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788 results for “genotypic data”
Benchmarking data for the KAGE and GKAGE genotypers
<p>Indexes and data for benchmarking KAGE and GKAGE genotypers.</p>
Microsatellite genotypes and associated data for: Tetrasporophyte bias coupled with heterozygote deficiency in Antarctic Plocamium sp. (Rhodophyta)
<p>Meiosis and syngamy generate an alternation between two ploidy stages, but the timing of these two processes varies widely across taxa, thereby generating life cycle diversity. One hypothesis suggests that life cycles with long-lived haploid stages are correlated with selfing, asexual reproduction, or both. Though mostly studied in angiosperms, selfing and asexual reproduction are often associated with marginal habitats. Yet, in haploid-diploid macroalgae, these two reproductive modes have subtle, but unique consequences whereby predictions from angiosperms may not apply. Along the western Antarctic Peninsula, there is a thriving macroalgal community, providing an opportunity to explore reproductive system variation in haploid-diploid macroalgae at high latitudes where endemism is common. <em>Plocamium </em>sp. is a widespread and abundant red macroalga found within this ecosystem. We sampled twelve sites during 2017 and 2018 field seasons and used ten microsatellite loci to describe the reproductive system. Overall genotypic richness and evenness were high, suggesting sexual reproduction. Eight sites were dominated by tetrasporophytes, but there was strong heterozygote deficiency, suggesting intergametophytic selfing. We found slight differences in the prevailing reproductive mode among sites, possibly due to local conditions (e.g., disturbance) that may contribute to site-specific variation. It remains to be determined whether high levels of selfing are characteristic of macroalgae more generally at high latitudes or due to the haploid-diploid life cycle. Further investigations of algal life cycles will likely reveal the processes underlying the maintenance of sexual reproduction more broadly across eukaryotes, but more studies of natural populations are required.</p>
Data explanation for Manuscript "'An optimized hydroponic pipeline for large-scale identification of wheat genotypes with resilient biological nitrification inhibition (BNI) activity'"
<p>Data explanation for Manuscript "'An optimized hydroponic pipeline for large-scale identification of wheat genotypes with resilient biological nitrification inhibition (BNI) activity'"</p>
Data for: Immune genotypes, immune responses, and survival in a wild bird population
<p>Individuals vary in their immune genotype, inbreeding coefficient <em>f</em>, immune responses, survival to adulthood, and adult longevity. However, whether immune genes predict survival or longevity, whether such relationships are mediated through immune responses, and how f affects immune genotype remain unclear. We use a wild song sparrow (<em>Melospiza</em> <em>melodia</em>) population in which survival to adulthood, adult longevity, and <em>f</em> were measured precisely, and in which immune responses have previously been assessed. We investigate four toll-like receptors (TLR) and the major histocompatibility complex (MHC) class IIB exon 2 genes. We test: a) whether immune genes predict fitness (survival to adulthood or adult longevity); b) whether immune genes predict immune response; c) whether immune response predicts fitness; and d) whether fitness, immune responses, or immune genotypes are correlated with <em>f</em>. We find that survival to adulthood is not associated with immune gene variation, but adult longevity is decreased by high MHC allele diversity (especially in birds that were relatively outbred), and by the presence of a specific MHC supertype. Immune responses were affected by specific immune genotypes. Survival to adulthood and adult longevity were not predicted by immune response, implying caution in the use of immune response as a predictor for fitness. We also found no relationship between <em>f</em> and immune genotype. This finding indicates that immune gene associations with longevity and immune response are not artefacts of <em>f</em>, and suggests that pathogen-mediated selection at functional loci can slow the loss of genetic variation arising from genetic drift and small population size.</p>
The genotype data accompanying the paper titled "Reanalyzing the genetic history of Kra-Dai speakers from Thailand and new insights into their genetic interactions beyond Mainland Southeast Asia"
<p>The newly generated genome-wide genotype data for 10 Lao individuals used in the paper "Reanalyzing the genetic history of Kra-Dai speakers from Thailand and new insights into their genetic interactions beyond Mainland Southeast Asia" ( https://www.nature.com/articles/s41598-023-35507-8 )</p>
Genotyping-by-sequencing data of common quails from the Azores
<p>In this study, we focused on common quails (<em>Coturnix</em> <em>coturnix</em>) from the Azores archipelago and used morphological, stable isotope, genetic and genomic data to characterise this lineage and to assess the divergence from neighbouring common quail populations. We detected the presence of a large chromosomal inversion that had been already described in other populations and we studied its role in this remote archipelago. The genotyping-by-sequencing data generated in this project were analysed together with those from Sanchez-Donoso et al. 2022 (<a href="https://doi.org/10.1016/j.cub.2021.11.019" rel="noopener" title="Persistent link using digital object identifier">https://doi.org/10.1016/j.cub.2021.11.019</a>). </p>
Data for: Genotypes selected for early and late avian lay date differ in their phenotype, but not fitness, in the wild
<p><span>Global warming has shifted phenological traits in many species, but whether species are able to track further increasing temperatures depends on the fitness consequences of additional shifts in phenological traits. To test this, we conducted a genomic selection experiment on wild great tits from the Hoge Veluwe study population (The Netherlands) to obtain great tits (<em>Parus</em> <em>major</em>) with genotypes for extremely early and late egg lay dates and measured phenology and fitness of selected great tit females under wild conditions.</span></p> <p><span>Females with early genotypes advanced lay dates relative to females with late genotypes, but not relative to non-selected females. Females with early and late genotypes did not differ in the number of fledglings produced, in line with the weak effect of lay date on the number of fledglings produced by non-selected females in the years of the experiment. Our study is the first application of genomic selection in the wild and led to an asymmetric phenotypic response that indicates the presence of constraints toward early, but not late, lay dates.</span></p>
Perna perna metadata and genotypic data
<p>Studies investigating gene flow in sessile or sedentary marine species typically draw conclusions about larval dispersal by investigating genetic structure of adults. Here, we generated microsatellite data from adults, recruits, settlers and planktonic larvae of the brown mussel, <em>Perna</em> <em>perna</em>, from the south-east coast of South Africa, and identified a consistent mismatch in genetic structure between the adults and all earlier life stages. While adults could be assigned to two major geographical groups (western and eastern), most of the early-stage mussels were strongly affiliated with the eastern group. This result suggests that few of the early-stage individuals present in the western portion of the sampling range will become part of the adult population. Our findings highlight the importance of post-settlement processes as key drivers of population structure and caution against the exclusive use of genetic data generated from adults to assess population connectivity facilitated by the dispersal of planktonic propagules.</p>
Data from: Genotype x environment interaction obscures genetic sources of variation in seed size in Dithyrea californica but provides the opportunity for selection on phenotypic plasticity
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Data from: Local parasite pressures and host genotype modulate epigenetic diversity in a mixed-mating fish
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Data from: Assessing the potential of genotyping-by-sequencing-derived single nucleotide polymorphisms to identify the geographic origins of intercepted gypsy moth (Lymantria dispar) specimens: a proof-of-concept study
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Data from: 2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador
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Data from: A high-density exome capture genotype-by-sequencing panel for forestry breeding in Pinus radiata
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Genotyping-by-Sequencing data of weedy and domesticated Brassica rapa L.
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Data for: Immune genotypes, immune responses, and survival in a wild bird population
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Data from: Genotypic diversity and spatial-temporal distribution of Symbiodinium clones in an abundant reef coral
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Data from: Supplementary stocking selects for domesticated genotypes
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Data from: Globally invasive genotypes of the amphibian chytrid outcompete an enzootic lineage in coinfections
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Data from: Evidence for selection-by-environment but not genotype-by-environment interactions for fitness-related traits in a wild mammal population
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Data for: Genotypes selected for early and late avian lay date differ in their phenotype, but not fitness, in the wild
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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.