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2,721 results for “CONNECTIVITY”
Combining population genomics with demographic analyses highlights habitat patchiness and larval dispersal as determinants of connectivity in coastal fish species
<p>Gene flow shapes spatial genetic structure as well as the potential for local adaptation of populations. Among marine animals with non-migratory adults, the presence or absence of a pelagic larval stage is thought to be a key determinant in shaping gene flow and the genetic structure of populations. In addition, the spatial distribution of suitable habitats will influence the distribution of biological populations and their pattern of gene flow. We used whole genome sequencing to study demographic history and reduced representation (ddRAD) sequencing data to analyze spatial genetic structure in the broadnosed pipefish (<em>Syngnathus typhle</em>). Its main habitat are seagrass meadows, which along the study coast (SW Norway) have a patchy distribution. Combining the results from several analyses including scans for selection, suggests that stochastic genetic drift has shaped the observed population structure largely due to its patchy habitat distribution. The restricted gene flow is further driven by life history traits such as the presence of parental care combined with no pelagic life stages, resulting in a clear isolation-by-distance pattern spanning 100s of kilometers.</p> <p>The spatial scale of demographic connectivity was inferred from long-term (~30 year) census population counts that uncovered a sharp decline in spatial correlations in abundance with distance (37% decorrelation over 2 km). These findings were contrasted with data from two other fish species sampled along the same coastline, both having pelagic larval stages lasting ~20 days (corkwing wrasse, <em>Symphodus melops</em>, and black goby, <em>Gobus niger</em>) where the population structure is not that evident. For these species, we found a wider spatial scale of demographic connectivity (decorrelation distances of 14 and 28 km, respectively), and weaker isolation-by-distance except at one point along the coast where both species revealed a strong barrier to gene flow, seemingly due to a lack of suitable habitat. Combined, these findings suggest that habitat fragmentation and absence of a pelagic larval stage in pipefish strongly increases geographic structuring, while the pelagic larvae of wrasse and goby increase genetic and demographic connectivity, except over extensive habitat shifts.</p>
FIGURE 2. Connective, dorsal view. A in Revision of the genus Doratura Sahlberg (Hemiptera, Cicadellidae, Deltocephalinae) with particular regard to its distribution in Italy and description of four new species
FIGURE 2. Connective, dorsal view. A: Doratura stylata (Boheman), Germany, Bayern, Memmingen; B: D. exilis Horváth, Slovakia, Chlaba, (MNHN)EH 23384; C: D. impudica Horváth, Italy, Friuli-Venezia Giulia, Spilimbergo; D: D. marandica Dlabola, Holotype, Iran, Marand; E: D. jole sp. nov., Turkey, Tunceli, Ovacik; F: D. vefele sp. nov., Morocco, Marrakech, Tahanaout; G: D. butzele Guglielmino & Bückle, Paratype, Italy, Abruzzo, Chieti, Montemitro; H: D. gravis Emeljanov, Paratype D. jurtica Dlabola, Mongolia, Songino; I: D. heterophyla Horváth, Bulgaria, Strouma valley, Kozhuh Hill, Rupite; K: D. rikele Guglielmino & Bückle, Paratype, Italy, Calabria, Crotone, Caccuri; L: D. concors Horváth, Montenegro, Nikšić, Vidrovan; M: D. homophyla (Flor), Spain, Andalusia, Jaén, Cazorla; N: D. salina Horváth, Syntype, Romania, Cluj, Sik; O: D. lobele, sp. nov., Greece, Arcadia, Tripoli, Kandalos.
Connecting Amazonian historical biogeography and local assemblages of understorey birds: recurrent guild proportionality within areas of endemism.
<p><strong>Aim:</strong> Current diversity patterns in local communities result from historical and contemporary events that operate at distinct spatial and temporal scales. However, the contribution of local and large-scale processes in structuring species diversity remain a contentious topic in ecology. We investigated diversity patterns (species richness, composition and number of captures) of understorey bird assemblages in Amazonian unflooded (<em>terra firme</em>) forests. We sought to understand whether understorey bird assemblages in distinct areas of endemism show distinct patterns of diversity, and whether species replacements among areas of endemism occur while the proportion of species within guilds remains stable.</p> <p><strong>Location:</strong> Amazonia.</p> <p><strong>Taxon: </strong>Understorey birds.</p> <p><strong>Methods:</strong> To investigate diversity patterns, we compiled studies that mist-netted birds at 11 regions across seven Amazonian areas of endemism. We used coverage-based rarefaction curves, non-metric multidimensional scaling (NMDS) and created a heatmap based on the proportion of captures in each area of endemism to access patterns of richness, composition and captures of understorey birds, respectively. The relative variance (RVgp index) was calculated to investigate the existence of guild proportionality within each area of endemism.</p> <p><strong>Results:</strong> Bird assemblages diverged across the seven areas of endemism, in terms of species richness, composition and captures. However, the proportion of species and individuals within guilds was similar among areas of endemism, indicating that species replacements across areas of endemism occur while maintaining the same ecological functions. Guild proportionality suggests that interspecific competition and resource availability are more important than environmental heterogeneity in structuring understorey bird assemblages.</p> <p><strong>Main conclusions:</strong> The similar proportion of species within guilds suggest that interspecific competition and resource availability are more important than environmental heterogeneity in structuring local assemblages, possibly via a process of limiting similarity in morphological and functional traits. The observed congruent structure in understorey bird assemblages across areas of endemism shows that coupled historical and ecological processes, operating at local to large scales, have led to current patterns of diversity and composition in Amazonian bird communities.</p>
Last.fm Social Connections
<p>This dataset contains a social network of Last.fm users that are part of the LFM-1b dataset [1] and has been created using the Last.fm API [2].<br> More specifically, we have adopted the breadth-first-search sampling strategy with LFM-1b users as seed nodes and crawled friends up to two hops away (friends and friends of friends). We have kept only those edges where both nodes connected by an edge are part of the original LFM-1b dataset. These edges are stored in the 'LFM-1b_social_ties.txt' file which contains 78,989 edges between 11,792 unique users.<br> Additionally, we have stored demographic and playcount information for each of these users in the 'LFM-1b_users.txt' file.<br> This dataset has been used as input for the purposes of studying homophily and link prediction with user preferences for mainstream, novelty, and diversity in music [3] and to reproduce the experiments from that study, we have also provided an open-source GitHub repository [4].</p> <p>[1] http://www.cp.jku.at/datasets/LFM-1b/<br> [2] https://www.last.fm/api<br> [3] Duricic, T., Kowald, D., Schedl, M., & Lex, E. (2021, November). My friends also prefer diverse music: homophily and link prediction with user preferences for mainstream, novelty, and diversity in music. In Proceedings of the 2021 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (pp. 447-454).<br> [4] https://github.com/tduricic/homophily-lastfm</p>
Data from: Landscape genetics reveals contrasting patterns of connectivity in two newt species (Lissotriton montandoni and L. vulgaris)
<p><span>Ecologically distinct species may respond to landscape changes in different ways. </span>In addition to basic ecological data, <span>the extent of the</span> geographic range has been successfully used as an indicator of species sensitivity to anthropogenic landscapes, with widespread species usually found to be less sensitive compared to range-restricted species. <span>In this study, we investigate connectivity patterns of two closely related but ecologically distinct newt species – the range-restricted, <em>Lissotriton montandoni</em> and the widespread,<em> L. vulgari</em>s – using genomic data, a highly replicated setting (six geographic regions per species), and tools from landscape genetics. Our results show the importance of forest for connectivity in both species, but at the same time suggest differential use of forested habitat, with <em>L. montandoni</em> and <em>L. vulgaris</em> showing the highest connectivity at forest-core and forest-edges, respectively. Anthropogenic landscapes (i.e., higher crop- or urban-cover) increased resistance in both species, but the effect was one to three orders of magnitude stronger in <em>L. montandoni</em> than in <em>L. vulgaris</em>. </span><span>This result is consistent with a view of <em>L. vulgaris</em> as an ecological generalist. </span><span>Even so, currently, the negative impact of anthropogenic landscapes is mainly seen in connectivity among L. vulgaris populations, which show significantly stronger isolation and lower effective sizes relative to <em>L. montandoni</em>. Overall, this study emphasizes how habitat destruction is compromising genetic connectivity not only in endemic, range-restricted species of conservation concern but also in widespread generalist species, despite their comparatively lower sensitivity to anthropogenic landscape changes.</span></p>
New paleomagnetic insights into the Neoproterozoic connection between South China and India and their position in Rodinia
<p>These documents are supplementary tables for a manuscript submitted to Geophysical Research Letters entitled "New paleomagnetic insights into the Neoproterozoic connection between South China and India and their position in Rodinia" by Chang et al.</p>
Historical connections between Atlantic Forest and Amazonia drove genetic and ecological diversity in Lithobates palmipes (Anura, Ranidae)
<p>The Atlantic and Amazon rainforests have a shared but unclear past, with intermittent connections resulting from historical climate change. We investigate these connections by studying the phylogeography and climatic niche of the disjunct distributed frog<em> Lithobates palmipes</em>. We sequenced two fragments of mitochondrial DNA from Atlantic Forest (AtF) and Amazonia (AmF) individuals and evaluated how genetic diversity is distributed in space and whether past demographic changes occurred. Also, we evaluated the existence of past suitable connections between biomes for<em> L. palmipes</em> through ecological niche models (ENM) and tested for niche divergence. The AtF group is nested within the AmF group and closely related to individuals from eastern Amazonia, a pattern recovered in many species that used northeast connection routes. We found evidence of recurrent use of connections in different directions and time during the Pleistocene, resulting in genetic structure between biomes, with no signal of demographic change and evidence of niche divergence across both genetic groups. ENMs indicated suitable areas connecting forests throughout northeastern Brazil during the Pleistocene. Mitochondrial lineages do not match biomes exactly. One lineage is composed of AtF populations and eastern Amazonia individuals. The other is composed of western Amazonia individuals, suggesting an effect of past climatic heterogeneity within the Amazonia forest. This is the first evidence that this route drove genetic and ecological diversity for amphibians recently, a group with habits and ecological requirements different from other vertebrates that have been shown to use this putative corridor.</p>
Subspecies and Distribution. 1. t. truncatus Montagu, 1821 — worldwide in temperate and tropical waters as far S as New Zealand and generally as far as 45° N, but reaching the Faroe Is in the N Atlantic. 1: 1. ponticus Barabash-Nikiforov, 1940 — inhabits the Black Sea, Kerch Strait along with the connecting part of the Azov Sea, and the Turkish Straits system. in Delphinidae
Subspecies and Distribution. 1. t. truncatus Montagu, 1821 — worldwide in temperate and tropical waters as far S as New Zealand and generally as far as 45° N, but reaching the Faroe Is in the N Atlantic. 1: 1. ponticus Barabash-Nikiforov, 1940 — inhabits the Black Sea, Kerch Strait along with the connecting part of the Azov Sea, and the Turkish Straits system.
Distribution. SE Madagascar, in scattered localities between Ranomafana National Park (where it has been seen as far N as Miaranony and Bevoahazo), and as far S as Andringitra National Park and in the forest corridor that connects them, with the distribution possibly extending to the NE as far as the region of Betsakafandrika; there has recently been an unconfirmed sighting of this species to the S in the Vevembe Forest (W of Vondrozo). in Lemuridae
Distribution. SE Madagascar, in scattered localities between Ranomafana National Park (where it has been seen as far N as Miaranony and Bevoahazo), and as far S as Andringitra National Park and in the forest corridor that connects them, with the distribution possibly extending to the NE as far as the region of Betsakafandrika; there has recently been an unconfirmed sighting of this species to the S in the Vevembe Forest (W of Vondrozo).
Data from: Combining citizen science species distribution models and stable isotopes reveals migratory connectivity in the secretive Virginia rail
Stable hydrogen isotope (δD) methods for tracking animal movement are widely used yet often produce low resolution assignments. Incorporating prior knowledge of abundance, distribution or movement patterns can ameliorate this limitation, but data are lacking for most species. We demonstrate how observations reported by citizen scientists can be used to develop robust estimates of species distributions and to constrain δD assignments. We developed a Bayesian framework to refine isotopic estimates of migrant animal origins conditional on species distribution models constructed from citizen scientist observations. To illustrate this approach, we analysed the migratory connectivity of the Virginia rail Rallus limicola, a secretive and declining migratory game bird in North America. Citizen science observations enabled both estimation of sampling bias and construction of bias-corrected species distribution models. Conditioning δD assignments on these species distribution models yielded comparably high-resolution assignments. Most Virginia rails wintering across five Gulf Coast sites spent the previous summer near the Great Lakes, although a considerable minority originated from the Chesapeake Bay watershed or Prairie Pothole region of North Dakota. Conversely, the majority of migrating Virginia rails from a site in the Great Lakes most likely spent the previous winter on the Gulf Coast between Texas and Louisiana. Synthesis and applications. In this analysis, Virginia rail migratory connectivity does not fully correspond to the administrative flyways used to manage migratory birds. This example demonstrates that with the increasing availability of citizen science data to create species distribution models, our framework can produce high-resolution estimates of migratory connectivity for many animals, including cryptic species. Empirical evidence of links between seasonal habitats will help enable effective habitat management, hunting quotas and population monitoring and also highlight critical knowledge gaps.
Data from: Geographic differences in vertical connectivity in the Caribbean coral Montastraea cavernosa despite high levels of horizontal connectivity at shallow depths
The Deep Reef Refugia Hypothesis proposes that deep reefs can act as local recruitment sources for shallow reefs following disturbance. To test this hypothesis, nine polymorphic DNA microsatellite loci were developed and used to assess vertical connectivity in 583 coral colonies of the Caribbean depth-generalist coral Montastraea cavernosa. Samples were collected from three depth zones (≤10 m, 15-20 m and ≥25 m) at sites in Florida Upper Keys, Lower Keys and Dry Tortugas), Bermuda, and the U.S. Virgin Islands. Migration rates were estimated to determine the probability of coral larval migration from shallow to deep and from deep to shallow. Finally, algal symbiont (Symbiodinium spp.) diversity and distribution was assessed in a subset of corals to test whether symbiont depth zonation might indicate limited vertical connectivity. Overall, analyses revealed significant genetic differentiation by depth in Florida, but not in Bermuda or the U.S. Virgin Islands, despite high levels of horizontal connectivity between these geographic locations at shallow depths. Within Florida, greater vertical connectivity was observed in the Dry Tortugas compared to the Lower or Upper Keys. However, at all sites, and regardless of the extent of vertical connectivity, migration occurred asymmetrically, with greater likelihood of migration from shallow to intermediate/deep habitats. Finally, most colonies hosted a single Symbiodinium type (C3), ruling out symbiont depth zonation of the dominant symbiont type as a structuring factor. Together, these findings suggest that the potential for shallow reefs to recover from deep-water refugia in M. cavernosa is location-specific; varying among and within geographic locations likely as a consequence of local hydrology.
Data from: Habitat fragmentation in coastal southern California disrupts genetic connectivity in the Cactus Wren (Campylorhynchus brunneicapillus)
Achieving long-term persistence of species in urbanized landscapes requires characterizing population genetic structure to understand and manage the effects of anthropogenic disturbance on connectivity. Urbanization over the past century in coastal southern California has caused both precipitous loss of coastal sage scrub habitat and declines in populations of the cactus wren (Campylorhynchus brunneicapillus). Using 22 microsatellite loci, we found that remnant cactus wren aggregations in coastal southern California comprised 20 populations based on strict exact tests for population differentiation, and 12 genetic clusters with hierarchical Bayesian clustering analyses. Genetic structure patterns largely mirrored underlying habitat availability, with cluster and population boundaries coinciding with fragmentation caused primarily by urbanization. Using a habitat model we developed, we detected stronger associations between habitat-based distances and genetic distances than Euclidean geographic distance. Within populations, we detected a positive association between available local habitat and allelic richness and a negative association with relatedness. Isolation-by-distance patterns varied over the study area, which we attribute to temporal differences in anthropogenic landscape development. We also found that genetic bottleneck signals were associated with wildfire frequency. These results indicate that habitat fragmentation and alterations have reduced genetic connectivity and diversity of cactus wren populations in coastal southern California. Management efforts focused on improving connectivity among remaining populations may help to ensure population persistence.
Distribution. Disjunct range, recorded in NE India and Bangladesh (Chittagong) and in SE Asia (Thailand, Laos, Vietnam, and Cambodia). Presence in all Myanmar expected, which would connect these areas. in Pteropodidae
Distribution. Disjunct range, recorded in NE India and Bangladesh (Chittagong) and in SE Asia (Thailand, Laos, Vietnam, and Cambodia). Presence in all Myanmar expected, which would connect these areas.
Spatiotemporal connectivity dynamics in spatially structured populations
<p>Connectivity is a fundamental concept linking dispersal to the emergent dynamics and persistence of spatially structured populations. Functional measures of connectivity typically seek to integrate aspects of landscape structure and animal movement to describe ecologically meaningful connectedness at the landscape and population scale.</p> <p>Despite this focus on function, traditional measures of landscape connectivity assume it is a static property of the landscape, hence abstracting out the underlying spatiotemporal population dynamics. Connectivity is, arguably, a dynamic property of landscapes, and is inherently related to the spatial distribution of individuals and populations across the landscape. Static representations of connectivity potentially overlook this variation and therefore adopting a dynamic approach should offer improved insights about connectivity and associated ecological processes.</p> <p>Using a large scale, long-term time-series of occupancy data from a metapopulation of water voles (Arvicola amphibius), we tested competing hypotheses about how considering the dynamic nature of connectivity improves the ability of spatially-explicit occupancy models to recover population dynamics. Iteratively relaxing standing assumptions of connectivity metrics, these models ranged from spatially and temporally fixed connectivity metrics that are widely applied, to the more flexible, but lesser used model that allowed temporally-varying connectivity measures that incorporate spatiotemporally dynamic patch occupancy states.</p> <p>Our results provide empirical evidence that demographic-weighting using patch occupancy dynamics and temporal variability in connectivity measures are important for describing metapopulation dynamics.</p> <p>We highlight the implications of commonly held assumption in connectivity modeling and demonstrate how they result in different and highly variable predictions of metapopulation capacity. Thus, we argue that the concept of connectivity and its potential applications would benefit from recognizing inherent spatiotemporal variation in connectivity that is explicitly linked to underlying ecological state variables. </p>
Distribution. Known from scattered records in the Columbia Plateau and N Great Plains of SC British Columbia (SE Canada), N & SE Washington, Oregon, WC Idaho, Montana, NE California, N Nevada, W Wyoming, and N Utah, although these populations are probably connected and additional collecting efforts are needed. in Soricidae
Distribution. Known from scattered records in the Columbia Plateau and N Great Plains of SC British Columbia (SE Canada), N & SE Washington, Oregon, WC Idaho, Montana, NE California, N Nevada, W Wyoming, and N Utah, although these populations are probably connected and additional collecting efforts are needed.
Distribution. Sierra Madre Occidental and Sierra Madre Oriental, connecting S of the mountains, including Durango, Jalisco, Colima, Guanajuato, Michoacan, Coahuila, Nuevo Leon, Tamaulipas, Querétaro, Hidalgo, México, Puebla, Distrito Federal, Morelos, Guerrero, and Oaxaca (Mexico). in Soricidae
Distribution. Sierra Madre Occidental and Sierra Madre Oriental, connecting S of the mountains, including Durango, Jalisco, Colima, Guanajuato, Michoacan, Coahuila, Nuevo Leon, Tamaulipas, Querétaro, Hidalgo, México, Puebla, Distrito Federal, Morelos, Guerrero, and Oaxaca (Mexico).
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>
A Multiscale Simulation Platform for Connected and Automated Transportation Systems
<p>The uploaded set contains real-world vehicle, traffic, demand data, simulation network and simulation testing data.</p>
DC Ionic Conductivity in KTP and Its Isomorphs: Properties, Methods for Suppression, and Its Connection to Gray Tracking
<p>Dataset for the related publication "DC Ionic Conductivity in KTP and Its Isomorphs: Properties, Methods for Suppression, and Its Connection to Gray Tracking"</p>
Landscape features influencing gene flow and connectivity of an endangered passerine
<p>Effective exchange of individuals among populations (i.e. gene flow) is one crucial aspect to maintain genetic diversity and viability of populations, especially in the case of threatened species. Landscape composition and structure may facilitate or limit individual movement within and among populations. We used a landscape genetics (LG) approach to assess the connectivity patterns of the threatened Dupont's lark (<em>Chersophilus duponti duponti</em>), considering their genetic patterns and the landscape features associated with its gene flow in Spain. We analysed genetic structure and relatedness based on 11 species-specific polymorphic microsatellites on 416 Dupont's lark individuals sampled across peninsular Spain between 2017 and 2019, covering most of the European distribution of the species. To assess the relationship between the landscape configuration and the species gene flow, we estimated genetic distance at the individual level (<em>Dps</em>). Next, we built a set of environmental surfaces from two time points (1990 and 2018), based on factors (land use and topography) influencing individuals' movement. We then obtained resistance surfaces from an optimization process on landscape variables, and LG analyses were done for single and composite surface models for each year separately. Our findings from both time points demonstrate, for the first time, that scatter or mosaic structured vegetation composed by low agricultural and tree cover and high presence of sclerophyllous shrubs favoured Dupont's lark dispersal, while dense and continuous tree cover, as well as areas of intensive agriculture, were limiting factors. Our results suggest the importance of steppe habitat patches both for the species establishment and dispersal. Besides, our results provide key information to develop specific conservation measures, including focusing on conserving and restoring steppe habitats as scattered and/or mosaic structured vegetation that could warrant the connectivity and persistence of Dupont's lark populations.</p>
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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.