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2,721 results for “Connectivity”
A White Matter Atlas and Common Connectivity Space Facilitate the Pig as a Translational Model in Neuroscience
<p>Dataset accompanying the preprint <em>"A White Matter Atlas and Common Connectivity Space Facilitate the Pig as a Translational Model in Neuroscience"</em>. Contained here are the files used for the cross-species browser spec files, as well as the raw and preprocessed pig diffusion-weighted data, and their raw anatomical files and surfaces. </p> <p>The preprint is available here: <a href="https://www.biorxiv.org/content/10.1101/2020.10.13.337436">https://www.biorxiv.org/content/10.1101/2020.10.13.337436</a></p> <p>And the associated code and lighter files can be found here: <a href="https://github.com/neurabenn/pig_connectivity_bp_preprint">https://github.com/neurabenn/pig_connectivity_bp_preprint</a></p> <p> </p>
Data from: Connecting the data landscape of long-term ecological studies: the SPI-Birds data hub
<p>1. The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long-term studies of individually marked animals are not an exception. These studies are especially important as instrumental for understanding evolutionary and ecological processes in the wild. Further, their number and global distribution provides a unique opportunity to assess the generality of patterns and to address broad-scale global issues (e.g. climate change).</p> <p>2. To solve data integration issues and enable a new scale of ecological and evolutionary research based on long-term studies of birds, we have created the SPI-Birds Network and Database (www.spibirds.org) – a large-scale initiative that connects data from, and researchers working on, studies of wild populations of individually recognizable (usually ringed) birds. Within year and a half since the establishment, SPI-Birds has recruited over 120 members, and currently hosts data on almost 1.5 million individual birds collected in 80 populations over 2000 cumulative years, and counting.</p> <p>3. SPI-Birds acts as a data hub and a catalogue of studied populations. It prevents data loss, secures easy data finding, use and integration, and thus facilitates collaboration and synthesis. We provide community-derived data and meta-data standards and improve data integrity guided by the principles of Findable, Accessible, Interoperable, and Reusable (FAIR), and aligned with the existing metadata languages (e.g. ecological meta-data language).</p> <p>4. The encouraging community involvement stems from SPI-Bird's decentralized approach: research groups retain full control over data use and their way of data management, while SPI-Birds creates tailored pipelines to convert each unique data format into a standard format. We outline the lessons learned, so that other communities (e.g. those working on other taxa) can adapt our successful model. Creating community-specific hubs (such as ours, COMADRE for animal demography, etc.) will aid much-needed large-scale ecological data integration.</p>
Conservation planning across realms: enhancing connectivity for multi-realm species
<p>Connectivity plays a key role in biodiversity conservation as it sustains ecological processes important for the maintenance of populations such as migrations. Connectivity is especially relevant for species that rely on different realms during their life cycle or use different realms daily or seasonally (multi-realm species). However, effort to address conservation across multiple realms have focused on identifying priority areas for conservation in a single realm (mostly marine) accounting for threats propagating from other realms or single species needs. Here, we demonstrate how to identify priority areas for conservation across three different realms (freshwater-terrestrial, estuary and marine) for multiple species, including some multi-realm species, that inhabit or move across the three realms. We use the whole Tagus River Basin, its estuary and nearby marine area as a case study. We compared the allocation of priority areas and spatial connectivity achieved under three scenarios: no-connectivity, within-realm and cross-realm connectivity scenarios. There were some differences in the spatial allocation of priority areas across scenarios. The most remarkable difference laid on the connectivity achieved under each scenario, which experienced a 3-fold increase when considering connectivity across realms, compared to solutions that considered only connectivity within each realm independently. This improvement in connectivity was especially marked for some of the species that occur across the three realms. There were, however, trade-offs between this improvement in connectivity: i) an increase in the number of planning units selected, especially in the estuary, the realm that links the other two; and ii) a decline in connectivity achieved within the freshwater—terrestrial and marine realms. Synthesis and applications: Addressing connectivity across realms deserves especial attention when planning for conservation of multi-realm species to ensure adequacy of conservation recommendations to respond to the needs of these species. Given the potential trade-offs between enhanced cross-realm connectivity and total area needed or internal within-realm connectivity, consideration of cross-realm connectivity must be cautiously evaluated and integrated in multi-realm conservation plans.</p>
Data from: Visualizing connectivity of ecological and evolutionary concepts – an exploration of research on plant species rarity
<p>Understanding the ecological and evolutionary factors that influence species rarity has important theoretical and applied implications, yet the reasons why some species are rare while others are common remain unresolved. As a novel exploration of scientific knowledge, we used network analysis conceptually to visualize the foci of a comprehensive base of >800 studies on plant species rarity within the context of ecology and evolution. In doing so, we highlight existing research strengths that could substantiate novel syntheses and gaps that could inspire new research. Our results reveal strong integrated foci on population dynamics with other ecological concepts. In contrast, despite the potential for ecological and evolutionary processes to interact, few studies explored the interplay of environmental factors and microevolutionary patterns. The cellular and molecular biology, physiology, and plasticity of rare plant species within both ecological and evolutionary contexts similarly provide avenues for impactful future investigations.</p>
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>
Stochastic processes and ecological connectivity drive stream invertebrate community responses to short-term drought
1. Community responses to and recovery from disturbances depend on local (e.g. presence of refuges) and regional (connectivity to recolonization sources) factors. Droughts are becoming more frequent in boreal regions, and are likely to constitute a severe disturbance for boreal stream communities where organisms largely lack adaptations to such hydrological extremes. 2. We conducted an experiment in 24 seminatural stream flumes to assess the effects of local and regional factors on the responses of benthic invertebrate communities to a short-term drought. We manipulated flow (drought vs. constant-flow), spatial arrangement of leaf litter patches (aggregated vs. evenly distributed) and colonization from regional species pool (enhanced vs. ambient connectivity) to test the combined effects of disturbance, connectivity, and resource arrangement on the structural and functional responses of benthic invertebrate communities. 3. We found that a drought as short as one week reduced invertebrate richness and abundances, mainly through stochastic extinctions. Such changes in richness were not reflected in functional diversity. This suggests that communities were characterized by a high degree of functional redundancy, which allowed maintenance of functional diversity despite species losses. Feeding groups responded differently to drought, with organic matter decomposers responding more than scrapers and predators. 4. Three weeks was insufficient for a complete invertebrate community recovery from the drought. However, recovery was greater in channels subjected to enhanced connectivity, which increased taxonomic diversity and abundance of certain taxa. Spatial configuration of resources explained the least variation in our response variables, having a significant effect only on invertebrate abundance and evenness (both sampling occasions) and species richness (end of recovery period). 5. Even a short drought, if occurring late to the season, may not allow communities to recover before the onset of winter, thus having a potentially long-lasting effect on stream communities. For boreal headwaters, extreme dewatering poses a novel disturbance regime that may trigger substantial and potentially irreversible changes. An improved understanding of such changes is needed to underpin adaptive management strategies in these increasingly fragmented and disturbed ecosystems. 18-Dec-2020
Plant community assembly in suburban vacant lots depends on earthmoving legacy, habitat connectivity, and current mowing frequency
<p>In suburban regions, vacant lots potentially offer significant opportunities for biodiversity conservation. Recently, in Japan, due to an economic recession, some previously developed lands have become vacant. Little is known, however, about the legacy of earlier earthmoving, which involves topsoil removal and ground levelling before residential construction, on plant community composition in such vacant lots. To understand (dis)assembly processes in vacant lots, we studied 24 grasslands in a suburban region in Japan: 12 grasslands that had experienced earthmoving and 12 that had not. We surveyed plant community composition and species richness, and clarified compositional turnover (replacement of species) and nestedness (non-random species loss) by distance-based β-diversities, which were summarized by PCoA analysis. We used piecewise structural equation modeling to examine the effects of soil properties, mowing frequency, past and present habitat connectivities on compositional changes. As a result, past earthmoving, mowing frequency, soil properties, and past habitat connectivity were found to be the drivers of compositional turnover. In particular, we found legacy effects of earthmoving: earthmoving promoted turnover from native grassland species to weeds in arable lands or roadside by altering soil properties. Mowing frequency also promoted the same turnover, implying that extensive rather than intensive mowing can modify the negative legacy effects and maintain grassland species. Decrease in present habitat connectivity marginally enhanced non-random loss of native grassland species (nestedness). Present habitat connectivity had a positive effect on species richness, highlighting the important roles of contemporary dispersal. Our study demonstrates that community assembly is a result of multiple processes differing in spatial and temporal scales. We suggest that extensive mowing at local scale, as well as giving a high conservation priority to grasslands with high habitat connectivity at regional scale, are the promising actions to maintain endangered native grassland species in suburban landscapes with negative legacy effects of earthmoving.</p>
Data from: Large-scale connectivity, cryptic population structure, and relatedness in Eastern Pacific olive ridley sea turtles (Lepidochelys olivacea)
<p>Endangered species are grouped into genetically discrete populations to direct conservation efforts. Mitochondrial Control Region (mtCR) haplotypes are used to elucidate deep divergences between populations, as compared to nuclear microsatellites that can detect recent structuring. When prior populations are unknown, it is useful to subject microsatellite data to clustering and/or ordination population inference. Olive ridley sea turtles (Lepidochelys olivacea) are the most abundant sea turtle, yet few studies have characterized olive ridley population structure. Recently, clustering results of olive ridleys in the Eastern Tropical Pacific Ocean suggested weak structuring (FST=0.02) between Mexico and Central America. We analyzed mtCR haplotypes, new microsatellite genotypes from Costa Rica, and pre-existing microsatellite genotypes from olive ridleys across the Eastern Tropical Pacific, to further explore population structuring in this region. We subjected inferred populations to multiple analyses to explore the mechanisms behind their structuring. We found 10 mtCR haplotypes from 60 turtles nesting at three sites in Costa Rica, but did not detect divergence between Costa Rican sites, or between Central America and Mexico. In Costa Rica, clustering suggested one population with no structuring, but ordination suggested four cryptic clusters with moderate structuring (FST=0.08, p<0.001). Across the Eastern Tropical Pacific, ordination suggested nine cryptic clusters with moderate structuring (FST=0.103, p<0.001) that largely corresponded to Mexican and Central American populations. All ordination clusters displayed significant internal relatedness relative to global relatedness (p<0.001) and contained numerous sibling pairs. This suggests that broadly dispersed family lineages have proliferated in Eastern Tropical Pacific olive ridleys and corroborates previous work showing basin-wide connectivity and shallow population structure in this region. The existence of broadly dispersed kin in Eastern Tropical Pacific olive ridleys has implications for management of olive ridleys in this region, and adds to our understanding of sea turtle ecology and life-history, particularly in light of the natal-homing paradigm.</p>
Integrating stable isotopes, parasite and ring-reencounter data to quantify migratory connectivity - a case study with Barn Swallows breeding in Switzerland, Germany, Sweden and Finland
<p>Ecosystems around the world are connected by seasonal migration. The migrant animals themselves are influenced by migratory connectivity through effects on the individual and the population level. Measuring migratory connectivity is notoriously difficult due to the simple requirement of data conveying information about the non-breeding distribution of many individuals from several breeding populations. Explicit integration of data derived from different methods increases the precision and the reliability of parameter estimates.</p> <p>We combine ring-reencounter, stable isotope and blood parasite data of Barn Swallows <i>Hirundo rustica</i> in a single integrated model to estimate migratory connectivity for three large scale breeding populations across a latitudinal gradient from Central Europe and Scandinavia. To this end, we integrated a non-Markovian multi-state mark-recovery model for the ring-reencounter data with normal and binomial mixture models for the stable isotope and parasite data.</p> <p>The integration of different data sources within a mark-recapture modelling framework enables the most precise quantification of migratory connectivity on the given broad spatial scale. The results show that northern breeding populations and Southern Africa as well as southern breeding populations and Western-Central Africa are more strongly connected through Barn Swallow migration than central European breeding populations with any of the African wintering areas. The non-breeding distribution of Barn Swallows from central European breeding populations seems to be a mixture of those populations breeding further North and South, indicating a migratory divide.</p>
Species distribution, hybridization and connectivity in the genus Chionodraco: unveiling unknown icefish diversity in Antarctica
<p><strong>Aim</strong></p> <p>The species of the genus <em>Chionodraco</em> (Notothenioidei) are the most abundant icefish on the continental shelf of the Weddell Sea. While previous studies indicated that only <em>Chionodraco hamatus</em> and <em>Chionodraco myersi</em> inhabit the Weddell Sea, the third <em>Chionodraco</em> species, <em>Chionodraco rastrospinosus</em>, was recently sampled in the area. Since <em>C. rastrospinosus</em> is supposed to be found only at the Antarctic Peninsula and Scotia Arc, this study aimed at confirming the species classification of <em>C. rastrospinosus</em> by molecular methods and identifying its putative source population. Given the documented evidence of introgression among the three species, we tested whether the newly found <em>C. rastrospinosus</em> shared any genetic variability with the other <em>Chionodraco</em> species. To explain the pattern of distribution of the <em>Chionodraco</em> species, we aimed at estimating the hydrodynamic connectivity between the Antarctic Peninsula and the Weddell Sea.</p> <p><strong>Location</strong></p> <p>Antarctic Peninsula, southern Scotia Arc and the south-eastern Weddell Sea</p> <p><strong>Methods</strong></p> <p>We genotyped 19 microsatellites and sequenced the mitochondrial D-loop for 560 <em>Chionodraco</em> individuals. We simulated the dispersal of more than 3 million drifters (Lagrangian model).</p> <p><strong>Results</strong></p> <p>The molecular analyses support the presence of <em>C. rastrospinosus</em> in the Weddell Sea and its homogeneity with <em>C. rastrospinosus</em> from the Antarctic Peninsula. Bayesian clustering identifies three putative hybrids among <em>C. rastrospinosus</em> and the other congenerics. Lagrangian simulations do not support connectivity driven by the oceanographic features of the Antarctic Peninsula and Weddell Sea via passive larval dispersal only.</p> <p><strong>Main conclusions</strong></p> <p>This study documents, for the first time, the presence of <em>C. rastrospinosus</em> in the Weddell Sea unveiling more biodiversity than previously known in this region. The sympatry of the three <em>Chionodraco</em> species explains the occurrence of occasional, ongoing events of hybridization in the genus. Alternative possible hypotheses need to be tested in future studies about the mechanisms maintaining the interspecific connectivity in <em>Chionodraco</em> spp.</p>
Data from: Herbivore control in connected seascapes: habitat determines when population regulation occurs in the life history of a key herbivore
Herbivore outbreaks often trigger catastrophic overgrazing events in marine macrophyte ecosystems. The sea urchin Paracentrotus lividus, the dominant herbivore of shallow Mediterranean seascapes, is capable of precipitating shifts to barrens when its populations explode. P. lividus is found ubiquitously in rocky macroalgal communities and in sandy seagrass meadows of Posidonia oceanica, two of the most important subtidal habitats in the Mediterranean. We explored if habitat-specific regulation across the principal stages of the urchin life cycle could help explain the persistence of these populations in connected mosaics. We measured each of three relevant ecological process (i.e. settlement, post-settlement survival and predation) across a wide stretch of the Mediterranean coast (ca. 600km). Our results show that habitat-specific regulation is critical in determining urchin populations: each habitat limited urchin sub-populations at different life stages. Settlement was never limiting; urchins settled at similar rates in both habitats across the coast. Post-settlement survival was a clear bottleneck, particularly in seagrass meadows where no juvenile urchins were recorded. Despite this bottleneck in seagrasses, adult urchin populations were very similar in both seagrass and macroalgal habitats indicating that other processes (potentially migration) could be key in determining adult distributions across the mosaic. The fact that population regulation is clearly habitat-specific suggests that sea urchin populations may be significantly buffered from bottlenecks in mixed seascapes where both habitats co-occur. Sea urchin populations can therefore persist across the seascape despite strong habitat-specific regulation either by maintaining reproductive output in one habitat or by migrating between them. By affording these regulatory escapes to habitat-modifying species, patchy mosaics may be much more prone to herbivore outbreaks and a host of cascading effects that come in their wake.
Data from: Surface-water dynamics and land use influence landscape connectivity across a major dryland region
Landscape connectivity is important for the long-term persistence of species inhabiting dryland freshwater ecosystems, with spatiotemporal surface-water dynamics (e.g., flooding) maintaining connectivity by both creating temporary habitats and providing transient opportunities for dispersal. Improving our understanding of how landscape connectivity varies with respect to surface-water dynamics and land use is an important step to maintaining biodiversity in dynamic dryland environments. Using a newly available validated Landsat TM and ETM+ surface-water time series, we modelled landscape connectivity between dynamic surface-water habitats within Australia's 1 million km2 semi-arid Murray Darling Basin across a 25-year period (1987 to 2011). We identified key habitats that serve as well-connected 'hubs', or 'stepping-stones' that allow long-distance movements through surface-water habitat networks. We compared distributions of these habitats for short- and long-distance dispersal species during dry, average and wet seasons, and across land-use types. The distribution of stepping-stones and hubs varied both spatially and temporally, with temporal changes driven by drought and flooding dynamics. Conservation areas and natural environments contained higher than expected proportions of both stepping-stones and hubs throughout the time series; however, highly modified agricultural landscapes increased in importance during wet seasons. Irrigated landscapes contained particularly high proportions of well-connected hubs for long-distance dispersers, but remained relatively disconnected for less vagile organisms. The habitats identified by our study may serve as ideal high-priority targets for land-use specific management aimed at maintaining or improving dispersal between surface-water habitats, potentially providing benefits to biodiversity beyond the immediate site scale. Our results also highlight the importance of accounting for the influence of spatial and temporal surface-water dynamics when studying landscape connectivity within highly variable dryland environments.
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: Seascape genomics reveals adaptive divergence in a connected and commercially important mollusc, the greenlip abalone (Haliotis laevigata), along a longitudinal environmental gradient
Populations of broadcast spawning marine organisms often have large sizes and are exposed to reduced genetic drift. Under such scenarios, strong selection associated with spatial environmental heterogeneity is expected to drive localized adaptive divergence, even in the face of connectivity. We tested this hypothesis using a seascape genomics approach in the commercially important greenlip abalone (Haliotis laevigata). We assessed how its population structure has been influenced by environmental heterogeneity along a zonal coastal boundary in southern Australia linked by strong oceanographic connectivity. Our datasets include 9,109 filtered SNPs for 371 abalones from 13 localities and environmental mapping across ~800 km. Genotype-environment association analyses and outlier tests defined 8,786 putatively neutral and 323 candidate adaptive loci. From a neutral perspective, the species is better represented by a metapopulation with very low differentiation (global FST=0.0081) and weak isolation by distance following a stepping stone model. For the candidate adaptive loci, however, model-based and model-free approaches indicated five divergent population clusters. After controlling for spatial distance, the distribution of putatively adaptive variation was strongly correlated to selection linked to minimum sea surface temperature and oxygen concentration. Around 80 candidates were annotated to genes with functions related to high temperature and/or low oxygen tolerance, including genes that influence the resilience of abalone species found in other biogeographic regions. Our study includes a documented example about the uptake of genomic information in fisheries management and supports the hypothesis of adaptive divergence due to coastal environmental heterogeneity in a connected metapopulation of a broadcast spawner.
Data from: Phylogenetic signal in module composition and species connectivity in compartmentalized host-parasite networks
Across different taxa, networks of mutualistic or antagonistic interactions show consistent architecture. Most networks are modular, with modules being distinct species subsets connected mainly with each other and having few connections to other modules. We investigate the phylogenetic relatedness of species within modules and whether a phylogenetic signal is detectable in the within- and among module connectivity of species using 27 mammal-flea networks from the Palaearctic. In the 24 networks that were modular, closely-related hosts co-occurred in the same module more often than expected by chance; in contrast, this was rarely the case for parasites. The within- and among-module connectivity of the same host or parasite species varied geographically. However, among-module but not within-module connectivity of host and parasites was somewhat phylogenetically constrained. These findings suggest that the establishment of host-parasite networks results from the interplay between phylogenetic influences acting mostly on hosts and local factors acting on parasites, to create an asymmetrically constrained pattern of geographic variation in modular structure. Modularity in host-parasite networks seems to result from the shared evolutionary history of hosts and by trait convergence among unrelated parasites. This suggests profound differences between hosts and parasites in the establishment and functioning of bipartite antagonistic networks.
Data from: Connecting thermal performance curve variation to the genotype: a multivariate QTL approach
Thermal performance curves (TPCs) are continuous reaction norms that describe the relationship between organismal performance and temperature and are useful for understanding trade-offs involved in thermal adaptation. While thermal trade-offs such as those between generalists and specialists or between hot- and cold-adapted phenotypes are known to be genetically variable and evolve during thermal adaptation, little is known of the genetic basis to TPCs – specifically, the loci involved and the directionality of their effects across different temperatures. To address this, we took a multivariate approach, mapping QTL for locomotor activity TPCs in the fly, Drosophila serrata using a panel of 76 recombinant inbred lines. The distribution of additive genetic (co)variance in the mapping population was remarkably similar to the distribution of mutational (co)variance for these traits. We detected 11 TPC-QTLs in females and 4 in males. Multivariate QTL effects were closely aligned with the major axes genetic (co)variation between temperatures; most QTL effects corresponded to variation for either overall increases or decreases in activity with a smaller number indicating possible trade-offs between activity at high and low temperatures. QTLs representing changes in curve shape such as the 'generalist-specialist' trade-off, thought key to thermal adaptation, were poorly represented in the data. We discuss these results in light of genetic constraints on thermal adaptation.
Data from: Identifying patterns of dispersal, connectivity, and selection in the sea scallop, Placopecten magellanicus, using RAD-seq derived SNPs
Understanding patterns of dispersal and connectivity among marine populations can directly inform fisheries conservation and management. Advances in high-throughput sequencing offer new opportunities for estimating marine connectivity. We used Restriction-site Associated DNA sequencing to examine dispersal and realized connectivity in the sea scallop Placopecten magellanicus, an economically important marine bivalve. Based on 245 individuals sampled range-wide at 12 locations from Newfoundland to the Mid-Atlantic Bight we identified and genotyped 7163 Single Nucleotide Polymorphisms; 112 (1.6%) were identified as outliers potentially under directional selection. Bayesian clustering revealed a discontinuity between northern and southern samples and latitudinal clines in allele frequencies were observed in 42.9% of the outlier loci and in 24.6% of neutral loci. Dispersal estimates derived using these clines and estimates of linkage disequilibrium imply limited dispersal; 373.1 ± 407.0 km (mean ± SD) for outlier loci and 641.0 ± 544.6 km (mean ± SD) for neutral loci. Our analysis suggests restricted dispersal compared to the species range (>2000 km) and that dispersal and effective connectivity differ. These observations support the hypothesis that limited effective dispersal structures scallop populations along eastern North America. These findings can help refine the appropriate scale of management and conservation in this commercially valuable species.
Data from: Testing the consistency of connectivity patterns for a widely dispersing marine species
Connectivity is widely recognised as an important component in developing effective management and conservation strategies. While managers are generally most interested in demographic, rather than genetic connectivity, new analytic approaches are able to provide estimates of both demographic and genetic connectivity measures from genetic data. Combining such genetic data with mathematical models represents a powerful approach for accurately determining patterns of population connectivity. Here, we use microsatellite markers to investigate the genetic population structure of the New Zealand Rock Lobster, Jasus edwardsii, which has one of the longest known larval durations of all marine species (> 2 years), a very large geographic range (> 5500 km), and has been the subject of extensive dispersal modelling. Despite earlier mitochondrial DNA studies finding homogeneous genetic structure, the mathematical model suggests that there are source-sink dynamics for this species. We found evidence of genetic structure in J. edwardsii populations with three distinct genetic groups across New Zealand and a further Australian group; these groups and patterns of gene flow were generally congruent with the earlier mathematical model. Of particular interest was the consistent identification of a self-recruiting population/region from both modelling and genetic approaches. While there is the potential for selection and harvesting to influence the patterns we observed, we believe oceanographic processes are most likely responsible for the genetic structure observed in J. edwardsii. Our results, using a species at the extreme end of the dispersal spectrum demonstrate that source-sink population dynamics may still exist for such species.
Data from: Node-based measures of connectivity in genetic networks
At-site environmental conditions can have strong influences on genetic connectivity, and in particular on the immigration and settlement phases of dispersal. However, at-site processes are rarely explored in landscape genetic analyses. Networks can facilitate the study of at-site processes, where network nodes are used to model site-level effects. We used simulated genetic networks to compare and contrast the performance of 7 node-based (as opposed to edge-based) genetic connectivity metrics. We simulated increasing node connectivity by varying migration in two ways: we increased the number of migrants moving between a focal node and a set number of recipient nodes, and we increased the number of recipient nodes receiving a set number of migrants. We found that two metrics in particular, the average edge weight and the average inverse edge weight, varied linearly with simulated connectivity. Conversely, node degree was not a good measure of connectivity. We demonstrated the use of average inverse edge weight to describe the influence of at-site habitat characteristics on genetic connectivity of 653 American martens (Martes americana) in Ontario, Canada. We found that highly connected nodes had high habitat quality for marten (deep snow and high proportions of coniferous and mature forest) and were farther from the range edge. We recommend the use of node-based genetic connectivity metrics, in particular, average edge weight or average inverse edge weight, to model the influences of at-site habitat conditions on the immigration and settlement phases of 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.
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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.
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.