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1,598 results for “genetic diversity”
Figure 1 in PCR-RFLP Based genetic diversity of Plasmodium vivax genotypes in district Mardan, Pakistan
Figure 1. Prevalence of four different alleles of Pvmsp-3α (A, B, C and D) from PCR-RFLP
Figure 3 in PCR-RFLP Based genetic diversity of Plasmodium vivax genotypes in district Mardan, Pakistan
Figure 3. Prevalence of three different alleles of Pvmsp-3β (A, B, C) from PCR-RFLP.
Supplementary Materials for Respiratory Syncytial Virus Genetic Diversity and Lineage Changes in Ireland pre- and post-COVID-19 pandemic
<p><span>The datasets presented here are the list of publicly available reference sequences used in NextClade (</span><a href="https://github.com/rsv-lineages"><span>https://github.com/rsv-lineages</span></a><span>) to provide the lineage classification of samples and used as reference for analysis of Irish RSV sequences (Supplementary Table 1), the list of sequenced Human respiratory syncytial viruses (RSV) in the Republic of Ireland during the period 2015-2024 (Supplementary Table 2) and the details of sequences downloaded from GISAID corresponding to European RSV sequences for the same period of time.</span></p> <p><span> </span></p> <p><span>Description of the data and file structure</span></p> <p><span>The files in this dataset were formatted in Microsoft Excel 2019 to allow easy access and manipulation of the data. The data corresponds to details on the sequences used in the analysis of RSV in Europe during the 2015-2024 period. The contents of the files are described below: -<strong>Supplementary Table 1</strong>: NextClade Reference Sequences publicly available at </span><a href="https://github.com/rsv-lineages"><span>https://github.com/rsv-lineages</span></a><span>. -<strong>Supplementary Table 2</strong>: Irish RSV Sequence Details contains details on the sequences generated in our study with the GenBank accession number, the GISAID accession number, reported collection RSV season, Nextclade assigned taxonomical clade. -<strong><span>Supplementary Table 3</span></strong>: European RSV Sequence Details contains a list of European RSV sequences downloaded from GISAID (</span><a href="https://gisaid.org/"><span>https://gisaid.org/</span></a><span>) with details on the sampling RSV season, the accession number, country of collection, and lineage assigned by NextClade.</span></p> <p><span> </span></p> <p><span>Sharing/Access information</span></p> <p><span>The databases used to extract and deposit the data were:</span></p> <p><span>-GenBank: the North American repository of sequences and publicly available at: </span><a href="https://www.ncbi.nlm.nih.gov/genbank/"><strong><span>https://www.ncbi.nlm.nih.gov/genbank/</span></strong></a><span> </span></p> <p><span>-GISAID:International consortium of sequences with some metadata and clinical data. It is a semi-public repository with easy access requiring only to create an account. Available at: </span><a href="https://gisaid.org/"><strong><span>https://gisaid.org/</span></strong></a></p> <p><span>-Github: reference sequences of RSV are available at the repository </span><a href="https://github.com/"><strong><span>https://github.com/</span></strong></a></p>
Fig. 1 in Trypanosomes genetic diversity, polyparasitism and the population decline of the critically endangered Australian marsupial, the brush tailed bettong or woylie (Bettongia penicillata)
Fig. 1. Geographical origin of the different species of marsupials trapped in this study.
Fig. 1 in Marked genetic diversity within Blastocystis in Australian wildlife revealed using a next generation sequencing-phylogenetic approach
Fig. 1. Map showing Melbourne's water catchment areas where samples were collected (2009-2022).
Fig.1 in Preliminary Studies On The Genetic Diversity Of An Endemic And Endangered Species Saussurea Esthonica Baer Ex Rupr. In Latvia
Fig.1 Genetic diversity measures between populations based on retrotransposon markers
Fig.3 in Preliminary Studies On The Genetic Diversity Of An Endemic And Endangered Species Saussurea Esthonica Baer Ex Rupr. In Latvia
Fig.3 Principal coordinate analysis based on retrotransposon analysis
A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals (GWAS)
<p>GWAS summary statistics accompanying manuscript "A Comprehensive Assessment of Demographic, Environmental and Host Genetic Associations with Gut Microbiome Diversity in Healthy Individuals".</p>
Figure 1 in Phylogenetic status and genetic diversity of corsac fox (Vulpes corsac) in Golestan Province, Iran
Figure 1. Geographic location of collected samples.
Figure 2 in A Lessepsian invader round herring (Etrumeus golanii) with high genetic diversity without bottlenecking in the northeastern Mediterranean Sea
Figure 2. Neighbor-joining tree of E. golanii populations.
Figure 1 in A Lessepsian invader round herring (Etrumeus golanii) with high genetic diversity without bottlenecking in the northeastern Mediterranean Sea
Figure 1. Sampling localities (1. İskenderun, 2. Antalya, 3. Marmaris).
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.
Fig. 1 in Genetic diversity of Halyomorpha halys (Hemiptera, Pentatomidae) in Korea and comparison with COI sequence datasets from East Asia, Europe, and North America
Fig. 1. Halyomorpha halys collection sites in Korea and the USA.
FIGURE 5 in A new species of Knodus (Characiformes: Characidae), with deep genetic divergence, from the Mearim and Munim river basins, Northeastern Brazil, and evidence for hidden diversity in adjacent river basins
FIGURE 5 | Geographical distribution of Knodus guajajara.
RAD-seq generated single nucleotide polymorphisms resolve patterns of genetic diversity and structure of the freshwater mussel Ptychobranchus fasciolaris in glaciated and unglaciated regions of North America
<p>Included are the initial unfiltered SNP output from the STACKS pipeline, and the final filtered SNP dataset in VCF format used to do analysis in the manuscript titled "<span>RAD-seq generated single nucleotide polymorphisms resolve patterns of genetic diversity and structure of the freshwater mussel <em>Ptychobranchus fasciolaris </em>in glaciated and unglaciated regions of North America" which was submitted to <em>Hydrobiologia </em>in September 2024.</span></p>
Development of tools to rapidly identify cryptic species and characterize their genetic diversity in different European kelp species
<p>Marine ecosystems formed by kelp forests are severely threatened by global change and local coastline disturbances in many regions. In order to take appropriate conservation, mitigation and restoration actions, it is crucial to identify the most diverse populations which could serve as a "reservoir" of genetic diversity. This requires the development of specific tools, such as microsatellite markers to investigate the level and spatial distribution of genetic diversity. Here, we tested new polymorphic microsatellite loci from the genome of the kelp, <i>Lamina</i><i>ria digitata,</i> and tested them for cross-amplification and polymorphism in four closely related congeneric species (<i>Laminaria hyperborea, Laminaria ochroleuca, Laminaria rodriguezii and Laminaria pallida</i>). Adding these 20 new microsatellite loci to the ten <i>L. digitata</i> loci previously developed by Billot et al. (1998) and Brenan et al. (2014) and to the ten <i>L. ochroleuca</i> loci previously developed by Coelho et al. (2014), we retained a total of 30 polymorphic loci for <i>L. digitata</i>, 19 for <i>L. hyperborea</i>, 16 for <i>L ochroleuca</i>, 19 for<i> L. rodriguezii</i> and 12 for<i> L. pallida</i>. These markers have been tested for the first time in the last two species. As predicted, the proportion of markers that cross-amplified between species decreased with increasing genetic distance. In addition, as problems of species identification were reported in this genus, mainly between <i>L. digitata </i>and <i>Hedophyllum nigripes</i>,<i> </i>but also between <i>L. digitata, L. hyperborea </i>and<i> L. ochroleuca </i>in areas where their range distributions overlap, we report a rapid PCR identification method based on species-specific cox1 mitochondrial primers that allows these four species of kelp to be rapidly distinguished.</p>
Metapopulation connectivity retains genetic diversity following historical bottleneck in a federally endangered seabird
<p>Despite intensive management since the 1970s, recovery of the endangered northwestern Atlantic population of the Roseate Tern (<i>Sterna dougallii dougallii</i>) has not offset low productivity from a female-biased sex ratio, low adult survival, and habitat constriction. Now, >90% of individuals breed at three sites within 200 km from Long Island, NY to Buzzards Bay, MA (warm-water subregion). To characterize the impact of historical bottlenecks, metapopulation structure, and demographic fluctuations on genetic variation, Roseate Terns from the warm-water (1870s, 1970s, 1997, 2016) and cold-water (Nova Scotia, Canada; 2018) subregions were genotyped at 8-16 microsatellites and two-three mitochondrial regions. Diversity declined in the warm-water subregion from the 1870s (H<sub>E</sub>= 0.44, A<sub>R</sub>= 2.86) and 1970s (H<sub>E</sub> = 0.53, A<sub>R </sub>= 3.25) to 1997 (H<sub>E</sub> = 0.38, A<sub>R </sub>= 2.58). Genetic signatures of bottlenecks persisted in 1997 (<i>P</i> = 0.001 – 0.003) and 2016 (<i>P</i> = <0.001 – 0.005), but an increase in variation occurred by 2016 (H<sub>E</sub>= 0.50, A<sub>R</sub>= 2.85). Weak structure was detected between contemporary warm- and cold-water subregions (θ = 0.06) and within the warm-water subregion (θ = 0.04). Both demographic (<span><span></span></span>= 3439-3821) and genetic (<span><span></span></span>= 3040) estimates suggested effective population size stability over the last 100 years, despite large fluctuations in census size (4000 – 8662). Results suggest that 50 years of management (restoring habitat, preventing gull encroachment, controlling predators) at colony sites supported a small, stable <i>N<sub>e</sub></i> and maintained a hierarchical metapopulation that allowed gene flow to redistribute genetic variation throughout the NW Atlantic. The metapopulation remains highly vulnerable to stochastic events but harbors resiliency and redundancy through gene flow and a stable <i>Ne</i>. For long-term persistence from a genetic perspective, managers must maintain the major source colonies, increase availability of high-quality peripheral breeding sites, and protect concentrated non-breeding sites that facilitate gene flow.</p>
Temporally-balanced selection during development of larval Pacific oysters (Crassostrea gigas) inherently preserves genetic diversity within offspring
<p>Balancing selection is one of the mechanisms which has been proposed to explain the maintenance of genetic diversity in species across generations. For species with large populations and complex life histories, however, heterogeneous selection pressures may create a scenario in which the net effects of selection are balanced across developmental stages. With replicated cultures and a pooled sequencing approach, we show that genotype-dependent mortality in larvae of the Pacific oyster (Crassostrea gigas) is largely temporally dynamic and inconsistently in favor of a single genotype or allelic variant at each locus. Overall, the patterns of genetic change we observe to be taking place are more complex than what would be expected under classical examples of additive or dominant genetic interactions. They are also not easily explained by our current understanding of the effects of genetic load. Collectively, temporally heterogeneous selection pressures across different larval developmental stages may act to maintain genetic diversity in oysters, while also inherently sheltering genetic load within populations.</p>
Figure 1 in Genetic diversity, population structure and demographic history of Dugesia japonica in Taihang Mountains
Figure 1. Geographical distribution of Dugesia japonica populations sampled in Taihang Mountains.
Data and scripts from: Balanced polymorphism fuels rapid selection in an invasive crab despite high gene flow and low genetic diversity
<p><em>Carcinus maenas</em> is a globally invasive species which spreads and thrives across a range of temperate environments. In the northwestern Pacific, the species has spread across >12 degrees of latitude in 10 years from a single source, following its introduction <35 years ago. Using six locations spanning >1,500 km, we examined genetic structure and selection to temperature using 9,376 Single Nucleotide Polymorphisms (SNPs) derived from cardiac transcriptome sequencing.</p> <p>Data in this repository includes information on sequenced samples (*.csv, *.txt), a cleaned transcriptome assembly after expression filtering (*.fasta), transcriptome annotation from EnTAP (*.tsv), list of transcripts removed from analysis after mapping (*.txt), high-quality SNPs identified from the transcriptome sequencing with GATK (seven files representing different SNP sets used in the analysis; *.vcf), and four custom scripts used in processing SNP data (*.py and *.R).</p> <p>Raw sequence data is archived in GenBank's SRA. 2015-2016 samples: BioProject ID PRJNA690934 and BioSample IDs SAMN17267686–SAMN17267781. 2011 samples: BioProject ID PRJNA283611 and BioSample IDs SAMN03653390–SAMN03653413.</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
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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.