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423 results for “Haplotypes”
Fig. 4 Haplotype networks for ITS2 in Cryptic species of Notophyllum (Polychaeta: Phyllodocidae) in Scandinavian waters
Fig. 4 Haplotype networks for ITS2. (A, B) Notophyllum foliosum. (C, D) N. crypticum n. sp. For further explanations, see Figure 3 10 4 5 3 8 9 B T 6 7 2 T 1 B
Fig. 3 Haplotypic networks for the studied histone H1 in Estimating range disjunction time of the Palearctic Admirals (Limenitis L.) with COI and histone H1 genes
Fig. 3 Haplotypic networks for the studied histone H1 gene (a–c) and COI fragment (d) of L. camilla (a–b) and L. helmanni (c–d) from the eastern and western parts of their ranges; b shows representation of combinations of histone H1 gene haplotypic variants in individuals of L. camilla
Fig. 9 Single gene trees and haplotype networks. a, b in Two new bioluminescent Henlea from Siberia and lack of molecular support for Hepatogaster (Annelida, Clitellata, Enchytraeidae)
Fig. 9 Single gene trees and haplotype networks. a, b Gene-trees (a COI, b H3) estimated with Bayesian coalescent analysis in BEAST. Numbers above branches are posterior probabilities. Scales show expected numbers of substitution per site. The specimen shaded in red has a conflict between morphology and COI data. c, d Statistical parsimony
Fig. 2 in Novel haplotypes of the COI-COII mtDNA region in the dark forest bee, Apis mellifera mellifera L., 1758
Fig. 2. The pattern of the P element sequence (54 bp) and the Q element (Q1, Q2, and Q3) sequences (197, 195, 195 bp, respectively) of the COICOII intergenic region of haplotypes M4 and M4' in Apis mellifera mellifera bees from Siberia. Nucleotide substitutions are highlighted, deletions are indicated by a dash and highlighted. Рис. 2. Структура P-Элемента (54 п.н.) и Q-Элементов (Q1, Q2 и Q3) (197, 195, 195 п.н., соответственно) межгенной области COI-COII мтДНК (гаплотипы M4 и M4') у пчел Apis mellifera mellifera сибирских популЯций. Нуклеотидные Замены выделены цветом, делеции обоЗначены тире и выделены цветом.
Fig. 1 in Novel haplotypes of the COI-COII mtDNA region in the dark forest bee, Apis mellifera mellifera L., 1758
Fig. 1. The map of localization of areas in Siberia (the Tomsk Region, the Krasnoyarsk Krai, the Altai Krai) and apiaries (dots 1–20), where a dark forest bee is identified. The distribution of COI-COII mtDNA locus variants (PQQ and PQQQ) in Apis mellifera mellifera bees from Siberian apiaries and their frequency in three regions of Siberia are presented on the right side of the figure. Рис. 1. Карта регионов Сибири (ТомскаЯ область, КрасноЯрский край, Алтайский край) и локалиЗации пасек (точки 1–20) на территории Сибири, где выЯвлена темнаЯ леснаЯ пчела. Распределение вариантов локуса COI-COII мтДНК (PQQ и PQQQ) у темных лесных пчел на пасеках и их частота в трех регионах Сибири представлены в правой части рисунка.
FIGURE 3. Haplotypes network from rpl32 in Molecular and cytogenetic confirmation of the hybrid origin of Jacobaea ×mirabilis (Asteraceae, Senecioneae), with nomenclatural notes on this name
FIGURE 3. Haplotypes network from rpl32-trnL region in Jacobaea. Each circle corresponds to a haplotype and circles' size is proportional to haplotype frequency (from n=1 to n=5). Small white circles represent single mutational steps.
FIGURE 3. TCS haplotype network obtained for 521 in Mitochondrial DNA-based reassessment of Antennablennius Fowler (Blenniidae: Salariini) from the north-western Indian Ocean, with resurrection of A. persicus (Regan)
FIGURE 3. TCS haplotype network obtained for 521 bp fragment of mitochondrial COI of the genus Antennablennius. Numbers between haplotypes represent mutational steps between them.
FIGURE 3. Haplotype network showing relationships among ITS haplotypes between Lepra amaroides, L. pseudosubventosa and L. subventosa s in New species and records of lichens from Bolivia
FIGURE 3. Haplotype network showing relationships among ITS haplotypes between Lepra amaroides, L. pseudosubventosa and L. subventosa s.str. Sizes of circles are proportional to the number of specimens per haplotype. Chemotypes are described below specimen's data. Numbers in brackets near lines between haplotypes represent number of mutational steps.
FIGURE 4. TCS haplotype network inferred from ITS-2 in The polyphasic approach revealed new species of Chloroidium (Trebouxiophyceae, Chlorophyta)
FIGURE 4. TCS haplotype network inferred from ITS-2 rDNA sequences of Chloroidium saccharophilum. This network was inferred using the algorithm described by Clement et al. (2002). Sequence nodes corresponding to samples collected from different geographical region and from different habitats.
FIGURE 5. TCS haplotype network inferred from ITS-2 in The polyphasic approach revealed new species of Chloroidium (Trebouxiophyceae, Chlorophyta)
FIGURE 5. TCS haplotype network inferred from ITS-2 rDNA sequences of Chloroidium ellipsoideum and C. lichenum. This network was inferred using the algorithm described by Clement et al. (2002). Sequence nodes corresponding to samples collected from different geographical region and from different habitats.
Complete sequences of six major histocompatibility complex haplotypes rev2
<p>Sequences that the analysis in the paper <a title="Complete sequences of six major histocompatibility complex haplotypes, including all the major MHC class II structures" href="https://doi.org/10.1111/tan.15020" target="_blank" rel="noopener">Houwaart et. al. 2023</a> was based on</p>
FIGURE 3. Statistical parsimony haplotype network constructed from 621 in Description of two new species of Rhamphus related to R. oxyacanthae (Curculionidae, Curculioninae, Rhamphini) from Italy based on a morphological study supported by molecular data
FIGURE 3. Statistical parsimony haplotype network constructed from 621 bp of the mtCOI gene of Rhamphus bavierai n. sp. (GenBank accession number MW879286- MW879303). Circle sizes are proportional to haplotype frequency (for details see supplementary Table S1). Numbers in brackets above/beside the solid broken line represent the number of mutations connecting mitochondrial lineages.
FIGURE 2. Statistical parsimony haplotype network constructed from 621 in Description of two new species of Rhamphus related to R. oxyacanthae (Curculionidae, Curculioninae, Rhamphini) from Italy based on a morphological study supported by molecular data
FIGURE 2. Statistical parsimony haplotype network constructed from 621 bp of the mtCOI gene of Rhamphus oxyacanthae in Italy (GenBank accession number MW879276- MW879285). Circles sizes are proportional to haplotype frequency (for details see supplementary S1).
Haplotype genome data for InfoGenomeR
<p>Reference genomes and haplotype directed-acyclic graphs (DAGs) used for InfoGenomeR.</p> <p> </p>
FIGURE 20. Haplotype Group 18 in COI haplotype groups in Mesocriconema (Nematoda: Criconematidae) and their morphospecies associations
FIGURE 20. Haplotype Group 18 (A, B, C, D, E, F, G, H, I, J, K, L). Specimens conforming to morphospecies Mesocriconema curvatum. Adult females=A–L.
FIGURE 18. Haplotype Group 17 in COI haplotype groups in Mesocriconema (Nematoda: Criconematidae) and their morphospecies associations
FIGURE 18. Haplotype Group 17 (A, B, C, D, E, F, G, H, I, J, K, L, M, N, O). Specimens conforming to morphospecies Mesocriconema inaratum. Adult females=A–E, G–O. Juvenile=F. Specimens G,O=from type locality. SEM images of specimens from Nine-mile Prairie, NE.
FIGURE 4. Haplotype Groups 1 in COI haplotype groups in Mesocriconema (Nematoda: Criconematidae) and their morphospecies associations
FIGURE 4. Haplotype Groups 1 (G, H, I, J, K, L, M) and 15 (A, B, C, D, E, F). Specimens conforming to morphospecies Mesocriconema ornatum. Location data for NID numbers are in Table 1. Adult females=A, B, C, D, E, H, L, M. Juveniles=F, G, I, J, K. Specimens for SEM images I, J, K were from a peach orchard in Alabama
FIGURE 14. Haplotype Groups 10 in COI haplotype groups in Mesocriconema (Nematoda: Criconematidae) and their morphospecies associations
FIGURE 14. Haplotype Groups 10 (A, B, C, D, E, F) and 11 (G, H, I, J, K). Specimens conforming to morphospecies Mesocriconema xenoplax. Juvenile=A, Adult females=B–K. SEM images of specimens from a peach orchard in Georgia.
Data from: Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize
<p><span><span><span><span><span><span><span><span><span><span><span>Genomic prediction typically relies on associations between single-site polymorphisms and traits of interest. This representation of genomic variability has been successful for prediction within populations. However, it usually cannot capture the complex effects due to combination of alleles in haplotypes. Therefore, accuracy across populations has usually been low. Here we present a novel and cost-effective method for imputing <i>cis</i> haplotype associated RNA expression (HARE, RNA expression of genes by haplotype), studied their transferability across tissues, and evaluated genomic prediction models within and across populations. HARE focuses on tightly linked <i>cis</i> acting causal variants in the immediate vicinity of the gene, while excluding <i>trans</i> effects from diffusion and metabolism, so it would be more transferrable across different tissues and populations. We showed that HARE estimates captured one-third of the variation in gene expression and were more transferable across diverse tissues than the measured transcript expression. HARE estimates were used in genomic prediction models evaluated within and across two diverse maize panels – a diverse association panel (Goodman Association panel) and a large half-sib panel (Nested Association Mapping panel) – for predicting 26 complex traits. HARE resulted in up to 15% higher prediction accuracy than control approaches that preserved haplotype structure, suggesting that HARE carried functional information in addition to information about haplotype structure. The largest increase was observed when the model was trained in the Nested Association Mapping panel and tested in the Goodman Association panel. Additionally, HARE yielded higher within-population prediction accuracy as compared to measured expression values. The accuracy achieved by measured expression was variable across tissues whereas accuracy using HARE was more stable across tissues. Therefore, imputing RNA expression of genes by haplotype is stable, cost-effective, and transferable across populations.</span></span></span></span></span></span></span></span></span></span></span></p>
Figure 1. Haplotype network derived from 704 in Repeated sampling adds to the genetic diversity of Lepidochelys olivacea (Eschscholtz 1829) olive ridley sea turtle
Figure 1. Haplotype network derived from 704 bp mitochondrial D-loop fragment. Circle sizes are proportional to the frequency of each haplotype. The black circles are hypothetical haplotypes not sampled. Each colour represents the ocean basin where the sample was taken: blue is Pacific Ocean, yellow is Indian Ocean, red is Atlantic Ocean, and green is Indo-Pacific Ocean.
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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.