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Supplementary material 1 from: Pontoppidan M, Nachman G (2013) Changes in behavioural responses to infrastructure affect local and regional connectivity – a simulation study on pond breeding amphibians. Nature Conservation 5: 13-28. https://doi.org/10.3897/natureconservation.5.4611
Full model description following the ODD-template suggested by Grimm et al. (2006, 2010) and model parameterisation. (doi: 10.3897/natureconservation.5.4611.app). File format: Adobe PDF document (pdf).:
FIGURE 3 in Knowledge connections for conservation of the Atlantic Goliath Grouper, Epinephelus itajara: records of tropical Brazilian coast
FIGURE 3 | A. Number of sightings of Atlantic Goliath Grouper (AGG) Epinephelus itajara in Alagoas (between 1960 and 2021) by length category. B. Percentage of required AGG recorded by habitats arranged in length category. Color-differentiated total length (TL) categories: juvenile (<50); subadult (50–100 cm); adult (101–150 cm); large adult (151–200 cm).
FIGURE 2 in Knowledge connections for conservation of the Atlantic Goliath Grouper, Epinephelus itajara: records of tropical Brazilian coast
FIGURE 2 | Percentage of Atlantic Goliath Grouper records for Sport fishing (Spo), Spearfishing (Spe), Professional fisher (Art), Recreational diving (Rec), and Stranding (Str).
FIGURE 6 in Knowledge connections for conservation of the Atlantic Goliath Grouper, Epinephelus itajara: records of tropical Brazilian coast
FIGURE 6 | A. Percentage of Atlantic Goliath Grouper (AGG) Epinephelus itajara registered along the coast of Alagoas, arranged in length category and; B. Percentage of individuals registered alive and dead (fished and stranded), along the division of the coast of Alagoas. C. Percentage of AGG recorded along the coast of Alagoas, distributed by habitats. Stranded animals also make up the graph. D. Distribution of AGG with estimated TL, arranged along the coast of Alagoas. Boxplots present the maximum and minimum limits (upper and lower rush). In the interquartile range are the third and first quartiles at the ends, median and mean (x) of the total length of the subjects. Colordifferentiated total length (TL) categories and separated by habitats.
FIGURE 5 in Knowledge connections for conservation of the Atlantic Goliath Grouper, Epinephelus itajara: records of tropical Brazilian coast
FIGURE 5 | A. Sightings of individuals of Atlantic Goliath Grouper (AGG) Epinephelus itajara in Alagoas, between 1960 and 2021, arranged by habitat and; B. Distribution of AGG with estimated Total Length arranged by habitat. Stranded animals also make up the boxplot. Habitats are separated by color, boxplots presents the maximum and minimum limits (upper and lower rush). In the interquartile range are the third and first quartiles at the ends, median and mean (x) of the AGG total length.
FIGURE 4 in Knowledge connections for conservation of the Atlantic Goliath Grouper, Epinephelus itajara: records of tropical Brazilian coast
FIGURE 4 | Photographic records from the pre-moratorium period, from the 1970s, 1980s, and 1990s. All images are of captures made through spearfishing in shallow coastal reefs off the Alagoas coast.
FIGURE 1 in Knowledge connections for conservation of the Atlantic Goliath Grouper, Epinephelus itajara: records of tropical Brazilian coast
FIGURE 1 | Distribution of Atlantic Goliath Grouper (AGG) Epinephelus itajara from the coast of Alagoas. Sites with the occurrence of the AGG validated through photographic or scientific records (Image records); places cited by informants for the occurrence of the species (Reports). Alagoas State, Brazil. The Alagoas coast was separated into north, central and south sectors. The figure highlighted Federal Marine Protected Areas (MPA), on the north coast is the MPA "Costa dos Corais". To the south is located the Marine Extractive Reserve of Lagoa do Jequiá and Environmental Protection Area of Piaçabuçu in the extreme south of the coast.
Data from: Predicting habitat suitability and connectivity for management and conservation of urban wildlife: A real-time web application for grassland water voles
<ol> <li>Natural habitats in urban areas provide benefits for both humans and biodiversity. However, to achieve biodiversity gains we require new techniques to determine habitat suitability and ecological connectivity that will inform urban planning and development.</li> <li>Using an example of an urban population of water voles (<i>Arvicola amphibius</i>) we developed a habitat suitability model and a resistance-surface-based model of landscape connectivity to identify potential connectivity between areas of suitable habitat. We then updated the environmental variables according to new urban development plans and used our models to generate spatially explicit predictions of both habitat suitability and connectivity.</li> <li>To make models accessible to urban and conservation planners we developed an interactive mapping tool that provided users with a graphical user interface (GUI) to inform conservation planning for this species.</li> <li>The model found that habitat suitability for water voles was related to distance from key environmental variables, such as built-up areas and urban green spaces, while the connectivity model identified important corridors connecting areas of potential distribution for this species.</li> <li>Future development plans altered the potential spatial distribution of the water vole population, reducing the extent of suitable habitat in some core areas. The interactive mapping tool made available suitable habitat and connectivity maps for conservation managers to assess new planning applications and for the development of a conservation action plan for water voles.</li> <li>Synthesis and applications: We believe this approach provides a framework for future development of nature conservation tools that can be used by planners to inform ecological decision making, increase biodiversity and reduce human-wildlife conflict in urban environments.</li> </ol>
Data from: Network analysis of sea turtle movements and connectivity: a tool for conservation prioritization
<p><strong>Aim</strong>: Understanding the spatial ecology of animal movements is a critical element in conserving long-lived, highly mobile marine species. Analysing networks developed from movements of six sea turtle species reveals marine connectivity and can help prioritize conservation efforts.</p> <p><strong>Location</strong>: Global.</p> <p><strong>Methods</strong>: We collated telemetry data from 1,235 individuals and reviewed the literature to determine our dataset's representativeness. We used the telemetry data to develop spatial networks at different scales to examine areas, connections, and their geographic arrangement. We used graph theory metrics to compare networks across regions and species and to identify the role of important areas and connections.</p> <p><strong>Results</strong>: Relevant literature and citations for data used in this study had very little overlap. Network analysis showed that sampling effort influenced network structure and the arrangement of areas and connections for most networks was complex. However, important areas and connections identified by graph theory metrics can be different than areas of high data density. For the global network, marine regions in the Mediterranean had high closeness while links with high betweenness among marine regions in the South Atlantic were critical for maintaining connectivity. Comparisons among species-specific networks showed that functional connectivity was related to movement ecology, resulting in networks composed of different areas and links.</p> <p><strong>Main conclusions</strong>: Network analysis identified the structure and functional connectivity of the sea turtles in our sample at multiple scales. These network characteristics could help guide the coordination of management strategies for wide-ranging animals throughout their geographic extent. Most networks had complex structures that can contribute to greater robustness, but may be more difficult to manage changes when compared to simpler forms. Area-based conservation measures would benefit sea turtle populations when directed towards areas with high closeness dominating network function. Promoting seascape connectivity of links with high betweenness would decrease network vulnerability.</p>
Identifying the environmental drivers of corridors and predicting connectivity between seasonal ranges in multiple populations of Alpine ibex (Capra ibex) as tools for conserving migration
<p># GPS locations of Alpine ibex</p> <p>This dataset contains migratory tracks of Alpine ibex identified using the application Migration Mapper (https://migrationinitiative.org/content/migration-mapper) and used in the work <strong>Identifying the environmental drivers of corridors and predicting connectivity between seasonal ranges in multiple populations of Alpine ibex (<em>Capra ibex</em>) as tools for conserving migration</strong></p> <p># Dataset structure</p> <p>Each row of the dataset represents a GPS location with its coordinates contained in the x (longitude) and y(latitude) columns. Coordinates are given in wgs84 (epsg 4326).<br> The column t1_ informs on the date and time the location was recorded.<br> The id and pop columns provide information about the identity of the animal and the population to which it belongs.</p> <p> </p>
Designing conservation networks to ensure connectivity in a changing climate: application to Spanish forests
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Data from: Predicting habitat suitability and connectivity for management and conservation of urban wildlife: A real-time web application for grassland water voles
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Data from: Network analysis of sea turtle movements and connectivity: a tool for conservation prioritization
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Data from: Potential distribution and landscape connectivity of the Antioquia Brushfinch (<em>Atlapetes blancae</em>): Implications for its conservation
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Data from: Agri-environment conservation set-asides have co-benefits for connectivity
<p>Widespread declines in farmland biodiversity have led to state-funded schemes which take land out of production to create (semi-)natural habitats for biodiversity (e.g. EU agri-environment schemes; US Conservation Reserve Program). Common features of such schemes are grassland strips at the edges of agricultural fields, and we examine potential co-benefits of these biodiversity set-asides for contributing to grassland connectivity. Although set-aside strips had negligible impact on landscape-scale species persistence (using metapopulation models parameterized for flying insects run on 267 landscapes of ~30 000 ha across England), they nonetheless improved connectivity in 74% (198/267) of landscapes (comparing landscapes with and without set-asides), as shown by range expansion rates increasing by up to 100%. Benefits of set-aside strips varied according to species type (high/low dispersal, high/low population density), but had little benefit for species with low dispersal and small population sizes, which enerally failed to expand. High dispersal/high density species were already successful expanders regardless of set-asides (> 75% of simulations were successful without set-sides) although expansion rates were still improved when set-asides were added. Whilst alternative strategies for placement of set-aside strips (more/less aggregated), revealed no consensus 'better' strategy across species types, set-aside benefits were generally greatest in landscapes with intermediate availability of semi-natural grassland (0.5-4% over). We conclude that small-scale set-asides have the potential to improve connectivity, which we expect to help some species track climate change, and connect habitat patches within existing climate space for others. However, set-asides are unlikely to benefit low dispersal species which are probably at greatest risk from agricultural intensification.</p> <p> </p> <p> </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: Predicting global population connectivity and targeting conservation action for snow leopard across its range
Movements of individuals within and among populations help to maintain genetic variability and population viability. Therefore, understanding landscape connectivity is vital for effective species conservation. The snow leopard is endemic to mountainous areas of Central Asia and occurs within 12 countries. We assess potential connectivity across the species' range to highlight corridors for dispersal and genetic flow between populations, prioritizing research and conservation action for this wide-ranging, endangered top-predator. We used resistant kernel modeling to assess snow leopard population connectivity across its global range. We developed an expert-based resistance surface that predicted cost of movement as functions of topographical complexity and land cover. The distribution of individuals was simulated as a uniform density of points throughout the currently accepted global range. We modeled population connectivity from these source points across the resistance surface using three different dispersal scenarios that likely bracket the lifetime movements of individual snow leopard: 100km, 500km and 1000km. The resistant kernel models produced predictive surfaces of dispersal frequency across the snow leopard range for each distance scenario. We evaluated the pattern of connectivity in each of these scenarios and identified potentially important movement corridors and areas where connectivity might be impeded. The models predicted two regional populations, in the north and south of the species range respectively, and revealed a number of potentially important connecting areas. Discrepancies between model outputs and observations highlight unsurveyed areas of connected habitat that urgently require surveying to improve understanding of the global distribution and ecology of snow leopard, and target land management actions to prevent population isolation. The connectivity maps provide a strong basis for directed research and conservation action, and usefully direct the attention of policy makers.
Data from: Seascape genetics and biophysical connectivity modelling support conservation of the seagrass Zostera marina in the Skagerrak-Kattegat region of the eastern North Sea
Maintaining and enabling evolutionary processes within meta-populations is critical to resistance, resilience and adaptive potential. Knowledge about which populations act as sources or sinks, and the direction of gene flow, can help to focus conservation efforts more effectively and forecast how populations might respond to future anthropogenic and environmental pressures. As a foundation species and habitat provider, Zostera marina (eelgrass) is of critical importance to ecosystem functions including fisheries. Here we estimate connectivity of Z. marina in the Skagerrak-Kattegat region of the North Sea based on genetic and biophysical modelling. Genetic diversity, population structure and migration were analysed at 23 locations using 20 microsatellite loci and a suite of analytical approaches. Oceanographic connectivity was analysed using Lagrangian dispersal simulations based on contemporary and historical distribution data dating back to the late 19th century. Population clusters, barriers and networks of connectivity were found to be very similar based on either genetic or oceanographic analyses. A single-generation model of dispersal was not realistic, whereas multi-generation models that integrate stepping-stone dispersal and extant and historic distribution data were able to capture and model genetic connectivity patterns well. Passive rafting of flowering shoots along oceanographic currents is the main driver of gene flow at this spatial-temporal scale and extant genetic connectivity strongly reflects the "ghost of dispersal past" sensu Benzie 1999. The identification of distinct clusters, connectivity hotspots and areas where connectivity has become limited over the last century is critical information for spatial management, conservation and restoration of eelgrass.
Conservation genetics of an island-endemic lizard: low Ne and the critical role of intermediate temperatures for genetic connectivity
<p>Island populations are at higher risk of extinction than mainland populations. Therefore, understanding the factors that facilitate connectivity is particularly pressing for the conservation of island taxa. <i>Sceloporus occidentalis becki</i>, the Island Fence Lizard, is an endemic taxon restricted to the Northern Channel Islands, part of a nearshore archipelago in Southern California, USA. Since the Last Glacial Maximum, fence lizard habitat on the Northern Channel Islands has decreased with rising sea levels and increasing temperatures that have reduced the availability of woody vegetation. More recently, the introduction (and subsequent removal) of invasive ungulates over the last 170 years and recovery of vegetation has resulted in further dramatic habitat modification. Given the potential for genetic bottlenecks, the history of habitat alteration, and topographic and landscape complexity, we used landscape and population genetic approaches to characterize patterns of genetic diversity and structure of Island Fence Lizards on Santa Cruz Island, the largest of the Northern Channel Islands. Our analyses revealed shallow population structure across the island, low effective population size (<i>N<sub>e</sub></i> = ~200), and evidence for a recent genetic bottleneck. Landscape genetic analyses showed that connectivity is facilitated by tree canopy cover and shrubland, as well as by intermediate temperatures, emphasizing the importance of woody vegetation and habitats with variable thermal regimes as the climate warms. Combined, these population and landscape genetic analyses suggest that the Island Fence Lizard is of greater conservation concern than currently appreciated, and increased conservation management focus is warranted for this island endemic.</p>
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.
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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.