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15,277 results for “GENETICS”
Mountain- and brown hare genetic polymorphisms to survey local adaptations and conservation status of the heath hare (Lepus timidus sylvaticus, Nilsson 1831)
<p class="MsoNormal">We provide the first whole genome sequences from three specimens of the mountain hare subspecies the heath hare (<em>Lepus timidus sylvaticus</em>), along with a sample subset of two mountain hares (<em>Lepus timidus timidus</em>) and two brown hares (<em>Lepus europaeus</em>) from Sweden. The heath hare has a unique grey winter pelage as compared to other mountain hares (white) and brown hares (mostly brown), and face regional extinction, likely due to competitive exclusion from the non-native brown hare. Whole genome resequencing from the eight hare specimens was mapped to the <em>Lepus timidus</em> pseudoreference genome and used for detection of 11,363,883 polymorphic nucleotide positions. We show that genomic data can be useful for addressing local adaptations and conservation status of mountain hares and brown hares in Sweden, including unique subspecies.</p>
Supp. Info. and Data for Forensic analysis of novel SARS2r-CoV identified in game animal datasets in China shows evolutionary relationship to Pangolin GX CoV clade and apparent genetic experimentation
<p>Supplementary Info. and Data to accompany: Forensic analysis of novel SARS2r-CoV identified in game animal datasets in China shows evolutionary relationship to Pangolin GX CoV clade and apparent genetic experimentation</p> <p>Supp_Info_2.xlsx</p> <p>Supp_Info_3.xlsx</p> <p>Supp. Data:</p> <p>Novel GX_ZC45r-CoV genome: GX_ZC45r-CoV.fa</p> <p>Gap filled GX_ZC45r-CoV genome: GX_ZC45-CoV_ZC45_gap_filled_no_polyA.fa</p> <p>Read alignments to gap filled GX_ZC45r-CoV genome using minimap2: GX_ZC45-CoV_ZC45_gap_filled_no_polyA_minimap2_16_SRA.sam</p> <p> </p>
Population structure and genetic variation of fragmented mountain birch forests in Iceland
<p>Data avilability for the manuscript JOH-2022-096.R2 accepted for application</p>
Data from: Increasing temperature weakens the positive effect of genetic diversity on population growth
Genetic diversity and temperature increases associated with global climate change are known to independently influence population growth and extinction risk. Whether increasing temperature may influence the effect of genetic diversity on population growth, however, is not known. We address this issue in the model protist system Tetrahymena thermophila. We test the hypothesis that at temperatures closer to the species' thermal optimum (i.e., the temperature at which population growth is maximal, or Topt), genetic diversity should have a weaker effect on population growth compared to temperatures away from the thermal optimum. To do so, we grew populations of T. thermophila with varying levels of genetic diversity at increasingly warmer temperatures and quantified their intrinsic population growth rate, r. We found that genetic diversity increases population growth at cooler temperatures, but that as temperature increases, this effect weakens. We also show that a combination of changes in the amount of expressed genetic diversity (G), plastic changes in population growth across temperatures (E), and strong GxE interactions, underlie this temperature effect. Our results uncover important but largely overlooked temperature effects that have implications for the management of small populations with depauperate genetic stocks in an increasingly warming world. --
Supplementary material 3 from: Goutte S, Reyes-Velasco J, Kassie A, Boissinot S (2022) Genetic and morphometric analyses of historical type specimens clarify the taxonomy of the Ethiopian Leptopelis gramineus species complex (Anura, Arthroleptidae). ZooKeys 1128: 63-97. https://doi.org/10.3897/zookeys.1128.82176
Maximum Likelihood phylogenetic inference, based on the ribosomal RNAs 16s for members of the Leptopelis gramineus complex
Genetic loci associated with winter survivorship in diverse lowland switchgrass populations: SNP read count data
<p>High winter mortality is the most important factor limiting biomass yield of lowland switchgrass planted in the northern latitudes of North America. Due to the perennial growth habit and strong dependence on weather conditions to generate sufficient selection pressure to identify winter-hardy individuals, breeding of cold tolerant switchgrass cultivars requires many years. Identification of causal genetic variants for winter survivorship would accelerate the improvement of switchgrass biomass production. The objective of this study was to identify allelic variation associated with winter survivorship in lowland switchgrass populations using bulk segregant analysis (BSA). Twenty-nine lowland switchgrass populations were evaluated for winter survival at two locations in southern Wisconsin and 21 population with differential winter survivorship was used for BSA. A maximum of 10% of the individuals per population (8-20) was bulked to create survivor and non-survivor DNA pools. The DNA pools were evaluated using exome capture sequencing and allele frequencies were used to conduct statistical tests. The BSA tests revealed nine QTL from tetraploid populations and seven QTL from octoploid populations. Some markers were identified in multiple populations that originated across a broad geographic landscape, while other markers were site-specific. QTL at positions 88 Mb on chromosome 2N, 115 Mb on chromosome 5K, and 1 and 100 Mb on chromosome 9N were potentially the most useful QTL. Markers associated with winter survivorship in this study can be used to accelerate breeding cycles of lowland switchgrass populations and should lead to improvements in adaptation within USDA hardiness zones 4 and 5.</p>
C.Origami: Cell type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening
<p>This data repository includes dataset generated from IMR-90, GM12878 cell lines and C.Origami pre-trained model weights.</p> <p>GitHub page: https://github.com/tanjimin/C.Origami</p>
Supplementary material 9 from: Testé E, Hernández-Rodríguez M, Veltjen E, Bécquer ER, Rodríguez-Meno A, Palmarola A, Samain M-S, González-Torres LR, Robert T (2022) Integrating morphological and genetic limits in the taxonomic delimitation of the Cuban taxa of Magnolia subsect. Talauma (Magnoliaceae). PhytoKeys 213: 35-66. https://doi.org/10.3897/phytokeys.213.82627
The Eigenvalue and percent of the total variance of the three first principal components (PC); and the relative weight of each variable to the Principal Component Analysis for the Cuban taxa of Magnolia subsect. Talauma
Supplementary material 8 from: Testé E, Hernández-Rodríguez M, Veltjen E, Bécquer ER, Rodríguez-Meno A, Palmarola A, Samain M-S, González-Torres LR, Robert T (2022) Integrating morphological and genetic limits in the taxonomic delimitation of the Cuban taxa of Magnolia subsect. Talauma (Magnoliaceae). PhytoKeys 213: 35-66. https://doi.org/10.3897/phytokeys.213.82627
Multiplex designed with the 21 microsatellites marker used for the genetic characterization of Magnolia subsect. Talauma in Cuba
Supplementary material 3 from: Testé E, Hernández-Rodríguez M, Veltjen E, Bécquer ER, Rodríguez-Meno A, Palmarola A, Samain M-S, González-Torres LR, Robert T (2022) Integrating morphological and genetic limits in the taxonomic delimitation of the Cuban taxa of Magnolia subsect. Talauma (Magnoliaceae). PhytoKeys 213: 35-66. https://doi.org/10.3897/phytokeys.213.82627
Graphic representation of the leaf´s morphological variables measured in the individuals of Magnolia subsect. Talauma in Cuba following the four taxa CS
Supplementary material 4 from: Testé E, Hernández-Rodríguez M, Veltjen E, Bécquer ER, Rodríguez-Meno A, Palmarola A, Samain M-S, González-Torres LR, Robert T (2022) Integrating morphological and genetic limits in the taxonomic delimitation of the Cuban taxa of Magnolia subsect. Talauma (Magnoliaceae). PhytoKeys 213: 35-66. https://doi.org/10.3897/phytokeys.213.82627
Graphic representation of the Sum of EDMA and Centroid Size calculated in the individuals of Magnolia subsect. Talauma in Cuba following the different CS
Supplementary material 1 from: Testé E, Hernández-Rodríguez M, Veltjen E, Bécquer ER, Rodríguez-Meno A, Palmarola A, Samain M-S, González-Torres LR, Robert T (2022) Integrating morphological and genetic limits in the taxonomic delimitation of the Cuban taxa of Magnolia subsect. Talauma (Magnoliaceae). PhytoKeys 213: 35-66. https://doi.org/10.3897/phytokeys.213.82627
Graphic representation of the leaf´s morphological variables measured in the individuals of Magnolia subsect. Talauma in Cuba following the two taxa CS
Supplementary material 2 from: Testé E, Hernández-Rodríguez M, Veltjen E, Bécquer ER, Rodríguez-Meno A, Palmarola A, Samain M-S, González-Torres LR, Robert T (2022) Integrating morphological and genetic limits in the taxonomic delimitation of the Cuban taxa of Magnolia subsect. Talauma (Magnoliaceae). PhytoKeys 213: 35-66. https://doi.org/10.3897/phytokeys.213.82627
Graphic representation of the leaf´s morphological variables measured in the individuals of Magnolia subsect. Talauma in Cuba following the three taxa CS
Supplementary material 10 from: Testé E, Hernández-Rodríguez M, Veltjen E, Bécquer ER, Rodríguez-Meno A, Palmarola A, Samain M-S, González-Torres LR, Robert T (2022) Integrating morphological and genetic limits in the taxonomic delimitation of the Cuban taxa of Magnolia subsect. Talauma (Magnoliaceae). PhytoKeys 213: 35-66. https://doi.org/10.3897/phytokeys.213.82627
F-values (F) of the NPMANOVA (one-way) based on Euclidian distance, 10 000 random permutations and Bonferroni-corrected p values (p); calculated on the individuals of Magnolia subsect. Talauma in Cuba
Supplementary material 11 from: Testé E, Hernández-Rodríguez M, Veltjen E, Bécquer ER, Rodríguez-Meno A, Palmarola A, Samain M-S, González-Torres LR, Robert T (2022) Integrating morphological and genetic limits in the taxonomic delimitation of the Cuban taxa of Magnolia subsect. Talauma (Magnoliaceae). PhytoKeys 213: 35-66. https://doi.org/10.3897/phytokeys.213.82627
Number of most probable (highest BIC score) groups resulting for the morphological data of the taxa of Magnolia subsect. Talauma in Cuba
Data from: Chromosome-scale reference genome and RAD-based genetic map of yellow starthistle (Centaurea solstitialis) reveal putative structural variation and QTLs associated with invader traits
<p>The data directory here includes all of the data and scripts necessary to recreate the results and plots for the manuscript titled "Chromosome-scale reference genome and RAD-based genetic map of yellow starthistle (Centaurea solstitialis) reveal putative structural variation and QTLs associated with invader traits". These data include a genetic map, QTL analysis, paleolog analysis, gene synteny analysis, and assembly validation for yellow starthistle (Centaurea solstitialis).</p>
Demographic changes and life-history strategies predict the genetic diversity in crabs
<p>Uncovering what predicts genetic diversity (GD) within species can help us access the status of populations and their evolutionary potential. Traits related to effective population size show a proportional association to GD, but evidence supports life-history strategies and habitat as the drivers of GD variation. Instead of investigating highly divergent taxa, focusing on one group could help to elucidate the factors influencing the GD. Additionally, most empirical data is based on vertebrate taxa; therefore, we might be missing novel patterns of GD found in neglected invertebrate groups. Here, we investigated the predictors of the GD in crabs (Brachyura) by compiling the most comprehensive cytochrome c oxidase subunit I (COI) available. Eight predictor variables were analyzed across 150 species (16,992 sequences) using linear models (multiple linear regression) and comparative methods (PGLS). Our results indicate that population size fluctuation represents the most critical trait predicting GD, with species that have undergone bottlenecks followed by population expansion showing lower GD. Egg size, pelagic larval duration, and habitat might play a role probably because of their association with how species respond to disturbances. Ultimately, K-strategists that have undergone bottlenecks are the species showing lower GD. Some variables do not show an association with GD as expected, most likely due to the taxon-specific role of some predictors, which should be considered in further investigations and generalizations. This work highlights the complexity underlying the predictors of GD and adds results from a marine invertebrate group to the current understanding of this topic.</p>
Multi-ancestry meta-analysis of host genetic susceptibility to tuberculosis identifies shared genetic architecture
<p><span>The heritability of susceptibility to tuberculosis disease (TB) has been well recognized. Over one-hundred genes have been studied as candidates for TB susceptibility, and several variants were identified by genome-wide association studies (GWAS), but few replicates. We established the International Tuberculosis Host Genetics Consortium (ITHGC) to perform a multi-ancestry meta-analysis of GWAS including 14,153 cases and 19,536 controls of African, Asian, and European ancestry. Our analyses demonstrate a substantial degree of heritability (pooled polygenic h<sup>2</sup>=26.3% 95% CI 23.7–29.0%) for susceptibility to TB that is shared across ancestries, highlighting an important host genetic influence on disease. We identified one global host genetic correlate for TB at genome-wide significance (p < 5x10<sup>-8</sup>) in the human leukocyte antigen (HLA)-II region (rs28383206, p-value = 5.2x10<sup>-9</sup>). These data demonstrate the complex shared genetic architecture of susceptibility to TB and the importance of large-scale GWAS analysis across multiple ancestries experiencing different levels of infection pressures. </span></p>
Supplementary material 14 from: Gloria-Soria A, Shragai T, Ciota AT, Duval TB, Alto BW, Martins AJ, Westby KM, Medley KA, Unlu I, Campbell SR, Kawalkowski M, Tsuda Y, Higa Y, Indelicato N, Leisnham PT, Caccone A, Armstrong PM (2022) Population genetics of an invasive mosquito vector, Aedes albopictus in the Northeastern USA. NeoBiota 78: 99-127. https://doi.org/10.3897/neobiota.78.84986
Population structure on Aedes albopictus samples from all Connecticut samples (no temporal series) based on 15 microsatellite markers
Supplementary material 12 from: Gloria-Soria A, Shragai T, Ciota AT, Duval TB, Alto BW, Martins AJ, Westby KM, Medley KA, Unlu I, Campbell SR, Kawalkowski M, Tsuda Y, Higa Y, Indelicato N, Leisnham PT, Caccone A, Armstrong PM (2022) Population genetics of an invasive mosquito vector, Aedes albopictus in the Northeastern USA. NeoBiota 78: 99-127. https://doi.org/10.3897/neobiota.78.84986
Population structure of Aedes albopictus at the United States northeastern invasion front (New York, Connecticut, Massachusetts) based on 15 microsatellite markers
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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.