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15,277 results for “GENETICS”
Data for: Harvest and decimation affect genetic drift and the effective population size in wild reindeer
<p>Harvesting and culling are methods used to monitor and manage wildlife diseases. An important consequence of these practices is a change in the genetic dynamics of affected populations that may threaten their long-term viability. The effective population size (N<sub>e</sub>) is a fundamental parameter for describing such changes as it determines the amount of genetic drift in a population. Here, we estimate N<sub>e</sub> of a harvested wild reindeer population in Norway. Then we use simulations to investigate the genetic consequences of management efforts for handling a recent spread of chronic wasting disease, including increased adult male harvest and population decimation. The N<sub>e</sub>/N ratio in this population was found to be 0.124 at the end of the study period, compared to 0.239 in the preceding 14-year period. The difference was caused by increased harvest rates with a high proportion of adult males (older than 2.5 years) being shot (15.2 % in 2005-2018 and 44.8 % in 2021). Increased harvest rates decreased N<sub>e</sub> in the simulations, but less sex-biased harvest strategies had a lower negative impact. For harvest strategies that yield stable population dynamics, shifting the harvest from calves to adult males and females increased N<sub>e</sub>. Population decimation always resulted in decreased genetic variation in the population, with higher loss of heterozygosity and rare alleles with more severe decimation or longer periods of low population size. A very high proportion of males in the harvest had the most severe consequences for the loss of genetic variation. This study clearly shows how the effects of harvest strategies and changes in population size interact to determine the genetic drift of a managed population. The long-term genetic viability of wildlife populations subject to disease will also depend on the population impacts of the disease and how these interact with management actions.</p>
The Genetic Background of Hearing Loss in Patients with EVA and Cochlear Malformation
<p>This dataset comprises likely pathogenic variants identified through next-generation sequencing (NGS) using a multigene panel (237 genes associated with hearing loss), as well as clinical exome sequencing (TruSightOne Sequencing Panel). Raw data obtained during variant validation using Sanger sequencing method are also included. Furthermore, audiometric data are attached, from which the average air-conduction thresholds for ears with EVA malformation were determined.</p> <p> </p> <p><strong>Abstract manuscripts: </strong></p> <p>The most frequently observed congenital inner ear malformation is enlarged vestibular aqueduct (EVA). It is often accompanied with incomplete partition type 2 (IP2) of the cochlea and a dilated vestibule, which together constitute Mondini malformation. Pathogenic SLC26A4 variants are considered the major cause of inner ear malformation but the genetics still needs clarification. The aim of this study was to identify the cause of EVA in patients with hearing loss (HL). Genomic DNA was isolated from HL patients with radiologically confirmed bilateral EVA (n = 23) and analyzed by next generation sequencing using a custom HL gene panel encompassing 237 HL-related genes or a clinical exome. The presence and segregation of selected variants and the CEVA haplotype (in the 5′ region of SLC26A4) was verified by Sanger sequencing. Minigene assay was used to evaluate the impact of novel synonymous variant on splicing. Genetic testing identified the cause of EVA in 17/23 individuals (74%). Two pathogenic variants in the SLC26A4 gene were identified as the cause of EVA in 8 of them (35%), and a CEVA haplotype was regarded as the cause of EVA in 6 of 7 patients (86%) who carried only one SLC26A4 genetic variant. In two individuals with a phenotype matching branchio-oto-renal (BOR) spectrum disorder, cochlear hypoplasia resulted from EYA1 pathogenic variants. In one patient, a novel variant in CHD7 was detected. Our study shows that SLC26A4, together with the CEVA haplotype, accounts for more than half of EVA cases. Syndromic forms of HL should also be considered in patients with EVA. We conclude that to better understand inner ear development and the pathogenesis of its malformations, there is a need to look for pathogenic variants in noncoding regions of known HL genes or to link them with novel candidate HL genes.</p>
Fig. 2. A in Genetic differentiation in populations of Aedes aegypti (Diptera, Culicidae) dengue vector from the Brazilian state of Maranhão
Fig. 2. A priori estimate of the probable groups of populations produced by the BAPS (Bayesian Analysis of Population Structure v 6.0) program, indicating a total of two groups.
F I G U R E 3 in Riverscape genetics of the orangethroat darter complex
F I G U R E 3 Orangethroat darter clade collection sites with colored circles corresponding to the proportion of individuals at the site that had predominant assignment to each genetic cluster identified in the STRUCTURE analysis for K=3. Inset shows region boundary between Upper Mississippi River and Ohio River regions.
F I G U R E 7 in Riverscape genetics of the orangethroat darter complex
F I G U R E 7 Principle component analysis (PCA) of Ceasia showing distribution of samples taken from glaciated, unglaciated, or the one basin that had both glaciated and unglaciated sampling sites ("Mix").
F I G U R E 8 in Genetic characteristics and growth patterns of the hybrid grouper derived from the hybridization of Epinephelus fuscoguttatus (female) Epinephelus polyphekadion (male)
F I G U R E 8 Allometric growth: regression curves for total length and body mass for the hybrid grouper in 5 months old (a), 6 months old (b) and 8 months old (c)
F I G U R E 7 in Genetic characteristics and growth patterns of the hybrid grouper derived from the hybridization of Epinephelus fuscoguttatus (female) Epinephelus polyphekadion (male)
F I G U R E 7 Correlation coefficients among morphological traits of the hybrid grouper in 5 months old (a), 6 months old (b) and 8 months old (c)
F I G U R E 5 Phylogenetic study using the 5S in Genetic characteristics and growth patterns of the hybrid grouper derived from the hybridization of Epinephelus fuscoguttatus (female) Epinephelus polyphekadion (male)
F I G U R E 5 Phylogenetic study using the 5S rDNA sequences from Epinephelus fuscoguttatus, Epinephelus polyphekadion and the hybrid grouper
F I G U R E 6 in Genetic characteristics and growth patterns of the hybrid grouper derived from the hybridization of Epinephelus fuscoguttatus (female) Epinephelus polyphekadion (male)
F I G U R E 6 Proportion of the total length and head length of the hybrid grouper, shown as percentages of body length
F I G U R E 8 in Riverscape genetics of the orangethroat darter complex
F I G U R E 8 FST isolation by distance plots. Segregation of allele frequencies is shown between pairs of basins v. geographic (river/land) distance. (a, b). All basin pairs in this study with comparisons within regions shown in black and between regions in gray for overland distance (a) and river distance (b). (c, d). Within region site comparisons, grouped by regions for overland distance (c) and river distance (d). The Tennessee River and Great Lakes regions were omitted because one basin was sampled in each region.
F I G U R E 1 in Riverscape genetics of the orangethroat darter complex
F I G U R E 1 Approximate collection sites of orangethroat species complex specimens used in this study. Colors indicate species. Numbers and region names correspond to USGS HUC2 watershed designations. Inset shows regional boundary between Upper Mississippi River and Ohio River regions.
F I G U R E 2 in Riverscape genetics of the orangethroat darter complex
F I G U R E 2 Results from STRUCTURE for (a) K = 3 and (b) K = 8. Each color corresponds to a distinct genetic cluster, and each bar represents an individual's assigned ancestry to each cluster. Names above chart correspond to river basin (HUC6). EB—E. burri, EP—E. pulchellum, ES— E. spectabile, and EU—E. uniporum. Glaciated and unglaciated correspond to areas that were/were not covered in ice during the last glacial maximum.
F I G U R E 4 Assigned ancestry plot using AIC criteria determining optimal K in Riverscape genetics of the orangethroat darter complex
F I G U R E 4 Assigned ancestry plot using AIC criteria determining optimal K of 5. Each color corresponds to a distinct genetic cluster, and each bar represents an individual's assigned ancestry to each cluster. Names above chart correspond to river basin (HUC6). EB—E. burri, EP— E. pulchellum, ES—E. spectabile, and EU—E. uniporum. Glaciated and unglaciated correspond to areas that were/were not covered in ice during the last glacial maximum.
F I G U R E 6 in Riverscape genetics of the orangethroat darter complex
F I G U R E 6 Principle component analysis (PCA) of Ceasia. Name indicates the basin where samples were collected.
F I G U R E 5 in Riverscape genetics of the orangethroat darter complex
F I G U R E 5 Cluster assignments at sampling locations under the AIC method and a K=5. Pie graphs represent proportion of individuals at the site assigned to a given cluster. Individuals with less than 85% assigned ancestry in either cluster are shown in gray.
F I G U R E 3 in Genetic characteristics and growth patterns of the hybrid grouper derived from the hybridization of Epinephelus fuscoguttatus (female) Epinephelus polyphekadion (male)
F I G U R E 3 Representative sequences of 5S rDNA. (a) Complete 5S coding regions from Epinephelus fuscoguttatus, Epinephelus polyphekadion and the hybrid grouper. Internal control regions of the coding region are shaded. (b) Comparison of the nontranscribed spacer (NTS) sequences from Epinephelus fuscoguttatus, Epinephelus polyphekadion and the hybrid grouper. The NTS upstream TATA elements are shaded and asterisks mark variable sites in the NTS
F I G U R E 1 in Genetic characteristics and growth patterns of the hybrid grouper derived from the hybridization of Epinephelus fuscoguttatus (female) Epinephelus polyphekadion (male)
F I G U R E 1 DNA content of (a) Epinephelus fuscoguttatus, (b) Epinephelus polyphekadion and (c) the hybrid grouper
F I G U R E 2 in Genetic characteristics and growth patterns of the hybrid grouper derived from the hybridization of Epinephelus fuscoguttatus (female) Epinephelus polyphekadion (male)
F I G U R E 2 Chromosome spreads at metaphase in Epinephelus fuscoguttatus, Epinephelus polyphekadion and the hybrid grouper. (a) The 48 chromosomes of Epinephelus fuscoguttatus. (b) The 48 chromosomes of Epinephelus polyphekadion. (c) The 48 chromosomes of the hybrid grouper
F I G U R E 3 A in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales
F I G U R E 3 A priori discriminant analysis of principal components (DAPC) plot of Camel trout. Each point represents the genotype of an individual fish, with centroids for each site labelled. Discriminant function 1 (DF1) is represented by the x axis, and discriminant function 2 (DF2) by the y-axis
F I G U R E 1 in A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales
F I G U R E 1 Map showing the location of rivers sampled for brown trout within the UK, France and Ireland. The left panel shows the rivers used to assess the performance of the single nucleotide polymorphisms (SNP) panel at characterising genetic parameters within and outside the target region. The top right (blue) panel shows the locations of the four sampled rivers in Mount's Bay, Cornwall (Case Study 1). The bottom right (red) panel shows the location of the sample locations in the Camel catchment (Case Study 2). The red box within the bottom right panel gives the position of the impassable De Lank quarry site
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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.