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Data from: Multiplexed microsatellite markers for genetic studies of beech
European beech (Fagus sylvatica L.) is one of the economically most important broadleaved tree species in Europe and has become a model for studying climate change effects. Multiplex PCR of microsatellites is a fast and cost-effective technique allowing high throughput genotyping. Here we present the procedure used to develop two multiplex kits (8-plexes) for European beech. We paid particular attention to quality control throughout all steps of the multiplex kits development (null allele detection, error rate measurements, linkage disequilibrium). Preliminary assays suggest that the multiplex kits amplify 16 loci largely devoid of null alleles and allow rapid and cost-effective genotyping of beech with low error rates. The two kits, which differ in their levels of polymorphism, most likely due to marker origin, were also informative in seven other beech species tested.
Data from: Musculoskeletal pain as a marker of health quality. Findings from the epidemiological sleep study among the adult population of São Paulo city
Background: We are witnessing the growth of urban populations, particularly in the developing world. São Paulo, the largest city in South America, continues to grow, and this growth is dramatically effecting the environment and human health. The aim of this study was to estimate the point prevalence of chronic pain in São Paulo city dwellers and to explore the influence of aspects related to urbanicity. Methods: A two-stage cluster randomized sample included 1100 individuals of the city of Sao Paulo, representing the population proportionally in terms of gender, age and social classes in 2007. For this observational cross-sectional study, the household sample was interviewed using validated questionnaires for sociodemographic aspects, the Beck inventories for anxiety and depression, the WHOQoL-REF for quality of life, the Chalder Fatigue Scale. Musculoskeletal pain was defined as diffuse pain or pain located in the back, joints or limbs. Data regarding sleep complaints and polysomnography were obtained from the Epidemiologic Sleep Study conducted in São Paulo city in 2007. Results: The prevalence estimate of chronic musculoskeletal pain was approximately 27%, with a female/male ratio of approximately 2.6/1. The predictors were being in the age-range of 30–39 years, low socioeconomic and schooling levels, obesity, sedentarism, fatigue, non-restorative sleep, daytime sleepiness, poor sleep quality, poor life quality, anxiety and depression symptoms. Psychological wellbeing was the main discriminator between responders with chronic musculoskeletal pain and the controls, followed by depression for the participants with poor psychological wellbeing, and fatigue, for the remaining ones. Insomnia syndrome was the third-level discriminator for those with fatigue, whereas sleep quality for those without fatigue. Conclusions: Musculoskeletal pain was frequently reported by São Paulo city dwellers and its correlates with psychological and sleep aspects are suggestive of a response to urbanicity. Trial Registration: ClinicalTrials.gov NCT00596713
Data from: Evolutionary factors affecting the cross-species utility of newly developed microsatellite markers in seabirds
Microsatellite loci are ideal for testing hypotheses relating to genetic segregation at fine spatio-temporal scales. They are also conserved among closely related species, making them potentially useful for clarifying interspecific relationships between recently diverged taxa. However, mutations at primer binding sites may lead to increased nonamplification, or disruptions that may result in decreased polymorphism in nontarget species. Furthermore, high mutation rates and constraints on allele size may also with evolutionary time, promote an increase in convergently evolved allele size classes, biasing measures of interspecific genetic differentiation. Here, we used next-generation sequencing to develop microsatellite markers from a shotgun genome sequence of the sub-Antarctic seabird, the thin-billed prion (Pachyptila belcheri), that we tested for cross-species amplification in other Pachyptila and related sub-Antarctic species. We found that heterozygosity decreased and the proportion of nonamplifying loci increased with phylogenetic distance from the target species. Surprisingly, we found that species trees estimated from interspecific FST provided better approximations of mtDNA relationships among the studied species than those estimated using DC, even though FST was more affected by null alleles. We observed a significantly nonlinear second order polynomial relationship between microsatellite and mtDNA distances. We propose that the loss of linearity with increasing mtDNA distance stems from an increasing proportion of homoplastic allele size classes that are identical in state, but not identical by descent. Therefore, despite high cross-species amplification success and high polymorphism among the closely related Pachyptila species, we caution against the use of microsatellites in phylogenetic inference among distantly related taxa.
Data from: Recurrent hybridisation events between Primula vulgaris, P. veris and P. elatior (Primulaceae, Ericales) challenge the species boundaries: Using molecular markers to re‐evaluate morphological identifications
Three Primula species, Primula vulgaris, P. veris and P. elatior, have been objects of fascination for gardeners and botanists over several centuries. The species are able to hybridise, and where they co-occur, hybrids are commonly found. In Denmark, Møns Klint on the island of Møn and Købelev Skov on Lolland are examples of localities where all three species occur and where the hybrids P. ×digenea, the hybrid between P. vulgaris and P. elatior, and P. ×polyantha, the hybrid between P. veris and P. vulgaris, can also be found. To investigate relations between the species and their hybrids, 168 specimens from 10 geographical locations were sampled for genetic analysis using DNA markers and identified based on morphological traits, primarily inflorescense structure, the size, shape, colour and markings of corolla and leaf basis, leaf blade texture and hairiness. After identifying species-specific SNPs in the internal transcribed spacer sequence, these were used to resolve species and hybrid boundaries and status through a cleaved amplified polymorphic sequence assay. Polymorphisms in the chloroplast trnL sequence were used as a high-throughput marker and used to determine the maternal parent of hybrids. Ten simple sequence repeat markers were applied to obtain further insight into the genetic makeup of the accessions using Structure and Introgress, providing information of genetic variability within and between populations. Data analyses indicated that backcrossing of P. ×digenea hybrids with parental species has occurred, and that many of the P. ×digenea found in the study were later-generation hybrids rather than F1s. Analyses of P. ×polyantha specimens show mostly the expected pattern for primary hybrids but indications of P. veris ancestry of a P. vulgaris plant was discovered. Our results further indicate that some of the specimens initially identified as P. elatior include P. vulgaris among their progenitors and thus challenge currently accepted species boundaries.
FIGURE 4 in Nuclear markers support the mitochondrial phylogeny of Vipera ursinii – renardi complex (Squamata: Viperidae) and species status for the Greek meadow viper
FIGURE 4. Species tree of the Vipera ursinii–renardi complex (with V. berus as outgroup) as inferred in *BEAST based on two mitochondrial and three nuclear loci (A); species-tree cloudogram of the complex based on 27 000 post-burn-in trees resulting from 3 runs of *BEAST, each producing 10,000 trees from which 10% was discarded as burn-in. Higher colour densities represent higher levels of certainty. Maximum clade credibility tree is superimposed upon the cloudogram in bold violet (B). Values of posterior probabilities are given. This figure is published in colour in the online version, the colours of the branches correspond with the colour of mitochondrial lineages in Fig. 2A.
FIGURE 1 in Nuclear markers support the mitochondrial phylogeny of Vipera ursinii – renardi complex (Squamata: Viperidae) and species status for the Greek meadow viper
FIGURE 1. Sampled localities inside the approximate distribution area of Vipera ursinii–renardi complex in Europe. Circles indicate sampling localities of Vipera ursinii–renardi complex, and triangles show the sampling of outgroup taxa. A diamond indicates the type locality of Vipera graeca stat. nov. This figure is published in colour in the online version, the colour of the patches corresponds to the colour of mitochondrial lineages in Fig. 2A.
FIGURE 2 in Nuclear markers support the mitochondrial phylogeny of Vipera ursinii – renardi complex (Squamata: Viperidae) and species status for the Greek meadow viper
FIGURE 2. (A) Current mitochondrial Bayesian phylogenetic hypothesis of Vipera ursinii–renardi complex based on CYT B dataset of Ferchaud et al. (2012) and Zinenko et al. (2015); (B) Phylogenetic reconstruction of the concatenated dataset (mtDNA+nDNA genes) obtained in MrBayes/Maximum likelihood (see Table 1). Sequences of Vipera berus (Vbbe-HU, Vbbo-AL, Vbni-RO) included as outgroup are not shown. Bayesian posterior probabilities/bootstrap pseudoreplicates are shown at nodes; (C) SplitsTree phylogenetic network (Huson & Bryant 2006) of the dataset for five mitochondrial and nuclear loci sequenced in the present study using the neighbornet algorithm. Asterisks in Fig. 2C indicate both phased sequences in one branch. Numbers along the edges are the bootstrap support values from 1000 replicates. The scale bar indicates one substitution per one hundred nucleotide positions. Taxon names of the phylogenetic network correspond with the Table 1. Inset shows a male Greek Meadow Viper from Dhëmbel Mountains, Albania.
FIGURE 3 in Nuclear markers support the mitochondrial phylogeny of Vipera ursinii – renardi complex (Squamata: Viperidae) and species status for the Greek meadow viper
FIGURE 3. Nuclear allele networks of the three analysed nuclear loci. Circle sizes are proportional to the number of samples/ sequences, small black circles indicate hypothetical haplotypes (alleles). This figure is published in colour in the online version, the colour of the circles in the network corresponds to the colour of mitochondrial lineages in Fig. 2A.
FIGURE 8 in Description of a new Notocomplana species (Platyhelminthes: Acotylea), new combination and new records of Polycladida from the northeastern Sea of Japan, with a comparison of two different barcoding markers
FIGURE 8. Baysian phylogenetic tree based on concatenated COI and 16S sequences (1142 bp in total). Numbers near nodes are the posterior probability and bootstrap values, respectively.
FIGURE 6 in Description of a new Notocomplana species (Platyhelminthes: Acotylea), new combination and new records of Polycladida from the northeastern Sea of Japan, with a comparison of two different barcoding markers
FIGURE 6. Notocomplana septentrionalis (Kato, 1937). A. Dorsal view in the living state, ICHUM5292 (non-type). B. Ventral view in the living state, ICHUM5292 (non-type). C. Eyespots in the living state, ICHUM5292 (non-type). D. Sagittal section of the male copulatory apparatus, anterior to the right, ICHUM5292 (non-type). E. Cross section of the male copulatory apparatus, ICHUM5295 (non-type). F. Weakly folded epithelium of the male atrium, ICHUM5291 (non-type). G. Extensively folded epithelium of the male atrium, ICHUM5294 (non-type). H. Sagittal section of the female copulatory apparatus, anterior to the right, ICHUM5292 (non-type). Abbreviations: cec, cerebral eye cluster; cg, cement glands; cov, common oviduct; exc, extra-vesicular gland's canal, fg, female gonopore; ied, intra-prostatic ejaculatory duct; ld, Lang's duct; lv, Lang's vesicle; ma, male atrium; mg, male gonopore; ov, oviduct; ped, post-prostatic ejaculatory duct; ph, pharynx; pp, penis papilla; pv, prostatic vesicle; sv, seminal vesicle; tec, tentacular eye cluster; v, vagina.
FIGURE 5 in Description of a new Notocomplana species (Platyhelminthes: Acotylea), new combination and new records of Polycladida from the northeastern Sea of Japan, with a comparison of two different barcoding markers
FIGURE 5. Notocomplana koreana (Kato, 1937). A. Dorsal view in the living state, ICHUM5281 (non-type). B. Ventral view in the living state, ICHUM5281 (non-type). C. Eyespots in the living state, ICHUM5278 (non-type). D. Sagittal section of the male copulatory apparatus, anterior to the right, ICHUM5278 (non-type). E. Cross section of the male copulatory apparatus, ICHUM5279 (non-type). F. Sagittal section of the female copulatory apparatus, anterior to the right, ICHUM5278 (non-type). Abbreviations: cec, cerebral eye cluster; cov, common oviduct; fg, female gonopore; ied, intra-prostatic ejaculatory duct; ld, Lang's duct; lv, Lang's vesicle; ma, male atrium; mg, male gonopore; ov, oviduct; ped, post-prostatic ejaculatory duct; ph, pharynx; pp, penis papilla; pv, prostatic vesicle; sd, sperm duct; sv, seminal vesicle; tec, tentacular eye cluster; v, vagina.
FIGURE 4. Diagrams showing the copulatory complex. A in Description of a new Notocomplana species (Platyhelminthes: Acotylea), new combination and new records of Polycladida from the northeastern Sea of Japan, with a comparison of two different barcoding markers
FIGURE 4. Diagrams showing the copulatory complex. A. Notocomplana japonica (Kato, 1937) comb. nov. B. Notocomplana koreana (Kato, 1937). C. Notocomplana septentrionalis (Kato, 1937). All anterior to the right. Abbreviations: cov, common oviduct; csd, common sperm duct; fg, female gonopore; ied, intra-prostatic ejaculatory duct; ld, Lang's duct; lv, Lang's vesicle; ma, male atrium; mg, male gonopore; ov, oviduct; ped, post-prostatic ejaculatory duct; pp, penis papilla; pv, prostatic vesicle; sd, sperm duct; sv, seminal vesicle; v, vagina.
FIGURE 3 in Description of a new Notocomplana species (Platyhelminthes: Acotylea), new combination and new records of Polycladida from the northeastern Sea of Japan, with a comparison of two different barcoding markers
FIGURE 3. Notocomplana japonica (Kato, 1937) comb. nov. A. Dorsal view in the living state, ICHUM5282 (non-type). B. Ventral view in the living state, ICHUM5282 (non-type). C. Eyespots in the living state, ICHUM5282 (non-type). D. Sagittal section of the male copulatory apparatus, anterior to the right, ICHUM5282 (non-type). E. Cross section of the male copulatory apparatus, ICHUM5286 (non-type). F. Sagittal section of female copulatory apparatus, anterior to the right, ICHUM5282 (nontype). Abbreviations: cec, cerebral eye cluster; cov, common oviduct; fg, female gonopore; ied, intra-prostatic ejaculatory duct; ld, Lang's duct; lv, Lang's vesicle; ma, male atrium; mg, male gonopore; ped, post-prostatic ejaculatory duct; ph, pharynx; pp, penis papilla; pv, prostatic vesicle; sv, seminal vesicle; tec, tentacular eye cluster; v, vagina.
FIGURE 2 in Description of a new Notocomplana species (Platyhelminthes: Acotylea), new combination and new records of Polycladida from the northeastern Sea of Japan, with a comparison of two different barcoding markers
FIGURE 2. Notocomplana hagiyai sp. nov. Diagram of the copulatory complex, anterior to the right. Abbreviations: cov, common oviduct; exc, extra-vesicular gland's canal; fg, female gonopore; ied, intra-prostatic ejaculatory duct; ld, Lang's duct; lv, Lang's vesicle; ma, male atrium; mg, male gonopore; ov, oviduct; ped, post-prostatic ejaculatory duct; pp, penis papilla; pv, prostatic vesicle; sd, sperm duct; sv, seminal vesicle; v, vagina.
FIGURE 1 in Description of a new Notocomplana species (Platyhelminthes: Acotylea), new combination and new records of Polycladida from the northeastern Sea of Japan, with a comparison of two different barcoding markers
FIGURE 1. Notocomplana hagiyai sp. nov. A. Dorsal view in the living state, ICHUM5267 (holotype). B. Ventral view in the living state, ICHUM5267 (holotype). C. Eyespots in the living state, ICHUM5267 (holotype). D. Sagittal section through the male copulatory apparatus, anterior to the right, ICHUM5267 (holotype). E. Cross section through the male copulatory apparatus, ICHUM5272 (paratype). F. Sagittal section through the female copulatory apparatus, anterior to the right, ICHUM5267 (holotype). Abbreviations: cec, cerebral eye cluster; cov, common oviduct; exc, extra-vesicular gland's canal; fg, female gonopore; ied, intra-prostatic ejaculatory duct; ld, Lang's duct; lv, Lang's vesicle; ma, male atrium; mg, male gonopore; ped, post-prostatic ejaculatory duct; ph, pharynx; pp, penis papilla; pv, prostatic vesicle; sd, sperm duct; sv, seminal vesicle; tec, tentacular eye cluster; v, vagina.
Dataset for Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas, All SNP markers
<p>Dataset for Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas. All SNP markers were included in the dataset. U designates a missing datapoint. The data was not inputed.</p>
Dataset for Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas with data for 330 markers
<p>Dataset for Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas with data for 330 markers. This dataset is associated with the dissertation entitled, Quantitative Trait Loci Associated with Lodging, Stem Strength, Yield, and Other Important Agronomic Traits in Dry Field Peas.</p>
Artificial Light at Night weakens body condition but does not negatively affect physiological markers of health in great tits.
Open the record for dataset details and reuse information.
Conserved genetic markers reveal widespread diatom reproduction in the global ocean
<p>Datasets associated with the study "Conserved genetic markers reveal widespread diatom reproduction in the global ocean" (post second revision, V3)</p>
Cryo-electron microscopy images of thin, vitreous biological samples with gold fiducial markers
<div> <p lang="EN-US"><span lang="EN-US"><span>Set of images compiled from EMPIAR </span><span>and </span><span>the </span><span>CryoET</span><span> Data Portal </span><span>with</span><span> corresponding segmentations of gold fiducial markers.</span></span><span> </span></p> </div> <div> <p lang="EN-US"><span lang="EN-US"><span>All images have been rescaled to a pixel size of 8 Å/</span><span>px</span></span><span> </span></p> </div> <div> <p lang="EN-US"><span lang="EN-US"><span>Annotations performed manually using </span><span>napari</span><span>.</span></span><span> </span></p> </div> <div> <p lang="EN-US"><span lang="EN-US"><span>EMPIAR-10009 - Cryo-electron tomography of an C1-IgG complex</span></span><span><span> </span><br></span><span lang="EN-US"><span>EMPIAR-10046 - Mouse 5-HT3 receptors in lipid vesicles</span></span><span><span> </span><br></span><span lang="EN-US"><span>EMPIAR-10164 - immature HIV-1 </span><span>dMACANC</span><span> VLPs</span></span><span><span> </span><br></span><span lang="EN-US"><span>EMPIAR-10304 - Improved applicability and robustness of fast cryo-electron</span></span><span><span> </span><br></span><span lang="EN-US"><span>tomography data acquisition<br></span></span><span lang="EN-US"><span>EMPIAR-10364 - E. coli minicells (collected with a volta phase plate)</span></span><span><span> </span><br></span><span lang="EN-US"><span>EMPIAR-10453 - SARS-CoV-2</span></span><span><span> </span><br></span><span lang="EN-US"><span>EMPIAR-10631 - fungal membrane-assembled </span><span>retromer:Grd</span><span>19 coat </span><span>containing</span><span> Kex2</span></span><span><span> </span><br></span><span lang="EN-US"><span>cargo motif</span></span><span><span> </span><br></span><span lang="EN-US"><span>EMPIAR-10814 - mouse DRG axons</span></span><span><span> </span><br></span><span lang="EN-US"><span>DS-10431 - Plasma membranes isolated by unroofing</span></span><span> </span></p> </div>
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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.