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114 results for “Structural Connectivity”
Structural and Molecular Analysis of Adult Mouse Astrocytes and Vascular Connectivity in the Cortex and Hippocampus
<p>After image acquisition (0-RAW_CL230331_E2_serie1) and deconvolution (1-Deconvolved_CL230331_E2_serie1) using confocal microscopy and the SVI Huygens software,respectively, the image processing was conducted using Imaris, Fiji, and Matlab software. This process involved a sequence of manual operations (2-Imaris_surfaces_CL230331_E2_serie1) and custom Groovy scripts (5-Groovy scripts).</p> <p>The dataset analysis (3-Imaris_final_CL230331_E2_serie1_ims) allowed for a deeper investigation of morphological and molecular properties of adult mouse astrocytes (4-Image analysis_CL230331_E2_serie1) in two brain regions, the Isocortex and the Hippocampus, known to be interconnected to support multiple cognitive functions.</p>
Data for: Brain structural connectivity predicts brain functional complexity
<p>Data used in analyses for "Brain structural connectivity predicts brain functional complexity: DTI derived centrality accounts for variance in fractal properties of fMRI signal"</p>
The genetic structure and connectivity in two sympatric rodent species with different life histories are similarly affected by land use disturbances
<p><strong>Microsatellite dataset of the wood mouse (<em>Apodemus sylvaticus)</em> and the bank vole (<em>Myodes glareolus).</em></strong></p> <p>The dataset of the wood mouse is constituted of 194 samples and 7 microsatellite markers: WM_194ind_7STRs.txt</p> <p>The dataset of the bank vole is constituted of 199 samples and 8 microsatellite markers: BV_199ind_8STRs.txt</p> <p>Each locus is encoded in the three-digit format (e.g., 126126) and each column corresponds to a locus specified in the order at the beginning of the file, following the GENEPOP format.</p> <p>Pop indicates the beginning of a new location.</p> <p> </p> <p><em><strong>Locus name in WM_194ind_7STRs.txt</strong></em></p> <p>Locus_1 AS-7-FAM<br> Locus_2 AS-12-PET<br> Locus_3 AS-20-NED<br> Locus_4 AS-34-FAM<br> Locus_5 GTTD9A-PET<br> Locus_6 AS-11-VIC<br> Locus_7 MS-AF-8-NED</p> <p> </p> <p><em><strong>Locus name in BV_199ind_8STRs.txt</strong></em></p> <p>Locus_1 Cg13B8-F_FAM<br> Locus_2 Cg6A1-F_VIC<br> Locus_3 Cg3F12-F_PET<br> Locus_4 Cg13H9-F_PET<br> Locus_5 Cg2E2-F_VIC<br> Locus_6 Cg3E10-F_FAM<br> Locus_7 Cg2A4-F_FAM<br> Locus_8 Cg3A8-F_NED</p>
Text-fig. 13. Enamel ultrastructure of I1, Equus hydruntinus (Kabazi 2). a: vertical sections, scale bar = 100 Μm; b: horizontal and vertical arrangement of prisms in the HSB structure, scale bar = 10 Μm; c: unstructured PLEX enamel at the end of the root, scale bar = 100 Μm. in The Ultrastructure Of The Tooth Enamel Of Small Equus Of The "Tarpan" Group And Their Possible Phylogenetic Connections
Text-fig. 13. Enamel ultrastructure of I1, Equus hydruntinus (Kabazi 2). a: vertical sections, scale bar = 100 Μm; b: horizontal and vertical arrangement of prisms in the HSB structure, scale bar = 10 Μm; c: unstructured PLEX enamel at the end of the root, scale bar = 100 Μm.
Text-fig. 11. Enamel ultrastructure of first (a) and second (b, c) lower incisors, Equus caballus (konik polski), vertical sections. a: enamel row, scale bar = 100 Μm; b: arranging the prisms in the HSB structure, scale bar = 20 Μm; c: arranging the prisms in PI structure, scale bar = 20 Μm. in The Ultrastructure Of The Tooth Enamel Of Small Equus Of The "Tarpan" Group And Their Possible Phylogenetic Connections
Text-fig. 11. Enamel ultrastructure of first (a) and second (b, c) lower incisors, Equus caballus (konik polski), vertical sections. a: enamel row, scale bar = 100 Μm; b: arranging the prisms in the HSB structure, scale bar = 20 Μm; c: arranging the prisms in PI structure, scale bar = 20 Μm.
Fig. 3 in Fig. 3 in Genetic Structure of the Mangrove Killifish Costa, 2011 (Cyprinodontiformes: Aplocheiloidei) Supports A Wide Connection among its Populations.
Fig. 3. Haplotype network of the Kryptolebias marmoratus species group. Maps represent the distribution of each group.
Fig. 2 in Fig. 3 in Genetic Structure of the Mangrove Killifish Costa, 2011 (Cyprinodontiformes: Aplocheiloidei) Supports A Wide Connection among its Populations.
Fig. 2. Distribution of K. hermaphroditus: Orange star indicates type locality; and Green circles indicate recorded localities for the species (Costa 2011; 2016; Sarmento-Soares et al. 2014; Lira et al. 2015; Berbel-Filho et al. 2016; Guimarães-Costa et al. 2017; Tatarenkov et al. 2017a; This study).
Fig. 1 in Fig. 3 in Genetic Structure of the Mangrove Killifish Costa, 2011 (Cyprinodontiformes: Aplocheiloidei) Supports A Wide Connection among its Populations.
Fig. 1. Kryptolebias hermaphroditus from Tutóia, Maranhão State, Delta do Parnaíba, north eastern Brazil; UFRJ12666: A: Hermaphrodite, 35.5 mm SL; B: Male, 20.3 mm SL; C: Male, 28.9 mm SL.
The dataset on structural connectivity in high-mountain Asia
<p>This is the inaugural version of the dataset, comprising 10 slices in GeoTIFF format at a resolution of 30 meters, provided for reviewers to assess our manuscript. We will release the full version of the dataset upon acceptance of the article. For any inquiries, please contact the following email address. jinlongli@stu.scu.edu.cn.</p>
Fig. 2 in Influence of habitat connectivity and seasonality on the ichthyofauna structure of a riverine knickzone
Fig. 2. Non-metric multidimensional plots of the abundance of fish assemblage sampled in isolated (I) and connected (C) pools during the rainy and dry season in the Sapucaí-Mirim River knickzone, Southeast Brazil.
Text-fig. 28. Scanning electron microscope (SEM) images of stamens and pollen of Endressistemon cateficensis gen. et sp. nov.; Catefica locality, Portugal. a, b) Staminal structure with two lateral stamens and one median structure seen in ventral and dorsal view (orientation unknown) showing that each stamen has a prominent apical extension and two pairs of pollen sacs separated by a narrow connective; both stamens are borne on a common base together with the median structure and their anthers are sessile on the common stalk; note the apical projection of the median structure (asterisk) between the two stamens and the ribs over probable vascular bundles that extend from the common base into the apical projections of both stamens and the median structure (arrows); c) Staminal structure showing two stamens with prominent apical projections and median axis-like structure between the two stamens (arrow); d) Staminal structure showing two stamens with prominent apical projections borne on a common base; e) Staminal structure in (a) and (b), from the same orientation as (b), showing the ribs over probable vascular bundles (yellow) that extend into the apical projections; f) Detail of staminal structure in (a) and (b) showing the fused or strongly adhering apical projections of the two lateral stamens and the median structure (asterisk); g) Monocolpate, reticulate pollen grains from the pollen sacs of stamen in (d). Specimens, Catefica 49-S107778 (holotype, a, b, e, f), Catefica 49-S107769 (c), Catefica 49-S107751 (d, g). Scale bars = 600 Μm (a–d), 300 Μm (e), 100 Μm (f), 6 Μm (g). in The Early Cretaceous Mesofossil Flora Of Catefica, Portugal: Angiosperms
Text-fig. 28. Scanning electron microscope (SEM) images of stamens and pollen of Endressistemon cateficensis gen. et sp. nov.; Catefica locality, Portugal. a, b) Staminal structure with two lateral stamens and one median structure seen in ventral and dorsal view (orientation unknown) showing that each stamen has a prominent apical extension and two pairs of pollen sacs separated by a narrow connective; both stamens are borne on a common base together with the median structure and their anthers are sessile on the common stalk; note the apical projection of the median structure (asterisk) between the two stamens and the ribs over probable vascular bundles that extend from the common base into the apical projections of both stamens and the median structure (arrows); c) Staminal structure showing two stamens with prominent apical projections and median axis-like structure between the two stamens (arrow); d) Staminal structure showing two stamens with prominent apical projections borne on a common base; e) Staminal structure in (a) and (b), from the same orientation as (b), showing the ribs over probable vascular bundles (yellow) that extend into the apical projections; f) Detail of staminal structure in (a) and (b) showing the fused or strongly adhering apical projections of the two lateral stamens and the median structure (asterisk); g) Monocolpate, reticulate pollen grains from the pollen sacs of stamen in (d). Specimens, Catefica 49-S107778 (holotype, a, b, e, f), Catefica 49-S107769 (c), Catefica 49-S107751 (d, g). Scale bars = 600 Μm (a–d), 300 Μm (e), 100 Μm (f), 6 Μm (g).
Going with the flow? Relative importance of riverine hydrologic connectivity versus tidal influence for spatial structure of genetic diversity and relatedness in a foundational submersed aquatic plant
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Data from: Population structure, connectivity and demographic history of an apex marine predator, the bull shark Carcharhinus leucas
Knowledge of population structure, connectivity and effective population size remains limited for many marine apex predators, including the bull shark Carcharhinus leucas. This large-bodied coastal shark is distributed worldwide in warm temperate and tropical waters, and uses estuaries and rivers as nurseries. As an apex predator, the bull shark likely plays a vital ecological role within marine food webs, but is at risk due to inshore habitat degradation and various fishing pressures. We investigated the bull shark's global population structure and demographic history by analysing the genetic diversity of 370 individuals from 11 different locations using 25 microsatellite loci and three mitochondrial genes (CR, nd4, cytb). Both types of markers revealed clustering between sharks from the Western Atlantic and those from the Western Pacific and the Western Indian Ocean, with no contemporary gene flow. Microsatellite data suggested low differentiation between the Western Indian Ocean and the Western Pacific, but substantial differentiation was found using mitochondrial DN A. Integrating information from both types of markers and using Bayesian computation with a random forest procedure (ABC-RF), this discordance was found to be due to a complete lack of contemporary gene flow. High genetic connectivity was found both within the Western Indian Ocean and within the Western Pacific. In conclusion, these results suggest important structuring of bull shark populations globally with important gene flow occurring along coastlines , highlighting the need for management and conservation plans on regional scales rather than oceanic basin scale.
Data from: Population structure, genetic connectivity, and adaptation in the Olympia oyster (Ostrea lurida) along the west coast of North America
Effective management of threatened and exploited species requires an understanding of both the genetic connectivity among populations and local adaptation. The Olympia oyster (Ostrea lurida), patchily distributed from Baja California to the central coast of Canada, has a long history of population declines due to anthropogenic stressors. For such coastal marine species, population structure could follow a continuous isolation-by-distance model, contain regional blocks of genetic similarity separated by barriers to gene flow, or be consistent with a null model of no population structure. To distinguish between these hypotheses in O. lurida, 13,424 single-nucleotide polymorphisms (SNPs) were used to characterize rangewide population structure, genetic connectivity, and adaptive divergence. Samples were collected across the species range on the west coast of North America, from southern California to Vancouver Island. A conservative approach for detecting putative loci under selection identified 235 SNPs across 129 GBS loci, which were functionally annotated and analyzed separately from the remaining neutral loci. While strong population structure was observed on a regional scale in both neutral and outlier markers, neutral markers had greater power to detect fine-scale structure. Geographic regions of reduced gene flow aligned with known marine biogeographic barriers, such as Cape Mendocino, Monterey Bay, and the currents around Cape Flattery. The outlier loci identified as under putative selection included genes involved in developmental regulation, sensory information processing, energy metabolism, immune response, and muscle contraction. These loci are excellent candidates for future research and may provide targets for genetic monitoring programs. Beyond specific applications for restoration and management of the Olympia oyster, this study lends to the growing body of evidence for both population structure and adaptive differentiation across a range of marine species exhibiting the potential for panmixia. Computational notebooks are available to facilitate reproducibility and future open-sourced research on the population structure of <i>Ostrea lurida</i>.
Population structure and connectivity among coastal and freshwater Kelp Gull (Larus dominicanus) populations from Patagonia
<p>The genetic identification of significant evolutionary units and information on their connectivity can be used to design effective management and conservation plans. Despite having high dispersal capacity, several seabird species show population structure due to both abiotic and biotic barriers to gene flow. The Kelp Gull is the most abundant species of gull in the southern hemisphere. In Argentina it reproduces in both marine and freshwater environments, with more than 100,000 pairs following a metapopulation dynamic across 140 colonies in the Atlantic coast of Patagonia. However, little is known about the demography and connectivity of inland populations. We aim to provide information on the connectivity of the largest freshwater colonies (those from Nahuel Huapi Lake) with the closest Pacific and Atlantic populations to evaluate if these freshwater colonies are being subsidized by the larger coastal populations. We sampled three geographic regions (Nahuel Huapi Lake and the Atlantic and Pacific coasts) and employed a reduced-representation genomic approach to genotype individuals for single-nucleotide polymorphisms (SNPs). We found, using clustering and phylogenetic analyses, that there are three genetic groups, each corresponding to one of our sampled regions. Individuals from marine environments are more closely related to each other than to those from Nahuel Huapi Lake, indicating that the latter population constitutes the first freshwater Kelp Gull colony to be identified as a significant evolutionary unit in Patagonia.</p>
Differences in network structure and connectivity of four (protected) Palearctic-Afrotropical flyways
<p class="MsoNormal"><em><span>Aim – </span></em><span>Waterbirds that travel seasonally between Europe and Africa use wetlands along four major Palearctic-Afrotropical flyways. However, it is unknown to what extent the overall connectivity of these flyways may be threatened by ongoing habitat loss and degradation. Here, we contrasted the wetland connectivity along these four flyways, applying graph-theoretic connectivity metrics on an intercontinental scale. We also explored for which flyway connectivity is most at risk. We then identified the most important wetlands by their contribution to connectivity in each flyway. </span></p> <p class="MsoNormal"><em><span>Location – </span></em><span>Western Palearctic, Afrotropics</span></p> <p class="MsoNormal"><em><span>Methods – </span></em><span>Based on high-resolution wetland maps, we calculated directional probabilistic connectivity metrics. Estimates of overall connectivity of each flyway were obtained, as well as the relative importance of wetlands, for birds with different migration strategies: short-distance hoppers and long-distance jumpers.</span></p> <p class="MsoNormal"><em><span>Results – </span></em><span>The East-Atlantic flyway and Eastern Mediterranean flyway had higher overall functional connectivity than the two central routes, reflecting the larger barrier represented by the Mediterranean Sea and Sahara Desert. Fewer than 5% of all wetlands supported more than 70% of the total connectivity of the network in each flyway, regardless of the considered migration strategy. These wetlands were either large, strategically positioned, or both. Removing non-protected wetlands from the analysis showed that the connectivity of some flyways could be jeopardised and that the East-Atlantic and Eastern Mediterranean flyway may be most vulnerable to additional habitat loss. </span></p> <p class="MsoNormal"><em><span>Main conclusions – </span></em><span>Our results illustrate (1) the major contribution of unprotected wetlands to flyway connectivity, (2) the importance of integrating migration ecology into site-based connectivity analyses, and (3) the utility of graph-based connectivity metrics to inform conservation prioritisation under present and future scenarios.</span></p>
Landscape connectivity and genetic structure in a mainstem and a tributary stonefly (Plecoptera) species using a novel reference genome
<p>Abstract Understanding how environmental variation influences population genetic structure can help predict how environmental change influences population connectivity, genetic diversity, and evolutionary potential. We used riverscape genomics modelling to investigate how climatic and habitat variables relate to patterns of genetic variation in two stonefly species, one from mainstem river habitats (Sweltsa coloradensis) and one from tributaries (Sweltsa fidelis) in 40 sites in northwest Montana, USA. We produced a draft genome assembly for S. coloradensis (N50 = 0.251 Mbp, BUSCO &gt; 95% using "insecta_ob9" reference genes). We genotyped 1930 SNPs in 372 individuals for S. coloradensis and 520 SNPs in 153 individuals for S. fidelis. We found higher genetic diversity for S. coloradensis compared to S. fidelis, but nearly identical genetic differentiation among sites within each species (both had global loci median FST = 0.000), despite differences in stream network location. For landscape genomics and testing for selection, we produced a less stringently filtered data set (3454 and 1070 SNPs for S. coloradensis and S. fidelis, respectively). Environmental variables (mean summer precipitation, slope, aspect, mean June stream temperature, land cover type) were correlated with 19 putative adaptive loci for S. coloradensis. but there was only one putative adaptive locus for S. fidelis (correlated with aspect). Interestingly, we also detected potential hybridization between multiple Sweltsa species which has never been previously detected. Studies like ours, that test for adaptive variation in multiple related species are needed to help assess landscape connectivity and the vulnerability of populations and communities to environmental change.</p>
Connectivity and succession of open structures as a key to sustaining light-demanding biodiversity in deciduous forests
<p>1. European forests are facing a rapid decline of light-demanding biota. This has prompted active interventions to re-establish and maintain partial habitat openness in protected areas. Managers of protected areas, however, need substantially more scientific evidence to support their decisions on where, when, and how to intervene.</p> <p>2. We investigated the importance of spatial continuity of open forest habitats in different years of succession, using six pairs of experimental clearings established in the formerly open, oak-dominated forests of the Podyji National Park (Czech Republic). In each pair, one clearing was connected to the forest edge, while the other was isolated in closed forest. We sampled butterflies (74 spp.), moths (435 spp.), saproxylic beetles (465 spp.), and vascular plants (567 spp.) on the 12 clearings during the first five years of succession. We then compared species richness, abundance, and composition of the four taxa between the two clearing types and along the succession.</p> <p>3. All studied insect groups were substantially more species-rich and more abundant in connected than in isolated clearings. Species composition of plants, moths, and butterflies differed between the clearing types.</p> <p>4. The number of species of all studied taxa generally increased from the first to the second or third year after cutting; species composition of all taxa differed among years. This suggests rapid changes in habitat quality and thus limited time for colonisation by light-demanding organisms.</p> <p>5. <i>Synthesis and applications</i>: Our results offer an evidence that spatial connectivity and rapid temporal dynamics are important habitat features for light-demanding insects. Attempts to create or restore habitats for light-demanding forest biota should take into account that: (i) Insects benefit from direct connection of new open patches to open habitats or flight corridors such as forest edges. (ii) Considering plants, the optimal solution is to connect newly created open forest habitats to existing habitats with established biota of high conservation value. (iii) Interventions should be carried out within short time intervals, i.e. within years rather than decades. (iv) A fine mosaic of interconnected<span>, open woodland patches in various successional stages is more beneficial than a single large patch with a single successional stage.</span></p>
Data for submitted manuscript "Connections between Sub-cloud Coherent Structures and the Life Cycle of Shallow Cumulus Clouds: Evidence from Large Eddy Simulation"
<p>This is the dataset for a submitted manuscript "Connections between Sub-cloud Coherent Structures and the Life Cycle of Shallow Cumulus Clouds: Evidence from Large Eddy Simulation" for peer review.</p> <p>The NetCDF file includes masked objects for sub-cloud coherent structures and cloud for tracking.</p>
Data from: Population structure, genetic connectivity, and adaptation in the Olympia oyster (Ostrea lurida) along the west coast of North America
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Allen Brain Atlas
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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.