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4,566 results for “marker”
Data from: Genetic diversity, linkage disequilibrium and selection signatures in Chinese and Western pigs revealed by genome-wide SNP markers
To investigate population structure, linkage disequilibrium (LD) pattern and selection signature at the genome level in Chinese and Western pigs, we genotyped 304 unrelated animals from 18 diverse populations using porcine 60 K SNP chips. We confirmed the divergent evolution between Chinese and Western pigs and showed distinct topological structures of the tested populations. We acquired the evidence for the introgression of Western pigs into two Chinese pig breeds. Analysis of runs of homozygosity revealed that historical inbreeding reduced genetic variability in several Chinese breeds. We found that intrapopulation LD extents are roughly comparable between Chinese and Western pigs. However, interpopulation LD is much longer in Western pigs compared with Chinese pigs with average r20.3 values of 125 kb for Western pigs and only 10.5 kb for Chinese pigs. The finding indicates that higher-density markers are required to capture LD with causal variants in genome-wide association studies and genomic selection on Chinese pigs. Further, we looked across the genome to identify candidate loci under selection using FST outlier tests on two contrast samples: Tibetan pigs versus lowland pigs and belted pigs against non-belted pigs. Interestingly, we highlighted several genes including ADAMTS12, SIM1 and NOS1 that show signatures of natural selection in Tibetan pigs and are likely important for genetic adaptation to high altitude. Comparison of our findings with previous reports indicates that the underlying genetic basis for high-altitude adaptation in Tibetan pigs, Tibetan peoples and yaks is likely distinct from one another. Moreover, we identified the strongest signal of directional selection at the EDNRB loci in Chinese belted pigs, supporting EDNRB as a promising candidate gene for the white belt coat color in Chinese pigs. Altogether, our findings advance the understanding of the genome biology of Chinese and Western pigs.
Data from: Transcriptome characterization and screening of molecular markers in ecologically important Himalayan species (Rhododendron arboreum)
Rhododendron arboreum is an ecologically prominent species, which also lends commercial and medicinal benefits in the form of palatable juices and useful herbal drugs. Local abundance and survival of the species under a highly fluctuating climate make it an ideal model for genetic structure and functional analysis. However, a lack of genomic data has hampered additional research. In the present study, cDNA libraries from floral and foliar tissues of the species were sequenced to provide a foundation for understanding the functional aspects of the genome and to construct an enriched repository that will promote genomics studies in the genera. Illumina's platform facilitated the generation of ∼100 million high-quality paired-end reads. De novo assembly, clustering, and filtering out of shorter transcripts predicted 113 167 non-redundant transcripts with an average length of 1164.6 bases. Of these, 71 961 transcripts were categorized based on functional annotations in the Gene Ontology database, whereby 5710 were grouped into 141 pathways and 23 746 encoded for different transcription factors. Transcriptome screening further identified 35 419 microsatellite regions, of which, 43 polymorphic loci were characterized on 30 genotypes. Seven hundred and nineteen transcripts had 811 high-quality single-nucleotide polymorphic variants with a minimum coverage of 10, a total score of 20, and SNP% of 50.
Data from: Genetic population structure of the round whitefish (Prosopium cylindraceum) in North America: multiple markers reveal glacial refugia and regional subdivision.
Round whitefish (Prosopium cylindraceum) have a broad, disjunct range across northern North America and Eurasia, and little is known about their genetic population structure. We performed genetic analyses of round whitefish from 17 sites across its range using nine microsatellites, two mitochondrial DNA (mtDNA) loci, and 4918 to 8835 single-nucleotide polymorphism (SNP) loci. Our analyses identified deep phylogenetic division between eastern and western portions of the range, likely indicative of origins from at least two separate Pleistocene glacial refugia. Regionally, microsatellites and SNPs identified congruent patterns in subdivision, and population structure was consistent with expectations based on hydrologic connectivity. Within the Laurentian Great Lakes, Lake Huron and Lake Ontario were identified as key areas of interest. Lake Huron appears to be a contemporary source population for several other Great Lakes, and Lake Ontario contains a genetically discrete group of round whitefish. In all cases, multiple genetic markers yielded similar patterns, but SNPs offered substantially enhanced resolution. We conclude that round whitefish have population subdivision on several scales important for understanding their evolutionary history and conservation planning.
Data from: Genome-wide markers reveal a complex evolutionary history involving divergence and introgression in the Abert's squirrel (Sciurus aberti) species group
Background: Genetic introgression between divergent lineages is now considered more common than previously appreciated, with potentially important consequences for adaptation and speciation. Introgression is often asymmetric between populations and patterns can vary for different types of loci (nuclear vs. organellar), complicating phylogeographic reconstruction. The taxonomy of the ecologically specialized Abert's squirrel species group has been controversial, and previous studies based on mitochondrial data have not fully resolved the evolutionary relationships among populations. Moreover, while these studies identified potential areas of secondary contact between divergent lineages, the possibility for introgression has not been tested. Results: We used RAD-seq to unravel the complex evolutionary history of the Abert's squirrel species group. Although some of our findings reinforce inferences based on mitochondrial data, we also find significant areas of discordance. Discordant signals generally arise from previously undetected introgression between divergent populations that differentially affected variation at mitochondrial and nuclear loci. Most notably, our results support earlier claims (disputed by mitochondrial data) that S. aberti kaibabensis, found only on the north rim of the Grand Canyon, is highly divergent from other populations. However, we also detected introgression of S. aberti kaibabensis DNA into other S. aberti populations, which likely accounts for the previously inferred close genetic relationship between this population and those south of the Grand Canyon. Conclusions: Overall, the evolutionary history of Abert's squirrels appears to be shaped largely by divergence during periods of habitat isolation. However, we also found evidence for interbreeding during periods of secondary contact resulting in introgression, with variable effects on mitochondrial and nuclear markers. Our results support the emerging view that populations often diversify under scenarios involving both divergence in isolation and gene flow during secondary contact, and highlight the value of genome-wide datasets for resolving such complex evolutionary histories.
Activation markers plotted against nutrient sensors in CD4+ and CD8+ T-cells.
<p>Activation markers (CD69, CD25, CD71, and CD38) plotted against nutrient sensors (GLUT1, GLUT4, HK1, HK2, and CD36) in CD4+ T-cells.</p>
FIGURE 8 in Resolving the phylogenetic affinities of Kappaphycus inermis within the genus Kappaphycus (Gigartinales, Solieriaceae) using mitochondrial and plastid markers
FIGURE 8. Phylogenetic tree hypothesized from ML analysis of the genus Kappaphycus based on RuBisCo spacer gene sequences. Numbers above branches correspond to BI probability values and ML bootsrap percent values.
FIGURE 7 in Resolving the phylogenetic affinities of Kappaphycus inermis within the genus Kappaphycus (Gigartinales, Solieriaceae) using mitochondrial and plastid markers
FIGURE 7. Phylogenetic tree hypothesized from ML analysis of the genus Kappaphycus based rbcL gene sequences. Numbers above branches correspond to BI probability values and ML bootsrap percent values.
FIGURE 6 in Resolving the phylogenetic affinities of Kappaphycus inermis within the genus Kappaphycus (Gigartinales, Solieriaceae) using mitochondrial and plastid markers
FIGURE 6. Phylogenetic tree hypothesized from ML analysis of the genus Kappaphycus based on cox2–3 spacer gene sequences. Numbers above branches correspond to BI probability values and ML bootsrap percent values.
FIGURE 5 in Resolving the phylogenetic affinities of Kappaphycus inermis within the genus Kappaphycus (Gigartinales, Solieriaceae) using mitochondrial and plastid markers
FIGURE 5. Phylogenetic tree hypothesized from ML analysis of the genus Kappaphycus based on cox1 gene sequences. Numbers above branches correspond to BI probability values and ML bootsrap percent values.
FIGURES 1–4 in Resolving the phylogenetic affinities of Kappaphycus inermis within the genus Kappaphycus (Gigartinales, Solieriaceae) using mitochondrial and plastid markers
FIGURES 1–4. Morphology of K. inermis. 1. Gross habit of K. inermis specimen, AOL616. Scale = 1 cm. The arrow indicates the presence of crustose holdfast. 2. Cross section of near apical tip showing medium and uniformly sized central medullary cells (arrow), AOL616. Scale = 125 µm. 3. Gross habit of a female K. inermis specimen, AOL538. Scale = 3 cm. 4. A portion of an inflated apical branch tip showing the location of cystocarps (arrows), AOL538. Scale= 1 cm.
Figure 3 in A review on deep molluscan phylogeny: old markers, integrative approaches, persistent problems
Figure 3. Molluscan class tree based on rRNA-dominated multilocus markers (five-gene nucleotide analysis published by Stöger et al. 2013; 17 lophotrochozoan outgroup and 125 molluscan species, MAFFT alignment masked using ALISCORE; ML analysis was performed with RAxML v. 7.2.8 under the GTRCAT model of evolution and 1000 bootstraps, respectively with MrBayes v. 3.1.2). Support values are indicated above branches (first value is bootstrap support, second value is posterior probability). Molluscan classes are in bold.
Figure 1 in A review on deep molluscan phylogeny: old markers, integrative approaches, persistent problems
Figure 1. Major competing hypotheses on molluscan phylogeny and evolution. Left: Consensus tree from phylogenomics according to Telford and Budd (2011) and Kocot (2013), showing a basal split into Aculifera and Conchifera, and Monoplacophora sister to Cephalopoda; suggesting that worm-like body constructions of aplacophorans are secondary simplifications of a more complex ancestor (Scheltema 1993). Right: Morphocladistic tree from Haszprunar (2000), showing basal paraphyletic aplacophorans, monophyletic Testaria and Conchifera with basal Monoplacophora, implying progressive evolution from worm-molluscs to shell plate-bearing chitons and towards molluscs with true shell (Salvini-Plawen 2006). The taxon Serialia (Giribet et al. 2006) is incompatible with traditional Testaria, Aculifera and Conchifera concepts.
Figure 2 in A review on deep molluscan phylogeny: old markers, integrative approaches, persistent problems
Figure 2. Collapsed molluscan phylogenetic tree based on mitochondrial genomic nucleotide sequence data (analysis published by Stöger and Schrödl 2013; 13 protein mt genes analysed as nucleotides; 16 lophotrochozoan outgroup and 96 molluscan species; alignment masked using GBlocks with less stringent options; ML analysis was performed with RAxML v. 7.2.8 under the GTRCAT model of evolution and 500 bootstraps). Support values are indicated above branches; molluscan groups are in bold and indicated with black triangles.
Figure 3 in Localization and transcription patterns of LsVasa, a molecular marker of germ cells in Lepeophtheirus salmonis (Krøyer)
Figure 3. Localization of Lepeophtheirus salmonis Vasa (LsVasa) transcripts. (A) Light microscopy of sexually mature adult female with eggstrings attached. Most of the eggstrings extending from the genital segment have been cropped from the image. The position of various tissues is indicated: ∗ (ovaries), × (oocytes in the genital segment). Subcuticular tissue is found under the cuticula of most of the lice. The area used for in situ hybridization is indicated (+). Scale bar represents 5 mm. (B–F) In situ hybridization using an LsVasa-specific antisense RNA probe showing positive staining as dark colour. Small inserts illustrate corresponding locations in negative controls (using a LsVasa-sense RNA probe). (B) The two ovaries (Ov) of mature adult females. LsVasa transcripts are localized throughout the ovary including both proximal and the more distal zones. Scale bar represents 200 µm. (C) LsVasa is present in immature oocytes in the oviduct (ovd, scale bar 50 µm) as well as in mature oocytes in the unfertilized eggstring (D, scale bar 200 µm). LsVasa is also present in the gonads of earlier developmental stages (E, ovaries of preadult females, scale bar 200 µm) and in adult male testes (F, scale bar 100 µm).
Figure 2 in Localization and transcription patterns of LsVasa, a molecular marker of germ cells in Lepeophtheirus salmonis (Krøyer)
Figure 2. Ontogenic analysis of Lepeophtheirus salmonis Vasa (LsVasa) transcript levels. LsVasa transcripts levels were determined by the use of quantitative reverse transcription-polymerase chain reaction at different developmental stages. Levels were quantified relative to the level found in the nauplius stage. Error bars show 95% confidence intervals calculated from the ΔΔCT values from each dilution.
Figure 1 in Localization and transcription patterns of LsVasa, a molecular marker of germ cells in Lepeophtheirus salmonis (Krøyer)
Figure 1. Domain structure and copy number of Lepeophtheirus salmonis Vasa (LsVasa). (A) LsVasa with position of conserved protein domains. Position of DEAD box helicase core motifs (reviewed by Hilbert et al. 2009) are indicated with Roman numerals: (I) Motif I, (II) Motif Ia, (III) GG doublet, (IV) Motif Ib, (V) Motif II, (VI) Motif III, (VII) Motif IV, (VIII) QxxR, (IX) Motif V and (X) Motif VI. Triangles indicate the position of the three introns. (B) Southern blot using LsVasa as a probe. Genomic DNA was digested with XhoI (lane 1), PstI (lane 2), ClaI (lane 3), KpnI (lane 4), SacI (lane 5) and XbaI (lane 6) and electrophoresed together with a DNA marker (M).
Figure 8 in Discovery of new species of New Caledonian Arsipoda Erichson, 1842 (Coleoptera: Chrysomelidae) and insights on their ecology and evolution using DNA markers
Figure 8. Diet molecular phylogenetic inference for Arsipoda spp. Synthetic trees showing the phylogenetic placement of trnL(UAA) sequences obtained from (A, C) Arsipoda isola Samuelson and (B) Arsipoda geographica Gómez-Zurita sp. nov. (see main text for details).
Figure 6 in Discovery of new species of New Caledonian Arsipoda Erichson, 1842 (Coleoptera: Chrysomelidae) and insights on their ecology and evolution using DNA markers
Figure 6. Aedeagus (dorsal, lateral and ventral views) of Arsipoda geographica Gómez-Zurita sp. nov.
Figure 3 in Discovery of new species of New Caledonian Arsipoda Erichson, 1842 (Coleoptera: Chrysomelidae) and insights on their ecology and evolution using DNA markers
Figure 3. Spermathecae of (A) Arsipoda agalma Samuelson and of (B) Arsipoda geographica Gómez-Zurita sp. nov.
Figure 4 in Discovery of new species of New Caledonian Arsipoda Erichson, 1842 (Coleoptera: Chrysomelidae) and insights on their ecology and evolution using DNA markers
Figure 4. (A) Holotype of Arsipoda geographica Gómez-Zurita sp. nov. (male). (B) Holotype of Arsipoda rostrata Gómez-Zurita sp. nov. (male). Scale bar = 1 mm.
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.