Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
738
datasets available to search
ShareScore release 0.9.0
Dataset results
738 results for “Microsatellite”
Microsatellite fragment sizing of South African Cape vulture (Gyps coprotheres)
<p>Microsatellite genoytping fragment sizing of <em>Gyps coprotheres</em> individuals collected in South Africa.</p>
Microsatellite genotypes of Cercidiphyllum japonicum seeds and identity numbers of the seed parents
<p>Genotypes at five microsatellite loci of 361 <em>Cercidiphyllum japonicum </em>seeds and identity numbers of their seed-parents in a population distributed over about 80 ha along a stream within Iwanazawa Forest Reserve (43°13′N, 142°34′E), University of Tokyo Hokkaido Forest, in central Hokkaido, Japan. Based on this and another data (<a href="https://doi.org/10.5061/dryad.zcrjdfnb7">https://doi.org/10.5061/dryad.zcrjdfnb7</a>), pattern of gene dispersal via pollen in this population was estimated by neighborhood model approach and Two generation analysis (TwoGener). These data set can be reused for review of the study and would be useful for comparison with other studies on gene dispersal of tree species.</p>
Fig.1 in Testing The Microsatellites-Pcr Markers For Genetic Diversity Research Of Alien Ponto-Caspian Amphipod Pontogammarus Robustoides G. O. Sars, 1894
Fig.1. Localities of sampling sities in the Latvian reservoirs.
Microsatellite data for Cryptopygus antarcticus travei
<p>Biodiversity patterns are shaped by the interplay between geodiversity and organis-mal characteristics. Superimposing genetic structure onto landscape heterogeneity(i.e., landscape genetics) can help to disentangle their interactions and better under-stand population dynamics. Previous studies on the sub-Antarctic Prince EdwardIslands (located midway between Antarctica and Africa) have highlighted the im-portance of landscape and climatic barriers in shaping spatial genetic patterns andhave drawn attention to the value of these islands as natural laboratories for study-ing fundamental concepts in biology. Here, we assessed the fine-scale spatial geneticstructure of the springtail, Cryptopygus antarcticus travei, which is endemic to MarionIsland, in tandem with high-resolution geological data. Using a species-specific suiteof microsatellite markers, a fine-scale sampling design incorporating landscape com-plexity and generalised linear models (GLMs), we examined genetic patterns overlaidonto high-resolution digital surface models and surface geology data across two 1-kmsampling transects. The GLMs revealed that genetic patterns across the landscapeclosely track landscape resistance data in concert with landscape discontinuities andbarriers to gene flow identified at a scale of a few metres. These results show thatthe island's geodiversity plays an important role in shaping biodiversity patterns andintraspecific genetic diversity. This study illustrates that fine-scale genetic patternsin soil arthropods are markedly more structured than anticipated, given that previ-ous studies have reported high levels of genetic diversity and evidence of geneticstructing linked to landscape changes for springtail species and considering the ho-mogeneity of the vegetation complexes characteristic of the island at the scale oftens to hundreds of metres. By incorporating fine-scale and high-resolution landscapefeatures into our study, we were able to explain much of the observed spatial geneticpatterns. Our study highlights geodiversity as a driver of spatial complexity. Morewidely, it holds important implications for the conservation and management of thesub-Antarctic islands.</p>
Fig. 1 in Testing microsatellite loci and preliminary genetic study for Eurasian otter in South Korea
Fig. 1. Spraints collection sites along Ungokcheon Stream, Bonghwa-gun, Gyeongsangbuk-do.
Genotype data of 10 nuclear microsatellite loci for 30 Quercus acutissima populations in China
<p>This dataset includes genotype data of 10 nuclear microsatellite loci for 707 individuals of Quercus acutissima from 30 natural populations in China.</p>
Microsatellite genotypes of South African Cape vulture (Gyps coprotheres)
<p>Multilocus microsatellite genotypes of 605 <em>Gyps coprotheres</em> individuals. This first column contains the individual sample identity as provided in Supplementary Data 1 and subsequent columns are allele scores in single row format. Alleles are scored according to their molecular size (in base pairs); missing data is encoded as "0".</p>
Figure 1 in Microsatellite based genetic diversity of Mediterranean fruit fly (Ceratitis capitata, Diptera: Tephritidae) populations from Southwest Turkey
Figure 1. Map of Turkey with sampling sites.
FIGURE 1 in Population genetics of the endangered catfish Pseudoplatystoma magdaleniatum (Siluriformes: Pimelodidae) based on species-specific microsatellite loci
FIGURE 1 | Sampling sites of Pseudoplatystoma magdaleniatum in the Magdalena-Cauca basin.
Microsatellite-based analysis of genetic structure and gene flow of Mythimna separata (Walker) (Lepidoptera: Noctuidae) in China
<p>The oriental armyworm, <i>Mythimna separata</i>, is a serious agricultural pest in China. Seasonal and roundtrip migration has recently led to sudden, localized outbreaks and crop losses. To evaluate genetic differentiation between populations in eastern and western China and elucidate gene flow, the genetic structure of 20 natural populations from nine provinces was examined using seven microsatellite markers. The results indicated high genetic diversity. However, little to moderate (0 < <i>F</i><sub>ST</sub> < 0.15) genetic differentiation was detected, and there was no correlation between genetic distance and geographical distance. Bayesian clustering analysis identified three groups whereas discriminant analysis of principal components identified ten clusters that were considered as two clear‐cut clusters and one admixed group. Gene flow occurred frequently in most population pairs, and an asymmetrical migration rate was detected in several pairwise population comparisons. The bottleneck test showed that few populations had experienced recent bottlenecks. Correspondingly, large‐scale and long‐distance migration of <i>M. separata</i> has caused low genetic differentiation and frequent gene exchange. Our findings are important for studying genetic evolution and help to improve predictions of <i>M. separata</i> outbreaks in China.</p>
Data from: CHIIMP: an automated high-throughput microsatellite genotyping approach reveals greater allelic diversity in wild chimpanzees
Short tandem repeats (STRs), also known as microsatellites, are commonly used to non-invasively genotype wild-living endangered species, including African apes. Until recently, capillary electrophoresis has been the method of choice to determine the length of polymorphic STR loci. However, this technique is labor intensive, difficult to compare across platforms, and notoriously imprecise. Here we developed a MiSeq-based approach and tested its performance using previously genotyped fecal samples from long-term studied chimpanzees in Gombe National Park, Tanzania. Using data from eight microsatellite loci as a reference, we designed a bioinformatics platform that converts raw MiSeq reads into locus-specific files and automatically calls alleles after filtering stutter sequences and other PCR artifacts. Applying this method to the entire Gombe population, we confirmed previously reported genotypes, but also identified 31 new alleles that had been missed due to sequence differences and size homoplasy. The new genotypes, which increased the allelic diversity and heterozygosity in Gombe by 61% and 8%, respectively, were validated by replicate amplification and pedigree analyses. This demonstrated inheritance and resolved one case of an ambiguous paternity. Using both singleplex and multiplex locus amplification, we also genotyped fecal samples from chimpanzees in the Greater Mahale Ecosystem in Tanzania, demonstrating the utility of the MiSeq-based approach for genotyping non-habituated populations and performing comparative analyses across field sites. The new automated high-throughput analysis platform (available at https://github.com/ShawHahnLab/chiimp) will allow biologists to more accurately and effectively determine wildlife population size and structure, and thus obtain information critical for conservation efforts.
Accurate measurement of microsatellite length by disrupting its tandem repeat structure
<p>Read, first copy, and template tables for microsatellite data pertaining to the manuscript: "Accurate measurement of microsatellite length by disrupting its tandem repeat structure". </p>
Transitioning from microsatellites to SNP-based microhaplotypes in genetic monitoring programs: lessons from a 20-year time series of paired data.
<p>Many long-term genetic monitoring programs began before next-generation sequencing became widely available. Older programs can now transition to new marker systems usually consisting of 1000s of SNP loci, but there are still important questions about comparability, precision, and accuracy of key metrics estimated using SNPs. Ideally, transitioned programs should capitalize on new information without sacrificing continuity of inference across the time series. We combined existing microsatellite-based genetic monitoring information with SNP-based microhaplotypes obtained from archived samples of Rio Grande silvery minnow (<em>Hybognathus amarus</em>) across a 20-year time series to evaluate point estimates and trajectories of key genetic metrics. Demographic and genetic monitoring bracketed multiple collapses of the wild population, and included cases where captive-born repatriates comprised the majority of spawners in the wild. Even with smaller sample sizes, microhaplotypes yielded comparable and in some cases more precise estimates of variance genetic effective population size, multilocus heterozygosity and inbreeding compared to microsatellites because many more microhaplotype loci were available. Microhaplotypes also recorded shifts in allele frequencies associated with population bottlenecks. Trends in microhaplotype-based inbreeding metrics were associated with the fraction of hatchery-reared repatriates to the wild, and should be incorporated into future genomic monitoring. Although differences in accuracy and precision of some metrics were observed between marker types, biological inferences and management recommendations were consistent.</p>
Microsatellite data from Mediterranean mussels (Mytilus galloprovincialis) from the eastern coast of the Adriatic Sea
<p>Microsatellite data from eighteen populations of Mediterranean Mussels from the eastern coast of the Adriatic Sea collected between 9/2015 and 5/2017. </p>
Roe deer microsatellite genotype data
<p>In the early 1800s, the European roe deer (<em>Capreolus capreolus</em>) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was enacted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonised Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonisation and assess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies and explore the opportunity for development of forensic traceability tools. The results concerning the recolonisation origin support natural, multidirectional immigration from neighbouring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad scale geographic origin assignment using nuclear markers to support law enforcement.</p>
Microsatellite alleles of two species of Tetramorium ants in their native and invasive ranges
<p>Microsatellite alleles at 16 loci, for 80 individuals of <em>Tetramorium immigrans</em> and 84 individuals of <em>T. tsushimae</em> from both their native and invasive ranges.</p>
Microsatellite data
<p>Scored alleles of 15 microsatellite markers used in a population genetics study of <em>Harmonia axyridis. </em>Includes global samples, but with a strong focus on South Africa.</p>
American Crow SNPs and microsatellite data
<p>Infectious diseases can cause steep declines in wildlife populations, leading to changes in genetic diversity that may affect the susceptibility of individuals to infection and the overall resilience of populations to pathogen outbreaks. Here, we examine evidence for a genetic bottleneck in a population of American crows (<em>Corvus</em> <em>brachyrhynchos</em>) before and after the emergence of West Nile virus (WNV). More than 50% of marked birds in this population were lost over the two-year period of the epizootic, representing a 10-fold increase in adult mortality. Using analyses of SNPs and microsatellite markers, we tested for evidence of a genetic bottleneck and compared levels of inbreeding and immigration in the pre- and post-WNV populations. Counter to expectations, genetic diversity (allelic diversity and the number of new alleles) increased after WNV emergence. This was likely due to increases in immigration, as the estimated membership coefficients were lower in the post-WNV population. Simultaneously, however, the frequency of inbreeding appeared to increase: mean inbreeding coefficients were higher among SNP markers, and heterozygosity-heterozygosity correlations were stronger among microsatellite markers, in the post-WNV population. These results indicate that loss of genetic diversity at the population level is not an inevitable consequence of a population decline, particularly in the presence of gene flow. The changes observed in post-WNV crows could have very different implications for their response to future pathogen risks, potentially making the population as a whole more resilient to a changing pathogen community, while increasing the frequency of inbred individuals with elevated susceptibility to disease.</p>
Data from: Novel microsatellite markers for epiphytic bromeliad Tillandsia recurvata L., in an urban landscape in South-eastern Brazil
<p><span>The authors present seven novel microsatellite markers for </span><em>Tillandsia recurvata</em> L. The genome assemble sequences of <em>T. recurvata</em> were obtained from NCBI (7.2Gb) (Sayers <em>et al</em>. 2022). The BioProject Accession and accession numbers are PRJNA701548 and SRX10089449, respectively. The microsatellite identification software Krait (0.5.2) (Du <em>et al</em>. 2018) was used to detect suitable microsatellites, both genome-wide and in the noncoding regions of <em>T. recurvata</em>. The single sequence repeats (SSRs) were refined to a minimum number of seven repeats of di-, tri-, or tetra-nucleotide repeat motifs. These sequences were further limited to SSRs of more than 100bp in length and low GC content (<50%). Krait (0.5.2) (Du <em>et al</em>. 2018) was also used to design the primers for the selected SSR sequences, in conjunction with the integrated Primer3 software. The criteria for primer selection included: a primer length of 18-26bp, an optimal melting temperature (Tm) of 54-59°C and GC content of <50%. These designed primers were single-plexed and amplified using the following PCR cycle: initial denaturation (95°C for 3 min), 34 cycles of 95°C for 30s, annealing for 30s (JP01-JP12: 54°C, 4873TD + 35251TD: 56°C, 19286TD: 53°C, 5044TD + 186664TD + 214633TD: 58°C), 72°C for 1 min and a final extension of 72°C for 5 mins. The authors make this information available to other researchers, to continue the investigation of epiphyte genetics.</p>
Asian elephant microsatellite genotypes: Nakai Plateau and Sepon mines region, Lao PDR
<p class="MsoNormal">Habitat loss and fragmentation are leading contributors to the endangered status of species. In 2006, the Nakai Plateau contained the largest known Asian elephant (<em>Elephas maximus</em>) population in the Lao People's Democratic Republic (Lao PDR), and the population was among those with the highest genetic diversity reported for Asian elephants. In 2008, completion of the Nam Theun 2 hydroelectric dam inundated much of the Plateau, resulting in the loss of 40% of elephant habitat. We<span> studied elephant presence, movements, and the incidence of human–elephant conflict (HEC) on the Nakai Plateau and surrounding areas from 2004-2020, before and for 12 years after dam completion. To examine contemporary population dynamics in the Nakai elephants, we </span>used genetic sampling to compare <span>minimum population numbers, demography, and levels of genetic diversity from the wet and dry seasons in 2018/2019, 10 years after dam completion, </span>with those reported in a pre-dam-completion genetic survey.<span> </span>After dam completion, we found a major increase in HEC locally and the creation of new, serious, and persistent HEC problems as far as 100 km away.<span> </span>While we were unable to compare estimated population sizes before and after dam completion, our data revealed a decrease in genetic diversity, a male-biased sex ratio, and evidence of dispersal from the Plateau by breeding-age females. Our results raise concerns about the long-term viability of this important population as well as that of other species in this region. Given that hydropower projects are of economic importance throughout Laos and elsewhere in southeast Asia, this study has important implications for understanding and mitigating their impact.</p>
ScienceDex guides
Understand access before you commit
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.