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700 results for “molecular identification”
FIGURE 3 in Morphological and molecular identification of specimens in the genus Euseius (Acari: Phytoseiidae) from the Republic of Congo
FIGURE 3. Results of Hierarchical Ascending Classification on the Principal Component Analysis are shown. Clusters correspond to those in figure 2.
FIGURE 5 in Morphological and molecular identification of specimens in the genus Euseius (Acari: Phytoseiidae) from the Republic of Congo
FIGURE 5. Strict Bayesian consensus tree obtained with the combined molecular data sets (12S rRNA and ITSS) including three species Euseius sp., Euseius fustis and outgroup species Typhlodromus pyri. Two main clades within the genus Euseius are emphasised. The numbers below branches indicate the posterior probability values.
FIGURE 1 in Morphological and molecular identification of specimens in the genus Euseius (Acari: Phytoseiidae) from the Republic of Congo
FIGURE 1. Sampling locations of different populations of species considered in this study: Euseius sp. (Site 1, 2, 3 and, 4) and Euseius fustis (Site 1, 2 and, 3).
FIGURE 4 in Morphological and molecular identification of specimens in the genus Euseius (Acari: Phytoseiidae) from the Republic of Congo
FIGURE 4. Genetic distances between and within Euseius sp., Euseius fustis and outgroup species Typhlodromus pyri for the two molecular markers used 12S rRNA (a) and ITSS (b).
Data from: Friends and Family: a software program for identification of unrelated individuals from molecular marker data. And from: Genetic diversity, relatedness and inbreeding of ranched and fragmented Cape buffalo populations in southern Africa
The identification of related and unrelated individuals from molecular marker data is often difficult, particularly when no pedigree information is available and the data set is large. High levels of relatedness or inbreeding can influence genotype frequencies and thus genetic marker evaluation, as well as the accurate inference of hidden genetic structure. Identification of related and unrelated individuals is also important in breeding programmes, to inform decisions about breeding pairs and translocations. We present Friends and Family, a Windows executable program with a graphical user interface that identifies unrelated individuals from a pairwise relatedness matrix or table generated in programs such as COANCESTRY and GenAlEx. Friends and Family outputs a list of samples that are all unrelated to each other, based on a user-defined relatedness cut-off value. This unrelated data set can be used in downstream analyses, such as marker evaluation or inference of genetic structure. The results can be compared to that of the full data set to determine the effect related individuals have on the analyses. We demonstrate one of the applications of the program: how the removal of related individuals altered the Hardy-Weinberg equilibrium test outcome for microsatellite markers in an empirical data set. Friends and Family can be obtained from https://github.com/DeondeJager/Friends-and-Family.
FIGURE 1 in Pseudococcidae (Hemiptera: Coccomorpha) in Uruguay: morphological identification and molecular characterization, with descriptions of two new species
FIGURE 1. Mealybug species collected in Uruguay. A. Pseudococcus longispinus, B. Ps. viburni, C. Ps. scatoterrae, D. Ps. pabulum, E. Ps. sociabilis, F. Planococcus citri, G. Pl. ficus, H. Ferrisia cristinae, I. F. meridionalis, J. Phenacoccus peruvianus, K. Ph. madeirensis, L. Saccharicoccus sacchari. Photographs by VCPS
Data from: High-throughput molecular identification of fish eggs using multiplex suspension bead arrays
The location and abundance of fish eggs provide information concerning the timing and location of spawning activities and can provide fishery-independent estimates of spawning biomass. However, the full value of egg and larval surveys is severely restricted because many species' eggs and larvae are morphologically similar, making species-level identification difficult. Recent efforts have shown that nearly all species of fish may be identified by mitochondrial DNA (mtDNA) sequences (e.g., via "DNA barcoding"). By taking advantage of a DNA barcode database, we have developed oligonucleotide probes for 23 marine fish species that produce pelagic eggs commonly found in California waters. Probes were coupled to fluorescent microspheres to create a suspension bead array. Biotin-labeled primers were used to amplify the mitochondrial cytochrome oxidase subunit I (COI) and 16S ribosomal rRNA genes from individual fish eggs. The amplicons were then hybridized to the bead array and after addition of a reporter fluorophore, samples were analyzed by flow cytometry with Luminex 100 instrumentation. Probes specifically targeted eggs that are abundant and/or from morphologically indistinguishable species pairs. Results showed the 33 different probes designed for this study accurately identified all samples when PCR was successful. Suspension bead arrays have a number of benefits over other methods of molecular identification; these arrays permit high multiplexing, simple addition of new probes, high throughput, and lower cost than DNA sequencing. The increasing availability of DNA barcode data for numerous fish faunas worldwide suggests bead arrays could be developed and widely used for fish egg, larval and tissue identifications.
Data from: Identification of Swedish mosquitoes based on molecular barcoding of the COI gene and SNP analysis
Mosquito-borne infectious diseases are emerging in many regions of the world. Consequently, surveillance of mosquitoes and concomitant infectious agents is of great importance for prediction and prevention of mosquito-borne infectious diseases. Currently, morphological identification of mosquitoes is the traditional procedure. However, sequencing of specified genes or standard genomic regions, DNA barcoding, has recently been suggested as a global standard for identification and classification of many different species. Our aim was to develop a genetic method to identify mosquitoes and to study their relationship. Mosquitoes were captured at collection sites in northern Sweden and identified morphologically before the cytochrome c oxidase subunit I (COI) gene sequences of 14 of the most common mosquito species were determined. The sequences obtained were then used for phylogenetic placement, for validation and benchmarking of phenetic classifications, and finally to develop a hierarchical PCR-based typing scheme based on single nucleotide polymorphism sites (SNPs) to enable rapid genetic identification, circumventing the need for morphological characterization. The results showed that exact phylogenetic relationships between mosquito taxa were preserved at shorter evolutionary distances, but at deeper levels they could not be inferred with confidence by using COI gene sequence data alone. Fourteen of the most common mosquito species in Sweden were identified by the SNP/PCR-based typing scheme, demonstrating that genetic typing using SNPs of the COI gene is a useful method for identification of mosquitoes with potential for worldwide application.
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.
FIGURES 5–9. Bemisia afer. 5 in Morphological and molecular identification of all developmental stages of four whitefly species (Hemiptera: Aleyrodidae) commonly intercepted in quarantine
FIGURES 5–9. Bemisia afer. 5, ovum on Laurus nobilis from Italy; 6, first instar on L. nobilis from Italy; 7, second instar on L. nobilis from Italy; 8, third instar on L. nobilis from Italy; 9, fourth instar on Manihot esculenta from Mauritius.
FIGURE 48 in Morphological and molecular identification of all developmental stages of four whitefly species (Hemiptera: Aleyrodidae) commonly intercepted in quarantine
FIGURE 48. CO1 sequence alignments showing sequence polymorphisms between species in the annealing sites of primers and probes. Mismatches are shown in bold, forward primer, probe and reverse primer annealing sites are boxed, left to right respectively.
FIGURES 39–47. Trialeurodes vaporariorum. 39 in Morphological and molecular identification of all developmental stages of four whitefly species (Hemiptera: Aleyrodidae) commonly intercepted in quarantine
FIGURES 39–47. Trialeurodes vaporariorum. 39, third instar on E. pulcherrima from Italy; 40, fourth instar on E. pulcherrima from Italy; 41, diagrammatic representation of left compound eye of adult female; 42, upper and lower compound eyes separate; 43, mesotibia combs; 44, male abdomen with dorsal discoidal pores; 45, female antenna; 46, aedeagus; 47, female cement gland.
FIGURES 31–38. Trialeurodes spp. 31, T in Morphological and molecular identification of all developmental stages of four whitefly species (Hemiptera: Aleyrodidae) commonly intercepted in quarantine
FIGURES 31–38. Trialeurodes spp. 31, T. ricini, diagrammatic representation of left compound eye of adult female; T. ricini, 32, upper and lower compound eyes linked by two to four ommatidia; T. ricini, 33, male antenna; T. ricini, 34, aedeagus; T. ricini, 35, female cement gland; 36, T. vaporariorum, ovum on Euphorbia pulcherrima from Italy; 37, T. vaporariorum, first instar on E. pulcherrima from the UK; 38, T. vaporariorum, second instar on E. pulcherrima from Italy.
FIGURES 3–4 in Morphological and molecular identification of all developmental stages of four whitefly species (Hemiptera: Aleyrodidae) commonly intercepted in quarantine
FIGURES 3–4. General morphology of a whitefly. 3, third-larval instar; 4, fourth-larval instar (puparium).
FIGURES 25–30. Trialeurodes ricini. 25 in Morphological and molecular identification of all developmental stages of four whitefly species (Hemiptera: Aleyrodidae) commonly intercepted in quarantine
FIGURES 25–30. Trialeurodes ricini. 25, ovum on Ricinus communis from Gran Canaria; 26, first instar on R. communis from Gran Canaria; 27, second instar on R. communis from Gran Canaria; 28, third instar on R. communis from Gran Canaria; 29–30, fourth instar on Telfairia sp. from Nigeria showing variation in submarginal tubercles.
FIGURES 18–24. B. tabaci. 18 in Morphological and molecular identification of all developmental stages of four whitefly species (Hemiptera: Aleyrodidae) commonly intercepted in quarantine
FIGURES 18–24. B. tabaci. 18, third instar on E. pulcherrima; 19, fourth instar on E. pulcherrima; 20, diagrammatic representation of left compound eye of adult female; 21, upper and lower compound eyes linked by one ommatidium; 22, female antenna; 23, aedeagus; 24, female cement gland.
FIGURES 10–17. Bemisia spp. 10, B in Morphological and molecular identification of all developmental stages of four whitefly species (Hemiptera: Aleyrodidae) commonly intercepted in quarantine
FIGURES 10–17. Bemisia spp. 10, B. afer, diagrammatic representation of left compound eye of adult female; B. afer, 11, upper and lower compound eyes linked by one ommatidium; B. afer, 12, female antenna; B. afer, 13, aedeagus; B. afer, 14, female cement gland; 15, B. tabaci, ovum on Euphorbia pulcherrima; 16, B. tabaci, first larval instar on Solidago from Spain; 17, B. tabaci, second instar on E. pulcherrima.
FIGURE 6 in Molecular and morphological identification of pistachio armored scale insects (Hemiptera: Diaspididae), with description of a new species
FIGURE 6. Fifty percent majority rule consensus tree resulting from Bayesian analysis of the COI dataset. Numbers above branches are posterior probability and likelihood as well as parsimony bootstrap values, respectively. Values <50 % are not shown.
FIGURE 5 in Molecular and morphological identification of pistachio armored scale insects (Hemiptera: Diaspididae), with description of a new species
FIGURE 5. Second-instar female of Suturaspis davatchi Balachowsky & Kaussari, illustration by Hosseininaveh.
FIGURE 4 in Molecular and morphological identification of pistachio armored scale insects (Hemiptera: Diaspididae), with description of a new species
FIGURE 4. Adult female of Suturaspis davatchi Balachowsky & Kaussari, illustration by Hosseininaveh.
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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)
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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.