime: differential gene expression from farmed tambaqui juveniles raised in subtropical and tropical regions
Fig 1: Relative gene expression in tambaqui juveniles farmed in two Brazilian regions: Northern (Balbina; BA) and Southeast (Brumado; BRU). Different letters represent statistical differences between populations. The graphs show expression of A) hif-1α (p = 0.137), B) hsp-70 (p = 0.465), C) mstn (p = 0.907), D) ube3a (p = 0.205), E) ras (p = 0.041), F) cry-1 (p = 0.001), G) per-1 (p = 0.001), H) ogt (p = 0.001) and I) acly (p = 0.025).
Fig 3 in Colossoma macropomum (Characiformes: Serrasalmidae) adapted to new climate regime: differential gene expression from farmed tambaqui juveniles raised in subtropical and tropical regions
Fig 3: IBR analyses of relative gene expression in Balbina (BA) and Brumado (BRU) populations. The IBR values are 42.7 (Balbina) and 6.79 (Brumado).
Fig 2 in Colossoma macropomum (Characiformes: Serrasalmidae) adapted to new climate regime: differential gene expression from farmed tambaqui juveniles raised in subtropical and tropical regions
Fig 2: Heatmap of relative expression in Balbina (BA) and Brumado (BRU) populations. The colour scale ranges from blue (low transcript levels) to red (high transcript levels).
Elucidating gene expression adaptation of phylogenetically divergent coral holobionts under heat stress
<p>As coral reefs struggle to survive under climate change, it is crucial to know whether they have the capacity to withstand changing conditions, particularly increasing seawater temperatures. Thermal tolerance requires the integrative response of the different components of the coral holobiont (coral host, algal photosymbiont, and associated microbiome). Here, using a controlled thermal stress experiment across three divergent Caribbean coral species, we attempt to dissect holobiont member metatranscriptome responses from coral taxa with different sensitivities to heat stress and use phylogenetic ANOVA to study the evolution of gene expression adaptation. We show that coral response to heat stress is a complex trait derived from multiple interactions among holobiont members. We identify host and photosymbiont genes that exhibit lineage-specific expression level adaptation and uncover potential roles for bacterial associates in supplementing the metabolic needs of the coral-photosymbiont duo during heat stress. Our results stress the importance of integrative and comparative approaches across a wide range of species to better understand coral survival under the predicted rise in sea surface temperatures.</p>
The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data
<p>In our work, we implemented the ABC-model and could show that one assay for measuring the openness of enhancers is sufficient. Further, we propose a generalised calculation of the ABC-score, which describes enhancer activity in a gene-specific manner, and which includes all TSS, without requiring any additional data. We combined our implementation of the ABC-score with an approach to quantify TF binding affinity into STARE: a framework to derive TF affinities to genes. STARE was also designed for potential application on single-cell data. You can find the code in our <a href="https://github.com/schulzlab/stare">GitHub repository</a> and more details in our <a href="https://doi.org/10.1093%2Fbioinformatics%2Fbtad062">publication</a>.</p> <p>We provide the data for the validation of our ABC-implementation on two CRISPR-screens. We also provide the results of our analysis of single-cell data of the human heart with STARE. All data is in hg19.</p> <p>Content:</p> <ul> <li>CRISPRi_screens: One file for each CRISPRi-screen with interactions that were used to plot precision-recall curves, containing columns for different ABC scoring versions.</li> <li>Enformer: Similar to the CRISPRi_screens, but containing columns for different calculations for Enformer's predicted expression change upon in silico mutagenesis of the enhancer region.</li> <li>K562_CandidateEnhancer: K562 enhancer with the 4th column for enhancer activity, one file for each activity representation that was measured.</li> <li>K562_ABC_Predictions: Regular ABC-scores and generalised ABC-scores for each activity measurement. The files contain all scored interactions for a 10MB window, without any cut-off. We also included the results of the implementation of the ABC-score of Fulco et al. (2019).</li> <li>STARE_Hocker_*: Whole STARE output for human heart single-cell data, one for regular ABC, generalised ABC, generalised ABC with average Hi-C matrix and one based on co-accessibility analysis. All approaches were run with a 5 MB window (except for GeneralisedABC500kb), the ABC-based runs with a score cut-off of 0.02. Each folder contains two subdirectories, one for the ABC-scoring and one for the Gene-TF affinity matrices. The 'ABC_output' also contains a GeneInfo file for each cell type, summarising different attributes per gene.</li> <li>INVOKE_Hocker_*: Folder with the input and output of INVOKE (see https://github.com/schulzlab/tepic), based on the STARE runs. CS genes stands for cell type-specific genes, defined as genes with a z-score across cell types of ≥ 2 and TPM ≥ 0.5. The INVOKE commands were as follows: <ul> <li>Rscript INVOKE.R --dataDir=<TF-Gene matrix> --outDir=<out_path> --response=Expression --regularization=E --performance=TRUE --outerCV=10 --seed=1234</li> </ul> </li> </ul> <p>Importantly, the results are based on data from the following publications:</p> <ul> <li>CRISPRi-screens: <ul> <li>Gasperini, Molly, Andrew J. Hill, José L. McFaline-Figueroa, Beth Martin, Seungsoo Kim, Melissa D. Zhang, Dana Jackson, et al. “A Genome-Wide Framework for Mapping Gene Regulation via Cellular Genetic Screens.” <em>Cell</em> 176, no. 1–2 (January 2019): 377-390.e19. https://doi.org/10.1016/j.cell.2018.11.029.</li> <li> <p>Schraivogel, Daniel, Andreas R. Gschwind, Jennifer H. Milbank, Daniel R. Leonce, Petra Jakob, Lukas Mathur, Jan O. Korbel, Christoph A. Merten, Lars Velten, and Lars M. Steinmetz. “Targeted Perturb-Seq Enables Genome-Scale Genetic Screens in Single Cells.” <em>Nature Methods</em> 17, no. 6 (June 2020): 629–35. https://doi.org/10.1038/s41592-020-0837-5.</p> </li> <li> <p>Fulco, Charles P., Joseph Nasser, Thouis R. Jones, Glen Munson, Drew T. Bergman, Vidya Subramanian, Sharon R. Grossman, et al. “Activity-by-Contact Model of Enhancer–Promoter Regulation from Thousands of CRISPR Perturbations.” <em>Nature Genetics</em> 51, no. 12 (December 2019): 1664–69. https://doi.org/10.1038/s41588-019-0538-0.</p> </li> </ul> </li> <li>Enformer model: Avsec, Žiga, Vikram Agarwal, Daniel Visentin, Joseph R. Ledsam, Agnieszka Grabska-Barwinska, Kyle R. Taylor, Yannis Assael, John Jumper, Pushmeet Kohli, and David R. Kelley. “Effective Gene Expression Prediction from Sequence by Integrating Long-Range Interactions.” <em>Nature Methods</em> 18, no. 10 (October 2021): 1196–1203. https://doi.org/10.1038/s41592-021-01252-x.</li> <li>K562 predictions and average Hi-C matrix: Fulco, Charles P., Joseph Nasser, Thouis R. Jones, Glen Munson, Drew T. Bergman, Vidya Subramanian, Sharon R. Grossman, et al. “Activity-by-Contact Model of Enhancer–Promoter Regulation from Thousands of CRISPR Perturbations.” <em>Nature Genetics</em> 51, no. 12 (December 2019): 1664–69. https://doi.org/10.1038/s41588-019-0538-0.</li> <li>Hi-C matrix for K562 predictions: Rao, S. et al. (2014). A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell, 159(7), 1665–1680</li> <li>STARE and INVOKE runs: Hocker, J. D. et al. (2021). Cardiac cell type–specific gene regulatory programs and disease risk association. Science Advances, 7(20), eabf1444</li> <li>H3K27ac HiChIP for STARE runs: Anene-Nzelu, C. G. et al. (2020). Assigning Distal Genomic Enhancers to Cardiac Disease–Causing Genes. Circulation, 142(9), 910–912</li> <li>INVOKE software: Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction Schmidt et al., Nucleic Acids Research 2016; doi: 10.1093/nar/gkw1061</li> </ul> <p> </p>
VCF file from: Signatures of local adaptation to current and future climate in phenology-related genes in natural populations of Quercus robur
<p>Qrob_seqcap_87_18799.vcf - containing 18,799 single nucleotide variants (SNPs) in phenology-related genes in 87 individuals of Quercus robur from 6 populations, described in Meger et al.</p> <p> </p>
Semipermeable species boundaries create opportunities for gene flow and adaptive potential
<p><span>Hybridisation and gene flow can have both deleterious and adaptive consequences for natural populations and species. To better understand the extent of hybridisation in nature and the balance between its beneficial and deleterious outcomes in a changing environment, information on naturally hybridising non-model organisms is needed. This requires the characterisation of the structure and extent of natural hybrid zones. Here we study natural populations of five keystone mound-building wood ant species in the <em>Formica</em> <em>rufa</em> group across Finland. No genomic studies across the species group exist, and the extent of hybridisation and genomic differentiation in sympatry is unknown. Combining genome-wide and morphological data, we demonstrate more extensive hybridisation than was previously detected between all five species in Finland. Specifically, we reveal a mosaic hybrid zone between <em>F. aquilonia, F. rufa </em>and<em> F. polyctena</em>, comprising further generation hybrid populations. Despite this, we find that <em>Formica rufa, F. aquilonia, F. lugubris, </em>and<em> F. pratensis</em> form distinct gene pools in Finland. We also find that hybrids occupy warmer microhabitats than the non-admixed populations of cold-adapted F. aquilonia, and suggest that warm winters and springs, in particular, may benefit hybrids over <em>F. aquilonia</em>, the most abundant <em>F. rufa</em> group species in Finland. In summary, our results indicate that extensive hybridisation may create adaptive potential that could promote wood ant persistence in a changing climate. Additionally, they highlight the potentially significant ecological and evolutionary consequences of extensive mosaic hybrid zones, within which independent hybrid populations face an array of ecological and intrinsic selection pressures.</span></p>
Visual opsin gene expression evolution in the adaptive radiation of cichlid fishes of Lake Tanganyika
<p>Tuning the visual sensory system to the ambient light is essential for survival in many animal species. This is often achieved through duplication, functional diversification, and/or differential expression of visual opsin genes. Here, we examined 753 new retinal transcriptomes from 112 species of cichlid fishes from Lake Tanganyika to unravel adaptive changes in gene expression at the macro-evolutionary and ecosystem level of one of the largest vertebrate adaptive radiations. We found that, across the radiation, all seven cone opsins – but not the rhodopsin – rank among the most differentially expressed genes in the retina, together with other vision-, circadian-rhythm-, and haemoglobin-related genes. We propose two new visual palettes characteristic of very shallow- and deep-water living species, respectively, and show that visual system adaptations along two major ecological axes, macro-habitat and diet, occur primarily via gene expression variation in a subset of cone opsin genes.</p>
Adaptive alien genes are maintained amidst a vanishing introgression footprint in a sea squirt
<p>This zenodo archive contains the multi-locus genotype tables for the paper "Falling shoulders ahead: adaptive alien genes maintained amidst vanishing introgression footprint in sea squirts". There are three files in this archive:</p> <ul> <li>Ci_KASP_genotypes_2012.csv: genotype table for individuals sampled in 2012</li> <li>Ci_KASP_genotypes_2021.csv: genotype table for individuals sampled in 2021 as well as control individuals from the two <em>Ciona</em> species</li> <li>Ci_KASP_genotypes_hybrids.csv: genotype table for control hybrids</li> </ul>
Data from: Signatures of local adaptation in candidate genes of oaks (Quercus spp.) in respect to present and future climatic conditions
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Semipermeable species boundaries create opportunities for gene flow and adaptive potential
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Data from: Restriction site-associated DNA sequencing reveals local adaptation despite high levels of gene flow in Sardinella lemuru (Bleeker, 1853) along the northern coast of Mindanao, Philippines
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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.
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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
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