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49 results for “spatial connectivity”
Research compendium for 'Refitting the Context: A Reconsideration of Cultural Change among Early Homo sapiens at Fumane Cave through Blade Break Connections, Spatial Taphonomy, and Lithic Technology'
<div> <h3>Compendium DOI:</h3> <p><a href="../doi/10.5281/zenodo.10965413">https://zenodo.org/doi/10.5281/zenodo.10965413</a> </p> </div> <p>The content available at the above provided URL will reproduce the results as documented in the publication. Instead, the files hosted at <a href="https://github.com/ArmandoFalcucci/Refitting-The-Context">https://github.com/ArmandoFalcucci/Refitting-The-Context</a> represent the developmental versions and might have undergone modifications since the paper's publication.</p> <div> <h3>Maintainer of this repository:</h3> </div> <p>Armando Falcucci (<a href="mailto:armando.falcucci@uni-tuebingen.de">armando.falcucci@uni-tuebingen.de</a>)</p> <div> <h3>Published paper:</h3> </div> <p>Armando Falcucci, Domenico Giusti, Filippo Zangrossi, Matteo De Lorenzi, Letizia Ceregatti, Marco Peresani. Refitting the Context: Revisiting the Aurignacian sequence at Fumane Cave through blade fragment connections, spatial taphonomy, and lithic technology. <em>Journal of Paleolithic Archaeology</em> (2024). DOI: <a href="https://doi.org/10.1007/s41982-024-00203-0" rel="nofollow">10.1007/s41982-024-00203-0</a></p> <div> <h3>Abstract:</h3> </div> <p>High-resolution stratigraphic frameworks are crucial for unraveling the biocultural processes behind the dispersals of Homo sapiens across Europe. Detailed technological studies of lithic assemblages retrieved from multi-stratified sequences allow archaeologists to precisely model the chrono-cultural dynamics of the early Upper Paleolithic. However, it is of paramount importance to verify the integrity of these assemblages before building explanatory models of cultural change. In this study, multiple lines of evidence suggest that the stratigraphic sequence of Fumane Cave in northeastern Italy experienced minor post-depositional reworking, establishing it as a pivotal site for exploring the earliest stages of the Aurignacian. By conducting a systematic search for break connections between blade fragments and applying spatial analysis techniques, we identified three well-preserved areas of the excavation containing assemblages suitable for renewed archaeological investigations. Subsequent technological analyses, incorporating attribute analysis, reduction intensity, and multivariate statistics, have allowed us to discern the spatial organization of the site during the formation of the Protoaurignacian palimpsest A2–A1. Moreover, diachronic comparisons between three successive stratigraphic units prompted us to reject the hypothesis of techno-cultural continuity of the Protoaurignacian in northeastern Italy after the onset of the Heinrich Event 4. Based on the variability of the lithic and osseous artifacts, the most recent assemblage analyzed, D3b alpha, is now ascribed to the Early Aurignacian, aligning the evidence from Fumane with the current understanding of the development of the Aurignacian across Europe. Overall, this study demonstrates the high effectiveness of the break connection method when combined with detailed spatial analysis and lithic technology, providing a methodological tool particularly amenable to be applied to sites excavated in the past with varying degrees of recording accuracy.</p> <div> <h3>Keywords:</h3> </div> <p>Protoaurignacian; Early Aurignacian; Lithics; Refittings; Assemblage integrity; Spatial analysis; Italy</p> <div> <h3>Overview of contents and how to reproduce:</h3> </div> <p>Within this repository, various folders house data (<code>data</code>), code (<code>script</code>), and output files (<code>output</code>) pertinent to the paper. The data folder encompasses the blank and core datasets from the Aurignacian of Fumane Cave and the dataset of the blade fragment connection study. To replicate the results, download the entire repository and employ <code>Refitting-The-Context.Rproj</code> and open the folder <code>script</code>. For ensuring reproducibility, the <code>renv</code> package (v. 1.0.3) was utilized, following the procedures detailed in its vignette. All analyses and visualizations in the paper were conducted using R 4.3.1 on Microsoft Windows 10.0.19045 (64-bit). As the necessary packages are available in the <code>renv</code> folder, they are not explicitly listed here.</p> <div> <h3>Licenses:</h3> </div> <p>Code: <strong>MIT</strong> <a href="http://opensource.org/licenses/MIT" rel="nofollow">http://opensource.org/licenses/MIT</a>, copyright holder: Armando Falcucci (2024).</p> <p>Data and intellectual work: <strong>Creative Commons Attribution 4.0 International License</strong> (<a href="http://creativecommons.org/licenses/by/4.0/" rel="nofollow">http://creativecommons.org/licenses/by/4.0/</a>), copyright holder: the authors (2024).</p>
Figure3. APCs A1-A4 connected within range of cohesion-factor-threshold form members of one ARB-AIDEN: A Density Conscious Artificial Immune System for Automatic Discovery of Arbitrary Shape Clusters in Spatial Patterns
<p>Figure3 depicts this process. The<br> model with the above specification then effectively detects self or non-self pathogens. In terms of<br> its application to the task of clustering, this interpretation means making the affinities high within<br> clusters and low across clusters. A pathogen corresponding to an outlier would not stimulate a TCR<br> sufficiently and may not form part of any ARB.</p>
Data and code for: Spatial cell type enrichment predicts mouse brain connectivity
<p>A fundamental neuroscience topic is the link between the brain's molecular, cellular and cytoarchitectonic properties and structural connectivity (SC). Recent studies relate inter-regional connectivity to gene expression, but the relationship to regional cell-type distributions remains understudied. Here, we utilize whole-brain mapping of neuronal and non-neuronal subtypes via the Matrix Inversion and Subset Selection (MISS) algorithm to model inter-regional connectivity as a function of regional cell-type composition with machine learning. We deployed random forest algorithms for predicting connectivity from cell type densities, demonstrating surprisingly strong prediction accuracy of cell types in general and particular cells like oligodendrocytes. We found evidence of a strong distance-dependency in the cell-connectivity relationship, with layer-specific excitatory neurons contributing the most for long-range connectivity, while vascular and astroglia are salient for short-range connections. Our results demonstrate a link between cell types and connectivity, providing a roadmap for examining this relationship in other species, including humans.</p>
Freshwater connectivity transforms spatially integrated signals of biodiversity
<p>Aquatic ecosystems offer a continuum of water flow from headwater streams to inland lakes and coastal marine systems. This spatial connectivity influences the structure, function and dynamics of aquatic communities, which are among the most threatened and degraded on earth. Here, we determine the spatial resolution of eDNA in dendritic freshwater networks, which we use as a model for connected metacommunities. Our intensive sampling campaign comprised over 430 eDNA samples across 21 connected lakes, allowing us to analyse detections at a variety of scales, from different habitats within a lake to entire lake networks. We found strong signals of within-lake variation in eDNA distribution reflective of typical habitat use by both fish and zooplankton. Most importantly, we also found that connecting channels between lakes resulted in an accumulation of downstream eDNA detections in lakes with a higher number of inflows, and as networks increased in length. Environmental DNA achieves biodiversity surveys in these habitats in a high-throughput, spatially integrated way. These findings have profound implications for the interpretation of eDNA detections in aquatic ecosystems in global-scale biodiversity monitoring observations.</p>
Data and code from: Determinants of species’ centrality in spatially-connected plant-frugivore networks
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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 and code for: Spatial cell type enrichment predicts mouse brain connectivity
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Freshwater connectivity transforms spatially integrated signals of biodiversity
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Spatial priorities for climate-change refugia and connectivity for British Columbia (Version 1.1)
<p>Climate-informed conservation priorities in British Columbia (Version 1.1)</p> <p>Territorial acknowledgement:</p> <p>We respectfully acknowledge that we live and work across diverse unceded territories and treaty lands and pay our respects to the First Nations, Inuit and Métis ancestors of these places. We honour our connections to these lands and waters and reaffirm our relationships with one another.</p> <p><br>Suggested citation:</p> <p>Stolar, J., D. Stralberg, I. Naujokaitis-Lewis, S.E. Nielsen, and G. Kehm. 2024. Spatial priorities for climate-change refugia and connectivity for British Columbia (Version 1.1). Place of publication: University of Alberta, Edmonton, Canada. doi: 10.5281/zenodo.10603162</p> <p>Corresponding author: stolar@ualberta.ca</p> <p><br>Summary:</p> <p>The purpose of this project is to identify spatial locations of (a) vulnerabilities within British Columbia’s current network of protected areas and (b) priorities for conservation and management of natural landscapes within British Columbia under a range of future climate-change scenarios. This involved adaptation and implementation of existing continental- and provincial-scale frameworks for identifying areas that have potential to serve as refugia from climate change or corridors for species migration.</p> <p>Outcomes of this work include the provision of practical guidance for protected areas network design and vulnerabilities identification under climate change, with application to other regions and jurisdictions. Project results, in the form of multiple spatial prioritization scenarios, may be used to evaluate the resilience of the existing protected area network and other conservation designations to better understand the risks to British Columbia’s biodiversity in our changing climate.</p> <p><br>Description:</p> <p>These raster layers represent different scenarios of Zonation rankings of conservation priorities for climate resilience and connectivity between current and 2080s conditions for a provincial-scale analysis. Input conservation features included metrics of macrorefugia (forward and backward climate velocity (km/year), overlapping future and current habitat suitability for ~900 rare species in BC), microrefugia (presence of old growth ecosystems, drought refugia, glaciers/cool slopes/wetlands, and geodiversity), and connectivity. Please see details in the accompanying report.</p> <p><br>File nomenclature:</p> <p>.zip folder (Stolar_et_al_2024_CiCP_Zenodo_upload_Version_1.1.zip):<br>Contains the files listed below.</p> <p>Macrorefugia (2080s_macrorefugia.tif):<br>Scenarios for each taxonomic group (equal weightings for all species) (Core-area Zonation Function)<br>Climate-type velocity + species scenarios from above (Core-area Zonation; equal weightings)</p> <p>Microrefugia (microrefugia.tif):<br>Scenario with old growth forest habitat, landscape geodiversity, wetlands/cool slopes/glaciers, drought refugia (Core-area Zonation; equal weightings)</p> <p>Overall scenario (2080s_macro_micro_connectivity.tif):<br>Inputs from above (with equal weightings) + connectivity metrics (each weighted at 0.1) (Additive Benefit Function Zonation)</p> <p>Conservation priorities (Conservation_priorities_2080s.tif):<br>Overall scenario from above extracted to regions of low human footprint.</p> <p>Restoration priorities (Restoration_priorities_2080s.tif):<br>Overall scenario from above extracted to regions of high human footprint.</p> <p>Accompanying report (Stolar_et_al_2024_CiCP_Zenodo_upload_Version_1.1.pdf):<br>Documentation of rationale, methods and interpretation.</p> <p>READ_ME file (READ_ME_PLEASE.txt):<br>Metadata.</p> <p><br>Legend interpretation:</p> <p>Ranked Zonation priorities increase from 0 (lowest) to 1 (highest).</p> <p>Raster information:</p> <p>Columns and Rows: 1597, 1368<br>Number of Bands: 1<br>Cell Size (X, Y): 1000, 1000<br>Format: TIFF<br>Pixel Type: floating point <br>Compression: LZW</p> <p><br>Spatial reference:</p> <p>XY Coordinate System: NAD_1983_Albers<br>Linear Unit: Meter (1.000000)<br>Angular Unit: Degree (0.0174532925199433)<br>false_easting: 1000000<br>false_northing: 0<br>central_meridian: -126<br>standard_parallel_1: 50<br>standard_parallel_2: 58.5<br>latitude_of_origin: 45<br>Datum: D_North_American_1983</p> <p><br>Extent:</p> <p>West -139.061502 East -110.430823 <br>North 60.605550 South 47.680823 </p> <p><br>Disclaimer: </p> <p>The University of Alberta (UofA) is furnishing this deliverable "as is". UofA does not provide any warranty of the contents of the deliverable whatsoever, whether express, implied, or statutory, including, but not limited to, any warranty of merchantability or fitness for a particular purpose or any warranty that the contents of the deliverable will be error-free.</p> <p><br>Funding:<br> <br>We gratefully acknowledge the financial support of Environment and Climate Change Canada, the Province of British Columbia through the Ministry of Water, Land and Resource Stewardship) and the Ministry of Environment and Climate Change Strategy, the BC Parks Living Lab for Climate Change and Conservation, and the Wilburforce Foundation.</p>
Country‐wide genetic monitoring over 21 years reveals lag in genetic recovery despite spatial connectivity in an expanding carnivore (Eurasian otter, Lutra lutra) population
<p>Numerous terrestrial mammal species have experienced extensive population declines during past centuries, due largely to anthropogenic pressures. For some species, including the Eurasian otter (<em>Lutra lutra</em>), environmental and legal protection has more recently led to population growth and recolonisation of parts of their historic ranges. While heralded as conservation successes, only a few such recoveries have been examined from a genetic perspective, i.e. whether genetic variability and connectivity have been restored. We here use large-scale and long-term genetic monitoring data from UK otters, whose population underwent a well-documented population decline between the 1950s to 1970s, to explore the dynamics of a population re-expansion over a 21-year period. We genotyped otters from across Wales and England at five time points between 1994 and 2014 using 15 microsatellite loci. We used this combination of long-term temporal and large-scale spatial sampling to evaluate 3 hypotheses relating to genetic recovery; that (i) gene flow between sub-populations would increase over time, (ii) genetic diversity of previously isolated populations would increase, and that (iii) genetic structuring would weaken over time. Although we found an increase in inter-regional gene flow and admixture levels among subpopulations, there was no significant temporal change in either heterozygosity or allelic richness. Genetic structuring among the main sub-populations hence remained strong and showed a clear historical continuity. These findings highlight an underappreciated aspect of population recovery of endangered species, that genetic recovery may often lag behind the processes of spatial and demographic recovery. In other words, the restoration of physical connectivity of populations does not necessarily lead to genetic connectivity. Our findings emphasise the need for genetic data as an integral part of conservation monitoring, to enable the potential vulnerability of populations to be evaluated.</p>
Spatial drivers of composition and connectivity across endangered tropical dry forests
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Hydrological connectivity and local environment alternately drive spatial structure of floodplain aquatic community across season
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Data from: Spatial structuring and life history connectivity of Antarctic silverfish along the southern continental shelf of the Weddell Sea
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Country‐wide genetic monitoring over 21 years reveals lag in genetic recovery despite spatial connectivity in an expanding carnivore (Eurasian otter, Lutra lutra) population
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Combining seascape connectivity with cumulative impact assessment in support of ecosystem-based marine spatial planning
<p>1. Cumulative impact assessment (CIA) is a promising approach to guide marine spatial planning (MSP) and management. One limitation of CIA is the neglect of seascape connectivity, which may spread the impact of localised pressures to ambient areas, e.g. through lost dispersal and recruitment of organisms.</p> <p>2. We here, for the first time, incorporate seascape connectivity into a traditional CIA model using a connectivity matrix, exemplified by dispersal of propagules estimated through biophysical modelling. Two <i>connectivity impacts</i>are identified: the <i>source impact</i> represents downstream areas losing recruits because of reduced larval dispersal from sites affected by the pressure, and the <i>sink impact</i> represents loss of recruits originating from upstream areas prevented from settlement in the site affected by the local pressure.</p> <p>3. By including seascape connectivity into the Swedish MSP-guiding CIA tool Symphony we demonstrate how to practically account for remote effects of local environmental impact. Our example on blue mussel shows how reducing mussel fitness in a given area may have impacts on mussels far from the acting pressures. Overall, results indicate that connectivity impact for blue mussels plays a minor role in most areas, less than 10% of the ordinary cumulative impact. However, in some smaller areas, e.g. on offshore banks and the Danish Straits, seascape connectivity may increase ordinary cumulative impact with 20-30%. In an example of scenario-based CIA analyses of MSP projections, we demonstrate how impacts of particular management actions, e.g. shipping rerouting and wind power developments, can be tracked far from the original area of influence.</p> <p>4. Depending on the dispersal ability of ecosystem components, a local pressure may impact a considerable area through seascape connectivity, transgressing management units and national borders. Although the mean connectivity impact may be modest for a single ecosystem component, the consideration of seascape connectivity across multiple ecosystem components may significantly alter the mapping of cumulative impact and the assessment of different MSP scenarios.</p> <p>5. Synthesis and applications.<span><span><span><span><span><span><span><span><span><span><span> Our extension of Cumulative Impact Assessment offers a new method for mapping and practically integrating seascape connectivity with ecosystem-based MSP and other spatial instruments for policy making, such as marine protected areas.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Genetic assessment of population structure and connectivity in the threatened Mediterranean coral Astroides calycularis (Scleractinia, Dendrophylliidae) at different spatial scales
Understanding dispersal patterns, population structure and connectivity among populations is helpful in the management and conservation of threatened species. Molecular markers are useful tools as indirect estimators of these characteristics. In this study we assess the population genetic structure of the endemic Mediterranean coral Astroides calycularis in the Alboran Sea at local and regional scales, and at three localities outside of this basin. Bayesian clustering methods, traditional F-statistics and Dest statistics were used to determine the patterns of genetic structure. Likelihood and coalescence approaches were used to infer migration patterns and effective population sizes. The results obtained reveal a high level of connectivity among localities separated by as much as one kilometer and moderate levels of genetic differentiation among more distant localities, somewhat corresponding with a stepping-stone model of gene flow and connectivity. These data suggest that connectivity among populations of this coral is mainly driven by the biology of the species, with low dispersal abilities; in addition, hydrodynamic processes, oceanographic fronts and the distribution of rocky substrate along the coastline may influence larval dispersal.
Data from: Understanding the spatial scale of genetic connectivity at sea: unique insights from a land fish and a meta-analysis
Quantifying the spatial scale of population connectivity is important for understanding the evolutionary potential of ecologically divergent populations and for designing conservation strategies to preserve those populations. For marine organisms like fish, the spatial scale of connectivity is generally set by a pelagic larval phase. This has complicated past estimates of connectivity because detailed information on larval movements are difficult to obtain. Genetic approaches provide a tractable alternative and have the added benefit of estimating directly the reproductive isolation of populations. In this study, we leveraged empirical estimates of genetic differentiation among populations with simulations and a meta-analysis to provide a general estimate of the spatial scale of genetic connectivity in marine environments. We used neutral genetic markers to first quantify the genetic differentiation of ecologically-isolated adult populations of a land dwelling fish, the Pacific leaping blenny (Alticus arnoldorum), where marine larval dispersal is the only probable means of connectivity among populations. We then compared these estimates to simulations of a range of marine dispersal scenarios and to collated FST and distance data from the literature for marine fish across diverse spatial scales. We found genetic connectivity at sea was extensive among marine populations and in the case of A. arnoldorum, apparently little affected by the presence of ecological barriers. We estimated that ~5000 km (with broad confidence intervals ranging from 810 - 11,692 km) was the spatial scale at which evolutionarily meaningful barriers to gene flow start to occur at sea, although substantially shorter distances are also possible for some taxa. In general, however, such a large estimate of connectivity has important implications for the evolutionary and conservation potential of many marine fish communities.
Data from: Grains of connectivity: analysis at multiple spatial scales in landscape genetics
Landscape genetic analyses are typically conducted at one spatial scale. Considering multiple scales may be essential for identifying landscape features influencing gene flow. We examined landscape connectivity for woodland caribou (Rangifer tarandus caribou) at multiple spatial scales using a new approach based on landscape graphs that creates a Voronoi tessellation of the landscape. To illustrate the potential of the method, we generated five resistance surfaces to explain how landscape pattern may influence gene flow across the range of this population. We tested each resistance surface using a raster at the spatial grain of available landscape data (200 m grid squares). We then used our method to produce up to 127 additional grains for each resistance surface. We applied a causal modelling framework with partial Mantel tests, where evidence of landscape resistance is tested against an alternative hypothesis of isolation-by-distance, and found statistically significant support for landscape resistance to gene flow in 89 of the 507 spatial grains examined. We found evidence that major roads as well as the cumulative effects of natural and anthropogenic disturbance may be contributing to the genetic structure. Using only the original grid surface yielded no evidence for landscape resistance to gene flow. Our results show that using multiple spatial grains can reveal landscape influences on genetic structure that may be overlooked with a single grain, and suggest that coarsening the grain of landcover data may be appropriate for highly-mobile species. We discuss how grains of connectivity and related analyses have potential landscape genetic applications in a broad range of systems.
Data from: Optimizing the trade-off between spatial and genetic sampling efforts in patchy populations: towards a better assessment of functional connectivity using an individual-based sampling scheme
Genetic data are increasingly used in landscape ecology for the indirect assessment of functional connectivity, i.e. the permeability of landscape to movements of organisms. Among available tools, matrix correlation analyses (e.g. Mantel tests or mixed models) are commonly used to test for the relationship between pairwise genetic distances and movement costs incurred by dispersing individuals. When organisms are spatially clustered, a population-based sampling scheme (PSS) is usually performed, so that a large number of genotypes can be used to compute pairwise genetic distances on the basis of allelic frequencies. Because of financial constraints, this kind of sampling scheme implies a drastic reduction in the number of sampled aggregates, thereby reducing sampling coverage at the landscape level. We used matrix correlation analyses on simulated and empirical genetic datasets to investigate the efficiency of an individual-based sampling scheme (ISS) in detecting isolation-by-distance and isolation-by-barrier patterns. Provided that pseudo-replication issues are taken into account (e.g. through restricted permutations in Mantel tests), we showed that the use of inter-individual measures of genotypic dissimilarity may efficiently replace inter-population measures of genetic differentiation: the sampling of only three or four individuals per aggregate may be sufficient to efficiently detect specific genetic patterns in most situations. The ISS proved to be a promising methodological alternative to the more conventional PSS, offering much flexibility in the spatial design of sampling schemes and ensuring an optimal representativeness of landscape heterogeneity in data, with few aggregates left unsampled. Each strategy offering specific advantages, a combined use of both sampling schemes is discussed.
Data from: Mountain metacommunities: climate and spatial connectivity shape ant diversity in a complex landscape
Understanding what drives biodiversity patterns across scales is the central goal of ecology. Both environmental gradients and spatial landscape structure have been found to be important factors influencing species distributions and community composition, and partly reflect the balance of underlying deterministic and stochastic community processes. In some systems, environmental gradients and spatial connectivity are intertwined in that steep environmental gradients serve as boundaries on species movements and impose environment-derived complex spatial structure to metacommunities. Mountainous landscapes are prime examples of this, and recent theory has linked principles of geomorphology, environmental gradients, and spatial structure to make predictions for resulting community patterns. In this context, we examine variation in taxonomic and phylogenetic ant diversity patterns along a geographic transect spanning >5000 m in elevational range in the Hengduan mountains of southern China. We found that environmental gradients dominate variation in both alpha and beta diversity in this landscape, with alpha diversity strongly declining with elevation and beta diversity driven by elevational differences. However, within an elevational band spatial connectivity predicts beta diversity better than geographic distance. Our findings deviate from theoretical predictions in several ways, notably alpha diversity is monotonically declining and within-band beta diversity is invariant with increasing elevation. The discrepancies between theory and observation may be explained by differences in the Hengduan landscape from idealized fluvial landscapes, such as a lack of a mid-elevation peak in connectivity, as well as evolutionary limits on the source pool of species available to populate metacommunities at different elevations. The latter is supported by variation in phylogenetic community structure with elevation. Our results demonstrate the power of conceptual, statistical, and theoretical frameworks that integrate the roles of environment and spatial structure in metacommunities, but that additional work is needed to bridge the gap between abstract theory and real systems.
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Allen Brain Atlas
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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.