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Dataset results
17 results for “Connectivity inference”
Data from: Integrating tracking and resight data enables unbiased inferences about migratory connectivity and winter range survival from archival tags
<p>Archival geolocators have transformed the study of small, migratory organisms but analysis of data from these devices requires bias correction because tags are only recovered from individuals that survive and are re-captured at their tagging location. Data and code provided in this repository can be used to replicate the simulation and Painted Bunting case study results presented by Rushing et al. (2021) showing that integrating geolocator recovery data and mark–resight data enables unbiased estimates of both migratory connectivity between breeding and nonbreeding populations and region-specific survival probabilities for wintering locations.</p>
Data for: Inferring population connectivity in Eastern Massasauga Rattlesnakes (Sistrurus catenatus) using landscape genetics
<p>Assessing the environmental factors that influence the ability of a threatened species to move through the landscape can be used to identify conservation actions that connect isolated populations. However, direct observations of species' movement are often limited making the development of alternate approaches necessary. Here we use landscape genetic analyses to assess the impact of landscape features on the movement of individuals between local populations of a threatened snake, the Eastern Massasauga Rattlesnake (<em>Sistrurus catenatus</em>). We linked connectivity data with habitat information from two landscapes of similar size: a large region of unfragmented habitat and a previously studied fragmented landscape consisting of isolated patches of habitat. We used this analysis to identify features of the landscape where modification or acquisition would enhance population connectivity in the fragmented region. We found evidence that current connectivity is impacted by both contemporary landcover features, especially roads, and inherent landscape features such as elevation. Next, we derived estimates of expected movement ability using a recently developed pedigree-based approach and Least Cost Paths through the unfragmented landscape. We then used our pedigree and resistance map to estimate resistance polygons of the potential extent for <em>S. catenatus</em> movement in the fragmented landscape. These polygons identify possible sites for future corridors connecting currently isolated populations in this landscape by linking the impact of future habitat modification or land acquisition to dispersal ability in this species. Overall, our study shows how modeling landscape resistance across differently fragmentated landscapes can identify habitat features that affect contemporary movement in threatened species in fragmented landscapes and how this information can be used to guide mitigation actions whose goal is to connect isolated populations.</p>
Data from: Integrating tracking and resight data enables unbiased inferences about migratory connectivity and winter range survival from archival tags
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Data from: Functional connectivity and home range inferred at a microgeographic landscape genetics scale in a desert-dwelling rodent
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Data for: Inferring population connectivity in Eastern Massasauga Rattlesnakes (Sistrurus catenatus) using landscape genetics
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Data from: An approach to incorporating inferred connectivity of adult movement into marine protected area design with limited data
Marine protected areas (MPAs) are important conservation tools that can support the resilience of marine ecosystems. Many countries, including Canada, have committed to protecting at least 10% of their marine areas under the Convention on Biological Diversity's Aichi Target 11, which includes connectivity as a key aspect. Connectivity, the movement of individuals among habitats, can enhance population stability and resilience within and among MPAs. However, little is known about regional spatial patterns of marine ecological connectivity, particularly adult movement. We developed a method to assess and design MPA networks that maximize inferred connectivity within habitat types for adult movement when ecological data are limited. We used the Northern Shelf Bioregion in British Columbia, Canada, to explore two different approaches: 1) evaluating sites important for inferred regional connectivity (termed hotspots); and 2) assessing MPA network configurations based on their overlap with connectivity hotspots and interconnectedness between MPAs. To assess inferred connectivity via adult movement, we used two different threshold distances (15 km and 50 km) to capture moderate home ranges, which are most appropriate to consider in MPA design. We applied graph theory to assess inferred connectivity within sixteen habitat and depth categories (proxies for distinct ecological communities), and used novel multiplex network methodologies to perform an aggregated assessment of inferred connectivity. We evaluated inferred regional connectivity hotspots based on betweenness and eigenvector centrality metrics, finding that the existing MPA network overlapped a moderate proportion of these regional hotspots, and identified key areas to be considered as candidate MPAs. Network density among existing MPAs was low within the individual habitat networks, as well as the multiplex. This work informs an ongoing MPA planning process, and approaches for incorporating connectivity into MPA design when data are limited, with lessons for other contexts.
Data from: An approach to incorporating inferred connectivity of adult movement into marine protected area design with limited data
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Data from: Inferring contemporary and historical genetic connectivity from juveniles
Measuring population connectivity is a critical task in conservation biology. While genetic markers can provide reliable long-term historical estimates of population connectivity, scientists are still limited in their ability to determine contemporary patterns of gene flow, the most practical time frame for management. Here, we tackled this issue by developing a new approach that only requires juvenile sampling at a single time period. To demonstrate the usefulness of our method, we used the Speartooth shark (Glyphis glyphis), a critically endangered species of river sharks found only in tropical northern Australia and southern Papua New Guinea. Contemporary adult and juvenile shark movements, estimated with the spatial distribution of kin pairs across and within three river systems, was contrasted with historical long-term connectivity patterns, estimated from mitogenomes and genome-wide SNP data. We found strong support for river fidelity in juveniles with the within-cohort relationship analysis. Male breeding movements were highlighted with the cross-cohort relationship analysis and female reproductive philopatry to the river systems was revealed by the mitogenomic analysis. We show that accounting for juvenile river fidelity and female philopatry is important in population structure analysis and that targeting sampling in nurseries and juveniles aggregation should be included in the genomic toolbox of threatened species management.
FIGURE 4. Phylogenetic tree with bootstrap values inferred from trnL-F in Revisit of European-Asiatic connections in Tayloria rudolphiana (Splachnaceae, Bryophyta) based on molecular data and new morphological evidence
FIGURE 4. Phylogenetic tree with bootstrap values inferred from trnL-F sequences (accession numbers after each species name obtained from Genbank) based on Maximum Likelihood and Maximum Parsimony analyses. Values above the branches indicate bootstrap (>50%) and numbers below the branches indicate PP values of Bayesian.
FIGURE 3. Phylogenetic tree with bootstrap values inferred from rps4 in Revisit of European-Asiatic connections in Tayloria rudolphiana (Splachnaceae, Bryophyta) based on molecular data and new morphological evidence
FIGURE 3. Phylogenetic tree with bootstrap values inferred from rps4 sequences (accession numbers after each species name obtained from Genbank) based on Maximum Likelihood and Maximum Parsimony analyses. Values above the branches indicate bootstrap (>50%) and numbers below the branches indicate PP values of Bayesian.
Data from: Inferring contemporary and historical genetic connectivity from juveniles
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Data from: Assessing the permeability of landscape features to animal movement: using genetic structure to infer functional connectivity
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◂Fig. 5 Cells of phylogenetically related strains (light microscopy). a Thecate cell in dorsal view. b Thecate cell in ventral view, note the sulcus extending onto the epitheca (arrow). c Putatively necrotic, thecate cell. d Thecate cell with one bulge on the epitheca (arrow), note that this was the only such cell among thousands of inspected cells. e, f Coccoid cells, apparently without thecae. g Two thecate cells enclosed in the parental theca. h Two connected, immotile cells enclosed in the parental thecae. j Lid of epitheca in dorsal-apical view (mirrored), composed of plates 2′‒4′, all intercalary plates and plates 2′′‒6′′. l‒m Same opened theca in ventral view (l) and dorsal view (m), note the sulcus extending onto the epitheca (arrow), the dorsal opening and all apical and all intercalary plates and plates 3′′‒5′′ remaining with the hypotheca. n Chloroplasts (as inferred from autofluorescence), note the space occupied by the nucleus. Plate labelling follows the Kofoidean notation, n′: apical plate; n′′: precingular plate; n′′′: postcingular plate; na: anterior intercalary plate. Scale= 10 µm in Bumps on the back: An unusual morphology in phylogenetically distinct Peridinium aff. cinctum (= Peridinium tuberosum; Peridiniales, Dinophyceae)
◂Fig. 5 Cells of phylogenetically related strains (light microscopy). a Thecate cell in dorsal view. b Thecate cell in ventral view, note the sulcus extending onto the epitheca (arrow). c Putatively necrotic, thecate cell. d Thecate cell with one bulge on the epitheca (arrow), note that this was the only such cell among thousands of inspected cells. e, f Coccoid cells, apparently without thecae. g Two thecate cells enclosed in the parental theca. h Two connected, immotile cells enclosed in the parental thecae. j Lid of epitheca in dorsal-apical view (mirrored), composed of plates 2′‒4′, all intercalary plates and plates 2′′‒6′′. l‒m Same opened theca in ventral view (l) and dorsal view (m), note the sulcus extending onto the epitheca (arrow), the dorsal opening and all apical and all intercalary plates and plates 3′′‒5′′ remaining with the hypotheca. n Chloroplasts (as inferred from autofluorescence), note the space occupied by the nucleus. Plate labelling follows the Kofoidean notation, n′: apical plate; n′′: precingular plate; n′′′: postcingular plate; na: anterior intercalary plate. Scale= 10 µm
Figure 2 from: Carvalho-Batista A, Negri M, Pileggi LG, Castilho AL, Costa RC, Mantelatto FL (2014) Inferring population connectivity across the range of distribution of the stiletto shrimp Artemesia longinaris Spence Bate, 1888 (Decapoda, Penaeidae) from DNA barcoding: implications for fishery management. In: Wehrtmann IS, Bauer RT (Eds) Proceedings of the Summer Meeting of the Crustacean Society and the Latin American Association of Carcinology, Costa Rica, July 2013. ZooKeys 457: 271-288. https://doi.org/10.3897/zookeys.457.6569
Figure 2 - Dendrogram based on Neighbor-Joining distance method of COI gene sequences of individuals of Artemesia longinaris. Localities represent the analyzed specimens. Numbers are bootstrap support values (1000 replicates); values below 50% are not shown.
Figure 4 from: Carvalho-Batista A, Negri M, Pileggi LG, Castilho AL, Costa RC, Mantelatto FL (2014) Inferring population connectivity across the range of distribution of the stiletto shrimp Artemesia longinaris Spence Bate, 1888 (Decapoda, Penaeidae) from DNA barcoding: implications for fishery management. In: Wehrtmann IS, Bauer RT (Eds) Proceedings of the Summer Meeting of the Crustacean Society and the Latin American Association of Carcinology, Costa Rica, July 2013. ZooKeys 457: 271-288. https://doi.org/10.3897/zookeys.457.6569
Figure 4 - Haplotype network of Artemesia longinarisaccording to Median-Joining analysis. Each circle represent one haplotype found in the localities (53 haplotypes in 60 specimens). The size of the circle of each haplotype is proportional to its frequency in the sample. Each small dash represents a mutational step.
Figure 1 from: Carvalho-Batista A, Negri M, Pileggi LG, Castilho AL, Costa RC, Mantelatto FL (2014) Inferring population connectivity across the range of distribution of the stiletto shrimp Artemesia longinaris Spence Bate, 1888 (Decapoda, Penaeidae) from DNA barcoding: implications for fishery management. In: Wehrtmann IS, Bauer RT (Eds) Proceedings of the Summer Meeting of the Crustacean Society and the Latin American Association of Carcinology, Costa Rica, July 2013. ZooKeys 457: 271-288. https://doi.org/10.3897/zookeys.457.6569
Figure 1 - Southwest Atlantic collection sites. Map showing the localities of the specimens of Artemesia longinaris analyzed: 1 Macaé, Brazil 2 Ubatuba, Brazil 3 Santos, Brazil 4 Cananéia, Brazil 5 São Francisco do Sul, Brazil 6 Rio Grande, Brazil 7 Mar del Plata, Argentina. The gray band indicates the complete geographical distribution of Artemesia longinaris.
Figure 3 from: Carvalho-Batista A, Negri M, Pileggi LG, Castilho AL, Costa RC, Mantelatto FL (2014) Inferring population connectivity across the range of distribution of the stiletto shrimp Artemesia longinaris Spence Bate, 1888 (Decapoda, Penaeidae) from DNA barcoding: implications for fishery management. In: Wehrtmann IS, Bauer RT (Eds) Proceedings of the Summer Meeting of the Crustacean Society and the Latin American Association of Carcinology, Costa Rica, July 2013. ZooKeys 457: 271-288. https://doi.org/10.3897/zookeys.457.6569
Figure 3 - Phylogram for individuals of Artemesia longinaris inferred from Maximum Likelihood analysis of COI gene sequences. Localities represent analyzed specimens. Numbers are bootstrap support values (1000 replicates); values below 50% are not shown.
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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)
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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.