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738 results for “Microsatellites”
Data from: Ancient and modern genomes reveal microsatellites maintain a dynamic equilibrium through deep time
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Microsatellite data for Aedes aegypti populations in Florida and southern California
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Joint analysis of microsatellites and flanking sequences enlightens complex demographic history of interspecific gene flow and vicariance in rear-edge oak populations
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Waste not, want not: microsatellites remain an economical and informative technology for conservation genetics
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Datasets for microsatellite genotype for natural populations and seedlings from six mother trees, and seedling survival and growth records
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Evaluation of DNA extracted from timber rattlesnake (Cotalus horridus) cloacal and blood swabs for microsatellite genotyping
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Microsatellite genotypes of bearded vultures (Gypaetus barbatus)
<p>Multilocus microsatellite genotypes of 236 <em>Gypaetus barbatus </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 given as "0".</p>
Monitoring Plasmodium falciparum and Plasmodium vivax using microsatellite markers indicates limited changes in population structure after substantial transmission decline in Papua New Guinea
Monitoring the genetic structure of pathogen populations may be an economical and sensitive approach to quantify the impact of control on transmission dynamics, highlighting the need for a better understanding of changes in population genetic parameters as transmission declines. Here we describe the first population genetic analysis of the major human malaria parasites, <i>Plasmodium falciparum</i> (Pf) and <i>Plasmodium vivax</i> (Pv) populations following nationwide distribution of long-lasting insecticide treated nets (LLIN) in Papua New Guinea (PNG). Parasite isolates from pre- (2005-6) and post-LLIN (2010-2014) were genotyped using microsatellite markers. Despite parasite prevalence declining substantially (East Sepik: Pf=54.9-8.5%, Pv=35.7-5.6%, Madang: Pf=38.0-9.0%, Pv: 31.8-19.7%), genetically diverse and intermixing parasite populations remained. Pf diversity declined modestly post-LLIN relative to pre-LLIN (East Sepik: Rs = 7.1-6.4, He = 0.77-0.71; Madang: Rs= 8.2-6.1, He = 0.79-0.71). Unexpectedly, population structure present in pre-LLIN populations was lost post-LLIN, suggesting that more frequent human movement between provinces may have contributed to higher gene flow. Pv prevalence initially declined but increased again in one province, yet diversity remained high throughout the study period (East Sepik: Rs=11.4-9.3, He=0.83-0.80; Madang: Rs=12.2-14.5, He=0.85-0.88). Although genetic differentiation values increased between provinces over time, no significant population structure was observed at any time point. For both species, a decline in multiple infections and increasing clonal transmission and significant multilocus linkage disequilibrium (mLD) post-LLIN was a positive indicator of impact on the parasite population using microsatellite markers. These parameters may be useful adjuncts to traditional epidemiological tools in the early stages of transmission reduction.
Microsatellite genotypes
<p>Phylogeographic divergence and population genetic diversity within species reflect the impacts of habitat connectivity, demographics, and landscape level processes in both the recent and distant past. Characterizing patterns of differentiation across the geographic range of a species provides insight on the roles of organismal and environmental traits, on evolutionary divergence, and future population persistence. This is particularly true of habitat specialists where habitat availability and resource dependence may result in pronounced genetic structure as well as increased population vulnerability. We use DNA sequence data as well as microsatellite genotypes to estimate range-wide phylogeographic divergence, historical population connectivity, and historical demographics in an endemic habitat specialist, the dunes sagebrush lizard (<i>Sceloporus arenicolus</i>). This species is found exclusively in dune blowouts and patches of open sand within the shinnery oak-sand dune ecosystem of southeastern New Mexico and adjacent Texas. We find evidence of phylogeographic structure consistent with breaks and constrictions in suitable habitat at the range-wide scale. In addition, we find support for a dynamic and variable evolutionary history across the range of <i>S. arenicolus</i>. Populations in the Monahans Sandhills have deeply divergent lineages consistent with long-term demographic stability. In contrast, populations in the Mescalero Sands are not highly differentiated, though we do find evidence of demographic expansion in some regions and relative demographic stability in others. Phylogeographic history and population genetic differentiation in this species has been shaped by the configuration of habitat patches within a geologically complex and historically dynamic landscape. Our findings identify regions as genetically distinctive conservation units as well as underscore the genetic and demographic history of different lineages of <i>S. arenicolus</i>.</p>
Microsatellites genotyping for common and lesser cuckoos
<p>In a parasite species, the dispersal of individuals should be dependent on host species to which they are specialized; thus, any sexual/individual difference in host specificity may influence their dispersal patterns, and hence, population genetic structures. However, such predictions remain poorly verified in generalist avian brood parasites that is composed of multiple lineages of host-specific races. Here, we show the dispersal consequences inferred from spatial genetic structures and their association with host specificity in brood parasitic common cuckoos <i>Cuculus canorus</i> in which female-specific host race formation has been widely accepted. Genetic sampling from adult cuckoos confirmed restricted dispersal in both sexes and resultant genetic structures between populations where different host species breed allopatrically, whereas it was not the case between distant areas inhabited by the same host species. Contrary to the female host race hypothesis, our results demonstrate that male cuckoos may also have host specificity and disperse accordingly, conclusively allowing us to hypothesize the formation of host race including both sexes.</p>
Microsatellite genotypes and associated data for: The contribution of clonality to population genetic structure in the sea anemone Diadumene lineata
<p>Ecological and evolutionary processes differ depending on how genetic diversity is organized in space. For clonal organisms, the organization of both genetic and genotypic diversity can influence the fitness effects of competition, the mating system, and reproductive mode, which are key drivers of life cycle evolution. Understanding how individual reproductive behavior contributes to population genetic structure is essential for disentangling these forces, particularly in species with complex and plastic life cycles. The widespread sea anemone <i>Diadumene lineata</i> exhibits temperature-dependent fission which contributes to predictable variation in clonal rate along the Atlantic coast of the United States, part of its non-native range. Because warmer conditions lead to higher rates of clonality, we expected to find lower genotypic and genetic diversity in lower versus higher latitude populations. We developed primers for 11 microsatellite loci and genotyped 207 anemones collected from 8 sites ranging from Florida to Massachusetts. We found clonal influence at all sites, and as predicted, the largest clones were found at lower latitude sites. We also found genetic signatures of sex in the parts of the range where gametogenesis is most common. Evidence of sex outside the native range is novel for this species and provides insights into the dynamics of this successful invader. Our findings also illustrate challenges that partially clonal taxa pose for eco-evolutionary studies, such as difficulty sampling statistically robust numbers of genets and interpretating common population genetic metrics. For example, we found high among-locus variation in F<i><sub>is, </sub></i>which makes the meaning of mean multilocus F<i><sub>is</sub></i> unclear.</p>
Multiple drainage reversal episodes and glacial refugia in a Patagonian fish revealed by sequenced microsatellites
<p>The rise of the southern Andes and the Quaternary glacial cycles influenced the landscape of Patagonia, affecting the phylogeographic and biogeographic patterns of its flora and fauna. Here we examine the phylogeography of the freshwater fish, Percichthys trucha, using 53 sequenced microsatellite DNA markers. Fish (N=835) were collected from 16 river systems (46 locations) spanning the species range on both sides of the Andes. Eleven watersheds drain to the Pacific, five of which are trans-Andean (headwaters east of Andes). The remaining five drainages empty into the Atlantic. Three analytical approaches (neighbour-joining tree, hierarchical AMOVAs, STRUCTURE) revealed evidence of historic drainage reversals: Fish from four of the five trans-Andean systems (Puelo, Futalaufquen/Yelcho, Baker, Pascua) exhibited greater genetic similarity with Atlantic draining systems than with Pacific systems with headwaters west of Andes. Present-day drainage (Pacific vs. Atlantic) explained only 5% of total genetic variance, while ancestral drainage explained nearly 27% of total variance. Thus, the phylogeographic structure of Percichthys trucha is consistent with episodes of drainage reversal in multiple systems and suggests a major role for deglaciation in the genetic and indeed the geographic distribution of P. trucha in Patagonia. The study emphasizes the significant role of historical processes in the current pattern of genetic diversity and differentiation in a fish from a southern temperate region.</p>
Response Rates to Anti–PD-1 Immunotherapy in Microsatellite-Stable Solid Tumors With 10 or More Mutations per Megabase
<p>This dataset has been used to analyze the association between tumor mutational burden and response to treatment in immunotherapy-treated patients with microsatellite-stable solid tumors. The dataset contains clinical and genomic data for 1,678 patients with 16 cancer types.</p> <p> </p>
Metadata: Microsatellite genotypes for Seriatopora hystrix and Acropora millepora in Indonesia
<p>Microsatellite genotypes for <em>Seriatopora hystrix</em> and <em>Acropora millepora</em> in Indonesia as used in the paper "Differences in genetic diversity and divergence between brooding and broadcast spawning corals across two spatial scales in the Coral Triangle region."</p>
Microsatellite data of Vincetoxicum hirundinaria offspring and their inferred mother plants from 13 populations in the South-Western Finnish Archipelago
<p>Fragmented landscapes may have implications for the genetic structure of populations and for the microevolution of plant species. In particular, landscape fragmentation and/or population isolation might affect the evolution of plant mating systems. Here, we study the consequences of landscape fragmentation on the genetic structure of populations of a perennial herb, <i>Vincetoxicum hirundinaria </i>with a mixed mating system. Our study area, the south-western Finnish archipelago, was formed after the glacial ice sheet started to retreat 12 000 years ago. Due to the isostatic land uplift following the glacial retreat, suitable habitats have been formed gradually, and as a consequence, populations of <i>V. hirundinaria</i> differ in age, size and their degree of isolation in the area. We hypothesized that a mixed-mating system has been selected for in these populations due to the advantage of self-fertilization in newly colonized areas and the advantage of outcrossing in adaptation to heterogeneous environments. To test this hypothesis, we collected seeds of open-pollinated flowers from 13 <i>V. hirundinaria</i> populations differing in size, age and isolation, and used 15 microsatellite markers to perform progeny-array analysis to estimate population-level outcrossing rates, population genetic indices and population structure. We found that <i>V. hirundinaria</i> is almost completely outcrossing in the study area with no signs of past self-fertilization and/or mating among relatives. The overall low inbreeding coefficients indicate that even in small populations mating among relatives is rare. High allelic richness of both maternal and offspring genotypes as well as limited genetic differentiation among the studied populations indicate strong gene flow among them. Our findings suggest that <i>V. hirundinaria</i> has successful seed and pollen dispersal among populations that has allowed colonization of new habitats in this fragmented landscape and led to a genetically well-mixed group of populations at the scale of the study.</p>
Data from: Transcriptome profiles of sunflower reveal the potential role of microsatellites in gene expression divergence
The mechanisms by which natural populations generate adaptive genetic variation are not well understood. Some studies propose that microsatellites can function as drivers of adaptive variation. Here we tested a potentially adaptive role for transcribed microsatellites with natural populations of the common sunflower (Helianthus annuus L.) by assessing the enrichment of microsatellites in genes that show expression divergence across latitudes. Seeds collected from six populations at two distinct latitudes in Kansas and Oklahoma were planted and grown in a common garden. Morphological measurements from the common garden demonstrated that phenotypic variation among populations is largely explained by underlying genetic variation. An RNA–Seq experiment was conducted with 96 of the individuals grown in the common garden and differentially expressed (DE) transcripts between the two latitudes were identified. A total number of 825 DE transcripts were identified. DE transcripts and non-differentially expressed (NDE) transcripts were then scanned for microsatellites. The abundance of different motif lengths and types in both groups were estimated. Our results indicate that DE transcripts are significantly enriched with mononucleotide repeats and significantly depauperate in trinucleotide repeats. Further, the standardized mononucleotide repeat motif A and dinucleotide repeat motif AG were significantly enriched within DE transcripts while motif types, C, AT, ACC, and AAC in DE transcripts are significantly differentiated in microsatellite tract length between the two latitudes. The tract length differentiation at specific microsatellite motif types across latitudes and their enrichment within DE transcripts indicate a potential functional role for transcribed microsatellites in gene expression divergence in sunflower.
Ursus arctos microsatellite fragment sizing, Chilkoot Valley, Alaska, USA 2014
<p>Microsatellite genoytping fragment sizing for 460 non-invasively collected saliva and fecal samples from brown bears (<em>Ursus arctos</em>) in northern Southeast Alaska, USA during summer and fall 2014.<br /> </p>
Microsatellite allele length of Phytophthora ramorum in San Mateo County California
<p>We implement a population genetics approach to clarify the role that temporal and environmental variability, spatially distinct locations, and different hosts may have in the epidemiology of plant disease and the microevolution of its causative pathogen. In California and Southern Oregon (USA), the introduction of the invasive pathogen <em>Phytophthora ramorum</em>, causal agent of the widespread disease Sudden Oak Death (SOD), has resulted in extensive mortality of various oaks (<em>Quercus sp</em>.) and of tanoak (<em>Notholithocarpus densiflorus</em>). Although the disease can infect over a hundred hosts, California bay laurel (<em>Umbellularia californica</em>) is the most competent transmissive host but is not lethally affected by the disease. Using population genetics data, we identify the relationship among<em> P. ramorum </em>populations in bay laurels, oaks and tanoaks to clarify the contribution of each host on the epidemiology of SOD and the microevolution of its causal agent and to explore differences in population structure across sites and years. We conclude that bay laurel is the primary source for infections of both tanoak and oak, and that tanoak contributes minimally to oak infection but can infect bay laurel, creating a secondary pathogen amplification process. Overall, pathogen diversity is associated with rainfall and presence of bay laurels, which sustain the largest populations of the pathogen. Additionally, we clarify that while bay laurels are a common source of inoculum, oaks and tanoaks act as sinks that maintain host-specific pathogen genotypes not observed in bay laurel populations. Finally, we conclude that different sites support a dominance of different pathogen genotypes. Some genotypes were widespread, while others were limited to a subset of the plots. Sites with higher bay laurel densities sustained a higher genotypic diversity of the pathogen. This work provides novel insight into the ecology and evolutionary trajectories of SOD epidemics in natural ecosystems.</p>
Microsatellite exploration in the climbing hydrangea (Hydrangea petiolaris Siebold & Zucc.) transcriptome: A resource for population genetics and functional genomics
<p><strong>Background</strong></p> <p><em>Hydrangea petiolaris</em> Siebold & Zucc., also known as climbing hydrangea, is a vine native to the woodlands of Korea, Japan, and Sakhalin Island. It is an economically important ornamental plant with fertile and sterile flowers. Despite the recent increase in <em>Hydrangea</em> breeding and interest in germplasm conservation, relatively little is known about the relationships between <em>Hydrangea</em> species.</p> <p><strong>Results</strong></p> <p>We employed Illumina NovaSeq 6000 sequencing technology to generate a total of 39,945,480 reads, which were assembled into 137,715 contigs. A total of 109,092 filtered transcripts were used to identify microsatellites, and 54,587 microsatellite repeat motifs were revealed within 33,556 contigs. Among these, 4,510 transcripts harboring microsatellites had Gene Ontology annotations, and numerous microsatellite-containing transcripts exhibited associations with genes, including those encoding PPR proteins, aldehyde dehydrogenases, and bHLH transcription factors, related to the <em>restorer of fertility</em> (<em>Rf</em>) genes, which play a critical role in restoring fertility in plants with cytoplasmic male sterility. Validation of transcriptomic SSR markers demonstrated high levels of polymorphism, revealing significant genetic diversity within populations. However, null alleles and deviations from Hardy‒Weinberg equilibrium at specific loci suggested caution in genotyping accuracy. Population-level analysis disclosed high genetic differentiation and distinct clustering of populations.</p> <p><strong>Conclusions</strong></p> <p>The <em>H</em>. <em>petiolaris</em> transcriptomic SSR markers offer valuable insight for gaining insights into the population genetics, evolutionary background, and practical strategies for conserving this species. Moreover, the microsatellite loci we have identified and their associations with annotated genes hold promise for creating functional markers specifically tailored for <em>H</em>. <em>petiolaris</em>. These markers include valuable resources of transcriptomic SSR markers suitable for population genetic investigations and have a reasonable degree of applicability across different taxa.</p>
Development of twenty-four microsatellite markers for Afrotropical Ornithodoros ticks
<p><strong>Background: </strong>Soft ticks of the genus <em>Ornithodoros</em> are responsible for the maintenance and transmission of the <em>African swine fever </em>(ASF)<em> virus</em> in the sylvatic and domestic viral cycles in Southern Africa. They are also the main vectors of <em>Borrelia</em> species causing relapsing fevers. Currently, no genetic markers are available for Afrotropical <em>Ornithodoros </em>ticks. As ASF spreads globally, such markers are needed to assess the role of ticks in the emergence of new outbreaks. The aim of this study was to design microsatellite markers that could be used for ticks of the <em>Ornithodoros moubata</em> complex, particularly <em>Ornithodoros phacochoerus</em>, to assess population structure and tick movements in ASF endemic areas.</p> <p><strong>Methods: </strong>One hundred and fifty-one markers were designed using the <em>O. moubata </em>and <em>O. porcinus</em> genomes after elimination of repeated sequences in the genomes. All designed markers were tested on <em>O. phacochoerus </em>and <em>O. porcinus </em>DNA to select the best markers.</p> <p><strong>Results:</strong> Twenty-four microsatellite markers were genotyped on two populations of <em>O. phacochoerus</em> and on few individuals from four other <em>Ornithodoros</em> species. Nineteen markers were selected to be as robust as possible for population genetic studies on <em>O. phacochoerus</em>.</p> <p><strong>Conclusions:</strong> The microsatellite markers developed here represent the first genetic tool to study nidicolous populations of Afrotropical <em>Ornithodoros</em>. This dataset contains the genotyping results obtained for all twenty-four markers tested.</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)
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.