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PROVIDER: PRJNA1013179 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Mutation generates the heritable variation that genetic drift and natural selection shape. In classical quantitative genetic models, drift is a function of the effective population size and acts uniformly across traits, while mutation and selection act trait-specifically. We identified thousands of quantitative trait loci (QTL) influencing transcript abundance traits in a cross of two C. elegans strains; although trait-specific mutation and selection explained some of the observed pattern of QTL distribution, the pattern was better explained by trait-independent variation in the intensity of selection on linked sites. Our results suggest that traits in C. elegans exhibit different levels of variation less because of their own attributes than because of differences in the effective population sizes of the genomic regions harboring their underlying loci.
2010-10-01 | GSE23857 | GEO
Project description:The Lundehund is an old dog breed with remarkable anatomical features including polydactyly in all four limbs and extraordinary flexibility of the spine. We genotyped 28 Lundehund using the canine Illumina high density beadchip to estimate the effective population size (Ne) and inbreeding coefficients as well as to identify potential regions of positive selection. The decay of linkage disequilibrium was slow with r2=0.95 in 50 kb distance. The last 7-200 generations ago, Ne was at 10-13. An increase of Ne was noted in the very recent generations with a peak value of 19 for Ne at generation 4. The FROH estimated for 50-, 65- and 358-SNP windows were 0.87, 087 and 0.81, respectively. The most likely estimates for FROH after removing identical-by-state segments due to linkage disequilibria were at 0.80-0.81. The extreme loss of heterozygosity has been accumulated through continued inbreeding over 200 generations within a probably closed population with a small effective population size. The mean inbreeding coefficient based on pedigree data for the last 11 generations (FPed=0.10) was strongly biased downwards due to the unknown coancestry of the founders in this pedigree data. The long-range haplotype test identified regions with genes involved in processes of immunity, olfaction, woundhealing and neuronal development as potential targets of selection. The genes QSOX2, BMPR1B and PRRX2 as well as MYOM1 are candidates for selection on the Lundehund characteristics small body size, increased number of digits per paw and extraordinary mobility, respectively.
2015-03-09 | GSE66677 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE34280: Clonal Selection Drives Genetic Divergence of Metastatic Medulloblastoma [Affymetrix SNP6 Arrays] GSE34355: Clonal Selection Drives Genetic Divergence of Metastatic Medulloblastoma [Illumina Infinium HumanMethylation27 Beadchip v1.2] Refer to individual Series
2011-12-13 | E-GEOD-34356 | biostudies-arrayexpress
Project description:The Lundehund is an old dog breed with remarkable anatomical features including polydactyly in all four limbs and extraordinary flexibility of the spine. We genotyped 28 Lundehund using the canine Illumina high density beadchip to estimate the effective population size (Ne) and inbreeding coefficients as well as to identify potential regions of positive selection. The decay of linkage disequilibrium was slow with r2=0.95 in 50 kb distance. The last 7-200 generations ago, Ne was at 10-13. An increase of Ne was noted in the very recent generations with a peak value of 19 for Ne at generation 4. The FROH estimated for 50-, 65- and 358-SNP windows were 0.87, 087 and 0.81, respectively. The most likely estimates for FROH after removing identical-by-state segments due to linkage disequilibria were at 0.80-0.81. The extreme loss of heterozygosity has been accumulated through continued inbreeding over 200 generations within a probably closed population with a small effective population size. The mean inbreeding coefficient based on pedigree data for the last 11 generations (FPed=0.10) was strongly biased downwards due to the unknown coancestry of the founders in this pedigree data. The long-range haplotype test identified regions with genes involved in processes of immunity, olfaction, woundhealing and neuronal development as potential targets of selection. The genes QSOX2, BMPR1B and PRRX2 as well as MYOM1 are candidates for selection on the Lundehund characteristics small body size, increased number of digits per paw and extraordinary mobility, respectively. The objectives of the present study were to genotype 28 Lundehund using the canine Illumina high density beadchip (Illumina, San Diego, CA, USA) to estimate the effective population size (Ne) from data on linkage disequilibria (LD). We identified runs of homozygosity (ROH) as regions with a local loss of genetic variation. Inbreeding coefficients were calculated on the basis of pedigree data (FPed) and genotype information (FROH, FIS) to compare the results of these different methods for this population. We applied the long-range haplotype test to search for potential selective sweeps.
2015-03-09 | E-GEOD-66677 | biostudies-arrayexpress
Project description:In the presence of environmental change, natural selection can shape the transcriptome. Under a scenario of environmental change, genotypes that are better able to modulate gene expression to maximize fitness will tend to be favored. Therefore, it is important to examine gene expression at the population level in order to distinguish random or neutral gene expression variation from the pattern produced by natural selection. This study investigates the natural variation in transcriptional response to a cactus host shift utilizing the mainland Sonora population of Drosophila mojavensis. Drosophila mojavensis is a cactophilic species composed of four cactus host populations endemic to the deserts of North America. Overall, the change in cactus host was associated with a significant reduction in larval viability, as well as the differential expression of 21% of the genome (3,109 genes). Among the genes identified were a set of genes previously known to be involved in xenobiotic metabolism, as well as genes involved in cellular energy production, oxidoreductase/carbohydrate metabolism, structural components and mRNA binding. Interestingly, of the 3,109 genes whose expression was affected by host use, there was a significant overrepresentation of genes that lacked an orthologous call to the D. melanogaster genome, suggesting the possibility of an accelerated rate of evolution in these genes. Of the genes with a significant cactus effect, the majority, 2,264 genes, did not exhibit a significant cactus-by-line interaction. This population level approach facilitated the identification of genes involved in past cactus host shifts. Dataset from Population transcriptomics of cactus host shifts in Drosophila mojavensis, Matzkin, LM. Molecular Ecology.
2012-06-18 | GSE35937 | GEO
Project description:Functional genomic analyses of exopolysaccharide-producing Streptococcus thermophilus ASCC 1275 in response to shifts in milk fermentation conditions
2019-05-02 | MSV000083741 | MassIVE
Project description:Poecilia reticulata brain size selection raw sequence reads
| PRJNA284588 | ENA