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44 results for “Microsatellite Diversity”
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: Genotypic diversity and differentiation among populations of two benthic freshwater diatoms as revealed by microsatellites
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Data from: Rapid microsatellite marker development for African mahogany (Khaya senegalensis, Meliaceae) using next-generation sequencing and assessment of its intra-specific genetic diversity.
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Microsatellite markers for assessing genetic diversity and kinship relationships in one of the largest South American fur seal (Arctocephalus australis) populations of the Pacific Ocean
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Data from: Microsatellite analyses across three diverse vertebrate transcriptomes (Acipenser fulvescens, Ambystoma tigrinum, and Dipodomys spectabilis)
Historically, many population genetics studies have utilized microsatellite markers sampled at random from the genome and presumed to be selectively neutral. Recent studies, however, have shown that microsatellites can occur in transcribed regions, where they are more likely to be under selection. In this study, we mined microsatellites from transcriptomes generated by 454-pyrosequencing for three vertebrate species: lake sturgeon (Acipenser fulvescens), tiger salamander (Ambystoma tigrinum), and kangaroo rat (Dipodomys spectabilis). We evaluated (i) the occurrence of microsatellites across species; (ii) whether particular gene ontology terms were over-represented in genes that contained microsatellites; (iii) whether repeat motifs were located in untranslated regions or coding sequences of genes; and (iv) in silico polymorphism. Microsatellites were less common in tiger salamanders than in either lake sturgeon or kangaroo rats. Across libraries, trinucleotides were found more frequently than any other motif type, presumably because they do not cause frameshift mutations. By evaluating variation across reads assembled to a given contig, we were able to identify repeat motifs likely to be polymorphic. Our study represents one of the first comparative data sets on the distribution of vertebrate microsatellites within expressed genes. Our results reinforce the idea that microsatellites do not always occur in noncoding DNA, but commonly occur in expressed genes.
Data from: Microsatellite analysis of genetic diversity and population structure of Arabian horse populations
The Arabian horse ignites imagination throughout the world. Populations of this breed exist in many countries, and recent genetic work has examined the diversity and ancestry of a few of these populations in isolation. Here we explore seven different populations of Arabians represented by 682 horses. Three of these are Middle Eastern populations from near the historical origin of the breed, including Syrian, Persian, and Saudi Arabian. The remaining Western populations are found in Europe (the Shagya-Arabian and Polish-Arabian) and America (American-Arabian). Analysis of genetic structure was carried out using 15 microsatellite loci. Genetic distances, AMOVA, factorial correspondence analysis and a Bayesian method were applied. The results consistently show higher level of diversity within the Middle Eastern populations than the Western populations. The Western Arabian populations were the main source of among populations variation. Genetic differentiation was not strong among all Middle Eastern populations, but all American-Arabians showed differentiation from Middle Eastern populations and were somewhat uniform among themselves. Here, we explore the diversities of many different populations of Arabian horses, and find that populations not from the Middle East have noticeably lower levels of diversity, which may adversely affect the health of these populations.
Data from: Polyploidy and microsatellite variation in the relict tree Prunus lusitanica L.: how effective are refugia in preserving genotypic diversity of clonal taxa?
Refugia are expected to preserve genetic variation of relict taxa, especially in polyploids, because high gene dosages could prevent genetic erosion in small isolated populations. However, other attributes linked to polyploidy, such as asexual reproduction, may strongly limit the levels of genetic variability in relict populations. Here, ploidy levels and patterns of genetic variation at nuclear microsatellite loci were analysed in Prunus lusitanica, a polyploid species with clonal reproduction that is considered a paradigmatic example of a Tertiary relict. Sampling in this study considered a total of 20 populations of three subspecies: mainland lusitanica (Iberian Peninsula and Morocco), and island azorica (Azores) and hixa (Canary Islands and Madeira). Flow cytometry results supported an octoploid genome for lusitanica and hixa, whereas a 16-ploid level was inferred for azorica. Fixed heterozygosity of a few allele variants at most microsatellite loci resulted in levels of allelic diversity much lower than those expected for a high-order polyploid. Islands as a whole did not contain higher levels of genetic variation (allelic or genotypic) than mainland refuges, but island populations displayed more private alleles and higher genotypic diversity in old volcanic areas. Patterns of microsatellite variation were compatible with the occurrence of clonal individuals in all but two island populations, and the incidence of clonality within populations negatively correlated with the estimated timing of colonization. Our results also suggest that gene flow has been very rare among populations, and thus population growth following founder events was apparently mediated by clonality rather than seed recruitment, especially in mainland areas. This study extends to clonal taxa the idea of oceanic islands as important refugia for biodiversity, since the conditions for generation and maintenance of clonal diversity (i.e. occasional events of sexual reproduction, mutation and/or seed immigration) appear to have been more frequent in these enclaves than in mainland areas.
Fig. 3 in Testing The Microsatellites-Pcr Markers For Genetic Diversity Research Of Alien Ponto-Caspian Amphipod Pontogammarus Robustoides G. O. Sars, 1894
Fig. 3. Microsatellites amplification of Pontogammarus robustoides from Pļaviņas Reservoir used primer Gapu-17.
Fig. 1 in Genetic diversity and population structure of endangered Neofinetia falcata (Orchidaceae) in South Korea based on microsatellite analysis
Fig. 1. Geographic distribution of N. falcata populations. Abbreviations are shown in Table 1. Pie charts represent assignment probability of belonging to each K = 2 clusters identified by STRUCTURE based on microsatellite allele frequencies, with probability values normalized using CLUMPP.
Figure 2 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Figure 2 Total number of shared haplotypes between populations of Usnea subfloridana in the south-eastern (SE), the western (W) and northern (N) regions of Estonia; the thickness of lines reflects the number of shared haplotypes between populations.
Figure 3 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Figure 3 Usnea subfloridana multilocus genotypes in the principal component analysis (PCA) ordination plot of the first and second axes. Samples are grouped according to the presence of lichen substance: samples containing thamnolic (square) or squamatic acid (circle).
Figure 1 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Figure 1 Distribution map of Usnea subfloridana in Estonia (light grey squares) and study populations (black circles) on Hiiumaa island in the western region (W), in the south-eastern region (SE) and in the northern region of Estonia; the map of Scandinavia was taken from free map resource http://d-maps.com/carte.php?num_car=5977&lang=en.
Figure 6 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Figure 6 Alleles of Usnea subfloridana and explanatory variables mean annual air temperature ('Temp') and geographical longitude of populations ('Long') in the bi-plot of the redundancy analysis (RDA) of the first and second axes. Labels of alleles prefixed by '8' or '9' indicate that these alleles belong to loci Us08 or Us09, respectively; for example, 8201 means that allele 201 is from Us08
Figure 4 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Figure 4 Usnea subfloridana multilocus genotypes (Us02, Us03, Us04, Us05, Us06, Us08, Us09) and explanatory variables mean annual air temperature ('Temp') and the presence of thamnolic acid ('Tham') in a lichen sample in the bi-plot of the redundancy analysis (RDA) of the first and second axes.
Figure 5 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Figure 5 Sample populations of Usnea subfloridana and explanatory variables mean annual air temperature ('Temp') and geographical longitude of populations ('Long') in the bi-plot of the redundancy analysis (RDA) of the first and second axes. The shape of symbols indicates the geographical location of studied populations (square – south-eastern region of mainland, circle - western island and diamond – north-eastern region) and the size of symbols indicates the number of different alleles found in the studied populations.
Figure 3. K in Microsatellite based genetic diversity of Mediterranean fruit fly (Ceratitis capitata, Diptera: Tephritidae) populations from Southwest Turkey
Figure 3. K = 4 clustering assignment depending on the Bayesian method under an admixture model obtained by Structure software. Individuals are represented by a vertical line and each color indicates a different cluster. 1: Muğla; 2: Aydın; 3: Antalya; 4: İzmir; 5: Adana; 6: Yalova; 7: Mersin.
Data from: Microsatellites reveal origin and genetic diversity of Eurasian invasions by one of the world's most notorious marine invader, Mnemiopsis leidyi (Ctenophora)
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Data from: Microsatellite analysis of museum specimens reveals historical differences in genetic diversity between declining and more stable Bombus species
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Data from: Microsatellite analyses across three diverse vertebrate transcriptomes (Acipenser fulvescens, Ambystoma tigrinum, and Dipodomys spectabilis)
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Data from: Development of MHC-linked microsatellite markers in the domestic cat and their use to evaluate MHC diversity in domestic cats, cheetahs and Gir lions.
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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.