Find research datasets worth reusing

Livorno, Urban driving, Automated and connected vehicle and smart traffic light

Scenario description: Test session for AD+connected car and connected cars approaching an intersection regulated by a "smart" traffic light. Session description: A "smart" traffic light sends SPaT and MAP messages describing the topology, actual status of the traffic light to other connected vehicles and to the oneM2M platform on the cloud. An AD vehicle consumes the information and autonomously adapts its speed in order to cross the intersection without violating the traffic light phases, considering also other vehicles moving in front. Goal is to record data for the technical evaluation. Datasets descriptions: AUTOPILOT_Livorno_UrbanDriving_Vehicle_all: Data generated from the vehicle sensors This dataset refers to the vehicle datasets generated from the vehicle sensors during Urban Drining in Livorno. This includes the data coming from the CAN bus and GPS. It includes following kind of dataset: Vehicle: general data (speed, battery); PositioningSystem: data from GPS; VehicleDynamics: data about dynamic (acceleration...); LateralControl: steering and lane control data AUTOPILOT_Livorno_UrbanDriving_V2X_all: V2V messages during platooning sessions This dataset refers to the V2V messages exchanged between ITS stations (vehicles and RSUs) during the Urban Drining in Livorno. AUTOPILOT_Livorno_UrbanDriving_IoT_all: Data extracted from IoT oneM2M platform This dataset refers to messages exchanged by Urban Driving devices, applications and services across the oneM2M platform.

Livorno, Highway pilot, one automated and connected car

Scenario description: Precondition: A vehicle is driving in the first lane of a “smart highway” at 90 km/h with all the devices working correctly and connected to all services needed. Actions or events: 1 The puddle monitoring system of the highway triggers a puddle hazard warning for a specific extended zone. 2 The AD car receives the information by IoT based services and sets a speed limitation according to the area interested by hazard conditions: it smoothly decelerates in order to enter in the area at the proper speed. 3 At the end of the dangerous area, as notified by the “smart road”, the vehicle will recover the legally allowed cruise speed. Relevant situations: How the AD function interacts with different IoT input: from oneM2M platform (advisory speed limit due to puddles); from I2V (DENM, puddle hazard warning); from V2V (CAM with info from other vehicles). Session description: Test session with one AD+connected car, lap of 12,3 km on the highway. Datasets description: AUTOPILOT_Livorno_HighwayPilot_Vehicle_all: Data generated from the vehicle sensors This dataset refers to the vehicle datasets generated from the vehicle sensors during Highway Piloting in Livorno. This includes the data coming from the CAN bus and GPS. It includes following kind of dataset: Vehicle: general data (speed, battery); PositioningSystem: data from GPS; VehicleDynamics: data about dynamic (acceleration...); LateralControl: steering and lane control data AUTOPILOT_Livorno_HighwayPilot_V2X_all: V2V messages during the Highway Pilot sessions This dataset refers to the V2V messages exchanged between ITS stations (vehicles and RSUs) during the Highway Piloting in Livorno. AUTOPILOT_Livorno_HighwayPilot_IoT_all: Data extracted from IoT oneM2M platform This dataset refers to messages exchanged by HighwayPilot devices, applications and services across the oneM2M platform.

Livorno, Highway pilot, connected car system and data management

Scenario description: Precondition: 1. AD cars with C-eHorizon and V2X OBU devices on board travels on the highway. The highway is equipped with IoT G5 RSUs. All the devices publish and share the information by the oneM2M platform in the cloud. Actions or events: 1 The Traffic Control Center publishes the presence of roadway works to the OneM2M platform. 2 The RSU (subscribed to the OneM2M platform) receives the information and it broadcasts to the vehicles the DENM message containing information about available lanes, speed limits, geometry, alternative routes etc. 3 At the same time, the CONTI cloud is subscribed to the oneM2M platform; it receives and shares with the FCA cloud the information of the road works, updating dynamically the maps of the Connected e-Horizon installed onboard the CRF AD car 4 The in-vehicle application fusing the information from the OBU, the C-eHorizon and on-board sensors, performs speed adaptation and lane-change maneuvers Relevant situations: How the AD function interacts with different IoT input: from I2V (DENM, Roadwork position and extension); from V2V (CAM with info from other vehicles). Session description: pre-test session with only connected cars, lap of 11,6 km on the highway. Goal is to check all the system and data management. Datasets description: AUTOPILOT_Livorno_HighwayPilot_Vehicle_all: Data generated from the vehicle sensors This dataset refers to the vehicle datasets generated from the vehicle sensors during Highway Piloting in Livorno. This includes the data coming from the CAN bus and GPS. It includes following kind of dataset: Vehicle: general data (speed, battery); PositioningSystem: data from GPS; VehicleDynamics: data about dynamic (acceleration...); LateralControl: steering and lane control data AUTOPILOT_Livorno_HighwayPilot_V2X_all: V2V messages during the Highway Pilot sessions This dataset refers to the V2V messages exchanged between ITS stations (vehicles and RSUs) during the Highway Piloting in Livorno. AUTOPILOT_Livorno_HighwayPilot_IoT_all: Data extracted from IoT oneM2M platform This dataset refers to messages exchanged by HighwayPilot devices, applications and services across the oneM2M platform.

Livorno, Highway pilot, one automated and two connected cars

Scenario description: Precondition: A vehicle is driving in the first lane of a “smart highway” at 90 km/h with all the devices working correctly and connected to all services needed. Actions or events:           1 The puddle monitoring system of the highway triggers a puddle hazard warning for a specific extended zone. 2 The AD car receives the information by IoT based services and sets a speed limitation according to the area interested by hazard conditions: it smoothly decelerates in order to enter in the area at the proper speed. 3 At the end of the dangerous area, as notified by the “smart road”, the vehicle will recover the legally allowed cruise speed. Relevant situations: How the AD function interacts with different IoT input: from oneM2M platform (advisory speed limit due to puddles); from I2V (DENM, puddle hazard warning); from V2V (CAM with info from other vehicles). Session description: Test session with one AD+connected car and two connected cars, lap of 12,3 km on the highway. Datasets description: AUTOPILOT_Livorno_HighwayPilot_Vehicle_all: Data generated from the vehicle sensors This dataset refers to the vehicle datasets generated from the vehicle sensors during Highway Pilot session in Livorno. This includes the data coming from the CAN bus and GPS. It includes following kind of dataset: Vehicle: general data (speed, battery); PositioningSystem: data from GPS; VehicleDynamics: data about dynamic (acceleration...); LateralControl: steering and lane control data AUTOPILOT_Livorno_HighwayPilot_V2X_all: V2V messages during Highway Pilot sessions This dataset refers to the V2V messages exchanged between ITS stations (vehicles and RSUs) during the Highway Pilot session in Livorno. AUTOPILOT_Livorno_HighwayPilot_IoT_all: Data extracted from IoT oneM2M platform This dataset refers to messages exchanged by HighwayPilot devices, applications and services across the oneM2M platform.

opencc-by-4.0May 2020View details →

Connecting digital citizen science data quality issue to solution mechanism table

A table explaining how to solve data quality issues in digital citizen science. A total of 35 issues and 64 mechanisms to solve them are proposed

opencc-zeroJul 2020View details →

Data from: Brain states govern the spatio-temporal dynamics of resting-state functional connectivity

Previously, using simultaneous resting-state functional magnetic resonance imaging (fMRI) and photometry-based neuronal calcium recordings in the anesthetized rat, we identified blood oxygenation level-dependent (BOLD) responses directly related to slow calcium waves, revealing a cortex-wide and spatially organized correlate of locally recorded neuronal activity (<a href="#_ENREF_68" title="Schwalm, 2017 #1">Schwalm et al., 2017</a>). Here, using the same techniques, we investigate two distinct cortical activity states: persistent activity, in which compartmentalized network dynamics were observed; and slow wave activity, dominated by a cortex-wide BOLD component, suggesting a strong functional coupling of inter-cortical activity. During slow wave activity we find a correlation between the occurring slow wave events and the strength of functional connectivity between different cortical areas. These findings suggest that down-up transitions of neuronal excitability can drive cortex-wide functional connectivity. This study provides further evidence that changes in functional connectivity are dependent on the brain's current state, directly linked to the generation of slow waves.

opencc-zeroNov 2020View details →

Invasion of freshwater ecosystems is promoted by network connectivity to hotspots of human activity

Aim: Hotspots of human activity are focal points for ecosystem disturbance and non-native introduction, from which invading populations disperse and spread. As such, connectivity to locations used by humans may influence the likelihood of invasion. Moreover, connectivity in freshwater ecosystems may follow the hydrological network. Here we tested whether multiple forms of connectivity to human recreational activities promotes biological invasion of freshwater ecosystems. Location: England, UK. Time period: 1990-2018. Major taxa studied: 126 non-native freshwater birds, crustaceans, fish, molluscs and plants. Methods: Machine learning was used to predict spatial gradients in human recreation and two high risk activities for invasion (fishing and water sports). Connectivity indices were developed for each activity, in which human influence decayed from activity hotspots according to Euclidean distance (spatial connectivity) or hydrological network distance (downstream, upstream and along-channel connectivity). Generalised linear mixed models identified the connectivity type most associated to invasive species richness of each group, while controlling for other anthropogenic and environmental drivers. Results: Connectivity to humans generally had stronger positive effects on invasion than all other drivers except recording effort. Recreation had stronger influence than urban land cover, and for most groups high risk activities had stronger effects than general recreation. Downstream human connectivity was most important for invasion by most of the groups, potentially reflecting predominantly hydrological dispersal. An exception was birds, for which spatial connectivity was most important, possibly because of overland dispersal capacity. Main conclusions: These findings support the hypothesis that freshwater invasion is partly determined by an interaction between human activity and species dispersal in the hydrological network. By comparing alternative connectivity types for different human activities, our approach could enable robust inference of specific pathways and spread mechanisms associated with particular taxa. This would provide evidence to support better prioritisation of surveillance and management for invasive non-native species.

opencc-zeroJul 2020View details →

Data from: Agri-environment conservation set-asides have co-benefits for connectivity

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.

opencc-zeroJul 2020View details →

Data from: Stressed connections: cortisol levels following acute psychosocial stress disrupt affiliative mimicry in humans

Mimicry, and especially spontaneous facial mimicry, is a rudimentary element of social–emotional experience that is well-conserved across numerous species. Although such mimicry is thought to be a relatively automatic process, research indicates that contextual factors can influence mimicry, especially in humans. Here, we extend this work by investigating the effect of acute psychosocial stress on spontaneous facial mimicry. Participants performed a spontaneous facial mimicry task with facial electromyography (fEMG) at baseline and approximately one month later, following an acute psychosocial stressor (Trier Social Stress Test). Results show that the magnitude of the endocrine stress response reduced zygomaticus major reactivity, and specifically spontaneous facial mimicry for positive social stimuli (i.e. smiles). Individuals with higher levels of the stress hormone cortisol showed a more blunted fEMG response to smiles, but not to frowns. Conversely, stress had no effect on corrugator supercilii activation (i.e. frowning to frowns). These findings highlight the importance of the biological stress response system in this basic element of social–emotional experience.

opencc-zeroNov 2018View details →

Node connectivity measurements for Hetionet v1.0 metapaths

<a href="https://github.com/hetio/hetionet">Hetionet</a> v1.0 is a hetnet (heterogeneous network) with 47,031 nodes of 11 types and 2,250,197 relationships of 24 types. This record contains computed connectivity measurements for Hetionet v1.0 for all metapaths (types of paths) up to length 3. These measurements are designed to assess the extent of connectivity between two nodes along a given metapath. Several types of data are included: <ol> <li>Path counts: Path counts measure the number of paths from a source node to a target node along a specified metapath. The path count is a special case of the degree-weighted path count (DWPC) metric where the damping exponent parameter is set to 0.0. Path counts for all source–target node combinations of a given metapath are stored in a matrix with source nodes as rows and target nodes as columns.</li> <li>Degree-weighted path counts: DWPCs measure the abundance of paths from a source to target node along a given metapath (like path counts), but are adjusted for the degrees along the path such that paths through higher degree nodes are downweighted according to a damping parameter. The DWPCs here use a damping exponent of 0.5 and the same matrix serialization as the path count datasets. The values are not scaled/transformed. To compare to the null DWPCs discussed below, divide each value by the mean DWPC for the entire matrix and apply an inverse hyperbolic sine transformation.</li> <li>Degree-grouped permutation summaries: Degree-grouped permutations (DGP) are used to compute the significance of DWPC values. Specifically, they are used to estimate null distribution for DWPCs from the unpermuted hetnet. DGP summaries provide summary statistics of DWPCs computed on permuted hetnets. The permuted hetnets are derived from Hetionet v1.0 using the XSwap algorithm. This approach preserves node degree but randomizes edges to muddle their meaning. DWPCs were computed for <a href="https://github.com/hetio/hetionet/tree/a95ae76581af604e91d744680aee3f888fa18887/hetnet/permuted/matrix">200 permuted networks</a> and grouped by source–target node degree within each metapath. Permuted DWPCs were scaled by dividing by the unpermuted DWPC mean and then inverse hyperbolic sine transformed. Every degree pair for a given metapath has corresponding statistics that summarize its values across permuted hetnets. These statistics include the number of observed DWPCs, the number of nonzero DWPCs, the sum of the DWPCs, and the sum of squared DWPCs. These values are sufficient to calculate the parameters of a gamma-hurdle null DWPC distribution.</li> </ol> Data Format: the .zip files are HetMat archive files. This simply means that the directory structure and file formats of the archived files conform to the HetMat data structure for storing hetnets on disk. Matrices are stored as scipy.sparse .npz files. .npz is a numpy array serialization format that scipy uses to write sparse matrices to disk. TSV files in this upload report information on the contents of the archives. The .zip-info.tsv files contain a list of all files included in the zip archives. metapath-dwpc-stats.tsv contains summary information on the unpermuted path counts and DWPCs. Note that results are archived by path length, such that all metapaths of length 1 are in a different archive than metapaths of length 2. Therefore, users who only need results for shorter metapaths, do not need to download the large archives for longer metapaths. There are 24 metapaths of length 1, 242 metapaths of length 2, and 1939 metapaths of length 3. Connectivity Search Database: connectivity-search-pg_dump.sql.gz is a PostgreSQL database dump for use with the <a href="https://github.com/greenelab/connectivity-search-backend">connectivity-search-backend</a> repository. Source code: These datasets were computed by the <a href="https://github.com/greenelab/hetmech/blob/34e95b9f72f47cdeba3d51622bee31f79e9a4cb8/explore/bulk-pipeline/bulk.ipynb">bulk.ipynb notebook</a> from <a href="https://github.com/greenelab/hetmech/commit/34e95b9f72f47cdeba3d51622bee31f79e9a4cb8">greenelab/hetmech@34e95b9</a>. Funding: This work was supported through a research collaboration with <a href="https://www.pfizer.com/partners/research-and-development">Pfizer Worldwide Research and Development</a>. This work is funded in part by the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through Grants <a href="https://www.moore.org/grant-detail?grantId=GBMF4552">GBMF4552</a> and <a href="https://www.moore.org/grant-detail?grantId=GBMF4560">GBMF4560</a>. More information: See the manuscript titled <a href="https://greenelab.github.io/connectivity-search-manuscript/">Hetnet connectivity search provides rapid insights into how two biomedical entities are related</a>. <ul> </ul>

The brains of elite soccer players are subject to experience-dependent alterations in white matter connectivity

Soccer is the only major sport with voluntary unprotected head-to-ball contact. It is crucial to determine if head impact through regular soccer sports training is manifested in brain structure and connectivity, and whether such alterations are due to sustained training per se. Using diffusion tensor imaging, we documented a comprehensive view of soccer players' brains in a sample of twenty-five right-handed male elite soccer players aged from 18 to 22 years and twenty-five non-athletic controls aged 19 to 24 years. Importantly, none had recalled a history of concussion. We performed a whole-brain tract-based spatial statistical analysis, and a tract-specific probabilistic tractography method to measure differences of white matter properties between groups. Whole-brain integrity analysis showed increased microstructural integrity within the corpus callosum tract in soccer players compared to controls. Further, tract-specific probabilistic tractography revealed that the anterior part of corpus callosum may be the brain structure most relevant to training experience, which may put into perspective prior evidence showing corpus callosum alteration in retired or concussed athletes practicing contact sports. Intriguingly, experience-related alterations showed left hemispheric lateralization of potential early signs of concussion-like effects. This is the first study to-date providing a definitive characterization of soccer-specific experience-related structural alterations. In sum, we concluded that the observed gains and losses may be due to a consequence of engagement in protracted soccer training that incurs prognostic hallmarks associated with minor injury-induced neural inflammation. Soccer is the only major sport with voluntary unprotected head-to-ball contact. It is crucial to determine if head impact through regular soccer sports training is manifested in brain structure and connectivity, and whether such alterations are due to sustained training per se. Using diffusion tensor imaging, we documented a comprehensive view of soccer players' brains in a sample of twenty-five right-handed male elite soccer players aged from 18 to 22 years and twenty-five non-athletic controls aged 19 to 24 years. Importantly, none had recalled a history of concussion. We performed a whole-brain tract-based spatial statistical analysis, and a tract-specific probabilistic tractography method to measure differences of white matter properties between groups. Whole-brain integrity analysis showed increased microstructural integrity within the corpus callosum tract in soccer players compared to controls. Further, tract-specific probabilistic tractography revealed that the anterior part of corpus callosum may be the brain structure most relevant to training experience, which may put into perspective prior evidence showing corpus callosum alteration in retired or concussed athletes practicing contact sports. Intriguingly, experience-related alterations showed left hemispheric lateralization of potential early signs of concussion-like effects. This is the first study to-date providing a definitive characterization of soccer-specific experience-related structural alterations. In sum, we concluded that the observed gains and losses may be due to a consequence of engagement in protracted soccer training that incurs prognostic hallmarks associated with minor injury-induced neural inflammation. Soccer is the only major sport with voluntary unprotected head-to-ball contact. It is crucial to determine if head impact through regular soccer sports training is manifested in brain structure and connectivity, and whether such alterations are due to sustained training per se. Using diffusion tensor imaging, we documented a comprehensive view of soccer players' brains in a sample of twenty-five right-handed male elite soccer players aged from 18 to 22 years and twenty-five non-athletic controls aged 19 to 24 years. Importantly, none had recalled a history of concussion. We performed a whole-brain tract-based spatial statistical analysis, and a tract-specific probabilistic tractography method to measure differences of white matter properties between groups. Whole-brain integrity analysis showed increased microstructural integrity within the corpus callosum tract in soccer players compared to controls. Further, tract-specific probabilistic tractography revealed that the anterior part of corpus callosum may be the brain structure most relevant to training experience, which may put into perspective prior evidence showing corpus callosum alteration in retired or concussed athletes practicing contact sports. Intriguingly, experience-related alterations showed left hemispheric lateralization of potential early signs of concussion-like effects. This is the first study to-date providing a definitive characterization of soccer-specific experience-related structural alterations. In sum, we concluded that the observed gains and losses may be due to a consequence of engagement in protracted soccer training that incurs prognostic hallmarks associated with minor injury-induced neural inflammation.

Genetic connectivity and population structure of African savanna elephants (Loxodonta africana) in Tanzania

Increasing human population growth, exurban development, and associated habitat fragmentation is accelerating the isolation of many natural areas and wildlife populations across the planet. In Tanzania, rapid and ongoing habitat conversion to agriculture has severed many of the country's former wildlife corridors between protected areas. To identify historically-linked protected areas, we investigated the genetic structure and gene flow of African savanna elephants in Tanzania using microsatellite and mitochondrial DNA markers in 688 individuals. Our results indicate distinct population genetic structure within and between ecosystems across Tanzania, and reveal important priority areas for connectivity conservation. Elephants sampled from the Tarangire-Manyara ecosystem appear marginally, yet significantly isolated from elephants sampled from the greater Serengeti ecosystem (mean FST = 0.03), where two distinct subpopulations were identified.Unexpectedly, elephants in the Lake Manyara region appear to be more closely related to those across the East African Rift wall in the Ngorongoro Conservation Area than they are to the neighboring Tarangire subpopulations. We concluded that the Rift wall has had a negligible influence on genetic differentiation up to this point, but differentiation may accelerate in the future because of ongoing loss of corridors in the area. Interestingly, relatively high genetic similarity was found between elephants in Tarangire and Ruaha although they are separated by >400 km. In southern Tanzania, there was little evidence of female-mediated gene flow between Ruaha and Selous, probably due to the presence of the Udzungwa Mountains between them. Despite observing evidence of significant isolation, the populations of elephants we examined generally exhibited robust levels of allelic richness (mean AR = 9.96), heterozygosity (mean µHE = 0.73), and effective population sizes (mean Ne = 148). Our results may inform efforts to restore wildlife corridors between protected areas in Tanzania in order to facilitate gene flow for long-term survival of elephants and other species.

Data from: Restricted connectivity and population genetic fragility in a globally endangered hammerhead shark

Vagile, large-bodied marine organisms frequently have wide range dispersion but also dependence on coastal habitats for part of their life-history. These characteristics may induce complex population genetic structure patterns, with resulting implications for the management of exploited populations. The scalloped hammerhead, Sphyrna lewini, is a cosmopolitan, migratory shark in tropical and warm temperate waters, inhabiting coastal bays during parturition and juvenile development and the open ocean as adults. Here, we investigated the genetic connectivity and diversity of S. lewini in the western Atlantic using large sample coverage (N=308), and data from whole mitochondrial control region (mtCR) sequences and ten nuclear microsatellite loci. We detected significant population genetic structure with both mtCR and microsatellites markers (mtCR: ΦST = 0.60; p < 0.001; microsatellites: Dest 0.0794, p = 0.001, FST = 0.046, p < 0.05), and isolation by distance (mtCR r = 0.363, p = 0.009; microsatellites r = 0.638, p = 0.007). The migration and gene flow patterns, based on mtCR and microsatellites were asymmetric, and female reproductive philopatry is postulated to explain such population subdivision patterns. The notable population differentiation at microsatellites markers indicates low-levels of male-mediated gene flow in the western Atlantic. The overall effective population size was estimated as 299 (215 – 412 Confidence Interval), and there was no evidence of strong or recent bottleneck effects. Findings of at least three management units, moderate genetic diversity, and low effective population size in the context of current overfishing calls for intensive management aimed at short and long-term conservation for this endangered species in the western Atlantic Ocean.

opencc-by-4.0Aug 2020View details →

Cryptic species and genetic connectivity among populations of the coral Pocillopora damicornis (Scleractinia) in the tropical southwestern Pacific

Studying population genetic connectivity (i.e., identifying gene flow among populations and understanding their impacts on the genetic structure and diversity of populations) is first a matter of knowing what we work on, that is, accurately delimiting evolutionary units. Here, we focused on Pocillopora damicornis sensu stricto (or Pocillopora PSH04 sensu Gélin et al. in Mol Phylogenet Evol 109:430–446. http://dx.doi.org/10.1016/j.ympev.2017.01.018, 2017). From 458 colonies sampled within the tropical southwestern Pacific [Chesterfield Islands and New Caledonia (Grande Terre and Loyalty Islands)], Bayesian assignments and network analyses were conducted with 11-microsatellite loci to first evaluate the genetic partitioning of the colonies in distinct Secondary Species Hypotheses (SSHs), then in distinct clusters. Population genetic connectivity was then assessed for each cluster separately. Pocillopora PSH04 was partitioned into two highly differentiated SSHs (SSH04a and SSH04b), regularly found in sympatry. Furthermore, SSH04a was subdivided into two clusters (SSH04a-1 and SSH04a-2). This pattern of genetic structuring seems not related to clonality, but rather to the establishment of reproductive barriers. Nevertheless, considering each cluster separately, the populations appeared highly differentiated, suggesting relatively weak gene flow. This low connectivity among populations, coupled with the existence of cryptic species, brings new insights to the connectivity pattern of this understudied Pacific region. This dataset contains the microsatellite genotypes analysed (458 Pocillopora PSH04 colonies × 13 loci).

Connectivity-based localization of human hypothalamic nuclei in functional images of standard voxel size

Despite their critical roles in autonomic functions, individual hypothalamic nuclei have not been extensively investigated in humans using functional magnetic resonance imaging, partly due to the difficulty in resolving individual nuclei contained in the small structure of the hypothalamus. Areal parcellation analyses enable discrimination of individual hypothalamic nuclei but require a higher spatial resolution, which necessitates long scanning time or large amounts of data to compensate for the low signal-to-noise ratio in 3T or 1.5T scanners. In this study, we present analytic procedures to estimate likely locations of individual nuclei in the standard 2-mm resolution based on our higher resolution dataset. The spatial profiles of functional connectivity with the cerebral cortex for each nucleus in the medial hypothalamus were calculated using our higher resolution dataset. Voxels in the hypothalamus in standard resolution images from the Human Connectome Project (HCP) database that predominantly shared connectivity profiles with the same nucleus were subsequently identified. Voxels representing individual nuclei, as identified with the analytic procedures, were reproducible across 20 HCP datasets of 20 subjects each. Furthermore, the identified voxels were spatially separate. These results suggest that these analytic procedures are capable of refining voxels that represent individual hypothalamic nuclei in standard resolution. Our results highlight the potential utility of these procedures in various settings such as patient studies, where lengthy scans are infeasible.

Integrating functional connectivity in designing networks of protected areas under climate change: a caribou case-study

Land-use change and climate change are recognized as two main drivers of the current biodiversity decline. Protected areas help safeguard the landscape from additional anthropogenic disturbances and, when properly designed, can help species cope with climate change impacts. When designed to protect the regional biodiversity rather than to conserve focal species or landscape elements, protected areas need to cover a representative sample of the regional biodiversity and be functionally connected, facilitating individual movements among protected areas in a network to maximize their effectiveness. We developed a methodology to define effective protected areas to implement in a regional network using ecological representativeness and functional connectivity as criteria. We illustrated this methodology in the Gaspésie region of Québec, Canada. We simulated movements for the endangered Atlantic-Gaspésie caribou population (Rangifer tarandus caribou), using an individual-based model, to determine functional connectivity based on this large mammal. We created multiple protected areas network scenarios and evaluated their ecological representativeness and functional connectivity for the current and future conditions. We selected a subset of the most effective network scenarios and extracted the protected areas included in them. There was a tradeoff between ecological representativeness and functional connectivity for the created networks. Only a few protected areas among those available were repeatedly chosen in the most effective networks. Protected areas maximizing both ecological representativeness and functional connectivity represented suitable areas to implement in an effective protected areas network. These areas ensured that a representative sample of the regional biodiversity was covered by the network, as well as maximizing the movement over time between and inside the protected areas for the focal population.

Permeability of Neotropical agricultural lands to a key native ungulate – are well-connected forests important?

Much of what remains of the Earth's tropical forests is embedded within agricultural landscapes, where forest is reduced and fragmented. As native forest ungulates are critical to maintaining forest function, it is imperative to understand how this functional group responds to declines in forest cover and connectivity resulting from agricultural expansion. We addressed this issue by evaluating selection of forest cover and forest connectivity by a key native ungulate of Neotropical forests, the white-lipped peccary (Tayassu pecari Link 1795, Tayassuidae, Cetartiodactyla), in agricultural landscapes of Brazil. We evaluated selection using compositional analysis at two hierarchical levels, landscape and home range. From 2013 to 2019, we GPS-tracked eight white-lipped peccary herds in Southwest Brazil, resulting in a total of 14,460 GPS locations. We found that herds can live in landscapes with a wide range of forest cover (35-81% of home ranges covered by native forest), with significant, but not strong, selection at the landscape level (p = 0.045). Nevertheless, herds strongly select for forest cover within their home ranges (81-97% of locations within native forest; highly significant selection at the home-range level: p = 0.008). As for connectivity, herds significantly select the largest, most connected forest fragments at the landscape level (p=0.04), but not at the home-range level (p=0.07). Our results support that Neotropical forests within agricultural landscapes need to be well-connected in order to preserve this key native ungulate, and maintain long-term forest function.

Data from: Broad-front migration leads to strong migratory connectivity in the lesser kestrel (Falco naumanni)

Aim: Migratory animals regularly move between often distant breeding and non-breeding ranges. Knowledge about how these ranges are linked by movements of individuals from different populations is crucial for unravelling temporal variability in population spatial structuring and for identifying environmental drivers of population dynamics acting at different spatio-temporal scales. We performed a large-scale individual-based migration tracking study of the lesser kestrel (Falco naumanni), an Afro-Palearctic migratory raptor, to determine the patterns of migratory connectivity of European breeding populations. Location: Europe, Africa. Methods: Migration data were recorded using different devices (geolocators, Argos PTTs, GPS loggers) from 87 individuals breeding in the three core European populations, located in the Iberian, Italian and Balkan peninsulas. We estimated connectivity by the Mantel correlation coefficient (rM), and computed both the degree of separation between the non-breeding areas of individuals from the same population (i.e., the population spread) and the relative size of the non-breeding range (i.e., the non-breeding range spread). Results: European lesser kestrels migrated on a broad-front across the Mediterranean Sea and Sahara Desert, with different populations using different routes. Iberian birds migrated to western Sahel (Senegal, Mauritania, western Mali), Balkan birds migrated chiefly to central-eastern Sahel (Niger, Nigeria, Chad), whereas Italian ones spread from eastern Mali to Nigeria. Spatial differentiation of non-breeding areas led to a strong migratory connectivity (rM = 0.58), associated with a relatively high population (637 km) and non-breeding range (1149 km) spread. Main conclusions: Our comprehensive analysis of the non-breeding distribution of European lesser kestrel populations revealed a strong migratory connectivity, a rare occurrence in long-distance avian migrants. The geographic conformation of the species' breeding and non-breeding ranges, together with broad-front migration across ecological barriers, promoted the differentiation of migratory routes and non-breeding areas. Strong connectivity could then arise because of both high population spread and broad non-breeding range.

Data from: Navigating the southern seas with small fins: Genetic connectivity of seahorses (Hippocampus abdominalis) across the Tasman Sea

Aim Historical patterns of ocean circulation in the Southern Hemisphere have been well studied, but the effects of coastal oceanography on marine biogeography in this region remain poorly understood relative to northern latitudes. Our study investigates historical and contemporary patterns of migration and dispersal across the Tasman Sea. Location Coastal regions of the Tasman Sea including southeastern Australia, Tasmania and New Zealand. Taxon Hippocampus abdominalis, the pot-bellied seahorse, one of the most broadly distributed seahorse species, and the only seahorse to have successfully colonized New Zealand from Australia across 2,000 km of open ocean. Methods We used a multilocus genetic dataset to measure population diversity and differentiation from seahorses across the full species range to investigate contemporary and historical demography, and to reconstruct colonization routes across the Tasman Sea. Results Genetic data indicate that seahorses colonized New Zealand from Australia during the previous interglacial-glacial cycle (12,000-120,000 ybp), and have evolved in relative isolation since the initial establishment event. Contemporary effective population sizes in the newly colonized range are substantially larger than those inferred in Australia, and both appear to be reduced relative to ancestral levels. Australian seahorses are genetically diverse and show high levels of population connectivity, while the distribution of genetic variation in New Zealand suggests an initial colonization of the South Island following by northward migration. Importantly, despite clear evidence that New Zealand seahorses are descendent from Australian ancestors, patterns of contemporary genetic diversity are consistent with trans-Tasman migration from New Zealand to Australia, suggesting that genetic variation accumulated in the newly colonized range is contributing to the genetic diversity of Australian seahorses. Main conclusions Despite a largely independent evolutionary trajectory of seahorses separated by the Tasman Sea, haplotype sharing between populations in Australia and New Zealand suggests that secondary genetic exchange is contributing to the contemporary phylogeography of the species. Patterns of genetic structure in H. abdominalis mirror those found in other rafting species, suggesting that adult dispersal via rafting has been an important vector of marine dispersal in this species.