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1,467 results for “Genetic structure”
Weak spatial-genetic structure in a native invasive, the southern pine beetle (Dendroctonus frontalis), across the eastern United States
<p>The southern pine beetle<i>, Dendroctonus frontalis</i>, is a native pest of pine trees that has recently expanded its range into the northeastern United States. Understanding its colonization, dispersal, and connectivity will be critical for mitigating negative economic and ecological impacts in the newly invaded areas. Characterization of spatial-genetic structure can contribute to this; however, previous studies have reached different conclusions about regional population genetic structure, with one study reporting a weak east-west pattern, and the most recent reporting absence of structure. Here we systematically assessed several explanations for the absence of spatial-genetic structure. To do this, we developed nine new microsatellite markers and combined them with an existing 24-locus data matrix for the same individuals. We then reanalyzed this full dataset alongside datasets in which certain loci were omitted with the goal of creating more favorable signal to noise ratios. We also partitioned the data based on the sex of <i>D. frontalis</i> individuals, and then employed a broad suite of genotypic clustering and isolation-by-distance (IBD) analyses. We found that neither inadequate information content in the molecular marker set, nor unfavorable signal-to-noise ratio, nor insensitivity of the analytical approaches could explain the absence of structure. Regardless of dataset composition, there was little evidence for clusters (i.e., distinct geo-genetic groups) or clines (i.e., gradients of increasing allele frequency differences over larger geographic distances), with one exception: significant IBD was repeatedly detected using an individual-based measure of relatedness whenever datasets included males (but not for female-only datasets). This is strongly indicative of broad-scale female-biased dispersal, which has not previously been reported for <i>D. frontalis</i>, in part owing to logistical limitations of direct approaches (e.g., capture-mark-recapture). Weak spatial-genetic structure suggests long-distance connectivity and that gene flow is high, but additional research is needed to understand range expansion dynamics in this species using alternate approaches.</p>
Figure 4 in Population genetic structure and demographic history of the Chinese endemic Mongoloniscus sinensis (Dollfus, 1901) (Isopoda: Oniscidea)
Figure 4. Pairwise mismatch distributions for six derived clades.
Figure 1 in Genetic diversity, population structure and demographic history of Dugesia japonica in Taihang Mountains
Figure 1. Geographical distribution of Dugesia japonica populations sampled in Taihang Mountains.
Strong population genetic structure and cryptic diversity in the Florida bonneted bat (Eumops floridanus)
<p>Knowledge of genetic structure is essential for the long-term management and conservation of endangered species. We report the results from a genetic examination of the federally endangered Florida bonneted bat (<i>Eumops floridanus</i>) sampled from its range in southern Florida, USA. Bonneted bats are primarily found in four regions separated by approximately 100 to 250 kms, including three western natural areas (BW, PC, and CC) and one urban population on the east coast [Miami-Dade County (MD)]. We used 22 microsatellite loci and cytochrome <i>b</i> sequences to assess the extent of connectivity and levels of genetic diversity. Regional populations were highly differentiated (<i>F</i><sub>ST</sub> = 0.178) and model-based and multivariate analyses showed that MD was the most distinct among pairwise comparisons. Regional populations are small (i.e., <i>N<sub>e</sub></i><sub> </sub>< 100) but demographically stable. Estimates of contemporary migration and historic gene flow suggest that regional populations do not frequently exchange migrants, but simulations suggest that the divergence among western regions is likely a result of recent genetic drift rather than long-term isolation. Significantly, mitochondrial DNA revealed that haplotypes from MD were similar or shared with those recognized as <i>Eumops ferox</i> from Cuba and Jamaica, and divergent (1.5%) from the remainder of bonneted bats in Florida. Our data support the management of each of the four populations as distinct population segments, and that BW, PC and CC combined are on an independent evolutionary trajectory from bats in MD. Critically, bonneted bats in Florida appear to harbor cryptic diversity that will require a reassessment of their taxonomy.</p>
Dataset 2 for Large‐ and small‐scale geographic structures affecting genetic patterns across populations of an Alpine butterfly
<p>Understanding factors influencing patterns of genetic diversity and the population genetic structure of species is of particular importance in the current era of global climate change and habitat loss. These factors include the evolutionary history of a species as well as heterogeneity in the environment it occupies, which in turn can change across time. Most studies investigating spatio-temporal genetic patterns have focused on patterns across wide geographical areas rather than local variation, but the latter can nevertheless be important particularly in topographically complex areas. Here we consider these issues in the Sooty Copper butterfly (<i>Lycaena tityrus</i>) from the European Alps, using genome-wide SNPs identified through RADseq. We found strong genetic differentiation within the Alps with four genetic clusters, indicating western, central, and eastern refuges, and a strong reduction of genetic diversity from west to east. This reduction in diversity may suggest that the southwestern refuge was the largest one in comparison to other refuges. Also, the high genetic diversity in the West may result from (1) admixture of different western refuges, (2) more recent demographic changes, or (3) introgression of lowland <i>L. tityrus</i> populations. At small spatial scales, populations were structured by several landscape features and especially by high mountain ridges and large river valleys. We detected 36 outlier loci likely under altitudinal selection, including several loci related to membranes and cellular processes. We suggest that efforts to preserve alpine <i>L. tityrus </i>should focus on the genetically diverse populations in the western Alps, and that the dolomite populations should be treated as genetically distinct management units, since they appear to be currently more threatened than others. This study demonstrates the usefulness of SNP-based approaches for understanding patterns of genetic diversity, gene flow and selection in a region that is expected to be particularly vulnerable to climate change.</p>
Limited seed dispersal shapes fine-scale spatial genetic structure in a Neotropical dioecious large-seeded palm
<p><span>Seed and pollen dispersal contribute to gene flow and shape the genetic patterns of plants over fine spatial scales. We inferred fine-scale spatial genetic structure (FSGS) and estimated realized dispersal distances in Phytelephas aequatorialis, a Neotropical dioecious large-seeded palm. We aimed to explore how seed and pollen dispersal shape this genetic pattern in a focal population. For this purpose, we genotyped 138 seedlings and 99 adults with 20 newly developed microsatellite markers. We tested if rodent-mediated seed dispersal has a stronger influence than insect-mediated pollen dispersal in shaping FSGS. We also tested if pollen dispersal was influenced by the density of male palms around mother palms in order to further explore this ecological process in large-seeded plants. Rodent-mediated dispersal of these large seeds occurred mostly over short distances (mean 34.76 ± 34.06 m) while pollen dispersal distances were two times higher (mean 67.91 ± 38.29 m). The spatial extent of FSGS up to 35 m and the fact that seed dispersal did not increase the distance at which male alleles disperse suggest that spatially limited seed dispersal is the main factor shaping FSGS and contributes only marginally to gene flow within the population. Pollen dispersal distances depended on the density of male palms, decreasing when individuals show a clumped distribution and increasing when they are scattered. Our results show that limited seed dispersal mediated by rodents shapes FSGS in P. aequatorialis, while more extensive pollen dispersal accounts for a larger contribution to gene flow and may maintain high genetic diversity.</span></p>
Illumina next generation ddRAD sequencing SNP data from: Contrasting genetic diversity and structure between endemic and widespread damselfishes are related to differing adaptive strategies
<p class="MsoNormal"><strong><u><span>Aim:</span></u></strong><span> Discerning when, where, and how processes of isolation lead to differing biogeography is especially complex for marine species with similar ecological niches and within the same geographic location. We assessed population genetics of congeneric and ecologically similar damselfishes within their overlapping distributions and across potential barriers to geneflow.</span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Taxon:</span></u></strong><span> <em>Dascyllus marginatus </em>(endemic) and <em>Dascyllus abudafur </em>(widespread)<em>.</em></span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Location:</span></u></strong><span> Coral reefs from the Red Sea, Djibouti, Yemen, Oman, and Madagascar. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Methods:</span></u></strong><span> We used RADseq derived SNPs to investigate key differences in population genetics between both species and discuss barriers shaping genetic differentiation (neutral vs. selective) and biogeography. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Results:</span></u></strong><strong><span> </span></strong><em><span>Dascyllus marginatus </span></em><span>inhabited the Red Sea, the coasts of Yemen (including Socotra), and the Gulf of Oman. <em>Dascyllus abudafur</em> species was present from the Red Sea to Madagascar but was absent from Yemen and Oman. Populations of <em>D. marginatus </em>had an order of magnitude higher genetic differentiation compared to <em>D. abudafur</em>, as well as several outlier loci (suggesting selective pressure), which were absent in <em>D. abudafur</em> despite equal sampling locations. In both species, specimens from the Red Sea and Djibouti formed one genetic cluster separated from all other locations. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Main conclusions:</span></u></strong><span> The stronger genetic structure at smaller geographic scale of the endemic species seems associated to faster adaptation to environmental differences; whereas the widespread species only experienced reduced geneflow and neutral differentiation at much larger geographic scales. Restrictive transitions (between the Gulf of Aqaba and the Red Sea or the Red Sea and the Gulf of Aden) did not affect the genetic architecture of either species, while the environmental shift within the Red Sea (at 22°N/20°N) affected the endemic but not the widespread species. Samples from continental Yemen revealed that a genetic break in the Gulf of Aden likely reflects historical colonization processes and not contemporary environmental regimes.</span></p>
Male diversity matters: Genetic structuring of insular male date palm (Phoenix dactylifera L.) revealed valuable breeding and conservation resources
Most male date palms available for pollinating different female cultivars have mainly originated from seed propagation resulting in many different local males that represent a source of genetic diversity. Favorable fruit production is related to quality of pollen and its compatibility with a certain female variety. Therefore, the genetic characterization of the male pollen as a superior one for each female cultivar should be the first step to establish an intensive program to produce superior males through different procedures. In this study, the genetic diversity and population structure of 72 male date palm accessions were investigated using 15 microsatellite loci. A total number of 125 alleles was detected with an average of 8.33 alleles per locus. Bayesian model-based clustering analysis indicated the presence of two differentiated endemic male date palm genetic clusters, continental and insular, with the presence of introduced accessions originating from the Middle East. The diversity analysis in the insular region of Tunisia, which had never been performed before, revealed that this germplasm enclosed valuable endemic resources supporting the hypothesis of the presence of wild material. These findings are crucial for identifying interesting genotypes that can be integrated into international coordinated actions of Phoenix dactylifera L. breeding programs as well as for the protection and conservation of valuable resources.
Genetic assessment reveals inbreeding, possible hybridization, and low levels of genetic structure in a declining goose population
<p>The population numbers of taiga bean goose (<i>Anser fabalis fabalis</i>) have halved during recent decades. Since this subspecies is hunted throughout most of its range, the decline is of management concern. Knowledge of the genetic population structure and diversity is important for guiding management and conservation efforts. Genetically unique subpopulations might be hunted to extinction if not managed separately, and any inbreeding depression or lack of genetic diversity may affect the ability to adapt to changing environments and increase extinction risk. We used microsatellite and mitochondrial DNA markers to study the genetic population structure and diversity among taiga bean geese breeding within the Central flyway management unit using non-invasively collected feathers. We found some genetic structuring with the maternally inherited mitochondrial DNA between four geographic regions (<i>ɸ</i><sub>ST</sub> = 0.11-0.20) but none with the nuclear microsatellite markers (all pairwise <i>F</i><sub>ST</sub>-values 0.002- 0.005). These results could be explained by female natal philopatry and male-biased dispersal, which completely homogenizes the nuclear genome. Therefore, the population could be managed as a single unit. Genetic diversity was still at a moderate level (average <i>H</i><sub>E</sub> = 0.69) and there were no signs of past population size reductions, although significantly positive inbreeding coefficients in all sampling sites (<i>F</i><sub>IS</sub> = 0.05-0.10) and high relatedness values (<i>r </i>= 0.60-0.86) between some individuals could indicate inbreeding. In addition, there was evidence of either incomplete lineage sorting or introgression from the pink-footed goose (<i>A. brachyrhynchus</i>). The current population is not under threat by genetic impoverishment but monitoring in the future is desirable.</p>
Data from: Multiple introductions, polyploidy and mixed reproductive strategies are linked to genetic diversity and structure in the most widespread invasive plant across Southern Ocean archipelagos
<p><span>Biological invasions in remote</span> <span>areas that experience low human activity provide unique opportunities to elucidate processes responsible for invasion success. Here we study the most widespread invasive plant species across the isolated islands of the Southern Ocean, the annual bluegrass, Poa annua. To </span><span>analyze</span><span> geographic variation in genome size, genetic diversity, and reproductive strategies, we sampled all major sub-Antarctic archipelagos in this region and generated microsatellite data for 470 individual plants representing 31 populations. We also estimated genome sizes for a subset of individuals using flow cytometry. Occasional events of island colonization are expected to result in high genetic structure among islands, overall low genetic diversity, and increased self-fertilization, but we show that this is not the case for Poa annua. Microsatellite data indicated low population genetic structure and lack of isolation-by-distance</span> <span>among the sub-Antarctic archipelagos we sampled, but high population structure within each archipelago. We identified high levels of genetic diversity, low clonality, and low selfing rates in sub-Antarctic P. annua populations (contrary to rates typical of continental populations). In turn, estimates of autogamy declined in populations as genetic diversity increased. Additionally, we found that most P. annua individuals are likely tetraploid and that only slight variation exists in genome size across the Southern Ocean. Our findings suggest multiple independent introductions of P. annua into the sub-Antarctic, which</span> <span>promoted the establishment of genetically diverse populations. Despite multiple introductions, the adoption of convergent reproductive strategies (outcrossing) happened independently in each major archipelago. The combination of polyploidy and a mixed reproductive strategy likely benefited P. annua in the Southern Ocean by increasing genetic diversity and its ability to cope with the novel environmental conditions.</span></p>
Genetic diversity and population structure from a Peruvian nucleus cattle herd using SNP data
<p>New-generation sequencing technologies, among them SNP chips for massive genotyping, have proven to be useful for the effective management of genetic resources. Also, developing nucleus herds is an effective method for genetic improvement work. To date, molecular studies in Peruvian cattle are still in their infancy. To close this gap, we here employed two SNP panels (BovineHD and Bovine100K) to determine for the first time the Peruvian nucleus herd's genetic diversity and population structure that belong to INIA. This nucleus comprises Brahman (N=16), Braunvieh (N=14), Gyr (N=11), and Fleckvieh (N=22) breeds. Additionally, samples from a locally adapted creole cattle, the Arequipa Fighting Bull (AFB, N=12), were incorporated into the study. The genetic diversity indices in all breeds showed a high proportion of polymorphic SNPs, varying from 69.37% in Gyr to 80.81% in Braunvieh. Also, Braunvieh possessed the highest observed heterozygosity (0.53±0.17), while Brahman possessed the lowest (0.44±0.10), indicating that the former is more diverse compared to the other cattle breed groups. According to the molecular variance analysis, 83.92% of the variance occurs within individuals, whereas 16.0% occurs between populations. The pairwise FST estimates between breeds showed values that ranged from 0.054 (Braunvieh vs AFB) to 0.266 (Brahman vs AFB). Pairwise Reynold's distance showed a pattern similar to the one obtained with the FST statistics, with values ranging from 0.058 to 0.309. A dendrogram was constructed using the Neighbor-Joining clustering algorithm, and similar to the principal coordinate analysis, three groups were identified. Results showed a clear separation between <em>Bos</em> <em>indicus</em> (Brahman and Gyr) and <em>B</em>. <em>taurus</em> breeds (Braunvieh and Fleckvieh). For Fleckvieh and Braunvieh, there were two subgroups each one of them grouping with the AFB group. Similar results were obtained with ADMIXTURE analysis with K= 3 as the most optimal number for the inferred genetic structure of the populations. The results from the current study would contribute to the appropriate management avoiding loss of genetic variability in these breeds and to future improvements for this nucleus. Additional work is needed to speed up the breeding process in the Peruvian cattle system.</p>
Historic and contemporary biogeographic perspectives on range-wide spatial genetic structure in a widespread seagrass
<p>This raw data set contains multilocus genotypes for 1,312 individual samples from 44 locations.</p> <p>Aim: Historical and contemporary processes drive spatial patterns of genetic diversity. These include climate-driven range shifts and gene flow mediated by biogeographical influences on dispersal. Assessments that integrate these drivers are uncommon, but critical for testing biogeographic hypotheses. Here, we characterise intraspecific genetic diversity and its spatial structure across the entire distribution of a temperate seagrass to test marine biogeographic concepts for southern Australia.</p> <p>Location: Temperate Australian coastal waters</p> <p>Methods: Predictive modelling was used to contrast the current <em>Posidonia australis</em> distribution to its historical distribution during the Last Glacial Maximum (LGM). Spatial genetic structure was estimated for 44 sampled meadows from across the geographical range of the species using nine microsatellite loci. </p> <p>Results: Historical and contemporary distributions were similar, with the exception of the Bass Strait. Genetic clustering was consistent with the three currently recognised biogeographic provinces and largely consistent with the finer-scale <span>IMCRA </span>bioregions. Discrepancies were found within the Flindersian province and southwest IMCRA bioregion, while two regions of admixture coincided with transitional bioregions. Clonal diversity was highly variable, but positively associated with latitude. Genetic differentiation among meadows was significantly associated with oceanographic distance.</p> <p>Main conclusions: Our approach suggests how shared seascape drivers have influenced the capacity of <em>P. australis</em> to effectively track sea level changes associated with natural climate cycles over millennia, <span>and in particular, the recolonisation of meadows across the Continental Shelf following the LGM</span>. Genetic structure associated with IMCRA bioregions reflects the presence of stable biogeographic barriers, such as oceanic upwellings. This study highlights the importance of biogeography to infer the role of historical drivers in shaping extant diversity and structure. </p>
Assessment of the Genetic Diversity and Population Structure of the Peruvian Andean Legume, Tarwi (Lupinus mutabilis), with High Quality SNPs
<p><em>Lupinus mutabilis</em> Sweet (Fabaceae), “tarwi” or “chocho”, is an important grain legume in the Andean region. In Peru, studies on tarwi have mainly focused on morphological features; however, they have not been molecularly characterized. Currently, it is possible to explore the genetic parameters of plants with reliable and modern methods such as genotyping by sequencing (GBS). Here, for the first time, we used single nucleotide polymorphism (SNP) markers to infer the genetic diversity and population structure of 89 accessions of tarwi from nine Andean regions of Peru. A total of 5922 SNPs distributed along all chromosomes of tarwi were identified. STRUCTURE analysis revealed that this crop is grouped into two clusters. A dendrogram was generated using the UPGMA clustering algorithm and, like the principal coordinate analysis (PCoA), it showed two groups that correspond to the geographic origin of the tarwi samples. AMOVA showed a reduced variation between clusters (7.59%) and indicated that variability within populations is 92.41%. Population divergence (F<sub>st</sub>) between clusters 1 and 2 revealed low genetic difference (0.019). We also detected a negative F<sub>is</sub> for both populations, demonstrating that, like other <em>Lupinus</em> species, tarwi also depends on cross-pollination. SNP markers were powerful and effective for the genotyping process in this germplasm. We hope that this information is the beginning of the path towards a modern genetic improvement and conservation strategies of this important Andean legume.</p>
Obuasi case study data: Performance of neutral SNP barcodes to determine genetic diversity and structure of Plasmodium falciparum in Africa
<p>A small number of informative biallelic single nucleotide polymorphisms (SNPs) have been proposed to be an economical method to fast-track the genotyping and relatedness analysis of <em>Plasmodium</em> <em>falciparum</em> in malaria-endemic areas. Whilst used successfully in low-transmission areas where infections are monoclonal and highly related, we present the first study to evaluate the performance of these 24- and 96-SNP molecular barcodes in African countries characterised by moderate-to-high transmission. Using haplotypes generated from the MalariaGEN <em>P. falciparum</em> Community Project version 6 database, 52.3% of infections were multiclonal, generating high frequencies of mixed-allele calls (MACs) per isolate. Both multiclonality and low heterozygosity of SNPs impeded haplotype construction for analyses of relatedness. Although fewer SNPs provided usable data, these SNP barcodes weakly identified genetic differentiation across large geographic distances. However, both minor and major alleles' frequencies were temporally unstable. We conclude that these standardised SNP barcodes are vulnerable to ascertainment bias. While large numbers of SNPs acquired by whole-genome sequencing and computational methods to construct haplotypes present a way forward, these approaches may not be practical or cost-effective for surveillance on large scales in malaria-endemic areas. </p>
Data for: Surrounding landscape, habitat and hybridization dynamics drive population structure and genetic diversity in the Saltmarsh Sparrow (Ammospiza caudacuta)
<p class="MsoNormal">Determining factors that shape a species' population genetic structure is beneficial for identifying effective conservation practices. We assessed population structure and genetic diversity for Saltmarsh Sparrow (<em>Ammospiza caudacuta</em>), an imperiled tidal marsh specialist, using 13 microsatellite markers and 964 individuals sampled from 24 marshes across the breeding range. We show that Saltmarsh Sparrow populations are structured regionally by isolation-by-distance, with gene flow occurring among marshes within ~110-135 km of one another. Isolation-by-resistance and isolation-by-environment also shape genetic variation; several habitat and landscape features are associated with genetic diversity and genetic divergence among populations. Human development in the surrounding landscape isolates breeding marshes, reducing genetic diversity and increasing population genetic divergence, while surrounding marshland and patch habitat quality (proportion high marsh and sea-level-rise trend) have the opposite effect. The distance of the breeding marsh to the Atlantic Ocean also influences genetic variation, with marshes farther inland being more divergent than coastal marshes. In northern marshes, hybridization with Nelson's Sparrow (<em>A. nelsoni</em>) strongly influences Saltmarsh Sparrow genetic variation, by increasing genetic diversity in the population; this has a concomitant effect of increasing genetic differentiation of marshes with high levels of introgression. From a conservation perspective, we found that the majority of population clusters have low effective population sizes, suggesting a lack of resiliency. To conserve the representative breadth of genetic and ecological diversity and to ensure redundancy of populations, it will be important to protect a diversity of marsh types across the latitudinal gradient of the species range, including multiple inland, coastal and urban populations, which we have shown to exhibit signals of genetic differentiation. It will also require maintaining connectivity at a regional level, by promoting high marsh habitat at the scale of gene flow (~130 km), while also ensuring "stepping stone" populations across the range. </p>
Low genetic diversity and shallow population structure in the broom hare, Lepus castroviejoi (Lagomorpha:Leporidae)
<p><span class="TextRun SCXW115721130 BCX4"><span class="NormalTextRun SCXW115721130 BCX4">Microsatellite dataset of 322 hare samples from five species: 76 samples from the broom hare (</span></span><em><span class="TextRun SCXW115721130 BCX4"><span class="NormalTextRun SCXW115721130 BCX4">Lepus </span><span class="NormalTextRun SCXW115721130 BCX4">castroviejoi</span></span></em><span class="TextRun SCXW115721130 BCX4"><span class="NormalTextRun SCXW115721130 BCX4">); 81 for the European hare (<em>L. europaeus</em>); 68 for the Iberian hare (<em>L. granatensis</em>); 77 for the mountain hare (<em>L. timidus</em>); and 20 for the Italian hare (<em>L. corsicanus</em>).</span></span></p>
The impact of genetically controlled splicing on exon inclusion and protein structure
<p><strong>This repository contains raw and processed files used in Einson et. al 2022. </strong></p> <p>Code used to generate these files can be found here: https://github.com/jeinson/sqtl_manuscript</p> <p><strong><em>Descriptions of files contained within each sub directory</em></strong></p> <p><strong>01_raw_psi</strong></p> <ul> <li><em>{GTEx_tissue_id}_v8.psi.tsv.gz: </em>Unfiltered PSI output from IPSA-nf, per tissue. See methods for details about how files were created. </li> <li><em>gtex_v8_exon_id_map.tsv: </em>Mapping file between exon coordinates and Ensembl gene IDs, with suffix used in GTEx v8 gencode annotation. </li> </ul> <p><strong>02_qtl_results</strong></p> <ul> <li><strong>cross_tissue</strong> <ul> <li><em>top_sQTLs_MAF05.tsv: </em>List of top GTEx v8 sQTLs across tissues, with one exon and top variant per tissue. See methods for details. See matching file for column descriptions. </li> <li><em>top_sQTLs_median_psi.tsv: </em>The median, mean, and standard deviation of PSI of each significant exon from the previous file, taken across all individuals from GTEx with data available.</li> <li><em>top_sQTLs_MAF05_w_anc_allele.tsv: </em>List of top sQTLs across tissues, with additional columns for the top ψQTL ancestral and derived alleles, where available. </li> </ul> </li> <li><strong>per_tissue</strong> <ul> <li><em>{GTEx_tissue_id}_combined_sQTLs.tsv.gz: </em>Raw output of ψQTL calling using QTLtools in grouped permutational mode per tissue, with groups specified by gene. See methods for more details, and https://qtltools.github.io/qtltools/ for column descriptions. </li> </ul> </li> </ul> <p><strong>03_qtl_credible_sets</strong></p> <ul> <li> <em>GTEx_psi_{GTEx_tissue_id}.collapsed.txt.gz: </em>Output of the QTL catalog fine mapping pipeline (https://github.com/eQTL-Catalogue/qtlmap), run on all exons and tissues, and collapsed using the procedure described in Methods. </li> </ul> <p><strong>04_qtl_coloc</strong></p> <ul> <li><em>combined_coloc_results_full.tsv.gz: </em>Combined output of running coloc on ψQTLs from the 18 GTEx tissues against 87 sets of GWAS summary statistics. This file contains all results, including non-significant associations. A nominal QTLtools pass was used as input. We do not include these files in this repository due to size limitations, but contact the authors if you need access to nominal QTL calls. </li> <li><em>top_sQTLs_with_top_coloc_event.tsv: </em>The QTLs in <em>top_sQTLs_MAF05.tsv</em> with additional columns for the GWAS with the highest posterior probability of a colocalization event. Importantly, the tissue and top variant may not match the main <em>top_sQTLs_MAF05.tsv </em>file for every gene. </li> </ul> <p><strong>05_exon_features: </strong>See matching files for description of each column. </p> <ul> <li><em>cross_tissue_constitutive_exons_with_AF.tsv: </em>Detailed features of cross tissue constitutive exons. See methods for definition of constitutive exons. </li> <li><em>cross_tissue_nonsignificant_genes_with_AF.tsv: </em>Detailed features of sufficiently variable exons with no significant variant across tissues. See methods for more details. </li> <li><em>top_sQTLs_MAF05_with_AF.tsv: </em>Detailed features of top sQTLs. </li> <li><em>top_sQTLs_with_top_coloc_with_AF.tsv: </em>Detailed features of sQTLs that colocalize with at least one GWAS trait. Contains columns for Euclidean distances between PAE matrices and RMSD between isoforms, among genes with a significant GWAS colocalization event. </li> </ul> <p><strong>06_predicted_structures: </strong>Each prediction was run 5 times, and we report the best model in the manuscript. </p> <ul> <li><strong>{protein.id}[_mutant].result</strong> <ul> <li><em>{protein.id}[_mutant]{_run.id}_coverage.png.gz: </em>Plot of the number of sequences per position in MSA</li> <li><em>{protein.id}[_mutant]{_run.id}_PAE.png.gz: </em>PAE matrix plots for each model</li> <li><em>{protein.id}[_mutant]{_run.id}_plddt.png.gz: </em>pLDDT plots for each model</li> <li><em>{protein.id}[_mutant]{_run.id}_predicted_aligned_error_v1.json.gz</em>: A PAE matrix for the best model using <a href="https://alphafold.ebi.ac.uk/faq#faq-7">AlphaFold-DB's format</a></li> <li><em>{protein.id}[_mutant]{_run.id}_unrelaxed_rank_{rank.num}_model_{model.num}_scores.json.gz</em>: Per model array (list of lists) with PAE, a list of the average pLDDT and the pTM score. </li> <li><em>{protein.id}[_mutant]{_run.id}_unrelaxed_rank_{rank.num}_model_{model.num}_pdb.gz: </em>Per model predicted structure in pd format</li> <li><em>{protein.id}[_mutant]{_run.id}.a3m.gz</em>: A3M formatted input MSA</li> <li><em>cite.bibtex: </em>BibTex file with citations for all used tools and databases</li> <li><em>config.json</em>: Model input parameters</li> </ul> </li> </ul> <p><strong>07_other_data</strong></p> <ul> <li><em>cross_tissue_constitutive_exons.tsv: </em>List of exons that are constitutively spliced across multiple tissues. See methods for details. </li> <li><em>cross_tissue_nonsignificant_genes.tsv</em>: List variably spliced exons with no significant sVariant in any tissue. See methods for details. </li> <li><em>gtex_v8_exon_id_map.rds: </em>rds representation of a map between exon IDs, as used in the modified version of gencode v26, and exon hg38 coordinates. </li> <li><em>gtex_v8_n_exons_per_gene.tsv: </em>Number of exons per gene, as annotated in the modified version of gencode v26 used in GTEx v8. </li> </ul> <p><strong>08_geuvadis</strong></p> <ul> <li><em>geuvadis_psi.tsv.gz: </em>Unfiltered PSI output from IPSA-nf, run on Geuvadis BAM files. See methods for details. (Raw data was downloaded from ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEUV)</li> <li><em>geuvadis_sQTLs.tsv.gz: </em>Raw output of ψQTL calling using QTLtools in grouped permutational mode for geuvadis data, with groups specified by gene. See methods for more details, and https://qtltools.github.io/qtltools/ for column descriptions. </li> <li><em>remapped_gencode.v26.GRCh37.GTEx_v8.nochr.genes.gtf.gz:</em> Lifted over version of the gencode v26 gtf file, used to define exons for PSI and qtl mapping in the geuvadis analysis. The original version that was used in the GTEx analysis is based on GRCh38, and is available here: https://storage.googleapis.com/gtex_analysis_v8/reference/gencode.v26.GRCh38.genes.gtf</li> </ul>
Data from: Philopatry influences the genetic population structure of the blacktip shark (Carcharhinus limbatus) at multiple spatial scales
<p>Understanding how interactions among microevolutionary forces generate genetic population structure of exploited species is vital to the implementation of management policies that facilitate population persistence. Philopatry displayed by many coastal shark species can impact gene flow and facilitate selection, and thus has direct implications for the spatial scales of management plans. Here, genetic structure of the blacktip shark (Carcharhinus limbatus) was examined using a mixed-marker approach based on mitochondrial control region sequences and 4,339 SNP-containing loci generated using ddRAD-Seq. Genetic variation was assessed among young-of-the-year sampled in 11 sites in waters of the United States in the western North Atlantic Ocean, including the Gulf of Mexico. Spatial and environmental analyses detected 68 nuclear loci putatively under selection, enabling separate assessments of neutral and adaptive genetic structure. Both mitochondrial and neutral SNP data indicated three genetically distinct units – the Atlantic, eastern Gulf, and western Gulf – that align with regional stocks and suggest regional philopatry by males and females. Heterogeneity at loci putatively under selection, associated with temperature and salinity, was observed among sites within Gulf units, suggesting local adaptation. Furthermore, five pairs of siblings were identified in the same site across timescales corresponding with female reproductive cycles. This indicates that females re-used a site for parturition, which has the potential to facilitate the sorting of adaptive variation among neighboring sites. The results demonstrate differential impacts of microevolutionary forces at varying spatial scales and highlight the importance of conserving essential habitats to maintain sources of adaptive variation that may buffer species against environmental change.</p>
Heterogeneous microgeographic genetic structure of the common cockle (Cerastoderma edule) in the Northeast Atlantic Ocean: biogeographic barriers and environmental factors
<p>Knowledge of genetic structure at the finest level is essential for conservation of genetic resources. Despite no visible barriers limiting gene flow, significant genetic structure has been shown in marine species. The common cockle (<em>Cerastoderma</em> <em>edule</em>) is a bivalve of great commercial and ecological value inhabiting the Northeast Atlantic Ocean. Previous population genomics studies demonstrated significant structure both across the Northeast Atlantic, but also within small geographic areas, highlighting the need to investigate fine-scale structuring. Here, we analysed two geographic areas that could represent opposite models of structure for the species: 1) the SW British Isles region, highly fragmented due to biogeographic barriers, and 2) Galicia (NW Spain), a putative homogeneous region. 9,250 SNPs genotyped by 2b-RAD on 599 individuals from 22 natural beds were used for the analysis. The entire SNP dataset mostly confirmed previous observations related to genetic diversity and differentiation, however, neutral and divergent SNP outlier datasets enabled disentangling physical barriers from abiotic environmental factors structuring both regions. While Galicia showed a homogeneous structure, the SW British Isles region was split into four reliable genetic regions related to oceanographic features and abiotic factors, such as sea surface salinity and temperature. The information gathered supports specific management policies of cockle resources in SW British and Galician regions also considering their particular socio-economic characteristics; further, these new data will be added to those recently reported in the Northeast Atlantic to define sustainable management actions across the whole distribution range of the species.</p>
Population genomic analyses reveal hybridization and marked differences in genetic structure and demographic history of Scurria limpet sister species with parapatric distributions across the southeastern pacific
<p>The study of sister species that occur in parapatry around biogeographic transition zones can help understand the evolutionary processes that underlie the changes in species composition across biogeographic transition zones. The South Eastern Pacific (SEP) coast is a highly productive coastal system that exhibits a broad biogeographic transition zone around 30–35ºS. Here, we present a comparative genome-wide analysis of the sister species <em>Scurria viridula</em> and <em>Scurria zebrina</em>, that occur in parapatry and whose poleward and equatorward range edges intersect in the 30–35ºS SEP biogeographic transition zone. We sampled 118 specimens sourced from nine sites from Tocopilla (22ºS) to Chiloé (41ºS) including one site where both species overlap and analyzed over 8,000 biallelic single nucleotide polymorphisms. We found evidence of hybridization between these species in the contact zone and found significant but contrasting population structures for both species. Our results indicate that the genetic structure in <em>S. viridula</em>, which is currently expanding its range poleward, follows a simple isolation-by-distance model with no traces of natural selection (no evidence of outlier loci). In contrast, <em>S. zebrina</em>, which finds its equatorward range edge at the transition zone, displayed a pronounced genetic break approximately at 32-34ºS, along a region of marked environmental heterogeneity in association with a semi-permanent coastal upwelling regime. For <em>S. zebrina</em>, we also found 43 outlier loci associated with this genetic break, with a significant proportion of them clustering in a single linkage group. This marked difference in the presence of outlier loci between species suggests that they could be responding differently to local environmental challenges found at their overlapping geographic range edges, thus providing important new insights about genomic changes around biogeographic transition zones in sister species and the forces that shape genetic diversity in intertidal marine species. </p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.