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15,277 results for “GENETICS”
Supplementary material 2 from: Astuti G, Roma-Marzio F, D'Antraccoli M, Bedini G, Carta A, Sebastiani F, Bruschi P, Peruzzi L (2017) Conservation biology of the last Italian population of Cistus laurifolius (Cistaceae): demographic structure, reproductive success and population genetics. Nature Conservation 22: 169-190. https://doi.org/10.3897/natureconservation.22.19809
Supplementary material 2 from: Astuti G, Roma-Marzio F, D'Antraccoli M, Bedini G, Carta A, Sebastiani F, Bruschi P, Peruzzi L (2017) Conservation biology of the last Italian population of Cistus laurifolius (Cistaceae): demographic structure, reproductive success and population genetics. Nature Conservation 22: 169-190. https://doi.org/10.3897/natureconservation.22.19809
Supplementary material 1 from: Astuti G, Roma-Marzio F, D'Antraccoli M, Bedini G, Carta A, Sebastiani F, Bruschi P, Peruzzi L (2017) Conservation biology of the last Italian population of Cistus laurifolius (Cistaceae): demographic structure, reproductive success and population genetics. Nature Conservation 22: 169-190. https://doi.org/10.3897/natureconservation.22.19809
Supplementary material 1 from: Astuti G, Roma-Marzio F, D'Antraccoli M, Bedini G, Carta A, Sebastiani F, Bruschi P, Peruzzi L (2017) Conservation biology of the last Italian population of Cistus laurifolius (Cistaceae): demographic structure, reproductive success and population genetics. Nature Conservation 22: 169-190. https://doi.org/10.3897/natureconservation.22.19809
Fig. 3. The genetic relatedness matrix summarising similarities and differences among the 90 in Morphological and molecular evidence refute a broad circumscription for Pultenaea glabra (Fabaceae: Mirbelieae), with implications for taxonomy, biogeography, and conservation
Fig. 3. The genetic relatedness matrix summarising similarities and differences among the 90 individuals included in the final, filtered dataset containing 2452 SNPs.
PRISMA 2009 Checklist - Phytoparasitic nematodes of Musa spp. with emphasis on sources of genetic resistance: a systematic review
<p>PRISMA 2009 Checklist da revisão sistemática Phytoparasitic nematodes of Musa spp. with emphasis on sources of genetic resistance: a systematic review</p>
Strong genetic structure and divergence of marginal populations of black poplar in Poland
<p><strong>The dataset comprises nuclear microsatellite data (PCR products lengths) used in the paper "Strong genetic structure and divergence of marginal populations of black poplar in Poland".</strong></p> <p>Abstract: Genetic diversity is crucial to secure the survival and sustainability of ecosystems. Given anthropogenic pressure, as well as the projected alterations connected with the level and circulation of water, riparian forests are of particular concern. In this paper, we assessed the genetic variation of black poplar – one of the keystone tree species of riverine forests. The natural habitats of black poplar have been severely transformed leading to a significant decline of its population size. Using a set of 18 nuclear microsatellites and geographic location data, we studied 26 remnant populations (1,261 trees) located along the biggest river valleys in Poland. Our main goal was to assess the overall genetic variation and to verify if range fragmentation and habitat transformation have disrupted gene exchange among populations. Genotyping revealed that 261 trees were clones. The level of clonality was generally higher in the two most transformed river valleys (the Oder and Warta). All populations have probably gone through a drastic genetic bottleneck in the distant past, and most of them have low effective population sizes. Still, the overall level of genetic variation remains high, but certain populations require attention due to their lower genetic variation, higher clonality and strong spatial genetic structure. Genetic differentiation was low, yet Bayesian clustering supported the existence of 11 separate gene pools. According to the results, the intensity of gene exchange is very low and limited to adjacent stands. Relatively free gene flow occurs only along the Vistula, particularly in its middle section which is characterized by the highest genetic variation. The greatest genetic structuring was observed along the Oder. Populations located at the range margin had unique gene pools and showed signs of genetic divergence and reduction of variation caused by genetic drift. We conclude that human activities have seriously impacted the gene pool of black poplar in Poland by disrupting landscape connectivity and preventing the species from generative reproduction. The study provides practical guidelines on how to develop and implement the conservation program for the gene pool of black poplar in Poland.</p>
Data For: City divided: Unveiling family ties and genetic structuring of coyotes in Seattle
<p>Included in the zip file:</p> <ol> <li>ReadMe file</li> <li>R Project</li> <li>3 R Markdown Files</li> <li>All necessary scripts and data files needed to replicate analyses</li> </ol>
Role of environmental factors in the genetic structure of a highly mobile seabird
<p><strong><span>Aim:</span></strong><span> Environmental features can act as selection pressures and barriers to gene flow between populations. The genetic structuring of highly mobile but philopatric seabirds creates a paradox, and the role of oceanographic and geographic variables is still poorly understood. In this study, we investigate the influence of environmental and geographic variables in the genetic and phenotypic diversity of a pantropical seabird breeding in islands and archipelagos separated by different geographic distances, up to thousand kilometers, and which differ in environmental characteristics.</span></p> <p><strong><span>Location:</span></strong><span> Islands and archipelagos in the southwestern Atlantic Ocean.</span></p> <p><strong><span>Taxon:</span></strong><span> <em>Sula dactylatra</em><span>, Lesson, 1831 (masked booby)</span><em>.</em></span></p> <p><strong><span>Methods:</span></strong><span> </span><span>The population structure of the species was accessed through mitochondrial and nuclear DNA. To test Isolation by Environment (IBE) <em>vs</em>. by Distance (IBD), sea surface temperature, primary productivity, and salinity, as well as isotopic niche based on carbon and nitrogen, and distances between colonies and from the continent, were used. We also tested the correlation between the genetic structure and the morphometry of individuals in each colony.</span></p> <p><strong><span>Results:</span></strong><span> We identified the presence of low genetic structure between populations. Nevertheless, differences were identified between inshore and offshore colonies, with the influence of landscape characteristics of these two types of environment. The morphometric and isotopic niche variations are consistent with this segregation. </span></p> <p><strong><span>Main conclusions:</span></strong><span> Environmental variables of coastal and oceanic environments seem to influence the genetic structure of masked boobies, </span><span>even though it is low in the SW Atlantic Ocean</span><span>, highlighting the role of environmental heterogeneity in shaping biodiversity.</span></p>
Data from: The genetic architecture of adaptations to high altitude in Ethiopia
<p>Genotype data for 260 high and low altitude Ethiopians from </p> <p>Alkorta-Aranburu G, Beall CM, Witonsky DB, Gebremedhin A, Pritchard JK, Di Rienzo A. The genetic architecture of adaptations to high altitude in Ethiopia. PLoS Genet. 2012</p> <p>Data is in PLINK format. </p> <p> </p>
Molecular screening and genetic diversity of tick-borne pathogens associated with dogs and livestock ticks in Egypt
Open the record for dataset details and reuse information.
Neutral processes and taxonomic scale drive beta species-genetic diversity correlations in a submesophotic tropical reef fish
<p>This dataset is associated to the following publication:</p> <p>Vilcot M, Faure N, Andrews KR, Bowen BW, Leprieur F, Manel S. (2024) <strong>Neutral processes and taxonomic scale drive beta species-genetic diversity correlations in a submesophotic tropical reef fish</strong>. <em>Molecular Ecology</em> <strong>33</strong>, e17423. (doi:<a href="https://doi.org/10.1111/mec.17423">10.1111/mec.17423</a>)</p> <p> </p> <h2><strong>Data: </strong></h2> <ul> <li> <p>"Report_DEtel22-6705_SNP_2_ordered_Bowen.csv": SNP data from Dart Sequencing on <em>Etelis coruscans</em>, from Andrews et al. (2020) samples</p> </li> <li>"PA_Mat_GaspObis.RDS": fish species presence data, gathered from an updated version of Albouy et al. (2019)</li> <li> <p>"metadata_samples_full.csv": all <em>Etelis coruscans</em> sample information, from Andrews et al. (2020) and the SEAMOUNTS project</p> </li> <li> <p>"metadata_samples.csv": <em>Etelis coruscans</em> sample information, only for samples that have passed the genetic filtering and were used for subsequent analyses </p> </li> <li> <p>"metadata_stations.csv": sampling station information</p> </li> <li> <p>"Taxonomy_Fishbase.csv": species taxonomic information, downloaded with rfishbase::load_taxa() </p> </li> <li> <p>"traits_Luiz_et_al_2013.csv": species trait information from Luiz et al. (2013) </p> </li> </ul> <h2><strong>Related dataset</strong><strong>: </strong></h2> <p><em>Etelis coruscans </em>SNP data on samples from the SEAMOUNTS project are available at <a href="https://doi.org/10.5281/zenodo.11201065">https://doi.org/10.5281/zenodo.11201065</a></p> <h2><strong>Scripts: </strong></h2> <p>Scripts used to reproduce the analyses and figures of the final article are available at <a href="https://github.com/mvilcot/etelis_SGDCs">https://github.com/mvilcot/etelis_SGDCs</a> </p> <p> </p> <h2><strong>References: </strong></h2> <p>Albouy, C., Archambault, P., Appeltans, W., Araújo, M. B., Beauchesne, D., Cazelles, K., Cirtwill, A. R., Fortin, M.-J., Galiana, N., Leroux, S. J., Pellissier, L., Poisot, T., Stouffer, D. B., Wood, S. A., & Gravel, D. (2019). The marine fish food web is globally connected. Nature Ecology & Evolution, 3(8), Article 8. <a href="https://doi.org/10.1038/s41559-019-0950-y" target="_blank" rel="noopener">https://doi.org/10.1038/s41559-019-0950-y</a> </p> <p>Andrews, K. R., Copus, J. M., Wilcox, C., Williams, A. J., Newman, S. J., Wakefield, C. B., & Bowen, B. W. (2020). Range-Wide population structure of 3 deepwater Eteline snappers across the Indo-Pacific Basin. Journal of Heredity, 111(5), 471‑485. <a href="https://doi.org/10.1093/jhered/esaa029" target="_blank" rel="noopener">https://doi.org/10.1093/jhered/esaa029</a> </p> <p>Luiz, O. J., Allen, A. P., Robertson, D. R., Floeter, S. R., Kulbicki, M., Vigliola, L., Becheler, R., & Madin, J. S. (2013). Adult and larval traits as determinants of geographic range size among tropical reef fishes. Proceedings of the National Academy of Sciences, 110(41), 16498‑16502. <a href="https://doi.org/10.1073/pnas.1304074110" target="_blank" rel="noopener">https://doi.org/10.1073/pnas.1304074110</a> </p> <p>Boettiger, C., Lang, D. T., & Wainwright, P. C. (2012). rfishbase: Exploring, manipulating and visualizing FishBase data from R. Journal of Fish Biology, 81(6), 2030‑2039. <a href="https://doi.org/10.1111/j.1095-8649.2012.03464.x" target="_blank" rel="noopener">https://doi.org/10.1111/j.1095-8649.2012.03464.x</a></p> <p> </p>
Supplemental files associated with the the manuscript "Genetic screening and metabolomics identify glial adenosine metabolism as a therapeutic target in Parkinson's disease"
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Orthopedic Diseases in the Pura Raza Española Horse: The Prevalence and Genetic Parameters of Angular Hoof Deviations
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Genetic diversity and spread dynamics of SARS-CoV-2 variants present in African populations
<p>The dynamics of coronavirus disease-19 (COVID-19) have been extensively researched in many settings around the world, but little is known about these patterns in Africa. 7540 complete nucleotide genomes from 51 African nations were obtained and analysed from the National Center for Biotechnology Information (NCBI) and Global Initiative on Sharing Influenza Data (GISAID) databases to examine genetic diversity and spread dynamics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) lineages circulating in Africa. Utilising a variety of clade and lineage nomenclature schemes, we looked at their diversity, and used maximum parsimony inference methods to recreate their evolutionary divergence and history. According to this study, only 465 of the 2610 Pango lineages found to have existed in the world circulated in Africa after three years of the COVID-19 pandemic outbreak, with five different lineages dominating at various points during the outbreak. We identified South Africa, Kenya, and Nigeria as key sources of viral transmissions between Sub-Saharan African nations. These findings provide insight into the viral strains that are circulating in Africa and their evolutionary patterns.</p>
Data for: Genetic relatedness shapes social dynamics in a threatened finch: Implications for population assessment
<p>Tropical granivorous finches often form large flocks around resources. The composition of these flocks, whether they are random groups of individuals or comprise related birds travelling together, is currently unknown. Understanding this distinction would aid in assessing the accuracy of population counts. To bridge this knowledge gap, we combined high-frequency location tracking with comprehensive genetic sequencing to investigate the relationship between pairwise association strength and genetic relatedness in Gouldian finches (<em>Erythrura gouldiae</em>). Our study revealed that birds captured near each other were more inclined to travel together, and their relatedness was significantly linked to the strength of their association. These findings suggest that within-flock associations are influenced by genetic relatedness, contributing to the stability of the flock size. We propose that juvenile kin associations play a pivotal role in this dynamic, potentially enhancing survival rates by forming sibling subgroups. The consistent flock sizes of Gouldian finches during movement have implications for estimating population sizes from waterhole counts, allowing flocks to be considered as distinct units for concurrent counts at multiple waterholes. This approach would offer a reasonably accurate method for estimating local populations, and conducting repeated counts on consecutive days could provide reliable and replicable results.</p>
A comparative evaluation of ChatGPT 3.5 and ChatGPT 4 in responses to selected genetics questions - Full study data
<p><strong>Objective</strong>:</p> <p>Our objective is to evaluate the efficacy of ChatGPT 4 in accurately and effectively delivering genetic information, building on previous findings with ChatGPT 3.5. We focus on assessing the utility, limitations, and ethical implications of using ChatGPT in medical settings.</p> <p><strong>Materials and Methods</strong>:</p> <p>A structured questionnaire, including the Brief User Survey (BUS-15) and custom questions, was developed to assess ChatGPT 4's clinical value. An expert panel of genetic counselors and clinical geneticists independently evaluated ChatGPT 4's responses to these questions. We also involved comparative analysis with ChatGPT 3.5, utilizing descriptive statistics and using R for data analysis.</p> <p><strong>Results</strong>:</p> <p>ChatGPT 4 demonstrated improvements over 3.5 in context recognition, relevance, and informativeness. However, performance variability and concerns about the naturalness of the output were noted. No significant difference in accuracy was found between ChatGPT 3.5 and 4.0. Notably, the efficacy of ChatGPT 4 varied significantly across different genetic conditions, with specific differences identified between responses related to BRCA1 and HFE.</p> <p><strong>Discussion and Conclusion</strong>:</p> <p>This study highlights ChatGPT 4's potential in genomics, noting significant advancements over its predecessor. Despite these improvements, challenges remain, including the risk of outdated information and the necessity of ongoing refinement. The variability in performance across different genetic conditions underscores the need for expert oversight and continuous AI training. ChatGPT 4, while showing promise, emphasizes the importance of balancing technological innovation with ethical responsibility in healthcare information delivery.</p>
Data from: On the importance of scale in evolutionary quantitative genetics
<p>The informed use of scales and units in evolutionary quantitative genetics is often neglected, and naïve standardizations can cause misinterpretations of empirical results. A potentially influential example of such neglect can be found in the recent book by Stevan J. Arnold (2023. Evolutionary Quantitative Genetics Oxford University Press). There, Arnold championed the use of heritability over mean-scaled genetic variance as a measure of evolutionary potential arguing that mean-scaled genetic variances are correlated with trait means while heritabilities are not. Here, we show that Arnold's empirical result is an artifact of ignoring the units in which traits are measured. More importantly, Arnold's argument mistakenly assumes that the goal of mean scaling is to remove the relationship between mean and variance. In our view, mean scaling is useful because it puts traits with different units on a common scale that makes evolutionary changes, or their potential, readily interpretable and comparable in terms of proportions of the mean.</p>
List of NDD candidate genes - Insitute of Human Genetics in Leipzig, Germany
<p>This dataset is a list a NDD candidate genes which was created by the Institute of Human Genetics, University of Leipzig Medical Center in Leipzig, Germany on 10th of June 2024. </p>
FIGURE 9 in A new species of Ducetia (Tettigoniidae, Phaneropterinae) from Mindanao, Philippines based on bioacoustics, stridulatory file morphology and genetic data
FIGURE 9. Dendrogram and the first-four best species partitions from ASAP analyses of COI sequences of 165 Ducetia specimens. ASAP, the header [x, y] represents the number of species delimited and the asap score; and the number in each partition represents the number of specimens grouped within the delimited species.
FIGURE 8 in A new species of Ducetia (Tettigoniidae, Phaneropterinae) from Mindanao, Philippines based on bioacoustics, stridulatory file morphology and genetic data
FIGURE 8. Habitats in the municipalities of Sibagat (A) and Bunawan (B), Agusan del Sur where Ducetia laniae sp. nov. was found.
FIGURE 7 in A new species of Ducetia (Tettigoniidae, Phaneropterinae) from Mindanao, Philippines based on bioacoustics, stridulatory file morphology and genetic data
FIGURE 7. Ducetia laniae sp. nov. ♂ calling song: oscillogram (A) and spectrogram (B) showing two echeme-sequences; oscillograms showing four echemes (C) and one echeme (D); power spectra of an echeme (E) where the gray line represents the power [dB] (axis name and scale in gray) and the black solid peak represents the relative amplitude (axis name in black).
ScienceDex guides
Understand access before you commit
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.