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738 results for “microsatellites”
Arctic grayling neutral genomic microsatellite loci from the Kuparuk, the Sagavanirktok (primarily Oksrukuyik Creek) and the Itkillik (primarily the I-Minus outlet stream) watersheds, 2010-2014
Since 2009, The FISHSCAPE Project (National Science Foundation grants: 1719267, 1417754, and 0902153), based at Toolik Field Station, has monitored physical, chemical, and biological parameters within three watersheds: The Kuparuk (including Toolik Lake and Toolik outlet stream), The Sagavanirktok (primarily Oksrukuyik Creek, but also including sections of the Atigun River and Tea and Galbraith Lakes), and Itkillik (primarily the I-Minus outlet stream a tributary that that feeds into the Itkilik River). Goals of the FISHSCAPE project are to understand and predict the adaptability and persistence of a key Arctic species, the Arctic grayling (Thymallus arcticus), to changing climate and hydrology. Research questions include: (1) Does landscape structure determine movement within and among watersheds; (2) do populations adapt to stream characteristics at local and regional scales; and (3) will the relative adaptability of populations determine their persistence under future climate change. We used genetics to investigate population structure and landscape genetics for Arctic grayling. Adult and young-of-the-year fish were captured at sampling locations and coordinates and/or specific station locations were noted. Fin clip samples (adults) or whole fish (young-of-the-year) were collected and preserved in 95% ethanol until Deoxyribonucleic acid (DNA) was extracted. Polymerase chain reaction (PCR) products from neutral genomic microsatellite loci were scored and used to assess population genetic structure and other population parameters. Adult capture and movement data, including length, weight and Passive Integrated Transponder (PIT) tag information, can be found in a separate data package.
Cichlasoma urophthalmus microsatellite fragment size collected from the Florida Everglades (FCE) and Central America from June 2010 to March 2013
Fragment sizes for 17 microsatellite markers obtained from samples of Cichlasoma urophthalmus collected from fin clippings of fish caught by angling and/or cast netting within the Florida Everglades and Central America. DNA was extracted, amplified and sizes of microsatellite fragments were rounded to nearest unit. Data were used to determine population genetic structure using GenAlex, Structure and DIYABC programs.
SBC LTER: Reef: Microsatellite markers for the giant kelp, Macrocystis pyrifera
These data were published as a technical note: Alberto, F., A. C. Whitmer, N. C. Coelho, M. Zippay, E. Varela-Alvarez, P. T. Raimondi, D. C. Reed and E. A. Serrão. 2009. Microsatellite markers for the giant kelp Macroystis pyrifera. Conservation Genetics. 10:1915-1917 doi: 10.1007/s10592-009-9853-9 Abstract: We report the isolation and characterization of 16 microsatellite loci to study the population genetics of the giant kelp, Macrocystis pyrifera. Markers were obtained by screening a genomic library enriched for microsatellite motifs. Of the 37 primer pairs defined, 16 amplified clean polymorphic microsatellites and are described. These loci identified a number of alleles ranging from three to forty (mean= 16.5, and gene diversity ranging from 0.469 to 0.930 (mean= 0.774). The isolation and characterization of these highly polymorphic markers will greatly benefit much needed studies on the molecular ecology of this important macroalga. These data report the isolation and characterization of 16 microsatellite loci to study the population genetics of the giant kelp, Macrocystis pyrifera. 180 samples of blade tissue were collected at Carpinteria Reef, Santa Barbara Channel, CA (USA) in July 2006. Sequence data are available from GenBank. These data were published as a Technical Note in the journal Conservation Genetics in 2009.
SBC LTER: Reef: Geospatial structure of microsatellite markers for the giant kelp, Macrocystis pyrifera, Santa Barbara CA, 2009
Data package includes data and R code for the examination of geospatial genetic structure (SGS) and simulation of inbreeding in giant kelp (Macrocystis pyrifera) from the Santa Barbara Channel, California. Data are reported for microsatellite markers from individual giant kelp plants from Carpinteria Reef, Mohawk Reef and Goleta Bay, collected during September 2009. Relative X and Y coordinates (meters) were recorded for each specimen sampled. R code consists of two scripts, a) to calculate mean number of alleles per locus, and observed and expected heterozygosity, and b) to simulate self-fertilization and sibling/cousin relationships. These data were presented in: Johansson, Mattias L, Raimondi, Peter T, Reed, Daniel C, Coelho, Nelson C, Serrão, Ester A, Alberto, Filipe A. In press. Looking into the black box: simulating the role of self-fertilization and mortality in the genetic structure of Macrocystis pyrifera. Molecular Ecology, 22:4842–4854. These data are also available from: Johansson ML, Raimondi PT, Reed DC, Coelho NC, Serrão EA, Alberto FA (2013) Data from: Looking into the black box: simulating the role of self-fertilization and mortality in the genetic structure of Macrocystis pyrifera. Dryad Digital Repository. doi:10.5061/dryad.s1b07.
Sequence-based microsatellite data of Anadenanthera colubrina (Leguminosae)
<p>The file contains SSRseq genotyping data of <em>Anadenanthera colubrina</em> 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 <em>Anadenanthera colubrina</em> (Leguminosae).</p> <p>The file contains</p> <p>- Two different data sets:</p> <p>GS: Genotypes based on sequence identity.<br>GL: Genotypes based on amplicon length.</p> <p>- Allele sequence information</p>
Microsatellite genotypes for «Genetic diversity and spatial genetic structure support the specialist‑generalist variation hypothesis in two sympatric woodpecker species»
<p>Species are often arranged along a continuum from “specialists” to “generalists”. Specialists typically use fewer resources, occur in more patchily distributed habitats and have overall smaller population sizes than generalists. Accordingly, the specialist-generalist variation hypothesis (SGVH) proposes that populations of habitat specialists have lower genetic diversity and are genetically more differentiated due to reduced gene flow compared to populations of generalists. Here, expectations of the SGVH were tested by examining genetic diversity, spatial genetic structure and contemporary gene flow in two sympatric woodpecker species differing in habitat specialization. Compared to the generalist great spotted woodpecker (<em>Dendrocopos major</em>), lower genetic diversity was found in the specialist middle spotted woodpecker (<em>Dendrocoptes medius</em>). Evidence for recent bottlenecks was revealed in some populations of the middle spotted woodpecker, but in none of the great spotted woodpecker. Substantial spatial genetic structure and a significant correlation between genetic and geographic distances were found in the middle spotted woodpecker, but only weak spatial genetic structure and no significant correlation between genetic and geographic distances in the great spotted woodpecker. Finally, estimated levels of contemporary gene flow did not differ between the two species. Results are consistent with all but one expectations of the SGVH. This study adds to the relatively few investigations addressing the SGVH in terrestrial vertebrates.</p>
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"
<p>These data sets were used for analyses in the publication "Bidirectional gene flow between <em>Fagus sylvatica</em> L. and<em> F. orientalis</em> 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></p> <p>For details about the data, please read the corresponding ReadMe files.</p>
Kelp Metapopulations: Macrocystis pyrifera microsatellite marker biogeography study
Dataset contains microsatellite genotypes specific for Macrocystis pyrifera (giant kelp). Table 1 describes seven loci from blades collected from 62 sites from Alaska, USA, to Baja California, Mexico, and Table 2 blades collected at 38 sites (subpopulations) in central California (Monterey Bay). Each row is the multilocus genotype for a single specimen (individual). These data were described in <ulink url="http://dx.doi.org/10.1111/mec.13371">Johansson ML, Alberto F, Reed DC, Raimondi PT, Coelho NC, Young MA, Drake PT, Edwards CA, Cavanaugh K, Assis J, Ladah LB, Bell TW, Coyer JA, Siegel DA, Serrão EA (2015) Seascape drivers of Macrocystis pyrifera population genetic structure in the northeast Pacific. Molecular Ecology. 24, 4866–4885.</ulink>
Data from: Ancient and modern genomes reveal microsatellites maintain a dynamic equilibrium through deep time
<p>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.</p>
Fig. 2 in Microsatellite Variability Of Two Populations Of Clarias Gariepinus (Siluriformes, Clariidae) In Nigeria
Fig. 2. Genetic dendrogram of C. gariepinus from two vegetation zone (Lokoja and Asejire) of Nigeria.
Fig. 1 in Molecular Characterization Of Lates Niloticus (Perciformes, Latidae) Populations From Three Nigerian Waterbodies Using Random Amplified Polymorphic Dna And Microsatellite Markers
Fig. 1. Map showing the sample locations of L. niloticus (Linnaeus, 1758). Population 1 — Kainji lake, Population 2 — River Benue, Makurdi and Population 3 — Ikere-Gorge reservoir, Iseyin, Oyo state.
Joint analysis of microsatellites and flanking sequences enlightens complex demographic history of interspecific gene flow and vicariance in rear-edge oak populations
<p><span>Inference of recent population divergence requires fast evolving markers and necessitates to differentiate shared genetic variation caused by ancestral polymorphism and gene flow. Theoretical research shows that the use of compound marker systems integrating linked polymorphisms with different mutational dynamics, such as a microsatellite and its flanking sequences, can improve estimation of population structure and inference of demographic history, especially in the case of complex population dynamics. However, empirical application in natural populations has so far been limited by lack of suitable methods for data collection. A solution comes from the development of sequence-based microsatellite genotyping which we used to study molecular variation at 36 sequenced nuclear microsatellites in seven <em>Quercus canariensis</em> and four <em>Q. faginea</em> rear-edge populations across Algeria. We aim to decipher their taxonomic relationship, past evolutionary history and recent demographic trajectory. First, we compare the estimation of population genetics parameters and simulation-based inference of demographic history from microsatellite sequence alone, flanking sequence alone or the combination of linked microsatellite and flanking sequence variation. Second, we apply random forest approximate Bayesian computation to identify which of these sequence types is most informative. Whereas analysing microsatellite variation alone indicates recent interspecific gene flow, additional information gained by integrating nucleotide variation in flanking sequences, by reducing homoplasy, suggests ancient interspecific gene flow followed by drift in isolation instead. The weight of each polymorphism in the inference also demonstrates the value of linked variations with contrasted mutation dynamic to improve estimation of both demographic and mutational parameters.</span></p>
Evaluation of DNA extracted from timber rattlesnake (Cotalus horridus) cloacal and blood swabs for microsatellite genotyping
<p>Genetic research is a key component to modern wildlife conservation, but it is contingent on the collection of reliable and high-quality genetic samples. Invasive genetic sampling techniques have potential to negatively impact individuals, which may be prohibitive when working with threatened and endangered species. Prior to sample collection, project managers must try to balance the negative impact on individuals included in the study with the demand for DNA and the difficulty of obtaining samples. Although established methods for blood and tissue collection in reptiles meet the need for high-quantity and quality DNA, they inherently require longer handling times and more skill to obtain. Thus, non-invasive DNA collection methods, such as cloacal swabs, may be preferred when animal welfare is a priority. Cloacal swabs are quicker, easier, require less training and reduce handling time. To evaluate cloacal swabbing as an alternative to collecting blood, we obtained both cloacal and blood swabs. We extracted DNA from cloacal and blood cells that were collected from 23 Timber Rattlesnakes (Crotalus horridus). We assessed DNA by purity (A260/A280), concentration, and microsatellite genotyping. Our results show high-quality DNA can be obtained from both cloacal swabs and blood samples, but quality and concentration of DNA was significantly lower from cloacal swabs. Further, degradation and contamination affects the performance of cloacal DNA when compared to blood DNA in microsatellite-based genotyping. Although we recommend collecting blood samples whenever possible to obtain the highest-quality DNA, cloacal swabs represent a viable alternative for genetic sampling when using microsatellite loci as genetic markers.</p>
Figure 3 in Genome-wide characterization of microsatellites and development of polymorphic markers shared between two weevils of Eucryptorrhynchus (Coleoptera: Curculionidae)
Figure 3. Genetic structure of Eucryptorrhynchus brandti (a) and E. scrobiculatus (b) populations based on 14 microsatellite markers inferred using the software STRUCTURE. Each bin indicates an individual. Different colors show the identified clusters. The best number of clusters (K) is 3. Abbreviations: BJHD—Haidian District, Beijing; NXZW—Zhongwei, Ningxia; SDTA—Tai'an, Shandong; SXYL—Yangling, Shaanxi.
Figure 2 in Genome-wide characterization of microsatellites and development of polymorphic markers shared between two weevils of Eucryptorrhynchus (Coleoptera: Curculionidae)
Figure 2. Frequency distribution of microsatellites among different motifs in the Eucryptorrhynchus brandti and E. scrobiculatus. The "others" category represents summed motifs with counts below 100.
Figure 1 in Genome-wide characterization of microsatellites and development of polymorphic markers shared between two weevils of Eucryptorrhynchus (Coleoptera: Curculionidae)
Figure 1. Collection sites for specimens of Eucryptorrhynchus brandti (red) and E. scrobiculatus (green). Abbreviations: BJHD— Haidian District, Beijing (116.22°E, 40.04°N); NXZW—Zhongwei, Ningxia (105.12°E, 37.50°N); SDTA—Tai'an, Shandong (116.72°E, 36.27°N); SXYL—Yangling, Shaanxi (108.07°E, 34.26°N).
FIG. 1 in Microsatellite development in the freshwater red alga Batrachospermum gelatinosum (L.) De Candolle (Batrachospermales, Rhodophyta)
FIG. 1. — Images of Batrachospermum gelatinosum (L.) De Candolle: A, gametophytes fixed to a log at Cedar Bog in Ohio. Often this species has a brown to olive-green color; B, multiple gametophytes in a 55 cm diameter bowl;C, a single gametophyte mounted on herbarium paper. Photo credits: A, Stacy A. KruegerHadfield; B, C, Morgan L. Vis. Scale bars: A, 10 cm; B, 1.5 cm; C, 1 cm.
Fig. 1 in Genetic Diversity In Peripheral And Central Populations Of Rusty-Necklaced Partridge (Alectoris Magna) Based On Mitochondrial And Microsatellite Dna
Fig. 1. Rusty-necklaced partridge sampling sites: 1 = Lanzhou, 2 = Jingyuan, 3 = Haiyuan, 4 = Dingxi, 5 = Huining, 6 = Wushan, 7 = Beidao, 8 = Lixian
FIGURE 1 in Development of microsatellite loci and population genetics in the bumblebee catfish species Pseudopimelodus atricaudus and Pseudopimelodus magnus (Siluriformes: Pseudopimelodidae)
FIGURE 1 | Sampling sites of Pseudopimelodus magnus and P. atricaudus in the middle and lower sectors of the Cauca River.
Fig. 2. Chromatograph comparing original and redesigned primers for Ccmic3 in Inheritance of fifeen microsatellite loci in Ceratitis capitata (Diptera: Tephritidae)
Fig. 2. Chromatograph comparing original and redesigned primers for Ccmic3 on sample A1-F1-07, Family A1. Both reactions were run simultaneously on the same fragment analysis plate using the same PCR conditions, DNA concentrations, and dilution factor. a) Chromatograph of progeny exhibiting an allele call of 74/74. Parents are 74/76 and 76/76. The observed 76 bp peak was considered to be weak. Cloning and sequencing confirmed the existence of this 76 bp fragment. b) Chromatograph of the same progeny as in Fig. 2a now exhibiting an allele call of 72/74 afer primer modification. Parents are now 72/74 and 74/74. The observed 74 bp peak is more pronounced compared to the previous 76 bp call. The intensity of the 74 bp peak also increased while the other 3 visible peaks decreased. This suggests an increase in adenylation has occurred.
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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
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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.