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2,785 results for “genotyping”
Genotypes of cave, surface and hybrid Astyanax mexicanus
<p>Genetic divergence in the presence of gene flow has been well documented, but there is little information on the specific factors maintaining divergence. The present study investigates this in the Mexican tetra (<em>Astyanax mexicanus</em>), an excellent model for studying this question because surface and cave populations differ markedly in phenotype and genotype, but are interfertile. Previous population studies documented significant gene flow among cave and surface populations but they focused on analyses of neutral markers, whose evolutionary dynamics likely differ from those of genes involved in cave adaptation. The present study advances our understanding of this question by focusing specifically on the genetics responsible for eye and pigmentation reduction, signature traits of cave populations. Direct observations of two cave populations over the course of 63 years verify that surface fish frequently move into the caves and even hybridize with the cavefish. Importantly, however, historical records show that surface alleles for pigmentation and eye size do not persist, but are rapidly eliminated from the cave gene pool. It has been argued that the regression of eyes and pigmentation was driven by drift, but the results of this study suggest that strong selection actively eliminates surface alleles from the cave populations. </p>
Influenza phenotype-genotype database beta version
<p>Beta version of a data base of genetic mutations in influenzaA viruses linked to phenotypic changes in the literature with references. Not exclusive and sources should be checked before use.</p>
Genotypes at 10 microsatellite loci for 8 perennial, polygyne colonies of Vespula squamosa
<p>Many highly social species show plasticity in their social structure in response to different environmental conditions. For example, typical colonies of the yellowjacket wasp <i>Vespula squamosa </i>are headed by a single reproductive queen and survive for only a single season. However, in warmer climates, <i>V. squamosa</i> colonies sometimes persist for multiple years and can grow to extremely large size. We used genetic markers to understand patterns of reproduction and recruitment within these perennial colonies. We genotyped <i>V. squamosa</i> workers, pre-reproductive queens, and males from perennial colonies in the southeastern United States at 10 polymorphic microsatellite loci and one mitochondrial DNA locus. We found that <i>V. squamosa</i> from perennial nests were produced by multiple reproductives, in contrast to typical annual colonies. Relatedness of nestmates from perennial colonies was significantly lower than relatedness of nestmates from annual colonies. Our analyses of mitochondrial DNA indicated that most <i>V. squamosa</i> perennial colonies represented semi-closed systems whereby all individuals belonged to a single matriline despite the presence of multiple reproductive females. However, new queens recruited into perennial colonies apparently mated with non-nestmate males. Notably, perennial and annual colonies did not show significant genetic differences, supporting the hypothesis that perennial colony formation represents an instance of social phenotypic plasticity. Overall, our results indicate that perennial <i>V. squamosa</i> colonies show substantial changes to their social biology compared to typical annual colonies.</p>
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>
Figure 15 in The monophyly of Crenuchinae and description of two new species of Poecilocharax (Teleostei: Crenuchidae) based on phenotypic and genotypic evidence
Figure 15. Igarapé Mutum, tributary of Rio Juma, Rio Aripuanã Basin, Apuí, Amazonas, Brazil, type-locality of Poecilocharax rhizophilus sp. nov. Inset details the microenvironment where P. rhizophilus sp. nov. was captured.
Figure 12 in The monophyly of Crenuchinae and description of two new species of Poecilocharax (Teleostei: Crenuchidae) based on phenotypic and genotypic evidence
Figure 12. Poecilocharax rhizophilus sp. nov.: A, holotype, male, 20.3 mm SL, MZUSP 121652; B, paratype, male, 23.1 mm SL, MZUSP 121651; C, paratype, female, 23.3 mm SL, MZUSP 121651.
Figure 10 in The monophyly of Crenuchinae and description of two new species of Poecilocharax (Teleostei: Crenuchidae) based on phenotypic and genotypic evidence
Figure 10. Type-locality (red square) of Poecilocharax callipterus sp. nov. and P. rhizophilus sp. nov. (blue dot), tributary of the Rio Juma, Rio Aripuanã drainage, Rio Madeira Basin, Apuí, Amazonas, Brazil.
Figure 8 in The monophyly of Crenuchinae and description of two new species of Poecilocharax (Teleostei: Crenuchidae) based on phenotypic and genotypic evidence
Figure 8. Superficial neuromasts (white arrows) on lateral body scales of Poecilocharax callipterus sp. nov., MZUSP 117568, paratype, 29.4 mm SL.
Figure 7 in The monophyly of Crenuchinae and description of two new species of Poecilocharax (Teleostei: Crenuchidae) based on phenotypic and genotypic evidence
Figure 7. Poecilocharax callipterus sp. nov., lateral line with a single perforated scale, MZUSP 117568, paratype, 27.5 mm SL.
Figure 4 in The monophyly of Crenuchinae and description of two new species of Poecilocharax (Teleostei: Crenuchidae) based on phenotypic and genotypic evidence
Figure 4. SEM photograph of the of neurocranium of Poecilocharax callipterus sp. nov. in frontal view, paratype, male, 28.1 mm SL. Epiphyseal branch of the supraorbital laterosensory canal (EP), foramina (FO), frontal bone (FR), mesethmoid (ME) and parietal branch of supraorbital laterosensory canal (P).
Figure 3 in The monophyly of Crenuchinae and description of two new species of Poecilocharax (Teleostei: Crenuchidae) based on phenotypic and genotypic evidence
Figure 3. Poecilocharax callipterus sp. nov.: A, holotype, male, 30.9 mm SL, MZUSP 121653; B, paratype, female, 27.7 mm SL, MZUSP 117568.
Figure 11 in The monophyly of Crenuchinae and description of two new species of Poecilocharax (Teleostei: Crenuchidae) based on phenotypic and genotypic evidence
Figure 11. Tributary of Rio Canadá, Rio Juma drainage, Rio Aripuanã Basin, Apuí, Amazonas, Brazil, type-locality of Poecilocharax callipterus sp. nov. In detail the microenvironment where P. callipterus sp. nov. was captured.
Figure 2 in The monophyly of Crenuchinae and description of two new species of Poecilocharax (Teleostei: Crenuchidae) based on phenotypic and genotypic evidence
Figure 2. Results from ABGD analysis on Crenuchinae data shown in the IB topology. Analyses were run with a minimum slope increase (X) of 1.0. Distances were calculated based on the Kimura 2-parameter (K80) model. Graphs indicate the histogram of distances (right, above) and ranked distances (right, below).
Figure 1 in The monophyly of Crenuchinae and description of two new species of Poecilocharax (Teleostei: Crenuchidae) based on phenotypic and genotypic evidence
Figure 1. Abbreviated phylogenetic trees of Crenuchidae obtained in this study based on mitochondrial gene cytochrome c oxidase subunit I (COI, 666 bp), indicating the monophyly of Crenuchinae (highlighted) and the relationships among its representatives. A, Bayesian tree, numbers at branches are posterior probabilities; B, maximum likelihood tree, numbers at branches are bootstrap values. Values below 75% (-) are not shown.
Figure 6 in The monophyly of Crenuchinae and description of two new species of Poecilocharax (Teleostei: Crenuchidae) based on phenotypic and genotypic evidence
Figure 6. Poecilocharax callipterus sp. nov., left medial view of premaxilla, maxilla and dentary, MZUSP 117568, paratype, male, 28.1 mm SL.
Figure 9 in The monophyly of Crenuchinae and description of two new species of Poecilocharax (Teleostei: Crenuchidae) based on phenotypic and genotypic evidence
Figure 9. Poecilocharax callipterus sp. nov., immediately after capture, paratypes: A, male, 30.6 mm SL, MZUSP 121653; B, female, 27.2 mm SL, MZUSP 117568.
Figure 5 in The monophyly of Crenuchinae and description of two new species of Poecilocharax (Teleostei: Crenuchidae) based on phenotypic and genotypic evidence
Figure 5. Infraorbital series of Poecilocharax callipterus sp. nov., depicting antorbital bone and infraorbitals 1–6, MZUSP 117568, paratype, male, 28.1 mm SL, left lateral view.
Figure 14 in The monophyly of Crenuchinae and description of two new species of Poecilocharax (Teleostei: Crenuchidae) based on phenotypic and genotypic evidence
Figure 14. Poecilocharax rhizophilus sp. nov., immediately after capture. A, holotype, male, 20.3 mm SL, MZUSP 121652. Paratypes: B, male, 23.1 mm SL; C, female, 23.3 mm SL, MZUSP 121651.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.