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394 results for “Microsatellite data”

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zenodo44/100

Sequence-based microsatellite data of Anadenanthera colubrina (Leguminosae)

The file contains SSRseq genotyping data of Anadenanthera colubrina populations. Individuals from two life stages were scored at 25 SSRseq loci. Goncalves AL, García MV, Chancerel E, Lepais O, Heuertz M. High-throughput sequence-based microsatellite genotyping for the non-model Neotropical tree species Anadenanthera colubrina (Leguminosae). The file contains - Two different data sets: GS: Genotypes based on sequence identity. GL: Genotypes based on amplicon length. - Allele sequence information

opencc-by-4.0May 2024View details →

zenodo44/100

Microsatellite genotype data and leaf morphological data of the publication "Bidirectional gene flow between Fagus sylvatica L. and F. orientalis Lipsky despite strong genetic divergence"

These data sets were used for analyses in the publication "Bidirectional gene flow between Fagus sylvatica L. and F. orientalis Lipsky despite strong genetic divergence" accepted in Forest Ecology and Management <a href="https://www.sciencedirect.com/journal/forest-ecology-and-management/vol/537/suppl/C">Volume 537</a>, 1 June 2023, 120947, <a href="https://doi.org/10.1016/j.foreco.2023.120947">https://doi.org/10.1016/j.foreco.2023.120947</a> For details about the data, please read the corresponding ReadMe files.

opencc-by-4.0Apr 2023View details →

dryad40/100

Data from: Ancient and modern genomes reveal microsatellites maintain a dynamic equilibrium through deep time

Microsatellites are widely used in population genetics, but their evolutionary dynamics remain poorly understood. It is unclear whether microsatellite loci drift in length over time. This is important because the mutation processes that underlie these important genetic markers are central to the evolutionary models that employ microsatellites. We identify more than 27 million microsatellites using a novel and unique dataset of modern and ancient Adélie penguin genomes along with data from 63 published chordate genomes. We investigate microsatellite evolutionary dynamics over two time scales: one based on Adélie penguin samples dating to approximately 46.5 kya, the other dating to the diversification of chordates more than 500 Mya. We show that the process of microsatellite allele length evolution is at dynamic equilibrium; while there is length polymorphism among individuals, the length distribution for a given locus remains stable. Many microsatellites persist over very long time scales, particularly in exons and regulatory sequences. These often retain length variability, suggesting that they may play a role in maintaining phenotypic variation within populations.

opencc-zeroFeb 2024View details →

dryad40/100

Microsatellite data for Aedes aegypti populations in Florida and southern California

In the affiliated paper we compare likely the oldest populations of Aedes aegypti in continental North America with some of the newest to illuminate the range of genetic diversity and structure that can be found within the invasive range of this important disease vector. Aedes aegypti populations in Florida have likely persisted since the 1600-1700s, while populations in southern California derive from new invasions that occurred in the last ten years. For this comparison, we genotyped 1,193 individuals from 29 sites at 12 highly variable microsatellites and a subset of these individuals at 23,961 single nucleotide polymorphisms (SNPs).

opencc-zeroJul 2021View details →

zenodo40/100

Microsatellite data for Gekko hokouensis and G. yakuensis from southern Kyushu and Tanegashima Island, Japan

README_file.txt This file explains the contents of the dataset.   Microsatellite_data_for_Gekko_hokouensis_and_G._yakuensis.csv This file is in STRUCTURE format and contains the raw data of allele lengths collected from 330 individuals using microsatellite genotyping. The first line lists the names of 16 microsatellite loci. The first column lists sample IDs, and the second column lists the names of sampling sites. Two alleles for each sample are listed in two consecutive columns in the subsequent columns. Missing data is represented with -9. These data include genotypic data for 20 pure G. hokouensis and 20 pure G. yakuensis used in Okamoto et al. (2020).

opencc-by-4.0Jun 2023View details →

zenodo40/100

Microsatellite data of the paper "A putatively new ant species from the Cataglyphis cursor group displays low levels of polyandry with standard sexual reproduction"

Fifty colonies of the ant Cataglyphis cursor were sampled at their nest entrance in two localities separated by 79km in the plain of Avila, west of Madrid, in July 2015 for Salobralejo (27 colonies) and in April 2014 for Castrillo de Guareña (23 colonies). Only workers near the nest entrance were collected. In Salobralejo, we also collected nine gynes at the nest entrance in three colonies. After collection, the individuals were preserved in 95% Ethanol (with 5% Tris-EDTA). From the 50 colonies sampled, we genotyped a single worker per colony for 37 colonies (Table S1). For the other 13 colonies, 114 workers were collected and genotyped to assess the colony genetic structure (86 workers from nine colonies in Salobralejo and 28 workers from four colonies in Castrillo). We also genotyped the nine gynes found in three colonies in Salobralejo. A total of 160 individuals were screened for thirteen microsatellite loci used by Eyer et al. (2023) and two supplementary loci (L76 and L3653) were amplified. The L26 locus was excluded because of amplification failures in nine individuals (18% of samples) and a highly significant Hardy-Weinberg disequilibrium (P < 00001 for both sites).  The file contain the locality (Salobralejo or Castrillo), the colony number and individual identification number (code), the caste (worker or gyne). For each locus, the two alleles are provided and characterised by their size.

opencc-by-4.0May 2023View details →

dryad40/100

Data from: Ancient and modern genomes reveal microsatellites maintain a dynamic equilibrium through deep time

Open the record for dataset details and reuse information.

publicFeb 2024View details →

dryad40/100

Microsatellite data for Aedes aegypti populations in Florida and southern California

Open the record for dataset details and reuse information.

publicJul 2021View details →

dryad36/100

Microsatellite genotypes and associated data for: The contribution of clonality to population genetic structure in the sea anemone Diadumene lineata

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 Diadumene lineata 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 Fis, which makes the meaning of mean multilocus Fis unclear.

opencc-zeroNov 2020View details →

dryad36/100

Microsatellite data of Vincetoxicum hirundinaria offspring and their inferred mother plants from 13 populations in the South-Western Finnish Archipelago

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, Vincetoxicum hirundinaria 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 V. hirundinaria 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 V. hirundinaria 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 V. hirundinaria 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 V. hirundinaria 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.

opencc-zeroJan 2021View details →

dryad36/100

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.

opencc-zeroDec 2017View details →

zenodo36/100

GMATA derived ssr files containing Microsatellite data for 128 Phytophthora strains

These 128  files are GMATA software-derived .ssr files, containing Microsatellite data for each Phytophthora strain.

opencc-by-4.0Oct 2021View details →

dryad36/100

Landscape genetics Afromontane forest birds - microsatellite data

<a name="_Hlk61564128"></a>Species confined to naturally fragmented habitats may exhibit intrinsic population complexity which may challenge interpretations of species response to anthropogenic landscape transformation. In South Africa, where native forests are naturally fragmented, forest‐dependent birds have undergone range declines since 1992, most notably among insectivores. These insectivores appear sensitive to the quality of natural matrix habitats, and it is unknown whether transformation of the landscape matrix has disrupted gene flow in these species. We undertook a landscape genetics study of four forest‐dependent insectivorous songbirds across southeast South Africa. Microsatellite data were used to conduct a priori optimization of landscape resistance surfaces (land cover, rivers and dams, and elevation) using cost‐distances along least‐cost pathway (LCP), and resistance distances (IBR). We detected pronounced declines in effective population sizes over the past two centuries for the endemic forest specialist Cossypha dichroa and Batis capensis, alongside recent gene flow disruption in B. capensis, C. dichroa and Pogonocichla stellata. Landscape resistance modelling showed both native forest and dense thicket configuration facilitates gene flow in P. stellata, B. capensis and C. dichroa. Facultative dispersal of P. stellata through dense thicket likely aided resilience against historic landscape transformation, whereas combined forest‐thicket degradation adversely affected the forest generalist B. capensis. By contrast, Phylloscopus ruficapilla appears least reliant upon landscape features to maintain gene flow and was least impacted by anthropogenic landscape transformation. Collectively, gene flow in all four species is improved at lower elevations, along river valleys, and riparian corridors— where native forest and dense thicket better persist. Consistent outperformance of LCP over IBR land‐cover models for P. stellata, B. capensis and C. dichroa demonstrates the benefits of wildlife corridors for South African forest‐dependent bird conservation, to ameliorate the extinction debts from past and present anthropogenic forest exploitation.

opencc-zeroNov 2021View details →

dryad36/100

Microsatellite data from various African buffalo (Syncerus caffer) populations throughout Africa

1280 African buffalo (Syncerus caffer) samples genotyped with up to 19 microsatellites. 1275 samples are from East (12 populations) and southern Africa (4 populations). 5 samples are from central Africa (2 populations).

opencc-zeroDec 2019View details →

dryad36/100

Microsatellite genotype data from: Male-biased dispersal in a fungus-gardening ant symbiosis (Matthews et al, Ecology and Evolution)

For nearly all organisms, dispersal is a fundamental life history trait that can shape their ecology and evolution. Variation in dispersal capabilities within a species exists and can influence population genetic structure and ecological interactions. In fungus-gardening (attine) ants, co-dispersal of ants and mutualistic fungi is crucial to the success of this obligate symbiosis. Female-biased dispersal (and gene flow) may be favored in attines because virgin queens carry the responsibility of dispersing the fungi, but a paucity of research has made this conclusion difficult. Here, we investigate dispersal of the fungus-gardening ant Trachymyrmex septentrionalis using a combination of maternally- (mitochondrial DNA) and biparentally-inherited (microsatellites) markers. We found three distinct, spatially isolated mitochondrial DNA haplotypes; two were found in the Florida panhandle and the other in the Florida peninsula. In contrast, biparental markers illustrated significant gene flow across this region and minimal spatial structure. The differential patterns uncovered from mitochondrial DNA and microsatellite markers suggest that most long-distance ant dispersal is male-biased and that females (and concomitantly the fungus) have more limited dispersal capabilities. Consequently, the limited female dispersal is likely an important bottleneck for the fungal symbiont. This bottleneck could slow fungal genetic diversification, which has significant implications for both ant hosts and fungal symbionts regarding population genetics, species distributions, adaptive responses to environmental change, and coevolutionary patterns.

opencc-zeroDec 2021View details →

dryad36/100

Data from: Demographic and ecogeographic factors limit wild grapevine spread at the southern edge of its distribution range - wild grapevine sampling locations, Maxent input files, morphological and microsatellite data

This dataset contains raw data described in the paper: "Rahimi O., Ohana-Levi N., Brauner H., Inbar N., Hübner S. and Drori E. (2021) "Demographic and ecogeographic factors limit wild grapevine spread at the southern edge of its distribution range", accepted for publication in "Ecology and Evolution". The spatial distribution of plants is constrained by demographic and eco-geographic factors that determine the range and abundance of the species. In this study, we performed genetic and morphological analyzes based on SSR and OIV datasets. In addition, according to the spatial distribution model performed by Maxent software we found that distance to water sources, Normalized difference vegetation index, and precipitation are the main environmental factors constraining V.v. sylvestris distribution at its southern distribution range. All raw data used for this study can be found in this deposit which contains a table with grapevine locations, Maxent input files, morphological and microsatellite data.

opencc-zeroApr 2022View details →

dryad36/100

Microsatellite data for Bull Trout

Freshwater ecosystems are negatively impacted by a variety of anthropogenic stressors, with concomitant elevated rates of population decline for freshwater aquatic vertebrates. Because reductions in population size and extent can negatively impact genetic diversity and gene flow, which are vital for sustained local adaptation, it is important to measure these characteristics in threatened species that may yet be rescued from extinction. Across its native range, Bull Trout (Salvelinus confluentus) extent and abundance are in decline due to historic overharvest, invasive nonnative species, and habitat loss. In Alberta's Eastern Slope region, populations at the range margin have progressively been lost, motivating us to better understand the amount and distribution of genetic variation in headwater habitats and some downstream sites where they continue to persist. Across this region, we sampled 431 Bull Trout from 20 sites in the Athabasca and Saskatchewan River basins and assayed 10 microsatellite loci to characterize within- and among-population genetic variation. The Saskatchewan and Athabasca River basins contained similar levels of heterozygosity but were differentiated from one another. Within the Athabasca River basin, five genetically differentiated clusters were found. Despite the evidence for genetic differentiation, we did not observe significant isolation-by-distance patterns among these sites. Our findings of ample genetic diversity and no evidence for hybridization with non-native Brook Trout in headwater habitats provide motivation to ameliorate downstream habitats and remove anthropogenic barriers to connectivity towards the goal of long-term persistence of this species.

opencc-zeroSep 2022View details →

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Microsatellite data for Cryptopygus antarcticus travei

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.

opencc-zeroJul 2024View details →

zenodo36/100

Genotype data of 10 nuclear microsatellite loci for 30 Quercus acutissima populations in China

This dataset includes genotype data of 10 nuclear microsatellite loci for 707 individuals of Quercus acutissima from 30 natural populations in China.

opencc-by-4.0Sep 2018View details →

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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.

opencc-zeroDec 2017View details →

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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.

allen-brain-atlas

neuroscienceopenDocumentation, web resources, and API references are available online.

Last verified 2026-04-30Open record

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.

abode-home-cage

behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.

Last verified 2026-04-30Open record

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.

dandi-nwb

electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.

Last verified 2026-04-30Open record

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.

ibl

behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.

Last verified 2026-04-29Open record

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.

openneuro

neuroscienceopenPublished datasets are available on demand over the internet.

Last verified 2026-04-29Open record