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62 results for “microsatellite DNA”
Data from: Noninvasive individual and species identification of jaguars (Panthera onca), pumas (Puma concolor) and ocelots (Leopardus pardalis) in Belize, Central America using cross-species microsatellites and fecal DNA
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Data from: Genetic diversity and population structure of three traditional horse breeds of Bhutan based on 29 DNA microsatellite markers
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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 ...
Figure 5 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Figure 5 - Simplified network of Bactrocera carambolae and Bactrocera dorsalis groups, and the sequential disconnection of the network. The network was constructed using eight SSRs. Scanning was done for decreasing thresholds A is the fully connected network B is the percolation threshold (Dp = 0.20, with all links corresponding to distances superior to Dp excluded). DP, JK, and NT are connecting between Bactrocera carambolae and Bactrocera dorsalis groups. Red dashed lines with number are corresponded to the threshold values, revealing serial disconnection of the network C is the lowest threshold (thr = 0.15).
Figure 4 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Figure 4 - Simplified network of seven Bactrocera carambolae populations, and the sequential forms of cluster. The network was constructed using eight SSRs. Scanning was done for decreasing thresholds A is the fully connected network B is the percolation threshold (Dp = 0.52, with all links corresponding to distances superior to Dp excluded). JK plays an important role connecting between native and introduced populations C–D are the lower thresholds chosen (thr = 0.40 and 0.15, respectively) to reveal sub-structured network.
Figure 3 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Figure 3 - The individual admixture plot for K = 3. Each bar reveals a single individual. Each color of bars represents each genetic cluster. Samples of Bactrocera carambolae belong to clusters 2 and 3 (green and blue, respectively) while samples of Bactrocera dorsalis belong to cluster 1 (red). Potential hybrids have a proportion of genetic cluster (Q) between 0.100 to 0.900 (0.100 ≤ Q ≤ 0.900) as identified with asterisk (*).
Figure 1 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Figure 1 - Sampling collections of Bactrocera carambolae and Bactrocera dorsalis in this study. Seven populations of Bactrocera carambolae (blue dots) were collected from Southeast Asia and Suriname. Three populations of Bactrocera dorsalis (red dots) were sampled from East and Southeast Asia. Two other unidentified populations (purple dots) were included. Information for each population is described in Table 1.
Figure 6 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Figure 6 - Simplified network of the SY5 strain and wild populations, and the sequential disconnection of the network. The network was constructed using seven SSRs. Scanning was done for decreasing thresholds A is the fully connected network B is the percolation threshold (Dp = 0.23, with all links corresponding to distances superior to Dp excluded). DP, JK, and NT are connecting between Bactrocera carambolae and Bactrocera dorsalis groups C is the lowest threshold (thr = 0.15). Red dashed lines with number are corresponded to the threshold values, revealing serial disconnection of the network.
Figure 2 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Figure 2 - Three-dimensional plot of Principal Coordinate Analysis (PCoA) and STRUCTURE analysis. A the planes of the first three principal coordinates explain 43.65%, 20.13%, and 16.91% of total genetic variation, respectively, for seven Bactrocera carambolae populations using eight SSRs B the planes of the first three principal coordinates explain 33.05%, 23.17%, and 15.87%, respectively, for Bactrocera carambolae and Bactrocera dorsalis groups using eight SSRs C the planes of the first three principal coordinates explain 30.50%, 22.14%, and 18.53%, respectively, for the SY5 strain and wild populations using seven SSRs. Pie graphs, consisting of different colored sections, represent co-ancestor distribution of 185, 289, and 321 individuals in A two, B three, and C two hypothetical clusters, respectively.
Spotted turtle dispersal microsatellite DNA sex and site data
<p>Sex-biased dispersal is common in many animals, with male-biased dispersal often found in studies of mammals and reptiles, including interpretations of spatial genetic structure, ostensibly as a result of male-male competition and a lack of male parental care. Few studies of sex-biased dispersal have been conducted in turtles, but a handful of studies, in saltwater turtles and in terrestrial turtles, have detected male-biased dispersal as expected. We tested for sex-biased dispersal in the endangered freshwater turtle, the spotted turtle (<em>Clemmys</em> <em>guttata</em>) by investigating fine-scale genetic spatial structure of males and females. We found significant spatial genetic structure in both sexes, but the patterns mimicked each other. Both males and females typically had higher than expected relatedness at distances < 25 km, and in many distance classes greater than 25 km, less than expected relatedness. Similar patterns were apparent whether we used only loci in Hardy-Weinberg equilibrium (n = 7) or also included loci with potential null alleles (n = 5). We conclude that, contrary to expectations, sex-biased dispersal is not occurring in this species, possibly related to the reverse sexual dimorphism in this species, with females having brighter colors. We did, however, detect significant spatial genetic structure in males and females, separate and combined, showing philopatry within a genetic patch size of < 25 km in <em>C</em>. <em>guttata</em>, which is concerning for an endangered species whose populations are often separated by distances greater than the genetic patch size.</p>
Data from: High-throughput microsatellite genotyping in ecology: improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA
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Data from: High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries
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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
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Data from: SSR_pipeline: a bioinformatic infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data
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Spotted turtle dispersal microsatellite DNA sex and site data
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Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage [RNA-seq]
GEO Series GSE140615. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Zscan4 binds nucleosomal microsatellite DNA and protects mouse two-cell embryos from DNA damage
GEO Series GSE140621. Mus musculus. 25 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
T a b l e 7 in Molecular Characterization Of Lates Niloticus (Perciformes, Latidae) Populations From Three Nigerian Waterbodies Using Random Amplified Polymorphic Dna And Microsatellite Markers
T a b l e 7. Conformity to Hardy-Weinberg equilibrium
Study of HRO761 Alone or in Combination in Cancer Patients With Specific DNA Alterations Called Microsatellite Instability or Mismatch Repair Deficiency.
ClinicalTrials.gov study NCT05838768. IPD Sharing: NO. Countries: 15. Publications: 0.
Ladder-like multimerization of FoxP3 enables microsatellite recognition and DNA bridging
GEO Series GSE243606. Mus musculus. 48 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
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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.