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24 results for “homozygosity”
High MHC gene copy number maintains diversity despite homozygosity in a Critically Endangered single-island endemic bird, but no evidence of MHC-based mate choice
<p>Raw sequence data from two amplicon libraries of MHC class I exon 3 of Raso Lark <em>Alauda razae</em>, sequenced on an Illumina Miseq. The two different libraries (two different Illumina runs) are collected in separat tar archive (.tar). Within each of those are individual sequence reads as gzipped fastq files (.fastq.gz). Each sample has two files, one for read 1 (R1) and one for read 2 (R2), with file names structured as follows. Delimited by underscore (_) are:</p> <ol> <li>sample name as referred to in the data and paper (“RingNo” in the Supporting data table);</li> <li>formal ID (also referred to in data table, often corresponding to full ring number);</li> <li>Illumina sample number (i.e. based on the order that samples are listed in the sample sheet);</li> <li>Illumina lane number (static as L001, as Miseq instruments have a single lane on their flow cells);</li> <li>read number (R1 [forward] or R2 [reverse]);</li> <li>static identifier from Illumina (001).</li> </ol> <p>Thus, the file 83304_TJ83304_S163_L001_R2_001.fastq.gz is the reverse (read 2) MHC class I exon 3 sequence of individual 83304 (ring number TJ83304).</p>
Homozygosity mapping reveals population history and trait architecture in self- incompatible pear (Pyrus spp.)
<p>Runs of homozygosity (ROH) are successive homozygous segments of the genome where the two haplotypes inherited from the parents are identical-by-descent. A key focus of this project is to investigate ROH distribution patterns in the genomes of outbred fruit crops using pear as a study case</p>
Homozygosity mapping reveals population history and trait architecture in self- incompatible pear (Pyrus spp.)
<p>Runs of homozygosity (ROH) are successive homozygous segments of the genome where the two haplotypes inherited from the parents are identical-by-descent. A key focus of this project is to investigate ROH distribution patterns in the genomes of outbred fruit crops using pear as a study caseRuns of homozygosity (ROH) are successive homozygous segments of the genome where the two haplotypes inherited from the parents are identical-by-descent. A key focus of this project is to investigate ROH distribution patterns in the genomes of outbred fruit crops using pear as a study case</p>
Homozygosity mapping reveals population history and trait architecture in self- incompatible pear (Pyrus spp.)
<p>Runs of homozygosity (ROH) are successive homozygous segments of the genome where the two haplotypes inherited from the parents are identical-by-descent. A key focus of this project is to investigate ROH distribution patterns in the genomes of outbred fruit crops using pear as a study case</p>
Silva, Harder et al. Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history Data
<p>Dataset used in the "Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history" paper by Silva, Harder et al.</p> <p>This dataset includes Fasta files for Simulated dataset and VCF files for both Empirical and Simulated datasets.</p>
Runs of homozygosity reveal past bottlenecks and contemporary inbreeding across diverging populations of an island-colonizing bird
<p>Genomes retain evidence of the demographic history and evolutionary forces that have shaped populations. Across island systems, contemporary patterns of genetic diversity reflect complex population demography, including colonisation events, bottlenecks, gene flow and genetic drift. Here, we investigate whether island founder events have prolonged effects on genome-wide diversity and runs of homozygosity (ROH) distributions, using whole genome resequencing from six populations across three archipelagos of Berthelot's pipit (<em>Anthus</em> <em>berthelotii</em>) – a passerine which has undergone island speciation relatively recently. Pairwise sequential Markovian coalescent (PSMC) analyses estimated divergence from its sister species approximately two million years ago. Results indicate that all Berthelot's pipit populations had shared ancestry until approximately 50,000 years ago, when the Madeiran archipelago populations were founded, while the Selvagens were colonised within the last 8,000 years. We identify extensive long ROH (>1 Mb) in genomes in the most recently colonised populations of Madeira and Selvagens which have experienced sequential island founder events and population crashes. Population expansion within the last 100 years may have eroded long ROH in the Madeiran archipelago, resulting in a prevalence of short ROH (<1 Mb). Extensive long and short ROH in the Selvagens reflects strong recent inbreeding, small contemporary effective population size and past bottleneck effects, with as much as 37.7% of the autosomes comprised of ROH >250 kb in length. These findings highlight the importance of demographic history, as well as selection and genetic drift, in shaping contemporary patterns of genomic diversity across diverging populations. </p>
Data from: Multi-locus homozygosity promotes actuarial senescence in a wild mammal
<ol> <li>Genome-wide homozygosity, caused for example by inbreeding, is expected to have deleterious effects on survival and/or reproduction. Evolutionary theory predicts that any fitness costs are likely to be detected in late life because natural selection will filter out negative impacts on younger individuals with greater reproductive value.</li> <li>Here we infer associations between multi-locus homozygosity, sex, disease, and age-dependent mortality risks using Bayesian analysis of the life histories of wild European badgers (<em>Meles</em> <em>meles</em>) in a population naturally infected with <em>Mycobacterium</em> <em>bovis</em> (the causative agent of bovine tuberculosis).</li> <li>We find important effects of multi-locus homozygosity on all parameters of the Gompertz-Makeham mortality hazard function, but particularly in later-life.</li> <li>Our findings confirm the predicted association between genomic homozygosity and actuarial senescence. Increased homozygosity is particularly associated with an earlier onset, and greater rates of actuarial senescence, regardless of sex. The association between homozygosity and actuarial senescence is further amplified among badgers putatively infected with bovine tuberculosis.</li> <li>These results recommend further investigation into the ecological and behavioural processes that result in genome-wide homozygosity, and focused work on whether homozygosity is harmful or beneficial during early life-stages.</li> </ol>
Data from: Multi-locus homozygosity promotes actuarial senescence in a wild mammal
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Runs of homozygosity reveal past bottlenecks and contemporary inbreeding across diverging populations of an island-colonizing bird
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Synteny enabled upgrade of the Galapagos giant tortoise genome improves inferences of runs of homozygosity
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Data from: Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds
A dataset consisting of 787 animals with high density SNP chip genotypes (346,774 SNP) and 939 animals with medium density SNP chip genotypes (33,828 SNP) from a total of 8 indigenous Swiss sheep breeds was analyzed to characterize population structures, quantify genomic inbreeding based on runs of homozygosity and identify selection signatures. In concordance with the recent known history of these breeds, the highest genetic diversity was observed in Engadine Red sheep and the lowest in Valais Blacknose sheep. Correlation between FPED and FROH was around 0.50 and thereby lower than that found in similar studies in cattle. Mean FROH estimates from medium density data and HD data were highly correlated (0.95). Signatures of selection and candidate gene analysis revealed that the most prominent signatures of selection were found in the proximity of genes associated with body size (NCAPG, LCORL, LAP3, SPP1, PLAG1, ALOX12, TP53), litter size (SPP1), milk production (ABCG2, SPP1), coat color (KIT, ASIP, TBX3) and horn status (RXFP2). For the Valais Blacknose sheep the private signatures in proximity of genes/QTL influencing body size, coat color and fatty acid composition were confirmed based on runs of homozygosity analysis. These private signatures underline the genetic uniqueness of the Valais Blacknose sheep breed. In conclusion we identified differences in the genetic make-up of Swiss sheep breeds and we present relevant candidate genes responsible for breed differentiation in locally adapted breeds.
Detecting selection using extended haplotype homozygosity (EHH)-based statistics in unphased or unpolarized data
<p>Analysis of population genetic data often includes the search for genomic regions with signs of recent positive selection. One of the approaches involves the concept of Extended Haplotype Homozygosity (EHH) and its associated statistics. These statistics typically need phased haplotypes and, some of them, polarized variants.<br> Here, we unify and extend previously proposed modifications to loosen these requirements. We compare the modified versions with the original ones by measuring the False Discovery Rate in simulated whole-genome scans and quantifying the overlap of inferred candidate regions in empirical data. We find that phasing information is indispensable for the accurate estimation of within-population statistics for all but very large samples and of cross-population statistics for small samples. Ancestry information, in contrast, is of lesser importance for both.<br> Our publicly available R package rehh incorporates the modified statistics presented here.</p>
Detecting selection using extended haplotype homozygosity (EHH)-based statistics in unphased or unpolarized data
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Data from: Runs of homozygosity and signatures of selection: a comparison among eight local Swiss sheep breeds
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Genomic patterns of homozygosity and inbreeding depression in Murciano-Granadina goats
<p>Genotypic data from 1,040 Murciano-Granadina female goats genotyped with the Goat SNP50 BeadChip, as well as milk production records of 817 Murciano-Granadina goats for the traits milk yield measured in kilograms at 210 days (MY210), 240 days (MY240) and 305 days (MY305), the natural logarithm of the somatic cell count divided by 1,000 (lnSCC, to convert this value into a somatic cell count please use the formula: e<sup>lnSCC</sup> × 10<sup>3</sup> cells/mL), fat percentage (FP), protein percentage (PP) and lactose percentage (LP).</p>
Genomic patterns of homozygosity and inbreeding depression in Murciano-Granadina goats
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Affymetrix SNP array data for homozygosity mapping of segregating anhidrosis
GEO Series GSE61122. Homo sapiens. 4 samples. Type: SNP genotyping by SNP array.
Homozygosity mapping in a consanguineous family with osteogenesis imperfecta (OI)
GEO Series GSE21958. Homo sapiens. 2 samples. Type: SNP genotyping by SNP array; Genome variation profiling by SNP array.
Generation of targeted homozygosity in the genome of human induced pluripotent stem cells
GEO Series GSE137657. Homo sapiens. 7 samples. Type: Expression profiling by high throughput sequencing.
Combinatorial Conflicting Homozygosity (CCH) analysis enables the rapid identification of shared genomic regions in the presence of multiple phenocopies
GEO Series GSE65312. Homo sapiens. 17 samples. Type: Genome variation profiling by SNP array; SNP genotyping by SNP array.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.