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172 results for “DNA markers”
Data from: Predominant east to west colonisations across major oceanic barriers: insights into the phylogeographic history of the hydroid superfamily Plumularioidea, suggested by a mitochondrial DNA barcoding marker
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Data from: Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach
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Data from: Measuring population differentiation using GST or D? A simulation study with microsatellite DNA markers under a finite island model and nonequilibrium conditions
Genetic differentiation of populations is a key question in population genetic investigations. Wright's FST (and its relatives such as GST) has been a standard measure of differentiation. However, the deficiencies of these indexes and their significance have been increasing realized in recent years, leading to some new measures being proposed, such as Jost's (2008) D. This has also stimulated some considerable debate which, in certain sense, makes empirical biologists even more confused, for example, on statistics which should be used for estimating population differentiation. Here we report a simulation study with neutral microsatellite DNA loci under a finite island model to compare the performance of GST and D, under non-equilibrium conditions, in particular. Our results suggest that there exist fundamental differences between the two statistics and neither GST nor D operate satisfactorily in all situations for quantifying differentiation. D is very sensitive to mutation models but GST noticeably less so ...
Supplementary material 2 from: Sildever S, Laas P, Kolesova N, Lips I, Lips U, Nagai S (2021) Plankton biodiversity and species co-occurrence based on environmental DNA – a multiple marker study. Metabarcoding and Metagenomics 5: e72371. https://doi.org/10.3897/mbmg.5.72371
Supplementary tables
Supplementary material 1 from: Sildever S, Laas P, Kolesova N, Lips I, Lips U, Nagai S (2021) Plankton biodiversity and species co-occurrence based on environmental DNA – a multiple marker study. Metabarcoding and Metagenomics 5: e72371. https://doi.org/10.3897/mbmg.5.72371
Supplementary figures
Supplementary material 1 from: Leite BR, Vieira PE, Troncoso JS, Costa FO (2021) Comparing species detection success between molecular markers in DNA metabarcoding of coastal macroinvertebrates. Metabarcoding and Metagenomics 5: e70063. https://doi.org/10.3897/mbmg.5.70063
Table S1, Figures S1–S5
Supplementary material 2 from: Leite BR, Vieira PE, Troncoso JS, Costa FO (2021) Comparing species detection success between molecular markers in DNA metabarcoding of coastal macroinvertebrates. Metabarcoding and Metagenomics 5: e70063. https://doi.org/10.3897/mbmg.5.70063
Tables S2, S3
Figures 3-4 from: Li X-M, Bai X-L, Ren G-D (2018) A new species of the genus Blaptogonia from the Himalayas with four DNA markers (Coleoptera, Tenebrionidae, Blaptini). ZooKeys 773: 69-78. https://doi.org/10.3897/zookeys.773.24656
Figures 3-4 Habitus of Blaptogonia zhentanga sp. n. 3.male, holotype, 12.2 mm 4 female, paratype, 13.5 mm.
Figure 2 from: Li X-M, Bai X-L, Ren G-D (2018) A new species of the genus Blaptogonia from the Himalayas with four DNA markers (Coleoptera, Tenebrionidae, Blaptini). ZooKeys 773: 69-78. https://doi.org/10.3897/zookeys.773.24656
Figure 2 Characters of Blaptogonia zhentanga sp. n. a–g male: a pronotum b antenna c1–c3 pro-, meso, metatibia d1–d3 pro-, meso-, metatarsus e1–e3 aedeagus in dorsal, ventral, and lateral view f spiculum astrale g. abdominal sternite VIII h–i female: h Speculum ventrale in ventral view i1–i2 ovipositor in dorsal and ventral view.
Figure 2 in Investigation of the effect of silymarin on oxidative DNA damage and inflammatory markers in ischemia/reperfusion injury following experimental testicular torsion/detorsion in rats
Figure 2. Testicular tissue, control group, negative Tnf-α expression (A). T 3 h / D 3 h group: very severe Tnf-α expression in the perivascular and intertubular intervals (arrowheads) (B). T 3 h / D 24 h group: severe Tnf-α expression in the perivascular and intertubular intervals (arrowheads) (C). T 3 h / D 3 h + silymarin group: medium level Tnf-α expression in the perivascular and intertubular intervals (arrowheads) (D). T 3 h / D 24 h + silymarin group: mild Tnf-α expression in the perivascular and intertubular intervals (arrowheads) (E). IHC-P, bar: 50 µm.
Figure 1 in Investigation of the effect of silymarin on oxidative DNA damage and inflammatory markers in ischemia/reperfusion injury following experimental testicular torsion/detorsion in rats
Figure 1. Testicular tissue, control group, normal histological view (A). T 3 h / D 3 h group: necrosis in spermatocytes (arrowheads); severe congestion in intertubular intervals (thick arrows); hemorrhage, thinning in the tubulus wall (B). T 3 h / D 24 h: necrosis in spermatocytes (arrowheads); severe edema in the intertubular space (stars); thinning of the tubulus wall (C). T 3 h / D 3 h + silymarin group: moderate edema in the intertubular intervals (star); congestion (thick arrow) (D). T 3 h / D 24 h + silymarin group: mild edema at intertubular intervals (star) (E); H and E, bar: 50 µm.
Figure 3 in Investigation of the effect of silymarin on oxidative DNA damage and inflammatory markers in ischemia/reperfusion injury following experimental testicular torsion/detorsion in rats
Figure 3. Testicular tissue, control group, negative 8-OHdG expression (A). T 3 h / D 3 h group: severe cytoplasmic 8-OHdG expression in spermatocytes (arrowheads) (B). T 3 h / D 24 h group: severe cytoplasmic 8-OHdG expression in spermatocytes (arrowheads) (C). T 3 h / D 3 h + silymarin group: moderate cytoplasmic 8-OHdG expression in spermatocytes (arrowheads) (D). T 3 h / D 24 h + silymarin group: mild cytoplasmic 8-OHdG expression in spermatocytes (E), IHC-P, bar: 50 µm.
Data from: ALG11 – a new variable DNA marker for sponge phylogeny: comparison of phylogenetic performances with the 18S rDNA and the COI gene
Phylogenetic relationships within sponge classes are highly debated. The low phylogenetic signal observed with some current molecular data can be attributed to the use of few markers, usually slowly-evolving, such as the nuclear rDNA genes and the mitochondrial COI gene. In this study, we conducted a bioinformatics search for a new molecular marker. We sought a marker that (1) is likely to have no paralogs; (2) evolves under a fast evolutionary rate; (3) is part of a continuous exonic region; and (4) is flanked by conserved regions. Our search suggested the nuclear ALG11 as a potential suitable marker. We next demonstrated that this marker can indeed be used for solving phylogenetic relationships within sponges. Specifically, we successfully amplified the ALG11 gene from DNA samples of representatives from all four sponge classes as well as from several cnidarian classes. We also amplified the 18S rDNA and the COI gene for these species. Finally, we analyzed the phylogenetic performance of ALG11 to solve sponge relationships compared to and in combination with the nuclear 18S rDNA and the COI mtDNA genes. Interestingly, the ALG11 marker seems to be superior to the widely-used COI marker. Our work thus indicates that the ALG11 marker is a relevant marker which can complement and corroborate the phylogenetic inferences observed with nuclear ribosomal genes. This marker is also expected to contribute to resolving evolutionary relationships of other apparently slow-evolving animal phyla, such as cnidarians.
Figure 7 in Discovery of new species of New Caledonian Arsipoda Erichson, 1842 (Coleoptera: Chrysomelidae) and insights on their ecology and evolution using DNA markers
Figure 7. Aedeagus dorsal, lateral and ventral views of Arsipoda rostrata Gómez-Zurita sp. nov.
Figure 5 in Discovery of new species of New Caledonian Arsipoda Erichson, 1842 (Coleoptera: Chrysomelidae) and insights on their ecology and evolution using DNA markers
Figure 5. Pronotum of Arsipoda geographica Gómez-Zurita sp. nov.
Figure 2 in Diet of the black rat (Rattus rattus) in a Canary laurel forest: species identification based on morphological markers and DNA sequences
Figure 2. Seed of Rubus bollei/palmensis found intact in rat dropping.
Figure 2 from: Ballardini M, Mercuri A, Littardi C, Abbas S, Couderc M, Ludeña B, Pintaud J (2013) The chloroplast DNA locus psbZ-trnfM as a potential barcode marker in Phoenix L. (Arecaceae). ZooKeys 365: 71-82. https://doi.org/10.3897/zookeys.365.5725
Figure 2 - Structure and variation of the minisatellite in the trnG-trnfM intergenic spacer. The repeats of the two mutational motifs (1 and 2) are indicated above the sequence alignment of the 7 haplotypes recorded. The pattern of inverted repeats generated by the two motifs and their reverse complements (RC) is shown below the alignment. See Table 1 for haplotype distribution among species.
Figure 1 from: Ballardini M, Mercuri A, Littardi C, Abbas S, Couderc M, Ludeña B, Pintaud J (2013) The chloroplast DNA locus psbZ-trnfM as a potential barcode marker in Phoenix L. (Arecaceae). ZooKeys 365: 71-82. https://doi.org/10.3897/zookeys.365.5725
Figure 1 - The sequenced cpDNA psbZ-trnfM region.The location of PCR primers used and polymorphisms found in this study are shown. DNA fragment length refers to the Phoenix dactylifera cv. Khalas cpDNA sequence (Yang et al. 2010), characterised by a 4-repetitions minisatellite haplotype (NCBI Reference Sequence: NC_013991.2).
Figure 2 from: Arriaga-Jiménez A, Roy L (2015) Co1 DNA supports conspecificity of Geomyphilus pierai and G. barrerai (Coleoptera, Scarabaeidae, Aphodiinae) and is a good marker for their phylogeographic investigation in Mexican mountains. ZooKeys 512: 77-88. https://doi.org/10.3897/zookeys.512.9646
Figure 2 - Example of the biotopes where the pocket gophers' burrows were dug: a scrubland in Malinche b grassland in Sierra Negra c pocket gopher nest at 50 cm depth d pocket gopher nest at more than 1.6 m depth.
Figure 5 from: Arriaga-Jiménez A, Roy L (2015) Co1 DNA supports conspecificity of Geomyphilus pierai and G. barrerai (Coleoptera, Scarabaeidae, Aphodiinae) and is a good marker for their phylogeographic investigation in Mexican mountains. ZooKeys 512: 77-88. https://doi.org/10.3897/zookeys.512.9646
Figure 5 - The size of the circles is proportional to the haplotype frequency. The length of links between haplotypes is proportional to the number of mutated positions. The median vectors that represent hypothetical intermediates or unsampled haplotypes are shown in small open dots. The haplotype circles' color corresponds to the sampling origin (one color per mountain).
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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.