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15,277 results for “GENETICS”
Supplementary tables for chapter 3: "Haplotype-resolved transcriptomics defines the inheritance and genetic architecture of response to Citrus Greening Disease"
<p>Dissertation chapter 3: "<span>Haplotype-resolved transcriptomics defines the inheritance and genetic architecture of response to Citrus Greening Disease"</span></p>
FIGURES 9–10 in The Rhyacophila fasciata Species Complex (Trichoptera: Rhyacophilidae) in Turkey with description of a new species, Rhyacophila anatolica Ekingen & Valladolid, sp. nov., based on morphological, genetic, and ecological evidence
FIGURES 9–10. Wings of Rhyacophila fasciata Hagen 1859 and Rhyacophila anatolica Ekingen & Valladolid sp. nov. 9a, forewing of R. fasciata, lectotype [Museum of Comparative Zoology of Harvard University, Cambridge, MA, USA (MCZH), with permission]; 9b, forewing of R. fasciata male from Slovakia; 9c, hind wing of R. fasciata male from Slovakia. 10a, forewing of R. anatolica male. 10b, hind wing of R. anatolica male. St = stigma. Major veins: C = costa, Sc = subcosta, R 1 –R = 5 radius, M 1 –M 4 = media, Cu1–Cu2 = cubitus, A1–A3 = anal; m-cu = crossvein between medial and cubital veins, cu-a = crossvein between second cubital and first anal veins (from Holzenthal et al. 2007). Scale bars: 2 mm. 9a: specimen preserved dry, 9b–c, 10a–b: specimens preserved in ethanol.
FIGURES 15–18 in The Rhyacophila fasciata Species Complex (Trichoptera: Rhyacophilidae) in Turkey with description of a new species, Rhyacophila anatolica Ekingen & Valladolid, sp. nov., based on morphological, genetic, and ecological evidence
FIGURES 15–18. Males and females of Rhyacophila anatolica Ekingen & Valladolid sp. nov. and Rhyacophila fasciata Hagen 1859. 15, male of R. anatolica: 15a, 2nd segment of left inferior appendage, left lateral; 15b, apicodorsal lobe of segment IX and preanal appendages, dorsal; 15c, parameres and ventral lobe of aedeagus (phallicata), ventral; 15d, left paramere, left lateral. 16, male of R. fasciata: 16a, 2nd segment of left inferior appendage, left lateral; 16b, apicodorsal lobe of segment IX and preanal appendages, dorsal; 16c, parameres and ventral lobe of aedeagus (phallicata), ventral; 16d, left paramere, left lateral. 17, female segments VIII–XI of R. anatolica: 17L, left lateral; 17D, dorsal; 17V, ventral. 18, female segments VIII–XI of R. fasciata: 18L, left lateral; 18D, dorsal; 18V, ventral. Scale bars: Figures 15a–c, 16a–c = 0.5 mm, Figures 15d, 16d = 200 μm, Figures 17, 18 = 1 mm.
FIGURE 8 in The Rhyacophila fasciata Species Complex (Trichoptera: Rhyacophilidae) in Turkey with description of a new species, Rhyacophila anatolica Ekingen & Valladolid, sp. nov., based on morphological, genetic, and ecological evidence
FIGURE 8. Rhyacophila anatolica Ekingen & Valladolid sp. nov., paired abdominal hook plates of male pupa. 8l and 8r, left and right hook plates, respectively. A = anterior hook plates, dorsal, P = posterior hook plates, dorsal; III–VII = abdominal terga III through VII, dorsal. Scale bars: 50 μm.
FIGURE 1 in The Rhyacophila fasciata Species Complex (Trichoptera: Rhyacophilidae) in Turkey with description of a new species, Rhyacophila anatolica Ekingen & Valladolid, sp. nov., based on morphological, genetic, and ecological evidence
FIGURE 1. Setae (S) and sensory pits (P) of the head and thorax of Rhyacophila larvae. 1a, head, dorsal; 1b, prothorax, right sclerite, dorsal (from Williams & Wiggins 1981).
FIGURES 11–12 in The Rhyacophila fasciata Species Complex (Trichoptera: Rhyacophilidae) in Turkey with description of a new species, Rhyacophila anatolica Ekingen & Valladolid, sp. nov., based on morphological, genetic, and ecological evidence
FIGURES 11–12. Male and female genitalia of Rhyacophila anatolica Ekingen & Valladolid sp. nov., respectively. 11, male: 11A, 2nd segment of left inferior appendage, left lateral; 11BV, 11BL, parameres: 11BV, parameres (p) and ventral lobe of aedeagus (phallicata) (vl), ventral; 11BL, left paramere, left lateral. 11CL, 11CD, aedeagus (phallicata) and lateroventral lobes: 11CL, aedeagus and its left lateroventral lobe, left lateral; 11CD, aedeagus and its lateroventral lobes (lvl), dorsal. 10DD, apicodorsal lobe of segment IX (al) and preanal appendages (pa), dorsal; 11DV, segment X, ventral, ab = apical band, as = anal sclerites, va = non-sclerotized ventral area. 12, female segments VIII–XI: 12L, left lateral; 12D, dorsal; 12V, ventral. Scale bars: unlabelled = 1 mm; ● = 0.5 mm; * = 200 μm.
FIGURES 2–7 in The Rhyacophila fasciata Species Complex (Trichoptera: Rhyacophilidae) in Turkey with description of a new species, Rhyacophila anatolica Ekingen & Valladolid, sp. nov., based on morphological, genetic, and ecological evidence
FIGURES 2–7. Larva of Rhyacophila anatolica Ekingen & Valladolid sp. nov. 2a–2d, head: 2a, dorsal; 2b, right lateral; 2c, ventral; 2d, frontoclypeus, dorsal. 3D–3V, mandibles from last instar larval exuviae, left (l) and right (r): 3D, dorsal; 3V, ventral. 4a–4b, prothorax: 4a, dorsal; 4b, left hemisclerite, left lateral. 5, abdominal segment III, dorsal, A = anterior edge. 6, abdominal tergite IX. 7a–7c, details of anal prolegs: 7a, right anal claw, right lateral; 7b, detail of basolateral plate with sword process (sp) and basoventral hook (bh), right lateral; 7c, detail of right claw, right lateral. Scale bars: unlabelled = 1 mm; ● = 0.5 mm.
FIGURE 20 in The Rhyacophila fasciata Species Complex (Trichoptera: Rhyacophilidae) in Turkey with description of a new species, Rhyacophila anatolica Ekingen & Valladolid, sp. nov., based on morphological, genetic, and ecological evidence
FIGURE 20. Spatial distribution of Rhyacophila anatolica Ekingen & Valladolid sp. nov. in Turkey. Star: specimens with DNA information. B. Bulgaria, C: Cyprus, Ge: Georgia, Gr: Greece, I: Iraq, R: Russia, S: Syria.
FIGURES 13–14 in The Rhyacophila fasciata Species Complex (Trichoptera: Rhyacophilidae) in Turkey with description of a new species, Rhyacophila anatolica Ekingen & Valladolid, sp. nov., based on morphological, genetic, and ecological evidence
FIGURES 13–14. Larvae of Rhyacophila anatolica Ekingen & Valladolid sp. nov. and Rhyacophila fasciata Hagen 1859. 13, R. anatolica: 13a, head, dorsal; 13b, prothorax, dorsal; 13c, abdominal tergite IX, dorsal; 13d, left anal proleg, left lateral. 14, R. fasciata: 14a, head, dorsal. 14b, prothorax, dorsal; 14c, abdominal tergite IX, dorsal; 14d, left anal proleg, left lateral. Scale bars: 1 mm.
FIGURE 19 in The Rhyacophila fasciata Species Complex (Trichoptera: Rhyacophilidae) in Turkey with description of a new species, Rhyacophila anatolica Ekingen & Valladolid, sp. nov., based on morphological, genetic, and ecological evidence
FIGURE 19. Phylogenetic relationships among the species of the "Rhyacophila fasciata Species Complex" included in this study. The ML tree represents a combination of Bayesian inference and maximum likelihood trees based on COI. Support for each node is represented by the posterior probabilities (PP) resulting from the Bayesian inference analysis and the bootstrap support values (BS) obtained for the maximum likelihood tree (PP/BS, respectively). 19a, Rhyacophila cf. obliterata, outgroup; 19b–19k, R. fasciata Complex: 19b, Rhyacophila septentrionis McLachlan 1865; 19c, R. viteceki Valladolid & Kučinić 2020 (by Valladolid et al. 2020); 19d, R. loeffleri Valladolid & Waringer (by Valladolid et al. 2023); 19e, R. macedonica Karaouzas, Valladolid & Ibrahimi 2022 (by Valladolid et al. 2022); 19f, R. fasciata Hagen 1859; 19g, R. delici Kučinić & Valladolid 2020 (by Valladolid et al. 2020); 19h, R. denticulata McLachlan 1879; 19i, R. sociata Navás 1916; 19j, R. anatolica sp. nov.; 19k, R. kykladica Malicky & Sipahiler 1993. Data for specimens are summarized in Table 1 (R. anatolica) and by Valladolid et al 2024. Scale bar: mean number of nucleotide substitutions per site or nucleotide position on the respective branch.
Systematic Identification of Needlefish (Belonidae) Species using Molecular Genetic and Morphological Markers in the Mediterranean and Black Seas
<p><span>In this study, we aimed to clarify the taxonomic status of Belonidae species distributed in the Mediterranean Sea and the Black Sea by conducting detailed genetic and morphological markers. A total of 550 needlefish samples were caught between January 2022 and January 2024.<span> </span>The data set used in the study contains a total of 171 sequences for the <em>COI</em> gene and 120 sequences for the <em>12s rRNA</em> gene from different Belonidae species, including data from GenBank. Systematic analysis of needlefish species was investigated by using sequencing of mtDNA <em>COI</em> and <em>12s rRNA</em> gene regions and morphological characters in the Turkish Marine Waters. A separate analysis of the two mitochondrial genes supported by morphological characters revealed that each species is grouped within itself. The genetic and morphological analyses showed that <em>Belone belone acus</em> and <em>Belone belone euxini</em> which are considered as the subspecies of <em>Belone belone</em> are not subspecies of the genus <em>Belone</em> and should be considered at the species level, <em>Belone belone</em>.<span> </span><em>Belone svetovidovi</em> is also considerably different from <em>Belone belone</em> and should be considered as a different species. <em>T. acus imperialis</em>, which is thought to be distributed in the Mediterranean Sea, is not a subspecies of <em>Tylosorus acus and should be revised as Tylosorus imperialis </em><span>which genetically </span>differs from<em> Tylosorus acus </em>and also other<em> Tylosorus </em><span>species</span><em> </em>at the species level<em>. </em></span></p>
Implementation of Genetic Algorithms to Optimize Metal-Organic Frameworks for CO2 Capture
<p>Dataset associated with the publication "Implementation of Genetic Algorithms to Optimize Metal-Organic Frameworks for CO2 Capture".</p> <p> </p> <p>Changelog:</p> <p>- Include sample input files for GCMC using RASPA2 and geometry optimization using LAMMPS.</p>
Unveiling genetic signatures of immune response in immune-related diseases through single-cell eQTL analysis across diverse conditions
<p><em><strong>Unveiling genetic signatures of immune response in immune-related diseases through single-cell eQTL analysis across diverse conditions</strong></em></p> <p> </p> <p>Tools and scripts were used to generate results in Zhang et al 2024.</p> <p>Supplementary files that were not included in the initial submission.</p> <p>Full summary statistics of eQTLs including top eQTLs and all SNP-gene pairs of each cell type, consistent.tar.gz for consistent eQTLs per cell and response.tar.gz for response eQTLs, respectively.</p>
Evaluation of Cas13d as a tool for genetic interaction mapping
<p>This zenodo upload contains the scripts for the calculation of tau values and genetic interaction scores (GI) in knockdown experiments with Cas13d. In addition to the scripts for determining the tau values and GI scores (Calculate_tau_and_GI.zip), the script for creating the plots used and the reference files for the publication “On the utility of Cas13d for genetic interaction mapping” are also provided. Further information can be found in the README. </p>
Contrasting reproductive traits affect the genetic diversity and fine-scale genetic structure of two sympatric and epiphytic tropical bromeliads.
<p>This database contains the coordinates of individuals of <em>Aechmea mariae-reginae</em> and <em>Werauhia ampla</em> in phorophytic trees and the genotypes for 8 microsatellite loci.</p>
Integrative genome-wide analyses identify novel loci associated with kidney stones and provide insights into its genetic architecture
Open the record for dataset details and reuse information.
Genetic basis of growth, spring phenology and susceptibility to biotic stressors in maritime pine
<p>Forest ecosystems are increasingly challenged by extreme events, e.g. drought, storms, pest and pathogenic fungi outbreaks, causing severe ecological and economical losses. Understanding the genetic basis of adaptive traits in tree species is of key importance to preserve forest ecosystems, as genetic variation in a trait (i.e. heritability) determines its potential for human-mediated or evolutionary change. Maritime pine (<i>Pinus pinaster</i> Aiton), a conifer widely distributed in southwestern Europe and northwestern Africa, grows under contrasted environmental conditions promoting local adaptation. Genetic variation at adaptive phenotypes, including height, growth phenology and susceptibility to two fungal pathogens (<i>Diplodia sapinea</i> and <i>Armillaria ostoyae</i>) and an insect pest (<i>Thaumetopoea pityocampa</i>), were assessed in a range-wide clonal common garden of maritime pine. Broad-sense heritability was significant for height (0.219), growth phenology (0.165-0.310) and pathogen susceptibility (necrosis length caused by <i>D. sapinea</i>, 0.152; and by <i>A. ostoyae</i>, 0.021) measured after inoculation under controlled conditions, but not for pine processionary moth incidence in the common garden. The correlations of trait variation among populations revealed contrasting trends for pathogen susceptibility to <i>D. sapinea</i> and <i>A. ostoyae</i> with respect to height. Taller trees showed longer necrosis length caused by <i>D. sapinea </i>while shorter trees were more affected by <i>A. ostoyae</i>. Moreover, maritime pine populations from areas with high summer temperatures and frequent droughts were less susceptible to <i>D. sapinea </i>but more susceptible to <i>A. ostoyae</i>. Finally, an association study using 4,227 genome-wide SNPs revealed several loci significantly associated to each trait (range of 3-26), including a possibly disease-induced translation initiation factor, eIF-5. This study provides important insights to develop genetic conservation and breeding strategies integrating species responses to biotic stressors.</p>
Genetic data from the extinct giant rat from Tenerife (Canary Islands)
<p>Evolution of vertebrate endemics in oceanic islands follows a predictable pattern, known as the island rule, according to which gigantism arises in originally small-sized species and dwarfism in large ones. Species of extinct insular giant rodents are known from all over the world. In the Canary Islands, two examples of giant rats, <em>Canariomys bravoi </em>and <em>Canariomys tamarani</em>, endemic to Tenerife and Gran Canaria islands, respectively, disappeared soon after human settlement. The highly derived morphological features of these insular endemic rodents hamper the identification of their mainland relatives and the reconstruction of their evolutionary histories. We have retrieved partial mitochondrial (mtDNA) data from <em>C. bravoi</em> and used this information to explore its evolutionary history. The resulting dated phylogeny confidently places <em>C. bravoi</em> within the African grass rat clade (<em>Arvicanthis niloticus</em>). The estimated divergence time, 650,000 years ago, is roughly coincident with the onset of the Günz-Mindel interglacial stage. <em>C. bravoi</em> ancestors would have reached the island via passive rafting and then underwent a yearly increase of mean body mass calculated between 0.0015 g and 0.0023 g; this corresponds to fast evolutionary rates (in darwins [d], ranging from 7.09 d to 2.78 d) that are well above those observed for non-insular mammals.</p>
Data files for: Hazardous loss of genetic diversity through selective sweeps in asexual populations
<p>With the two-fold cost of sex, derived asexual organisms have an immediate reproductive advantage over their sexual sisters. Yet the "twiggy'' phylogenetic distribution of asexual lineages implies that they go extinct relatively quickly over evolutionary time. Meanwhile, bacteria and archaea have persisted for billions of years without requiring sexual reproduction. A simple explanation for this difference is that prokaryotes have very large population sizes that are not subject to the accumulation of deleterious mutations, but this implies that drift and mutational meltdown dominate derived asexual populations. </p> <p>We explored a different hazard, quantifying the degree to which genetic variation is lost in asexual populations experiencing selective sweeps. Even though large populations generate diversity by mutation during sweeps, we find that populations that are safe from mutational meltdown may still be reduced to dangerous effective population sizes by sweeps. Thus, ironically, adaptation itself reduces further adaptive potential and may predispose asexual populations to extinction. Our data give results for the probability of mutational meltdown across various population sizes, the critical population size required to avoid meltdown, and the effect of selective sweeps on heterozygosity. Analytical predictions are confirmed by simulation.</p> <p>We also derive a simple approximation for the effective population size after a hard sweep, and quantify the impact of recent sweeps on evolutionary rescue. These factors may help to explain the phylogenetic twigginess of asexuals, the maintenance of sex and recombination, and the evolutionary persistence of prokaryotes.</p>
The evolutionary genetics of paternal care: how good genes and extra-pair copulation affect the trade-off between paternal care and mating success
<p>We investigate the evolution of a gene for paternal care, with pleiotropic effects on male mating fitness and offspring viability, with and without extra pair copulations (EPCs). We develop a population genetic model to examine how pleiotropic effects of a male mating advantage and paternal care are affected by 'good genes' and EPCs. Using this approach, we show that the relative effects of each on fitness do not always predict the evolutionary change. We then find the line of combinations of mating success and paternal care that bisects the plane of possible values into regions of positive or negative gene frequency change. This line shifts when either good genes or EPCs are introduced, thereby expanding or contracting the region of positive gene frequency change and significantly affecting the evolution of paternal care. Predictably, a direct viability effect of 'good genes' that enhances offspring viability constrains or expands the parameter space over which paternal care can evolve, depending on whether the viability effect is associated with the paternal care allele or not. In either case, the effect of a 'good gene' that enhances offspring viability is substantial; when strong enough, it can even facilitate the evolution of <i>poor</i>paternal care, where males harm their young. When non-random mating is followed by random EPCs, the genetic regression between sire and offspring is reduced and, consequently, the relative strengths of selection are skewed away from paternal care and toward the male mating advantage. However, when random mating is followed by non-random EPCs, a situation called "trading up" by females, we show that selection is skewed in the opposite direction, away from male mating advantage and toward paternal care across the natural range of EPC frequencies.</p>
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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)
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.