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2,785 results for “genotyping”
Figure 1 from: Moreno-González JA, Pinto-da-Rocha R, Gallão JE (2021) Bringing order to a complex system: phenotypic and genotypic evidence contribute to the taxonomy of Tityus (Scorpiones, Buthidae) and support the description of a new species. ZooKeys 1075: 33-75. https://doi.org/10.3897/zookeys.1075.67459
Figure 1 Phylogeny of Tityus representatives from South America obtained by analysis of DNA sequences (12S rDNA, 16S rDNA, 28S rDNA, and Cytochrome c Oxidase I- COI). Maximum likelihood tree (Log-likelihood= -12896.086), showing species-groups and subgenera. Values on nodes correspond to ultrafast-bootstrap (Ubst) values.
Figure 13 from: Moreno-González JA, Pinto-da-Rocha R, Gallão JE (2021) Bringing order to a complex system: phenotypic and genotypic evidence contribute to the taxonomy of Tityus (Scorpiones, Buthidae) and support the description of a new species. ZooKeys 1075: 33-75. https://doi.org/10.3897/zookeys.1075.67459
Figure 13 Tityus (Tityus) spelaeus sp. nov., female paratypes under laboratory conditions A, B female paratype with scorpionlings A feeding upon scorpionlings B litter on female's back C specimens feeding on a cricket.
Figure 5 from: Moreno-González JA, Pinto-da-Rocha R, Gallão JE (2021) Bringing order to a complex system: phenotypic and genotypic evidence contribute to the taxonomy of Tityus (Scorpiones, Buthidae) and support the description of a new species. ZooKeys 1075: 33-75. https://doi.org/10.3897/zookeys.1075.67459
Figure 5 Tityus C. L. Koch, 1836, female pectinal basal piece and basal middle lamellae of the pectines, showing glandular regions A, C, E White light B, D, F UV light A, BTityus (Tityus) brazilae Lourenço & Eickstedt, 1984 (MZSP 75619) C, DTityus (Archaeotityus) clathratus C. L. Koch, 1844 (MZSP 31468) E, FTityus (Atreus) forcipula (Gervais, 1843) (MZSP). Abbreviations: BML, basal middle lamellae; GR, glandular region. Scale bars: 500 μm.
Figure 12 from: Moreno-González JA, Pinto-da-Rocha R, Gallão JE (2021) Bringing order to a complex system: phenotypic and genotypic evidence contribute to the taxonomy of Tityus (Scorpiones, Buthidae) and support the description of a new species. ZooKeys 1075: 33-75. https://doi.org/10.3897/zookeys.1075.67459
Figure 12 Tityus (Tityus) spelaeus sp. nov., female holotype (MZSP 74633), metasoma and telson A, B telson A lateral view B ventral view C, D metasoma C lateral view D ventral view. Scale bars: 2 mm (A, B); 5 mm (C, D).
Figure 3 from: Moreno-González JA, Pinto-da-Rocha R, Gallão JE (2021) Bringing order to a complex system: phenotypic and genotypic evidence contribute to the taxonomy of Tityus (Scorpiones, Buthidae) and support the description of a new species. ZooKeys 1075: 33-75. https://doi.org/10.3897/zookeys.1075.67459
Figure 3 Phylogeny of Tityus representatives from South America obtained by analysis of DNA sequences (12S rDNA, 16S rDNA, 28S rDNA, Cytochrome c Oxidase I), showing distribution of the characters states exhibited by the female basal pectinal piece (orange: GR absent; grey: medium-sized GR; turquoise: relatively large GR; blue: very large GR) across different Tityus subgenera and species-groups. Boxes on branches and associated values correspond to ultrafast-bootstrap (Ubst) values. Observations= Tityus (Tityus) spelaeus sp. nov. is marked in bold. Abbreviations= GR, glandular region.
Figure 7 from: Moreno-González JA, Pinto-da-Rocha R, Gallão JE (2021) Bringing order to a complex system: phenotypic and genotypic evidence contribute to the taxonomy of Tityus (Scorpiones, Buthidae) and support the description of a new species. ZooKeys 1075: 33-75. https://doi.org/10.3897/zookeys.1075.67459
Figure 7 Tityus (Tityus) spelaeus sp. nov., female holotype (MZSP 74633) A dorsal view B ventral view. Scale bars: 10 mm.
Figure 2 from: Moreno-González JA, Pinto-da-Rocha R, Gallão JE (2021) Bringing order to a complex system: phenotypic and genotypic evidence contribute to the taxonomy of Tityus (Scorpiones, Buthidae) and support the description of a new species. ZooKeys 1075: 33-75. https://doi.org/10.3897/zookeys.1075.67459
Figure 2 Phylogeny of Tityus representatives from South America obtained by analysis of DNA sequences (12S rDNA, 16S rDNA, 28S rDNA, and Cytochrome c Oxidase I- COI), showing the distribution of the characters states of the ventral setae of telotarsi I–IV (orange: an irregularly distributed tuft of setae (type I); turquoise: two ventro-submedian rows of setae (type II)) across different Tityus subgenera and species-groups. Boxes on branches and associated values correspond to ultrafast-bootstrap (Ubst) values. Observations= Tityus (Tityus) spelaeus sp. nov. is marked in bold.
Figure 6 from: Moreno-González JA, Pinto-da-Rocha R, Gallão JE (2021) Bringing order to a complex system: phenotypic and genotypic evidence contribute to the taxonomy of Tityus (Scorpiones, Buthidae) and support the description of a new species. ZooKeys 1075: 33-75. https://doi.org/10.3897/zookeys.1075.67459
Figure 6 Tityus C. L. Koch, 1836, female pectinal basal piece and basal middle lamellae of the pectines, showing glandular regions A, C, E White light B, D, F UV light A, BTityus (Atreus) obscurus Gervais, 1843 (MNRJ 07610) C, DTityus (Tityus) serrulatus Lutz & Mello, 1922 (MZSP 28205) E, FTityus (Tityus) spelaeus sp. nov. (MZSP 74633). Abbreviations: BML, basal middle lamellae; GR, glandular region of the pectinal basal piece. Scale bars: 500 μm.
Figure 9 from: Moreno-González JA, Pinto-da-Rocha R, Gallão JE (2021) Bringing order to a complex system: phenotypic and genotypic evidence contribute to the taxonomy of Tityus (Scorpiones, Buthidae) and support the description of a new species. ZooKeys 1075: 33-75. https://doi.org/10.3897/zookeys.1075.67459
Figure 9 Tityus (Tityus) spelaeus sp. nov., female holotype (MZSP 74633), right pedipalp segments A femur, dorsal view B, C patella B dorsal view C external view. Scale bars: 1.5 mm.
Hazelnut SSR database: genetic profiles of the accessions, list of synonyms, and true-to-type genotypes
<p>Hazelnut (<i>Corylus avellana</i> L.) is one of the most important tree nut crops in Europe. Germplasm accessions are conserved in <i>ex situ</i> repositories, located in countries where hazelnut production occurs. In this work, we used ten simple sequence repeat (SSR) markers as the basis to establish a core collection representative of the hazelnut genetic diversity conserved in different European collections. A total of 480 accessions were used: 430 from <i>ex situ</i> collections and 50 landraces maintained <i>on-farm</i>. SSR analysis identified 181 genotypes, that represented our whole hazelnut germplasm collection (WHGC). Four approaches (utilizing MSTRAT, Power Core, and Core Hunter's single- and multi-strategy) based on the maximization (M) strategy were used to determine the best sampling method. Core Hunter's multi-strategy, optimizing both allele coverage (Cv) and Cavalli-Sforza and Edwards (Dce) distance with equal weight, outperformed the others and was selected as the best approach. The final core collection (Cv-Dce30) comprised 30 entries (16.6% of genotypes). It recovered all SSR alleles and preserved parameter variations when compared to WHGC. Entries represented all six gene pools obtained from the population structure analysis of WHGC, further confirming the representativeness of Cv-Dce30. Our findings contribute towards improving the conservation and management of European hazelnut genetic resources and could be used to optimize future research by identifying a minimum number of accessions on which to focus.</p>
SNPs genotypes of Italian wild boar (Sus scrofa) populations
<p>Human activities can globally modify natural ecosystems determining ecological, demographic and range perturbations for several animal species. These changes can jeopardize native gene pools in different ways, leading either to genetic homogenization or, conversely, to the split into genetically divergent demes.</p> <p> </p> <p>In the past decades, most European wild boar (<i>Sus scrofa</i>) populations were heavily managed by humans. Anthropic manipulations have strongly affected also Italian populations through heavy hunting, translocations and reintroductions that might have deeply modified their original gene pools.</p> <p> </p> <p>In this study, exploiting the availability of the well-mapped porcine genome, we applied genomic tools to explore genome-wide variability in Italian wild boar populations, investigate their genetic structure and detect signatures of possible introgression from domestic pigs and non-native wild boar. Genomic data from 134 wild boar sampled in six areas of peninsular Italy and in Sardinia were gathered using the Illumina Porcine SNP60 Beadchip (60k Single Nucleotide Polymorphisms – SNPs) and compared with reference genotypes from European specimens and from domestic pigs (both commercial and Italian local breeds), using multivariate and maximum-likelihood approaches.</p> <p> </p> <p>Pairwise F<sub>ST</sub> values, multivariate analysis and assignment procedures indicated that Italian populations were highly differentiated from all the other analyzed European wild boar populations.</p> <p> </p> <p>Overall, a lower heterozygosity was found in the Italian population than in the other European regions. The most diverging populations in Castelporziano Presidential Estate and Maremma Regional Park can be the result of long-lasting isolation, reduced population size and genetic drift. Conversely, an unexpected similarity was found among Apennine populations, even at high distances. Signatures of introgression from both non-Italian wild boar and domestic breeds were very limited.</p> <p> </p> <p>To summarize, we successfully applied genome-wide procedures to explore, for the first time, the genomic diversity of Italian wild boar, demonstrating that they represent a strongly heterogeneous assemblage of demes with different demographic and manipulation histories. Nonetheless, our results suggest that a native component of genomic variation is predominant over exogenous ones in most populations.</p>
Data from: Genotyping-in-Thousands by sequencing of archival fish scales reveals maintenance of genetic variation following a severe demographic contraction in kokanee salmon
<p>Historical DNA analysis of archival samples has added new dimensions to population genetic studies, enabling spatiotemporal approaches for reconstructing population histories and informing conservation management. Here we tested the efficacy of Genotyping-in-Thousands by sequencing (GT-seq) for collecting targeted single nucleotide polymorphism (SNP) genotypic data from archival scale samples, and demonstrate its application to a study of kokanee salmon (<i>Oncorhynchus nerka</i>) in Kluane National Park and Reserve (KNPR; Yukon, Canada) that underwent a severe 12-year population decline followed by a rapid rebound. We genotyped archival scales sampled pre-crash and contemporary fin clips collected post-crash, revealing high coverage (>90% average genotyping across all individuals) and low genotyping error (<0.01% within-libraries, 0.60% among-libraries) despite the relatively poor quality of recovered DNA. We observed slight decreases in expected heterozygosity, allelic diversity, and effective population size post-crash, but none were significant, suggesting genetic diversity was retained despite the severe demographic contraction. Genotypic data also revealed the genetic distinctiveness of a now extirpated population just outside of KNPR, revealing biodiversity loss at the northern edge of the species distribution. More broadly, we demonstrate GT-seq as a valuable tool for genome-wide data collection from archival samples to address basic questions in ecology and evolution, and inform applied research in wildlife conservation and fisheries management.</p>
Genotype by environment interactions for chronic wasting disease in farmed U.S. white-tailed deer
<p>Despite the implementation of enhanced management practices, chronic wasting disease (CWD) in U.S. white-tailed deer (<em>Odocoileus virginianus</em>; hereafter WTD) continues to expand geographically. Herein, we perform the largest genome-wide association analysis (GWAA) to date for CWD (n = 412 CWD-positive; n = 758 CWD-non-detect) using a custom Affymetrix Axiom® single nucleotide polymorphism (SNP) array (n = 121,010 SNPs), and confirm that differential susceptibility to CWD is a highly heritable (h<sup>2</sup> = 0.611 ± 0.056) polygenic trait in farmed U.S. WTD, but with greater trait complexity than previously appreciated. We also confirm <em>PRNP</em> codon 96 (G96S) as having the largest effects on risk (<em>P</em> ≤ 3.19E-08; Phenotypic Variance Explained ≥ 0.025) across three U.S. regions (Northeast, Midwest, South). However, 20 CWD-positive WTD possessing codon 96SS genotypes were also observed, including one that was lymph node and obex positive. Beyond <em>PRNP</em>, we also detected 23 significant SNPs (<em>P</em>-value ≤ 5E-05) implicating ≥ 24 positional candidate genes; many of which have been directly implicated in Parkinson's, Alzheimer's, and prion diseases. Genotype-by-environment (GxE) interaction GWAA revealed a SNP in the lysosomal enzyme gene <em>ARSB</em> as having the most significant regional heterogeneity of effects on CWD (<em>P</em> ≤ 3.20E-06); with increasing copy number of the minor allele increasing susceptibility to CWD in the Northeast and Midwest; but with opposite effects in the South. In addition to <em>ARSB</em>, 38 significant GxE SNPs (<em>P</em>-value ≤ 5E-05) were also detected, thereby implicating ≥ 36 positional candidate genes; the majority of which have also been associated with aspects of Parkinson's, Alzheimer's, and prion diseases.</p>
Microsatellite genotypes for Gambusia marshi
<p>1. The valley of Cuatro Ciénegas in Coahuila, Mexico has the highest degree of local endemism of any habitat in North America. Despite the arid desert climate, the Cuatro Ciénegas basin harbors an extensive system of permanent streams, wetlands, and spring fed pools.</p> <p>2. Microsatellite loci were surveyed to infer genetic diversity and population structure of <i>Gambusia marshi</i>, a poeciliid fish endemic to the desert springs of the Cuatro Ciénegas basin and its outflow the Río Salado de Nadadores in Mexico.</p> <p>3. The Sierra de San Marcos and long-term isolation have played a vital role in shaping the current pattern of phylogeographic structure in<i> G. marshi</i>, and Bayesian clustering analysis revealed four genetic populations within <i>G. marshi</i> as well as a major east-west division of the of the species corresponding to the Sierra de San Marcos.</p> <p>4. Most sample sites exhibited high levels of genetic differentiation, although there is evidence for recent gene flow between some of these locations, presumably facilitated by irrigation canals. Although all populations exhibit genetic differentiation, the population of <i>G. marshi</i> in Poza Anteojo is extremely divergent and should be considered as an independent management unit.</p>
The genotypic data of elite European cultivar panel comprising 358 winter and 14 summer wheat varieties released from 1975 to 2007 at different marker densities
<p>This submission contains the genotpying data corresponding to the GABI-WHEAT and its subset TROST panel, at different densities i.e 35k, 90k for GABI-WHEAT and 135k for TROST panel. Additionally, the marker oligo sequences, envisioned to be used for mapping to wheat reference genome for obtaining marker phyical positions and thus assist genomic interoperability, are included. </p> <p>(35k, 135k and 90k are names given to markers originating from Affymetrix [Allen et al., 2017*; Muqaddasi et al., 2019, Muqaddasi et al., 2020**] and 90k iSELECT [Wang et al., 2014***] SNP array chips)</p> <p>*https://doi.org/10.1111/pbi.12635</p> <p>**https://doi.org/10.3835/plantgenome2018.05.0029</p> <p>***https://doi.org/10.1111/pbi.12183</p>
Supplementary material 1 from: Mojžišová M, Svobodová J, Kozubíková-Balcarová E, Štruncová E, Stift R, Bílý M, Kouba A, Petrusek A (2022) Long-term changes in the prevalence of the crayfish plague pathogen and its genotyping in invasive crayfish species in Czechia. NeoBiota 74: 105-127. https://doi.org/10.3897/neobiota.74.79087
Table S1
Microsatellite genotyping data for habitat-linked genetic structure for white-crowned sparrow (Zonotrichia leucophrys): local factors shape population genetic structure
<p>Ecological, environmental, and geographic factors all influence genetic structure. Species with broad distributions are ideal systems because they cover a range of ecological and environmental conditions allowing us to test which components predict genetic structure. This study presents a novel, broad geographic approach using molecular markers, morphology, and habitat modelling to investigate rangewide and local barriers causing contemporary genetic differentiation within the geographical range of three white-crowned sparrow (<i>Zonotrichia leucophrys</i>) subspecies: <i>Z. l. gambelii, Z. l. oriantha, </i>and <i>Z. l. pugetensis</i>. Three types of genetic markers showed geographic distance between sampling sites, elevation, and ecosystem type are key factors contributing to population genetic structure. Microsatellite markers revealed white-crowned<i> </i>sparrows<i> </i>do not group by subspecies, but instead indicated four groupings at a rangewide scale and two groupings based on coniferous and deciduous ecosystems at a local scale. Our analyses of morphological variation also revealed habitat differences; sparrows from deciduous ecosystems are larger than individuals from coniferous ecosystems based on principal component analyses. Habitat modeling showed isolation by distance was prevalent in describing genetic structure, but isolation by resistance also had a small but significant influence. Not only do these findings have implications concerning the accuracy of subspecies delineations, they also highlight the critical role of local factors such as habitat in shaping contemporary population genetic structure of species with high dispersal ability.</p>
Data from: Genotyping-in-Thousands by Sequencing panel development and application for high-resolution monitoring of introgressive hybridization within sockeye salmon
<p>Stocking programs have been widely implemented to re-establish extirpated fish species to their historical ranges; when employed in species with complex life histories, such management activities should include careful consideration of resulting hybridization dynamics with resident stocks and corresponding outcomes on recovery initiatives. Genetic monitoring can be instrumental for quantifying the extent of introgression over time, however, conventional markers typically have limited power for the identification of advanced hybrid classes, especially at the intra-specific level. Here, we demonstrate a workflow for developing, evaluating, and deploying a Genotyping-in-Thousands by Sequencing (GT-seq) SNP panel with the power to detect advanced hybrid classes to assess the extent and trajectory of intra-specific hybridization, using the sockeye salmon (<em>Oncorhynchus nerka)</em> stocking program in Skaha Lake, British Columbia, as a case study. Previous analyses detected significant levels of hybridization between the anadromous (sockeye) and freshwater resident (kokanee) forms of <em>O. nerka</em>, but were restricted to assigning individuals to pure-stock or "hybrid". Simulation analyses indicated our GT-seq panel had high accuracy, efficiency and power (> 94.5%) of assignment to pure-stock sockeye salmon/kokanee, F<sub>1</sub>, F<sub>2</sub>, and B<sub>2</sub> backcross-sockeye/kokanee. Re-analysis of 2016/2017 spawners previously analyzed using TaqMan<span> </span>assays and otolith microchemistry revealed shifts in assignment of some hybrids to adjacent pure-stock or B<sub>2</sub>-backcross classes, while new assignment of 2019 spawners revealed hybrids comprised 31% of the population, ~74% of which were B<sub>2</sub>-backcross or F<sub>2</sub>. Overall, the GT-seq panel development workflow presented here could be applied to virtually any system where genetic stock identification and intra-specific hybridization are important management parameters.</p>
Genotype by sequencing data from CHPRRU2, a panel of 282 maize inbred lines.
<p>Genotype by sequencing data from CHPRRU2, a panel of 282 maize inbred lines.</p>
Rocky Mountain Brook Trout harvest project genotypes
<p>Sustainable management of exploited populations benefits from integrating demographic and genetic considerations into assessments, as both play a role in determining harvest yields and population persistence. This is especially important in populations subject to size-selective harvest, because size selective harvesting has the potential to result in significant demographic, life-history, and genetic changes. We investigated harvest-induced changes in the effective number of breeders ( ) for introduced brook trout populations (<em>Salvelinus fontinalis</em>) in alpine lakes from western Canada. Three populations were subject to three years of size-selective harvesting, while three control populations experienced no harvest. The decreased consistently across all harvested populations (on average 60.8%) but fluctuated in control populations. There were no consistent changes in between control or harvest populations, but one harvest population experienced a decrease in of 63.2%. The / ratio increased consistently across harvest lakes; however we found no evidence of genetic compensation (where variance in reproductive success decreases at lower abundance) based on changes in family evenness ( ) and the number of full-sibling families ( ). We found no relationship between and or between / and . We posit that change in was buffered by constraints on breeding habitat prior to harvest, such that the same number of breeding sites were occupied before and after harvest. These results suggest that effective size in harvested populations may be resilient to considerable changes in Nc in the short-term, but it is still important to monitor exploited populations to assess the risk of inbreeding and ensure their long-term survival.</p>
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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.
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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.