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1,467 results for “Genetic structure”
FIGURE 5 in Phylogeography and Genetic Structure in the California Giant Salamander (Dicamptodon ensatus): Impacts of current and historic landscape features
FIGURE 5. Isolation by distance plot. P value calculated by Mantel test. (y = 0.00292 x + 0.07696, r2 = 0.809, P = 0.007).
FIGURE 3. a in Phylogeography and Genetic Structure in the California Giant Salamander (Dicamptodon ensatus): Impacts of current and historic landscape features
FIGURE 3. a) mtDNA TCS haplotype network of the control region. b) nuDNA haplotype TCS network of E16C7. Colors of clusters are coded to match the coalescent tree clade branches. Circle size is proportional to haplotype occurrence and numbers refer to occurrence sampled if greater then one.
Genetic structure, phylogeography, adaptive variation and speciation in the tropical tree genus Symphonia
<p>S9.2.1. SNP genotypes of <em>Symphonia globulifera</em> samples generated by Genotyping-by-sequencing</p> <p>S9.4.2. SNP genotypes of <em>Symphonia globulifer</em>a and Malagasy <em>Symphonia </em>samples generated by Sequenom technology</p> <p> </p>
Host genetics, phenotype and geography structure the microbiome of a foundational seaweed
<p>Interactions between hosts and their microbiota are critical to the functioning and resilience of eukaryotic macro-organisms. Critically, for hosts that play foundational roles in communities, understanding what drives these interactions is essential for informing restoration and conservation of entire ecosystems. Here, we investigated the relative influence of host traits and the surrounding environment on microbial communities associated with the foundational seaweed Phyllospora comosa. We collected data on 16 morphological and functional phenotypic traits, host genetics (using 354 Single Nucleotide Polymorphisms) and surface-associated microbial communities (using 16S rRNA gene amplicon sequencing) from 160 individuals sampled from eight sites spanning Phyllospora's entire latitudinal distribution (1300 km). Combined, these factors explained 54% of the overall variation in Phyllospora's associated microbial community structure, much of which was related to the local environment (~32%). We found that putative "core" microbial taxa (i.e. present on all Phyllospora individuals sampled) exhibited slightly higher association with host traits when compared to "variable" taxa (not present on all individuals). We identified several key genetic loci and phenotypic traits in Phyllospora that were strongly related to multiple microbial amplicon sequence variants, including taxa with known associations to seaweed defense, disease and tissue degradation. This information on how host-associated microbial communities vary with host traits and the environment enhances our current understanding of holobionts and how they are structured. Such understanding can be used to inform management strategies of these important and vulnerable habitats.</p>
Heterogeneous genetic structure in eastern North American peatmosses (Sphagnum)
<p><span><span><span>Bryophytes generally have broad geographic ranges that suggest high dispersal ability. The aim of this study was to test hypotheses about dispersal limitation, as indicated by isolation by distance (IBD), in four spore producing species of the moss genus <i>Sphagnum</i> (<i>S. carolinianum</i>, <i>S. missouricum</i>, <i>S. macrophyllum</i>, <i>S. pylaesii</i>), and to assess whether plants in the southern United States harbor high levels of unique alleles and/or other indicators of exceptional genetic diversity. IBD was detected in all four species, but regional patterns of genetic structure were very species-specific. One species, <i>S. macrophyllum</i>, exhibited differentiation between northern and southern genetic groups that appear to reflect more ancient phylogenetic diversification.</span></span></span></p>
Assessing the population genetic structure of introduced rainbow trout (Oncorhynchus mykiss) in the Lake Tahoe basin: A case for understanding hybridization potential during the reintroduction of the native Endangered Species Act listed Lahontan cutthroat trout (O. clarkii henshawi)
<p class="MsoNormal">Hybridization with introduced or invasive species is a major threat and driver of population declines in native salmonids. The rainbow trout (<em>Oncorhynchus mykiss</em>, RBT) has been widely introduced globally and represents an important invasive species, often establishing entrenched naturalized populations. The cutthroat trout (<em>Oncorhynchus clarkii</em>, CT), a close congener, is particularly susceptible to competition and hybridization from RBT introductions which has led to range-wide population declines and loss of CT genetic variation. The Lahontan CT (<em>O. c. henshawi</em>, LCT) whose historic distribution included the Lake Tahoe basin, was extirpated by the 1940s due to overfishing and introduction of nonnative salmonids, including now naturalized RBT. Here, we characterize genetic variation of RBT in a subset of Lake Tahoe tributaries to assess potential homing of RBT to streams for spawning, thereby informing LCT reintroduction. Diploid reproductively viable RBT were stocked annually into Lake Tahoe from the late 1800s until the mid-2000s by California and Nevada fish and wildlife agencies, planting the same commonly raised hatchery strains over time. Since 2007, triploid RBT comprise the bulk of RBT planted. Despite extensive dispersal from stocking locations, our analyses revealed variation in population differentiation among tributaries, with individuals from spatially proximate streams clustering across multiple population genetic analyses. Although subtle, we detected evidence for genetic differentiation among tributaries from the southern, western, and northern regions, including surprising structure involving a single tributary. These results illustrate the extent of differentiation within and among streams and could inform possibilities for and implications of RBT removal and LCT reintroduction.</p>
Conserving on the edge: genetic variation and structure in northern populations of the endangered plant Dracocephalum ruyschiana L. (Lamiaceae)
<p>Loss of biodiversity is accelerating, including the loss of genetic diversity. Conservation of small, isolated populations may be important, as they can provide valuable contributions to overall genetic variation and long-term viability of species. Furthermore, such populations may play an essential role in adaptation to new environments following changes in e.g. land-use and climate. <em>Dracocephalum ruyschiana</em> is a threatened plant species throughout its European distribution, but 25% of the European populations are situated within Norway. Therefore, the species has its own action plan in Norway, which includes demographic monitoring. However, this monitoring does not cover genetic variation nor is the selection of monitored populations based on genetic differentiation, therefore this fundamental level of biodiversity is overlooked. We analyzed 43 sites using 96 SNPs developed for <em>D. ruyschiana</em>, to investigate whether the monitored populations cover the genetic variation and differentiation found within the Norwegian distribution. The results show structuring and differentiation between populations and indicate that there are at least four distinct genetic groups, of which only two are covered extensively by current demographic monitoring. We suggest that two sites representing the two other genetic groups should be included in the national monitoring program to better conserve the genetic variation found in the Norwegian population of <em>D. ruyschiana</em>. Overall, our results highlight the importance of an integrated, interdisciplinary framework to better monitor and conserve biodiversity at several levels.</p>
Genetic structure and evolution of diploid Cochlearia in Iceland
<p>Within the northern European <em>Cochlearia</em> (Brassicaceae), considerable chromosome variation has taken place without corresponding morphological differentiation, which has resulted in an intricate species complex including two base chromosome numbers and several ploidy levels. Here, we dig into the<em> </em>situation in Iceland. The distribution, genetic structure, taxonomy and origin of the two <em>Cochlearia</em> cytotypes (2<em>n</em> = 12 and 2<em>n</em> = 14) present in Iceland are discussed. Chromosome counts indicate that the 2<em>n</em> = 12 populations are dominating along the coast, whereas only 2<em>n</em> = 14 has been reported for inland alpine populations. RADseq data support geographically structured genetic variation along the Icelandic coast, as well as environmentally structured genetic differentiation between coastal and alpine populations. The alpine populations show genetic and morphological affiliation with <em>C. groenlandica </em>(2<em>n</em> = 14), which is widely distributed in the Arctic, but more comprehensive sampling is needed to conclude on the taxonomical status of the Icelandic coastal plants. To uncover the origin of and phylogenomic relationship among the two chromosome variants, comparative whole-genome sequencing should be performed.</p> <div></div>
Data from: Traces of Genetic but Not Epigenetic Adaptation in the Invasive Goldenrod Solidago canadensis Despite the Absence of Population Structure
<p><strong>General information</strong></p> <p>This deposition contains the datasets that were used in the statistical analysis of the manuscript entitled <strong>Traces of genetic but not epigenetic adaptation in the invasive goldenrod <em>Solidago canadensis</em> despite the absence of population structure </strong>published in Frontiers in Ecology and Evolution (doi: <a href="https://doi.org/10.3389/fevo.2022.856453">10.3389/fevo.2022.856453</a>).</p> <p><strong>Uploaded files</strong></p> <ul> <li><strong>README</strong> file to explain the datasets</li> <li><strong>AFLP/MSAP metadata</strong> called EckertHerdenStiftDurkavanKleunenJoshi_2022_FrontEcolEvol_AFLPMSAP_meta_data.txt</li> <li><strong>AFLP scoring dataset</strong> called EckertHerdenStiftDurkavanKleunenJoshi_2022_FrontEcolEvol_AFLP_scoring_data.txt</li> <li><strong>MSAP scoring dataset</strong> called EckertHerdenStiftDurkavanKleunenJoshi_2022_FrontEcolEvol_MSAP_scoring_data.txt</li> <li><strong>MSAP mix1-scoring dataset</strong> called EckertHerdenStiftDurkavanKleunenJoshi_2022_FrontEcolEvol_MSAP_scoring_data_mix1.txt</li> <li>All files were combined in a <strong>.zip file</strong></li> </ul>
Genetic structure and dispersal in peripheral populations of a marine fish (Pacific cod, Gadus macrocephalus) and their importance for adaptation to climate change
<p>Small and isolated peripheral populations, which are often remnants of glacial refugia, offer an opportunity to determine the magnitude and direction of fine-scale connectivity in high gene flow marine species. When located at the equatorial edge of a species' range, these populations may also harbor genetic diversity related to survival and reproduction at higher temperatures, a critical resource for marine species facing warming ocean temperatures. Pacific cod (Gadus macrocephalus), a marine fish in the North Pacific, has already experienced major shifts in biomass and distribution linked to climate change. We estimated the magnitude and direction of connectivity between peripheral populations of Pacific cod at the southern edge of the species' range, by conducting restriction site-associated DNA (RAD) sequencing and individual assignment on fish collected around the Korean Peninsula during the spawning season. Three populations on the western, eastern, and southern Korean coasts were highly differentiated (FST =0.025 – 0.042) and relatively small (Ne = 433-1777). Ten putative dispersers and estimates of contemporary migration rates revealed asymmetrical, west-to-east movement around the Korean Peninsula, at a higher rate than predicted by indirect estimates of connectivity (FST). Allele frequencies at 87 RAD loci were decisively correlated with strong marine temperature gradients between the warmer southern coast and the cooler waters of the eastern and western coasts. Despite relatively small sample sizes, our data suggest asymmetrical dispersal and gene flow, potentially involving adaptive alleles, between peripheral populations inhabiting markedly different thermal regimes. Our study emphasizes the conservation value of peripheral populations in high gene flow marine fish species.</p>
Population genetic structure of wolves in the northwestern Dinaric-Balkan region
<p><span>The Balkan Peninsula and the Dinaric Mountains possess extraordinary biodiversity and </span>support one of the largest and most diverse wolf (<em>Canis lupus</em>) populations in Europe. Results obtained with diverse genetic markers show west-east substructure, also seen in various other species, despite the absence of obvious barriers to movement. However, the spatial extent of the genetic clusters remains unresolved, and our aim was to combine fine-scale sampling with population and spatial genetic analyses to improve resolution of wolf genetic clusters. We analyzed 16 autosomal microsatellites from 255 wolves sampled in Slovenia, Croatia, Bosnia and Herzegovina (BIH), and Serbia, and documented three genetic clusters. These comprised (1) Slovenia and the regions of Gorski kotar and Lika in Croatia, (2) the region of Dalmatia in southern Croatia and BIH, and (3) Serbia. <span>When we mapped the clusters geographically, we observed west-east genetic structure across the study area, together with some specific structure in BIH – Dalmatia. </span>We observed that cluster 1 had a smaller effective population size, consistent with earlier reports of population recovery since the 1980s. Our results provide foundation for future genomic studies that would further resolve the observed west-east population structure and its evolutionary history in wolves and other taxa in the region, and identify focal areas for habitat conservation. They also have immediate importance for conservation planning for the wolves in one of the most important parts of the species' European range.</p>
Genetic admixture and population structure analysis of Indian water buffaloes (Bubalus bubalis) using STR markers
<p><span>We generated genetic diversity data for 10 different buffalo populations of India using 20 highly polymorphic microsatellite markers. The buffalo populations of Odisha were the primary focus, viz. Chilika, Paralakhemundi, Kalahandi, Sambhalpuri, and Manda. The total observed number of alleles ranged between 143 (Manda) and 301 (Paralakhemundi) with an average of 204 alleles per breed. The minimal spanning network based on Bruvo's distance, PCA based on the Fst values, and genetic admixture analysis using both the STRUCTURE and 'snapclust' could identify the Manda population distinct from other Odisha buffalo breeds as well as Chhattisgarhi buffalo breed. The Sambhalpuri buffalo population also clustered into two separate subpopulations, half of the unique sub-population located geographically south-wards displayed no admixture with any of the adjacent buffalo populations. The Sambhalpuri population requires elaborate analysis to confirm the existence of two distinct sub-populations and if they could be recognized as separate breeds. The limited number of sires in the Manda population has resulted in excess of heterozygosity. Furthermore, the Manda population is left with very little allelic richness and this poses a huge threat to the population's existence. In another way, the study has led to the identification of the Manda buffalo as a distinct population, and the germplasm has been registered based on the study.</span></p>
FIGURE 4 in Population Structure and Genetic Diversity in Delphinium (Ranunculaceae) Using Scot Molecular Markers
FIGURE 4: WARD tree of SCoT data revealing species delimitation in the Delphinium sp1= D. teheranicum; sp2= D. camptocarpum; sp3= D. lorestanicum; sp4= D. leptocarpum; sp5= D. persicum; sp 6= D. aucheri; sp7= D. anthoroideum; sp8= D. hohenackeri; sp9= D. stocksianum; sp10: D. rugulosum; sp11: D. ambiguum; sp12= D. ajacis; sp13= D. consolida; sp14= D. oliverianum; sp15= D. flavum; sp16= D. trigonelloides; sp17= D. oliganthum; sp18= D. linarioides; sp19= D. paradoxum.
FIGURE. 3 in Population Structure and Genetic Diversity in Delphinium (Ranunculaceae) Using Scot Molecular Markers
FIGURE. 3. Electrophoresis gel of studied ecotypes from DNA fragments produced by SCoT-15. sp1= D. teheranicum; sp2= D. camptocarpum; sp3= D. lorestanicum; sp4= D. leptocarpum; sp5= D. persicum; sp 6= D. aucheri; sp7= D. anthoroideum; sp8= D. hohenackeri; sp9= D. stocksianum; sp10: D. rugulosum; sp11: D. ambiguum; sp12= D. ajacis; sp13= D. consolida; sp14= D. oliverianum; sp15= D. flavum; sp16= D. trigonelloides; sp17= D. oliganthum; sp18= D. linarioides; sp19= D. paradoxum. L = Ladder 100 bp,
FIGURE 2 in Population Structure and Genetic Diversity in Delphinium (Ranunculaceae) Using Scot Molecular Markers
FIGURE 2: PCA plot of morphological characters revealing species delimitation in the Delphinium species; sp1= D. teheranicum; sp2= D. camptocarpum; sp3= D. lorestanicum; sp4= D. leptocarpum; sp5= D. persicum; sp 6= D. aucheri; sp7= D. anthoroideum; sp8= D. hohenackeri; sp9= D. stocksianum; sp10: D. rugulosum; sp11: D. ambiguum; sp12= D. ajacis; sp13= D. consolida; sp14= D. oliverianum; sp15= D. flavum; sp16= D. trigonelloides; sp17= D. oliganthum; sp18= D. linarioides; sp19= D. paradoxum.
FIGURE. 1 in Population Structure and Genetic Diversity in Delphinium (Ranunculaceae) Using Scot Molecular Markers
FIGURE. 1. Map of Iran shows the collection sites and provinces where Delphinium species were obtained for this study; sp1= D. teheranicum; sp2= D. camptocarpum; sp3= D. lorestanicum; sp4= D. leptocarpum; sp5= D. persicum; sp 6= D. aucheri; sp7= D. anthoroideum; sp8= D. hohenackeri; sp9= D. stocksianum; sp10: D. rugulosum; sp11: D. ambiguum; sp12= D. ajacis; sp13= D. consolida
Unraveling hierarchical genetic structure of tea green leafhopper, Matsumurasca onukii, in East Asia based on SSRs and SNPs
<p><em>Matsumurasca onukii</em> (Matsuda, 1952), one of the dominant pests in major tea production areas in Asia, currently is known to occur in Japan, Vietnam, and China, and severely threatens tea production, quality, and international export trade. To elucidate the population genetic structure of this species, 1633 single nucleotide polymorphisms (SNPs) and 18 microsatellite markers (SSRs) were used to genotype samples from 27 sites representing 18 geographical populations distributed throughout the known range of the species in East Asia. Analyses of both SNPs and SSRs showed that <em>M</em>. <em>onukii</em> populations in Yunnan exhibit high genetic differentiation and structure compared to other populations. The Kagoshima (JJ) and Shizuoka (JS) populations from Japan were separated from populations from China by SNPs but clustered with Jinhua (JH), Yingde (YD), Guilin (GL), Fuzhou (FZ), Hainan (HQ), Leshan (CT), Chongqing (CY) and Zunyi (ZY) tea areas in China and the Vietnamese Vinh Phuc (VN) population based on SSR data. On the contrary, CT, CY, ZY, and Shaanxi (SX) populations clustered together based on SNPs, but were separated by SSRs. Both marker datasets identified significant geographic differentiation among the 18 populations. Various environmental and anthropogenic factors, including the geographical barriers to migration, human transport of hosts (<em>Camellia sinesis</em> (L.) O. Kuntze), and adaptability of <em>M. onukii</em> to various climatic zones possibly account for the rapid spread of this pest in Asia. The results demonstrate that SNPs from high-throughput genotyping data can be used to reveal subtle genetic substructure at broad scales in r-strategist insects.</p>
Supplementary material 1 from: Hermes C, Döpper A, Schaefer MH, Segelbacher G (2016) Effects of forest fragmentation on the morphological and genetic structure of a dispersal-limited, endangered bird species. Nature Conservation 16: 39-58. https://doi.org/10.3897/natureconservation.16.10905
Development of species-specific microsatellite primers : Explanation note: The supplementary material contains a detailed description of the development of a set of 10 microsatellite primers for the Ecuadorian Tapaculo, including primer sequences and gene bank accession numbers.
Supplementary material 2 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Component data at the four successive thresholds used to illustrate Figure 5: Explanation note: Component data are used to illustrate the structure of the subset of Bactrocera carambolae and Bactrocera dorsalis populations. The highest Betweenness-centrality is highlighted in blue.
Supplementary material 1 from: Aketarawong N, Isasawin S, Sojikul P, Thanaphum S (2015) Gene flow and genetic structure of Bactrocera carambolae (Diptera, Tephritidae) among geographical differences and sister species, B. dorsalis, inferred from microsatellite DNA data. In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 239-272. https://doi.org/10.3897/zookeys.540.10058
Component data at the five successive thresholds used to illustrate Figure 4: Explanation note: Component data are used to illustrate the structure of the subset of Bactrocera carambolae populations. The Highest Betweenness-centrality is highlighted in blue.
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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.
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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.