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114 results for “structural connectivity”
Data from: Genetic structure in a fragmented Northern Hemisphere rainforest: large effective sizes and high connectivity among populations of the epiphytic lichen Lobaria pulmonaria
An extraordinary diversity of epiphytic lichens is found in the boreal rainforest of central Norway, the highest-latitude rainforest in the world. These rainforest relicts are located in ravine systems, and clear cutting has increased the distance between remaining patches. We hypothesized that the relatively small lichen populations in the remaining forest stands have suffered a depletion of genetic diversity through bottlenecks and founder events. In order to test this hypothesis we assessed genetic diversity and structure in populations of the tripartite lichen Lobaria pulmonaria using eight SSR loci. We sampled thalli growing on Picea abies branches and propagules deposited in snow at three localities. Contrary to expectations, we found high genetic diversity in lichen and snow samples, and high effective sizes of the studied populations. Also, limited genetic differentiation between populations, high historical migration rates, and a high proportion of first generation immigrants were estimated, implying high connectivity across distances <30 km. Almost all genetic variation was due to variation within sites; spatial genetic structures within populations were absent or appeared on small scales (5–10 m). The high genetic diversity in the remaining old boreal rainforests shows that even relict forest patches might be suitable for conservation of genetic diversity.
Data from: A map-based approach to assessing genetic diversity, structure, and connectivity in the seagrass Halodule wrightii
Seagrass cover has declined in many areas of the world in a trend that has accelerated over the past several decades. This raises concern for both the impact the decline in cover has on coastal ecosystems and the effect it may have on seagrass evolutionary potential, as genotypic and genomic variation is lost. We used 8 microsatellite loci to investigate genetic diversity, structure, and connectivity in the seagrass Halodule wrightii from the Gulf of Mexico (Texas, USA) and western Atlantic (Bermuda). We examined how estimates correlated with changes in H. wrightii abundance and distribution on the Texas Gulf coast over the past 50 yr. Results show that, compared to other species, H. wrightii from this region exhibits variable clonal diversity (R = 0.02-0.81), moderate allelic diversity (mean AR = 4.09), and relatively high heterozygosity (mean He = 0.56). The patterns of genetic diversity and structure, however, do not entirely coincide with either geography or recent historical trends in seagrass distribution in this region. Results from a basin in which seagrasses have recently been expanding were consistent with expectations, as they were for an isolated site near the limit of H. wrightii's range. Results from basins in which seagrasses have been experiencing decline and/or fragmentation, however, were mixed. Genetic structure on the Texas coast was relatively weak and coincided more strongly with tidal range than with geographic barriers or distance. Rapid expansion and the discovery of identical multi-locus genotypes at several sites raises the possibility of migration via drifting vegetative fragments, as the geographic distance among certain multi-locus genotypes cannot be explained by rhizome growth models.
Data from: Genetic connectivity for two bear species at wildlife crossing structures in Banff National Park
Roads can fragment and isolate wildlife populations, which will eventually decrease genetic diversity within populations. Wildlife crossing structures may counteract these impacts, but most crossings are relatively new, and there is little evidence that they facilitate gene flow. We conducted a three-year research project in Banff National Park, Alberta, to evaluate the effectiveness of wildlife crossings to provide genetic connectivity. Our main objective was to determine how the Trans-Canada Highway and crossing structures along it affect gene flow in grizzly (Ursus arctos) and black bears (Ursus americanus). We compared genetic data generated from wildlife crossings with data collected from greater bear populations. We detected a genetic discontinuity at the highway in grizzly bears but not in black bears. We assigned grizzly bears that used crossings to populations north and south of the highway, providing evidence of bidirectional gene flow and genetic admixture. Parentage tests showed that 47% of black bears and 27% of grizzly bears that used crossings successfully bred, including multiple males and females of both species. Differentiating between dispersal and gene flow is difficult, but we documented gene flow by showing migration, reproduction and genetic admixture. We conclude that wildlife crossings allow sufficient gene flow to prevent genetic isolation.
Functional and structural computed connectivity profiles for pre-defined whole-brain and cortical hull maps
<p>This Repository holds Lead-DBS Lead-Mapper v.2.5.2 computed functional and structural estimated connectivity. The structural dMRI connectivity is computed based on the "HCP1000 6K" connecome and the fMRI connectivity "GSP 1000 Yeo 2011" connectome.</p> <p>Both connectivity metrices were computed using two pre-defined grids:</p> <ol> <li> Cortical hull (1025 points). The grid was estimated based on the <a href="https:/github.com/neuromodulation/py_neuromodulation/blob/main/py_neuromodulation/ConnectivityDecoding/_get_grid_hull.m">SPM cortex_20484 grid</a> and subsampled by every 20th point. The grid is saved as a <a href="(https:/github.com/neuromodulation/py_neuromodulation/blob/main/py_neuromodulation/ConnectivityDecoding/mni_coords_cortical_surface.mat)">.mat file</a> and can be acessed through the main repository .</li> <li>Whole-brain (1236 points). Given the Lead-DBS provided <a href="https://github.com/neuromodulation/py_neuromodulation/blob/main/py_neuromodulation/ConnectivityDecoding/Automated%20Anatomical%20Labeling%203%20(Rolls%202020).nii">AAL3 atlas</a> the whole-brain .nii grid is subsampled by a factor of 150. See here the <a href="https://github.com/neuromodulation/py_neuromodulation/blob/main/py_neuromodulation/ConnectivityDecoding/_get_grid_whole_brain.py">grid computation</a>.</li> </ol> <p>Both grids can be accessed trough the <a href="https://github.com/neuromodulation/py_neuromodulation/tree/main">py_neuromodulation</a> API using the <a href="https://github.com/neuromodulation/py_neuromodulation/blob/main/py_neuromodulation/nm_RMAP.py">nm_RMAP.py</a> module.</p>
Unleashing the power of data through organization: Structure and connections for meaning, learning, and discovery
<p><span>Knowledge organization is needed everywhere. Its importance is marked by its pervasiveness. This paper will show many areas, tasks, and functions where proper use of Knowledge Organization, construed as broadly as the term implies, provides support for learning and understanding, for sensemaking and meaning making, for inference, and for discovery by people and computer programs and thereby will make the world a better place. The paper focuses not on metadata but rather on structuring and representing the actual data or knowledge itself and argues for more communication between the largely separated KO, Ontology, Data Modeling, and Semantic Web communities to address the many problems that need better solutions. In particular, the paper discusses the application of knowledge organization in Knowledge bases for question answering and cognitive systems; Knowledge bases for information extraction from text or multimedia; Linked data; Big data and data analytics; Electronic health records as one example; Influence diagrams (causal maps), dynamic system models, process diagrams, concept maps, and other node-link diagrams; Information systems in organizations; Knowledge organization for understanding and learning; and Knowledge transfer between domains. The paper argues for moving beyond triples to a more powerful representation using entities and multi-way relationships but not attributes.</span></p>
Spatiotemporal connectivity dynamics in spatially structured populations
<p>Connectivity is a fundamental concept linking dispersal to the emergent dynamics and persistence of spatially structured populations. Functional measures of connectivity typically seek to integrate aspects of landscape structure and animal movement to describe ecologically meaningful connectedness at the landscape and population scale.</p> <p>Despite this focus on function, traditional measures of landscape connectivity assume it is a static property of the landscape, hence abstracting out the underlying spatiotemporal population dynamics. Connectivity is, arguably, a dynamic property of landscapes, and is inherently related to the spatial distribution of individuals and populations across the landscape. Static representations of connectivity potentially overlook this variation and therefore adopting a dynamic approach should offer improved insights about connectivity and associated ecological processes.</p> <p>Using a large scale, long-term time-series of occupancy data from a metapopulation of water voles (Arvicola amphibius), we tested competing hypotheses about how considering the dynamic nature of connectivity improves the ability of spatially-explicit occupancy models to recover population dynamics. Iteratively relaxing standing assumptions of connectivity metrics, these models ranged from spatially and temporally fixed connectivity metrics that are widely applied, to the more flexible, but lesser used model that allowed temporally-varying connectivity measures that incorporate spatiotemporally dynamic patch occupancy states.</p> <p>Our results provide empirical evidence that demographic-weighting using patch occupancy dynamics and temporal variability in connectivity measures are important for describing metapopulation dynamics.</p> <p>We highlight the implications of commonly held assumption in connectivity modeling and demonstrate how they result in different and highly variable predictions of metapopulation capacity. Thus, we argue that the concept of connectivity and its potential applications would benefit from recognizing inherent spatiotemporal variation in connectivity that is explicitly linked to underlying ecological state variables. </p>
Functional connectivity in the face of congenital structural changes – a case of homozygous LAMC3 Mutation
<p>Results of diffusion tensor imaging analysis for each participant. These results were summarized in a manuscript titled as " <strong>Functional connectivity in the face of congenital structural changes – a case of homozygous <em>LAMC3</em> Mutation</strong> "</p>
Data from: Contrasting patterns of population structure and gene flow facilitate exploration of connectivity in two widely distributed temperate octocorals
Connectivity is an important component of metapopulation dynamics in marine systems and can influence population persistence, migration rates and conservation decisions associated with Marine Protected Areas (MPAs). In this study, we compared the genetic diversity, gene flow and population structure of two octocoral species, Eunicella verrucosa and Alcyonium digitatum, in the northeast Atlantic (ranging from the northwest of Ireland and the southern North Sea, to southern Portugal), using two panels of 13 and 8 microsatellite loci, respectively. Our results identified regional genetic structure in E. verrucosa partitioned between populations from southern Portugal, northwest Ireland and Britain/France; subsequent hierarchical analysis of population structure also indicated reduced gene flow between southwest Britain and northwest France. However, over a similar geographical area, A. digitatum showed little evidence of population structure, suggesting high gene flow and/or a large effective population size; indeed, the only significant genetic differentiation detected in A. digitatum occurred between North Sea samples and those from the English Channel/northeast Atlantic. In both species the vast majority of gene flow originated from sample sites within regions, with populations in southwest Britain being the predominant source of contemporary exogenous genetic variants for the populations studied. Overall, historical patterns of gene flow appeared more complex, though again southwest Britain appeared to be an important source of genetic variation for both species. Our findings have major conservation implications, particularly for E. verrucosa, a protected species in UK waters and listed by the IUCN as 'Vulnerable', and for the designation and management of European MPAs.
Data from: Influence of the larval phase on connectivity: strong differences in the genetic structure of brooders and broadcasters in the Ophioderma longicauda species complex
Closely related species with divergent life-history traits are excellent models to infer the role of such traits in genetic diversity and connectivity. Ophioderma longicauda is a brittle star species complex composed of different genetic clusters, including brooders and broadcasters. These species diverged very recently and some of them are sympatric and ecologically syntopic, making them particularly suitable to study the consequences of their trait differences. At the scale of the geographic distribution of the broadcasters (Mediterranean Sea and north-eastern Atlantic), we sequenced the mitochondrial marker COI and genotyped an intron (i51) for 788 individuals. In addition, we sequenced 10 nuclear loci newly developed from transcriptome sequences, for six sympatric populations of brooders and broadcasters from Greece. At the large scale we found a high genetic structure within the brooders (COI: 0.07
Data from: Population genetic structure and connectivity of deep-sea stony corals (Order Scleractinia) in the New Zealand region: implications for the conservation and management of Vulnerable Marine Ecosystems
Deep-sea stony corals, which can be fragile, long-lived, late to mature and habitat-forming, are defined as vulnerable marine ecosystem indicator taxa. Under United Nations resolutions these corals require protection from human disturbance such as fishing. To better understand the vulnerability of stony corals (Goniocorella dumosa, Madrepora oculata, Solenosmilia variabilis) to disturbance within the New Zealand region, and to guide marine protected area design, genetic structure and connectivity were determined using microsatellite loci and DNA sequencing. Analyses compared population genetic differentiation between two biogeographic provinces, amongst three sub-regions (north-central-south), and amongst geomorphic features. Extensive population genetic differentiation was revealed by microsatellite variation, whilst DNA sequencing revealed very little differentiation. For G. dumosa, genetic differentiation existed amongst regions and geomorphic features, but not between provinces. For M. oculata, only a north-central-south regional structure was observed. For S. variabilis, genetic differentiation was observed between provinces, amongst regions and amongst geomorphic features. Populations on the Kermadec Ridge were genetically different from Chatham Rise populations in all three species. A significant isolation-by-depth pattern was observed for both marker types in G. dumosa, and also in ITS of M. oculata. An isolation-by-distance pattern was revealed for microsatellite variation in S. variabilis. Medium to high levels of self-recruitment were detected in all geomorphic populations, and rates and routes of genetic connectivity were species-specific. These patterns of population genetic structure and connectivity at a range of spatial scales indicate that flexible spatial management approaches are required for the conservation of deep-sea corals around New Zealand.
Data from: Connectivity explains local ant community structure in a Neotropical forest canopy: a large-scale experimental approach
Understanding how habitat structure and resource availability affect local species distributions is a key goal of community ecology. Where habitats occur as a mosaic, variation in connectivity among patches influences both local species richness and composition, and connectivity is a key conservation concern in fragmented landscapes. Similarly, availability of limiting resources frequently determines species co-existence or exclusion. For primarily cursorial arthropods like ants, gaps between neighboring trees are a significant barrier to movement through the forest canopy. Competition for limited resources such as nest sites also promotes antagonistic interactions. Lianas (woody vines) connect normally isolated neighboring tree crowns and often have hollow stems inhabited by ants. We used two large-scale liana removal experiments to determine how connectivity and nest site availability provided by lianas affect arboreal ant species richness, species composition, and β-diversity in a lowland tropical forest in Panama. Removing lianas from a tree crown reduced ant species richness up to 35%, and disproportionately affected species that require large foraging areas. Adding artificial connectivity to trees mitigated the effects of liana removal. Ant colonization of artificial nests was higher (73% occupied) in trees without lianas vs. trees with lianas (28% occupied). However, artificial nests typically were colonized by existing polydomous, resident ant species. As a result, nest addition did not affect ant community structure. Collectively, these results indicate that lianas are important to the maintenance of arboreal ant diversity specifically by providing connectivity among neighboring tree crowns. Anticipated increases in liana abundance in this forest could increase the local (tree-level) species richness of arboreal ants, with a compositional bias toward elevating the density of broad-ranging specialist predators.
Data from: The structural and functional connectivity of the grassland plant Lychnis flos-cuculi
Understanding the relationship between structural and functional connectivity is essential for successful restoration and conservation management, particularly in intensely managed agricultural landscapes. We evaluated the relationship between structural and functional connectivity of the wetland plant Lychnis flos-cuculi in a fragmented agricultural landscape using landscape genetic and network approaches. First, we studied the effect of structural connectivity, such as geographic distance and various landscape elements (forest, agricultural land, settlements and ditch verges), on gene flow among populations as a measurement of functional connectivity. Second, we examined the effect of structural graph-theoretic connectivity measures on gene flow among populations and on genetic diversity within populations of L. flos-cuculi. Among landscape elements, forests hindered gene flow in L. flos-cuculi, whereas gene flow was independent of geographic distance. Among the structural graph-theoretic connectivity variables, only intrapopulation connectivity, which was based on population size, had a significant positive effect on gene flow, that is, more gene flow took place among larger populations. Unexpectedly, interpopulation connectivity of populations, which takes into account the spatial location and distance among populations, did not influence gene flow in L. flos-cuculi. However, higher observed heterozygosity and lower inbreeding was observed in populations characterised by higher structural interpopulation connectivity. This finding shows that a spatially coherent network of populations is significant for maintaining the genetic diversity of populations. Nevertheless, lack of significant relationships between gene flow and most of the structural connectivity measures suggests that structural connectivity does not necessarily correspond to functional connectivity.
Phylogeography and population genetic structure of the cardinal tetra (Paracheirodon axelrodi) in the Orinoco basin and Negro River (Amazon basin): evaluating connectivity and historical patterns of diversification
<p class="MsoNormal"><span class="Fuentedeprrafopredeter1"><span>The Neotropics contain one of the most diverse assemblages of freshwater fishes worldwide. Part of this diversity is shared between the Orinoco and Amazon basins. These basins have been separated for a long time due to the Vaupes Arch, rising between 10 - 11 Ma. T</span></span><span class="Fuentedeprrafopredeter1"><span>oday, there is only one permanent connection between the Orinoco and Negro </span></span><span class="Fuentedeprrafopredeter1"><span>(Amazon) </span></span><span class="Fuentedeprrafopredeter1"><span>basins, known as the Casiquiare Canal</span></span><span class="Fuentedeprrafopredeter1"><span>. </span></span><span class="Fuentedeprrafopredeter1"><span>However, alternative corridors allowing fish dispersion between both basins have been proposed. The cardinal tetra (<em>Paracheirodon axelrodi),</em> the most important fish in the ornamental world market, is distributed in both basins. Here we investigated </span></span><span class="Fuentedeprrafopredeter1"><em><span>P. axelrodi </span></em></span><span class="Fuentedeprrafopredeter1"><span>phylogeography, population structure, and potential routes of migration and connectivity between the two basins. A total of 468 bp of the mitochondrial gene (COI), 555 bp of the nuclear gene fragment (MYH6), and 8 microsatellite loci were analyzed. </span></span><span class="Fuentedeprrafopredeter1"><span>As a result, we found two major genetic clusters as the most likely scenario (K=2), but they were not discreetly distributed between basins. A gradient of genetic admixture was observed in Cucui and </span></span><span class="Fuentedeprrafopredeter1"><span>São</span></span><span class="Fuentedeprrafopredeter1"><span> Gabriel da Cachoeira, between the upper Negro River and the upper Orinoco. Samples from the middle-lower Negro River were highly structured. </span></span><span class="Fuentedeprrafopredeter1"><span>Cucui (Negro basin) was more similar to the Orinoco than to the rest of the Negro basin populations. </span></span><span class="Fuentedeprrafopredeter1"><span>However, substructure was also observed by the discriminant analysis, fixation indices and other hierarchichal structure analyses (K=3-6), showing three major geographic clusters: Orinoco, Cucui, and the remaining of the Negro basin. </span></span><span class="Fuentedeprrafopredeter1"><span>Unidirectional migration patterns were detected between basins: via Cucui toward Orinoco and via the remaining of the Negro basin toward Orinoco. Results from the Relaxed Random Walk analysis support a very recent origin of this species in the headwater Orinoco basin (Western Guiana Shield, at late Pleistocene) with a later rapid colonization of the remaining Orinoco basin and almost simultaneously the Negro River via Cucui, between 0.115 until about 0.001 Ma. Historical biogeography and population genetic patterns observed here for Cardinal tetra, seem to be better explained by river capture, physical, or ecological barriers than due to the geographic distance.</span></span></p>
Altered Structural-functional Connectivity Coupling on Chronic Subcortical Stroke
ClinicalTrials.gov study NCT05648552. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
The Influence of in Utero Cannabis Exposure on Neonatal Brain Morphology and Structural Connectivity
ClinicalTrials.gov study NCT03718520. IPD Sharing: NO. Countries: 1. Publications: 0.
Bridging Brain Structure and Function by Correlating Structural Connectivity, Cortico-Cortical Transmission and Direct Electro-Stimulation
ClinicalTrials.gov study NCT03503110. IPD Sharing: NO. Countries: 1. Publications: 6.
Structural and Functional Connectivity of Frontostriatal and Frontoparietal Networks as Endophenotypes of ADHD
ClinicalTrials.gov study NCT01682915. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Developmental Trajectory of Brain Structural Connectivity and Cognitive Function From Childhood to Adulthood
ClinicalTrials.gov study NCT01677793. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Elucidating the Temporality of Structural and Functional Connectivity Changes in Essential Tremor After Successful Deep Brain Stimulation to the Dentato-rubro-thalamic Tract
ClinicalTrials.gov study NCT04758624. IPD Sharing: NO. Countries: 1. Publications: 1.
Structural and Functional Connectivity in Partial Epilepsies Studied with MRI and MEG
ClinicalTrials.gov study NCT01313260. IPD Sharing: Not stated. Countries: 1. Publications: 1.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.
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.