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79 results for “genetic crosses”
Data from: Genetic connectivity for two bear species at wildlife crossing structures in Banff National Park
Roads can fragment and isolate wildlife populations, which will eventually decrease genetic diversity within populations. Wildlife crossing structures may counteract these impacts, but most crossings are relatively new, and there is little evidence that they facilitate gene flow. We conducted a three-year research project in Banff National Park, Alberta, to evaluate the effectiveness of wildlife crossings to provide genetic connectivity. Our main objective was to determine how the Trans-Canada Highway and crossing structures along it affect gene flow in grizzly (Ursus arctos) and black bears (Ursus americanus). We compared genetic data generated from wildlife crossings with data collected from greater bear populations. We detected a genetic discontinuity at the highway in grizzly bears but not in black bears. We assigned grizzly bears that used crossings to populations north and south of the highway, providing evidence of bidirectional gene flow and genetic admixture. Parentage tests showed that 47% of black bears and 27% of grizzly bears that used crossings successfully bred, including multiple males and females of both species. Differentiating between dispersal and gene flow is difficult, but we documented gene flow by showing migration, reproduction and genetic admixture. We conclude that wildlife crossings allow sufficient gene flow to prevent genetic isolation.
Genetic Control of Reproductive Traits under Different Temperature Regimes in Inbred Line Populations Derived from Crosses between S. pimpinellifolium and S. lycopersicum Accessions
<p>Marker genotypes, linkage map and phenotypic data used for QTL analysis included in the manuscript by Gonzalo et al. <em>in press "</em>Genetic Control of Reproductive Traits under Different Temperature Regimes in Inbred Line Populations Derived from Crosses between <em>S. pimpinellifolium</em> and <em>S. lycopersicum</em> Accessions".</p>
Data from: The evolutionary stability of cross-sex, cross-trait genetic covariances
Although knowledge of the selective agents behind the evolution of sexual dimorphism has advanced considerably in recent years, we still lack a clear understanding of the evolutionary durability of cross-sex genetic covariances that often constrain its evolution. We tested the relative stability of cross-sex genetic covariances for a suite of homologous contact pheromones of the fruit fly Drosophila serrata, along a latitudinal gradient that these traits have diverged in mean. Using a Bayesian framework, which allowed us to account for uncertainty in all parameter estimates, we compared divergence in the total amounts and orientations of genetic variance across populations, finding divergence in orientation but not total variance. We then statistically compared orientation divergence of within-sex (G) to cross-sex (B) covariance matrices. In line with a previous theoretical prediction, we find that the cross-sex covariance matrix, B, is more variable than either male or female within-sex covariance matrix. Decomposition of B matrices into their symmetrical and non-symmetrical components revealed that instability is linked to the degree of asymmetry. We also find that the degree of asymmetry correlates with latitude suggesting a role for spatially varying natural selection in shaping genetic constraints on the evolution of sexual dimorphism.
Data from: Crossing the uncrossable: novel trans-valley biogeographic patterns revealed in the genetic history of low dispersal mygalomorph spiders (Antrodiaetidae, Antrodiaetus) from California
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Data from: Effects of arbuscular mycorrhizal fungi on aboveground tri-trophic interactions are contingent upon plant genetic effects of cross type in the perennial herb Ruellia nudiflora
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Insights into the genetic architecture of sexual dimorphism from an interspecific cross between two diverging Silene (Caryophyllaceae) species
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Data from: Genetic connectivity for two bear species at wildlife crossing structures in Banff National Park
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Data from: Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross-specific and species-specific amplifications
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Data from: Interspecific crossing and genetic mapping reveal intrinsic genomic incompatibility between two Senecio species that form a hybrid zone on Mount Etna, Sicily
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Data from: The evolutionary stability of cross-sex, cross-trait genetic covariances
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Data from: Heritability and cross-sex genetic correlations of early life circulating testosterone levels in a wild mammal
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Strong and weak cross-sex correlations govern the quantitative-genetic architecture of social group choice in Drosophila melanogaster
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Data from: Re-imagining maize inbred potential: identifying breeding crosses using genetic variance of simulated progeny
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Data from: Is there indirect selection on female extra-pair reproduction through cross-sex genetic correlations with male reproductive fitness?
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Genetic maps and marker effects of four maize biparental crosses
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Data from: Detection dog efficacy for collecting fecal samples from the critically endangered Cross River gorilla (Gorilla gorilla diehli) for genetic censusing
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Data from: Cross-sex genetic covariances limit the evolvability of wing-shape within and among species of Drosophila
The independent evolution of males and females is potentially constrained by both sexes inheriting the same alleles from their parents. This genetic constraint can limit the evolvability of complex traits; however, there are few studies of multivariate evolution that incorporate cross-sex genetic covariances in their predictions. Drosophila wing-shape has emerged as a model high-dimensional phenotype; wing-shape is highly evolvable in contemporary populations, and yet perplexingly stable across phylogenetic timescales. Here we show that cross-sex covariances in D. melanogaster, given by the B-matrix, may considerably bias wing-shape evolution. Using random skewers, we show that B would constrain the response to antagonistic selection by 90%, but would double the response to concordant selection. Both cross-sex within-trait and cross-sex cross-trait covariances determined the response to antagonistic selection, but only cross-sex within-trait covariances facilitated the response to concordant selection. Similar patterns were observed when selection was applied in the direction of extant sexual dimorphism in D. melanogaster, and in directions of most and least dimorphic variation across the Drosophila phylogeny. Our results highlight the importance of considering between-sex genetic covariances when making predictions about evolution on both macro- and micro- evolutionary timescales, and may provide one more explanatory piece in the puzzle of stasis.
Combining genome-wide studies of breast, prostate, ovarian and endometrial cancers maps cross-cancer susceptibility loci and identifies new genetic associations
<p>Data set linked to the paper, "Combining genome-wide studies of breast, prostate, ovarian and endometrial cancers maps cross-cancer susceptibility loci and identifies new genetic associations". Pre-print of the paper is here: <a href="https://doi.org/10.1101/2020.06.16.146803">https://doi.org/10.1101/2020.06.16.146803</a>.</p> <p> </p> <p>cross_cancer_sum_stats.txt.gz contains summary genome-wide association statistics for susceptibility to single cancers (breast (BR), prostate (PR), ovarian (OV), endometrial (EN), estrogen receptor (ER)-positive breast (POS), ER-negative breast (NEG), and high-grade serous ovarian (HGS) cancers) and from the cross-cancer meta-analysis (main [main] and subtype-focused [sub]). EA in the header refers to the effect allele, OA is the other allele, EAF is the effect allele frequency in the largest of the single cancer data sets (BR), IMPR2 is the imputation quality in the largest of the single cancer data sets (BR), SE is the standard error, PVAL is the P-value, RE2Cs1 is the RE2C statistic mean effect part, RE2Cs2 is the RE2C statistic heterogeneity part, RE2Cp* is the RE2C* P-value. More on RE2Cp* can be found here: <a href="http://software.buhmhan.com/RE2C/index.php?mid=contact&act=dispBoardWrite">http://software.buhmhan.com/RE2C/index.php?mid=contact&act=dispBoardWrite</a> and in <a href="https://academic.oup.com/bioinformatics/article/33/14/i379/3953957">https://academic.oup.com/bioinformatics/article/33/14/i379/3953957</a> SNP names in cross_cancer_sum_stats.txt.gz include the chromosome and build 37 position.</p> <p> </p> <p>main_tetrachoric_corr_matrix.txt and subtype_tetrachoric_corr_matrix.txt provide the tetrachoric correlation matrices used in the main and subtype-focused meta-analyses. These were also used to specify the cryptic.cor argument of the exh.abf function of MetABF. More on MetABF can be found here: <a href="https://github.com/trochet/metabf">https://github.com/trochet/metabf</a> and in <a href="https://onlinelibrary.wiley.com/doi/abs/10.1002/gepi.22202">https://onlinelibrary.wiley.com/doi/abs/10.1002/gepi.22202</a></p> <p> </p> <p>prior_sigmas_for_metabf.txt contains the values used to specify the prior.sigma argument of the exh.abf function in MetABF.</p> <p> </p> <p>The breast cancer data used are described in <a href="https://pubmed.ncbi.nlm.nih.gov/29059683/"><strong>PMID 29059683</strong></a> and can be downloaded from <a href="http://bcac.ccge.medschl.cam.ac.uk/bcacdata/oncoarray/oncoarray-and-combined-summary-result/gwas- summary-results-breast-cancer-risk-2017/">http://bcac.ccge.medschl.cam.ac.uk/bcacdata/oncoarray/oncoarray-and-combined-summary-result/gwas- summary-results-breast-cancer-risk-2017/</a> (this link also includes acknowledgements). The prostate cancer data are described in <a href="https://pubmed.ncbi.nlm.nih.gov/29892016/"><strong>PMID 29892016</strong></a> and can be downloaded from: <a href="http://practical.icr.ac.uk/blog/?page_id=8164">http://practical.icr.ac.uk/blog/?page_id=8164</a> (this link also includes acknowledgements). The ovarian cancer data used are described in <a href="https://pubmed.ncbi.nlm.nih.gov/28346442/"><strong>PMID 28346442</strong></a> and can be downloaded from <a href="https://www.ebi.ac.uk/gwas/studies/GCST004415">https://www.ebi.ac.uk/gwas/studies/GCST004415</a>. The endometrial cancer data are described in <a href="https://pubmed.ncbi.nlm.nih.gov/30093612/"><strong>PMID 30093612</strong></a> and can be downloaded from <a href="https://www.ebi.ac.uk/gwas/studies/GCST006464">https://www.ebi.ac.uk/gwas/studies/GCST006464</a>. These links point to the same data that form the basis of the cross_cancer_sum_stats.txt.gz file.</p> <p> </p> <p><strong>The sample size and precision of the data presented should preclude identification of any individual study participant. However, in downloading these data, you undertake not to attempt to identify individual study participant and not to re-post these data to a third-party website. Please cite the PMIDs highlighted above along with the appropriate acknowledements if you use the cross_cancer_sum_stats.txt.gz file.</strong></p> <p> </p> <p>If you have any questions about this repository, please email Siddhartha Kar at siddhartha dot kar at bristol dot ac dot uk</p>
Data from: QuLinePlus: extending plant breeding strategy and genetic model simulation to cross-pollinated populations – case studies in forage breeding
Plant breeders are supported by a range of tools that assist them to make decisions about the conduct or design of plant breeding programs. Simulations are a strategic tool that enable the breeder to integrate the multiple components of a breeding program into a number of proposed scenarios that are compared by a range of statistics measuring the efficiency of the proposed systems. A simulation study for the trait growth score compared two major strategies for breeding forage species, among half-sib family selection and among and within half-sib family selection. These scenarios highlighted new features of the QuLine program, now called QuLinePlus, incorporated to enable the software platform to be used to simulate breeding programs for cross pollinated species. Each strategy was compared across three levels of HS family mean heritability (0.1, 0.5 and 0.9), across three sizes of the initial parental population (10, 50, and 100), and across three genetic effects models (fully additive model, a mixture of additive, partial and over dominance model, and a mixture of partial dominance and over dominance model). Among and within half-sib selection performed better than among half-sib selection for all scenarios. The new tools introduced into QuLinePlus should serve to accurately compare among methods and provide direction on how to achieve specific goals in the improvement of plant breeding programs for cross breeding species.
Data from: Superiority of extra-pair offspring: maternal but not genetic effects as revealed by a mixed cross-fostering design
Extra-pair copulations (EPC) are a rule rather than an exception in socially monogamous birds. Despite widespread occurrences, the benefits of female infidelity remain illusive. Most attention has been paid to the possibility that females gain genetic benefits from EPC. Fitness comparison between maternal half-siblings is considered to be a defining test of this hypothesis. Recently it was shown that these comparisons may be confounded by within-brood maternal effects. One such effect may be the distribution of half-siblings in the laying order. This possibility is difficult to study since it would be necessary to detect from which egg the chick hatched. Here we used a new approach for egg-chick assignment. We cross-fostered eggs on an individual basis among a set of nests of the collared flycatcher Ficedula albicollis. After hatching, chicks were ascribed to mothers and therefore to individual eggs by molecular-genetic methods. Extra-pair young predominated early in the laying order. Under natural conditions, this should give them a competitive advantage over their half-siblings mediated by hatching asynchrony. However, we experimentally synchronized hatching. After this treatment extra-pair young did not outperform within-pair young in any studied trait including survival up to recruitment and several indicators of reproductive success and attractiveness. We obtained only modest sample size for the last two traits and did not test for extra-pair success of male offspring. Thus we cannot exclude the possibility of slight advantages of EPY during their adult phase of life. However, our data tentatively suggest that more likely reason for females' EPCs is the insurance against the infertility of a social mate.
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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.