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394 results for “Microsatellite data”
Data from: Challenges in analysis and interpretation of microsatellite data for population genetic studies
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Data from: Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species
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Data from: Isolation and characterization of microsatellite loci for the isopod crustacean Armadillidium vulgare and transferability in terrestrial isopods
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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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Data from: Transcriptome-wide mining, characterization, and development of microsatellite markers in Lychnis kiusiana (Caryophyllaceae)
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Microsatellite data from: Multiple colonizations and genetic differentiation from the mainland populations in insular populations of the perennial herb Solidago virgaurea complex (Asteraceae) on recently formed nearshore oceanic islands
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Data from: ‘True’ null allele detection in microsatellite loci: a comparison of methods, assessment of difficulties, and survey of possible improvements
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Data from: Limited usefulness of microsatellite markers from the malaria vector Anopheles gambiae when applied to the closely related species Anopheles melas
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Microsatellite data of Avicennia marina from Gazi Bay, Kenya
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Data from: Microsatellite analysis of genetic diversity and population structure of Arabian horse populations
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Spotted turtle dispersal microsatellite DNA sex and site data
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Microsatellite genotyping data for habitat-linked genetic structure for white-crowned sparrow (Zonotrichia leucophrys): local factors shape population genetic structure
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ETV6 Deficiency and Microsatellite Enhancers Drive Transcriptional Dysregulation in B-Lymphoblastic Leukemia: ChIP-Seq data
GEO Series GSE186941. Homo sapiens. 56 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Third-party reanalysis.
Data from: A single multiplex of twelve microsatellite markers for the simultaneous study of the brown hare (Lepus europaeus) and the mountain hare (Lepus timidus)
The management of hunted species is challenging, as it must conciliate the conservation of species and their sustainable exploitation. Non-genetic tools are widely used in this context but they may present limitations notably when species can hybridize or when large-scale spatial monitoring is required to establish optimal management actions. This is why genetic tools have been more and more integrated in wildlife management practices. However, the markers proposed are often amplified in small multiplexes when larger ones could allow to better cope with the small quantities of DNA obtained with non-invasive sampling methods. Here, we propose a unique multiplex of 12 autosomal microsatellite markers for the study of two hare species that exist in sympatry in some areas in Europe and are hunted notably in France: the brown hare Lepus europaeus and the mountain hare L. timidus. We tested 17 markers previously used in these two species or other lagomorph species, from which 12 were included in this single multiplex. Diversity was between 4 and 30 alleles per locus totalling 126 alleles and we showed that these markers possess appropriate genetic resolution for individual and species identification for the populations under study. This multiplex panel represents the largest number of microsatellites amplified in one reaction proposed for these two hare species and provides a cost-effective and valuable tool for further hybridization studies and the management of hares.
Data from: Microsatellite and major histocompatibility complex variation in an endangered rattlesnake, the Eastern Massasauga (Sistrurus catenatus)
Genetic diversity is fundamental to maintaining the long-term viability of populations, yet reduced genetic variation is often associated with small, isolated populations. To examine the relationship between demography and genetic variation, variation at hypervariable loci (e.g., microsatellite DNA loci) is often measured. However, these loci are selectively neutral (or near neutral) and may not accurately reflect genomewide variation. Variation at functional trait loci, such as the major histocompatibility complex (MHC), can provide a better assessment of adaptive genetic variation in fragmented populations. We compared patterns of microsatellite and MHC variation across three Eastern Massasauga (Sistrurus catenatus) populations representing a gradient of demographic histories to assess the relative roles of natural selection and genetic drift. Using 454 deep amplicon sequencing, we identified 24 putatively functional MHC IIB exon 2 alleles belonging to a minimum of six loci. Analysis of synonymous and nonsynonymous substitution rates provided evidence of historical positive selection at the nucleotide level, and Tajima's D provided support for balancing selection in each population. As predicted, estimates of microsatellite allelic richness, observed, heterozygosity, and expected heterozygosity varied among populations in a pattern qualitatively consistent with demographic history and abundance. While MHC allelic richness at the population and individual levels revealed similar trends, MHC nucleotide diversity was unexpectedly high in the smallest population. Overall, these results suggest that genetic variation in the Eastern Massasauga populations in Illinois has been shaped by multiple evolutionary mechanisms. Thus, conservation efforts should consider both neutral and functional genetic variation when managing captive and wild Eastern Massasauga populations.
Data from: Microsatellite evidence for high frequency of multiple paternity in the marine gastropod Rapana venosa
Background: Inferring of parentage in natural populations is important in understanding the mating systems of a species, which have great effects on its genetic structure and evolution. Muricidae, a large group (approximately 1,600 species) of marine gastropods, are poorly investigated in patterns of multiple paternity and sperm competition based on molecular techniques. The veined Rapa whelk, Rapana venosa, a commercially important muricid species with internal fertilization, is an ideal species to study the occurrence and frequency of multiple paternity and to facilitate understanding of their reproductive strategies. Methodology/Principal Findings: We developed five highly polymorphic microsatellites in R. venosa and applied them to identify multiple paternity in 19 broods (1381 embryos) collected from Dandong, China. Multiple paternity was detected in 17 (89.5%) of 19 broods. The number of sires per brood ranged from 1 to 7 (4.3 on average). Of the 17 multiply sired broods, 16 (94.1%) were significantly skewed from equal paternal contributions, and had a dominant sire which was also dominant in each assayed capsule. Conclusions: Our results indicate that a high level of multiple paternity occurs in the wild population of R. venosa. Similar patterns of multiple paternity in the 2–6 assayed capsules from each brood imply that fertilization events within the body of a female occur mostly (but not entirely) as random draws from a "well-but-not-perfectly blended sperm pool" of her several mates. Strongly skewed distributions of fertilization success among sires also suggest that sperm competition and/or cryptic female choice might be important for post-copulatory paternity biasing in this species.
Data from: Evaluation of genetic diversity and population structure of five Chinese indigenous donkey breeds using microsatellite markers
China had the largest population of raising donkeys in the world, however the number of Chinese indigenous donkey decreased dramatically due to the increase of agriculture mechanization in the last century. The species has still been important in China because of its edible and medical value, therefore the survey on its genetic diversity in China is necessary for its conservation and utilization. In this study, 15 microsatellite markers were used to evaluate genetic diversity and population structure of five Chinese indigenous donkey breeds. The mean values of expected heterozygosity, allelic richness, and total number of alleles for all the tested Chinese donkeys were 0.70, 6.04, and 6.28 respectively, suggesting that the genetic diversity of Chinese indigenous donkeys is rich. The Bayesian analysis and principal component analysis plot yielded the same clustering result, which revealed that Guanzhong donkey was the most differentiated breed in all detected samples, and Jinnan (JN) and Guangling (GL) were genetically closed together. Additionally, our results indicated that the heterozygote deficit was severe in two Chinese indigenous donkey breeds (GL and JN), and it warned us that animal conservation activities on this species should be considered carefully in near future.
microsatellite data
<p>This is the microsatellite raw data of the article 'Revelation of genetic diversity and structure of wild <em>Elymus excelsus</em> (Poaceae: Triticeae) collection from western China by SSR markers' published at Peer J.</p>
Data from: Cost effective microsatellite isolation and genotyping by high throughput sequencing
High throughput sequencing (HTS) has emerged as a valuable tool for the rapid isolation of genetic markers for population genetics and pedigree analysis. HTS-based SNP (single nucleotide polymorphism) genotyping protocols like RAD (Restriction-site associated DNA) sequencing or hybrid capture, allow for the isolation of thousands of markers from any non-model organism. However, these protocols are relatively laborious and expensive and the resulting high marker density is not always necessary. Since HTS technology has also greatly simplified the isolation and genotyping process of microsatellite markers, we develop microsatellite markers as a cost efficient and simple alternative to SNP genotyping. We present low coverage genome sequencing data from seven distantly related spider species (Argiope bruennichi, Larinia jeskovi, Oedothorax restusus, Pisaura mirabilis, Australomisidia ergandros, Cheiracanthium punctorium, Theridion grallator) and show the utility of HTS for microsatellite isolation. We also present a simple Illumina amplicon sequencing protocol to genotype microsatellites from multiplex PCR amplicons in the Hawaiian happy face spider T. grallator. We discuss advantages and drawbacks of the use of microsatellites for a range of research questions, and highlight an unexpectedly fast decay and gain of repeat loci for T. grallator.
Three oaks Microsatellite data
<p>Knowledge of interspecific divergence and population expansions/contractions of dominant forest trees in response to geological events and climatic oscillations is of major importance to understand their evolution and demography. However, the interspecific patterns of genetic differentiation and spatiotemporal population dynamics of three deciduous <i><span>Cerris</span></i> oak species (<i>Q. acutissima</i>, <i>Q. variabilis</i> and <i>Q. chenii</i>) that are widely distributed in China remain poorly understood. In this study, we genotyped 16 nuclear loci in 759 individuals sampled from 44 natural populations of these three sibling species to evaluate the plausible demographical scenarios of the closely related species. We also tested the hypothesis that macro- and microevolutionary processes of the three species had been triggered and molded by Miocene–Pliocene geological events and Quaternary climatic change. The Bayesian cluster analysis showed that <i>Q. acutissima</i> and<i> Q. chenii </i>were clustered in the same group, whereas <i>Q. variabilis </i>formed a different genetic cluster. An approximate Bayesian computation (ABC) analyses suggested that <i>Q. variabilis </i>and<i> </i><i>Q. acutissima</i> diverged from their most common ancestor around 19.84 Ma, and subsequently <i>Q. chenii </i>diverged from <i>Q. acutissima </i>at about<i> </i>9.6 Ma, which was significantly associated with the episodes of the Qinghai–Tibetan Plateau (QTP). In addition, ecological niche modeling and population history analysis showed that these three <i><span>Cerris</span></i><i> </i>oak<i> </i>species repeatedly underwent considerable 'expansion–contraction' during the interglacial and glacial periods of the Pleistocene, although they have varying degrees of tolerance for the climatic change. Overall, these findings indicated geological and climatic changes during the Miocene–Pliocene and Pleistocene as causes of species divergence and range shifts of dominant tree species in the subtropical and warm temperature areas in China.</p>
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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.