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Data for manuscript # 2021JA029122 JGR-Space Physics
<p>This is a collection of files that we have used to generate our figures for the manuscript 2021JA029122. </p>
Data from: Distance-dependent seedling mortality and long-term spacing dynamics in a neotropical forest community
Negative distance dependence (NDisD), or reduced recruitment near adult conspecifics, is thought to explain the astounding diversity of tropical forests. While many studies show greater mortality at near vs. far distances from adults, these studies do not seek to track changes in the peak seedling curve over time, thus limiting our ability to link NDisD to coexistence. Using census data collected over 12 years from central Panama in conjunction with spatial mark-connection functions, we show evidence for NDisD for many species, and find that the peak seedling curve shifts away from conspecific adults over time. We find wide variation in the strength of NDisD, which was correlated with seed size and canopy position, but other life-history traits showed no relationship with variation in NDisD mortality. Our results document shifts in peak seedling densities over time, thus providing evidence for the hypothesized spacing mechanism necessary for diversity maintenance in tropical forests.
Data from: Implications of shared predation for space use in two sympatric leporids
Spatial variation in habitat riskiness has a major influence on the predator–prey space race. However, the outcome of this race can be modulated if prey shares enemies with fellow prey (i.e., another prey species). Sharing of natural enemies may result in apparent competition, and its implications for prey space use remain poorly studied. Our objective was to test how prey species spend time among habitats that differ in riskiness, and how shared predation modulates the space use by prey species. We studied a one‐predator, two‐prey system in a coastal dune landscape in the Netherlands with the European hare (Lepus europaeus) and European rabbit (Oryctolagus cuniculus) as sympatric prey species and red fox (Vulpes vulpes) as their main predator. The fine‐scale space use by each species was quantified using camera traps. We quantified residence time as an index of space use. Hares and rabbits spent time differently among habitats that differ in riskiness. Space use by predators and habitat riskiness affected space use by hares more strongly than space use by rabbits. Residence time of hare was shorter in habitats in which the predator was efficient in searching or capturing prey species. However, hares spent more time in edge habitat when foxes were present, even though foxes are considered ambush predators. Shared predation affected the predator–prey space race for hares positively, and more strongly than the predator–prey space race for rabbits, which were not affected. Shared predation reversed the predator–prey space race between foxes and hares, whereas shared predation possibly also released a negative association and promoted a positive association between our two sympatric prey species. Habitat riskiness, species presence, and prey species' escape mode and foraging mode (i.e., central‐place vs. noncentral‐place forager) affected the prey space race under shared predation.
Data from: A place-based participatory mapping approach for assessing cultural ecosystem services in urban green space
1. Cultural Ecosystem Services (CES) encompass a range of social, cultural and health benefits to local communities, for example recreation, spirituality, a sense of place and local identity. However, these complex and place-specific CES are often overlooked in rapid land management decisions and assessed using broad, top–down approaches. 2. We use the Toolkit for Ecosystem Service Site-based Assessment (TESSA) to examine a novel approach to rapid assessment of local CES provision using inductive, participatory methods. We combined free-listing and participatory geographic information systems (GIS) techniques to quantify and map perceptions of current CES provision of an urban green space. The results were then statistically compared with those of a proposed alternative scenario with the aim to inform future decision-making. 3. By identifying changes in the spatial hotspots of CES in our study area, we revealed a spatially-specific shift toward positive sentiment regarding several CES under the alternative state with variance across demographic and stakeholder groups. Response aggregations in areas of proposed development reveal previously unknown stakeholder preferences to local decision-makers and highlight potential trade-offs for conservation management. Free-listed responses revealed deeper insight into personal opinion and context. 4. This work serves as a useful case study on how the perceptions and opinions of local people regarding local CES could be accounted for in the future planning of an urban greenspace and how thorough analysis of CES provision is important to fully-inform local-scale conservation and planning for the mutual benefit of local communities and nature.
Data from: SNPs across time and space: population genomic signatures of founder events and epizootics in the House Finch (Haemorhous mexicanus)
Identifying genomic signatures of natural selection can be challenging against a background of demographic changes such as bottlenecks and population expansions. Here, we disentangle the effects of demography from selection in the House Finch (Haemorhous mexicanus) using samples collected before and after a pathogen-induced selection event. Using ddRADseq, we genotyped over 18,000 SNPs across the genome in native pre-epizootic western US birds, introduced birds from Hawaii and the eastern United States, post-epizootic eastern birds, and western birds sampled across a similar time span. We found 14% and 7% reductions in nucleotide diversity, respectively, in Hawaiian and pre-epizootic eastern birds relative to pre-epizootic western birds, as well as elevated levels of linkage disequilibrium and other signatures of founder events. Despite finding numerous significant frequency shifts (outlier loci) between pre-epizootic native and introduced populations, we found no signal of reduced genetic diversity, elevated linkage disequilibrium, or outlier loci as a result of the epizootic. Simulations demonstrate that the proportion of outliers associated with founder events could be explained by genetic drift. This rare view of genetic evolution across time in an invasive species provides direct evidence that demographic shifts like founder events have genetic consequences more widespread across the genome than natural selection.
Data from: Inferring continuous and discrete population genetic structure across space
A classic problem in population genetics is the characterization of discrete population structure in the presence of continuous patterns of genetic differentiation. Especially when sampling is discontinuous, the use of clustering or assignment methods may incorrectly ascribe differentiation due to continuous processes (e.g., geographic isolation by distance) to discrete processes, such as geographic, ecological, or reproductive barriers between populations. This reflects a shortcoming of current methods for inferring and visualizing population structure when applied to genetic data deriving from geographically distributed populations. Here, we present a statistical framework for the simultaneous inference of continuous and discrete patterns of population structure. The method estimates ancestry proportions for each sample from a set of two-dimensional population layers, and, within each layer, estimates a rate at which relatedness decays with distance. This thereby explicitly addresses the "clines versus clusters" problem in modeling population genetic variation, and remedies some of the overfitting to which nonspatial models are prone. The method produces useful descriptions of structure in genetic relatedness in situations where separated, geographically distributed populations interact, as after a range expansion or secondary contact. We demonstrate the utility of this approach using simulations and by applying it to empirical datasets of poplars and black bears in North America.
Data from: Inter-individual spacing affects the finder's share in ring-tailed coatis (Nasua nasua)
<p>Social foraging models are often used to explain how group size can affect an individual's food intake rate and foraging strategies. The proportion of food eaten before the arrival of conspecifics, the finder's share, is hypothesized to play a major role in shaping group geometry, foraging strategy, and feeding competition. The variables which affect the finder's share in ring-tailed coatis were tested using a series of food trials. The number of grapes in the food trials had a strong negative effect on the finder's share and the probability that the finder was joined. The effect of group size on the finder's share and foraging success was not straightforward, and was mediated by socio-spatial factors. The finder's share increased when the time to arrival of the next individual was longer, the group was more spread out, and the finder was in the back of the group. Similarly, the total amount of food eaten at a trial was higher when more grapes were placed, arrival time was longer, and number of joiners was smaller. Individuals at the front edge of the group found far more food trials, but foraging success was higher at the back of the group where there were fewer conspecifics to join them. This study highlights the importance of social spacing strategies and group geometry on animal foraging tactics and the costs and benefits of sociality.</p>
Data from: The Bogert effect revisited: salamander regulatory behaviors are differently constrained by time and space
The use of behavior to buffer extreme environmental variation is expected to enable species to a) extend the breadth of environments they inhabit beyond that predicted from climatic data, and b) diminish the negative effects of broad-scale and chronic disturbances such as climate change. The term Bogert effect refers to behavioral compensation entailing microhabitat selection to maintain performance across a gradient of environmental conditions resulting in evolutionary inertia of physiological traits. Here we compare microhabitats used by plethodontid salamanders distributed along an elevational gradient to determine whether there is behavioral compensation that buffers them from deleterious temperatures and moisture levels. Overall, salamanders preferred cooler and more mesic environments and occupied microhabitats that maintained constant moisture conditions at both high and low elevation sites. Our results suggest that salamanders use microhabitats to regulate temperature and moisture levels, which is consistent with the Bogert effect. Maintenance of more moist conditions may help buffer these species from rising temperatures, but only in suitable high-elevation environments that are likely to disappear over the next century. We conclude that behavioral regulation of temperature and moisture is a potential mechanism for the Bogert effect in plethodontid salamanders.
Data: Greater local cooling effects of trees across globally distributed urban green spaces
<p>The dataset used for hierarchical linear mixed effects models in the R code during the study. </p><p>The description of the column names is provided in the readme file.</p>
Ocean Heat Content Anomalies in the North Atlantic based on mapping Argo data using local Gaussian processes defined over space
<p>Monthly Ocean Heat Content Anomalies (OHCA) in the top 2000 dbar of the ocean are calculated (during 2005-2022, in the North Atlantic, north of 20N) subtracting the time mean over the period 2005-2021 from the monthly time series of OHC. OHC fields are mapped using a locally stationary Gaussian process (defined over space) with data-driven decorrelation scales (Kuusela and Stein, 2018). A linear time trend was included in the estimate of the mean field (along with spatial terms and harmonics for the annual cycle). In this product, mapping is done in latitude and longitude with monthly subsets of data. Mapping is done separately for different vertical sections: 15-20 dbar, 15-300 dbar, 300-700 dbar, 700-1850 dbar, 1800-1850 dbar. The 15-20 dbar (1800-1850 dbar) section is used to estimate OHCA for 0-15 dbar (1850-2000 dbar), where observations are sparser. Different vertical sections are combined to estimate global OHCA for 0-2000 dbar. Regions of the ocean that are shallower than 300 m or are not sufficiently well sampled by the Argo array are not included. </p>
Supporting data for "Space weather in the popular media, and the opportunities the upcoming solar maximum brings"
<p>This contains the supporting data for the Space Weather Editorial "Space weather in the popular media, and the opportunities the upcoming solar maximum brings". It contains the Google Trends data (multiTimeline.csv) and the F10.7 and Kp data (omniweb.txt). </p>
Measurement data for septal spacing and conch morphology in Cretaceous ammonoids
<p>We analyzed the ontogenetic trajectories of conch morphology and septal spacing between successive chambers in Cretaceous ammonoids (suborders Perisphinctina and Ancyloceratina) collected from southern India, Madagascar, and Japan. All examined species, except for the family Collignoniceratidae, exhibited similar characteristics during early ontogeny. The common ontogenetic trajectories of septal spacing show a cycle comprising an increase and a subsequent decrease in septal spacing during early ontogeny. The conch diameters at the end of the cycle were estimated to be 1–4 mm. The conch shape (aperture height and whorl expansion rate) covariably changed at this conch diameter. Such covariable changes are commonly recognized in the suborders Perisphinctina and Ancyloceratina. The similarity in the ontogenetic trajectories of conch morphology implies a closer phylogenetic relationship between these suborders compared to Lytoceratina or Phylloceratina.</p>
Digisonde Data files used for JGR-Space Physics paper "A simplified method of true height analysis to estimate the real height of sporadic E layers"
<p>paper submitted for publication in JGR-Space Physics.</p> <p>Digisonde Data files used for analysis</p> <p> </p> <p>A simplified method of true height analysis to estimate the real height of sporadic E layers</p> <p> </p> <p>Christos Haldoupis</p> <p>Department of Physics, University of Crete, Heraklion, Greece</p> <p>Haris Haralambous</p> <p>Frederick University and Frederick Research Center, Nicosia, Cyprus</p> <p>Chris Meek</p> <p>Institute of Space and Atmospheric Studies, University of Saskatchewan, Saskatoon, SK, Canada</p>
Data from: neglected puzzle pieces of urban green infrastructure: richness, cover, and composition of insect-pollinated plants in traffic-related green spaces
<p>Insect-pollinated vascular plants in spontaneous vegetation provide essential ecosystem services and benefit wildlife. However, floral communities associated with traffic-related green spaces are rarely considered valuable elements of urban green infrastructure (UGI). The dataset contains information on species-based floral communities of vascular insect-pollinated plants in traffic-related green spaces in three highly populated Finnish cities. Those are Helsinki (665 558 inhabitants), Tampere (244 029 inhabitants), and Turku (175 645 inhabitants). Data were collected during the mean flowering phenophase of vascular plants in July-August 2022 from two types of locations: (i) urban (city centers) and (ii) suburban (city outskirts), and from three types of traffic-related green spaces: (i) traffic islands, (ii) parking lots, (iii) road verges. The dataset contains information for the 93 vascular insect-pollinated plant species flowering during the survey. Sampling campaign was conducted in 90 sampling sites, and the dataset contains information on the location coordinates. In addition, the dataset possesses information on the amount of garbage pieces (cigarette filters, plastic boxes, or scraps) revealed for each sampling point in traffic-related green spaces.</p>
Data associated with the manuscript: 'COLIS: An advanced light scattering apparatus for investigating soft matter onboard the International Space Station'
<p>Experimental data shown in the manuscript.</p>
Data files for "Genomic-to-space measurements reveal global ocean nutrient stress"
<p>Data files to be used with the following code: https://github.com/ljustick/genomic_to_space_nut_stress</p>
Data from: N-mixture models estimate abundance reliably: a field test on Marsh Tit using time-for-space substitution
<p>Imperfect detection in field studies on animal abundance, including birds, is common and can be corrected for in various ways. The binomial N-mixture (hereafter binmix) model developed for this task is widely used in ecological studies owing to its simplicity: it requires replicated count results as the input. However, it may overestimate abundance and be sensitive to even small violations of its assumptions. We used a 33-year dataset on the Marsh Tit, Poecile palustris, a sedentary forest passerine, from Białowieża Forest, Poland to validate inference from binmix models by comparing model-estimated abundances to the true number of breeding pairs within the plots, determined by exhaustive population study. The abundance estimates, derived from six springtime (April-May) counts of males on each plot in each year, were highly reliable: 116 out of 132 year-plot estimates (88%) included the true number of pairs within the 95% confidence intervals. Over- and underestimations were thus rare and similarly frequent (9 and 12 cases, respectively), with a tendency to overestimate at low densities and underestimate at high densities. Marsh Tits sing rarely but the frequency of countersinging increases with abundance, leading to non-independence in detections. When accounted for in a submodel for detection, the per-survey number of countersinging events positively affected detection probability but only weakly affected abundance estimates. Simulations further demonstrate that this property, overestimation at low densities and underestimation at high densities, may be a systematic bias of binmix model even if density-dependent detection is absent. While the behaviour of binmix models in specific situations requires more study, we conclude that these models are a valid tool to estimate abundance reliably when intensive population monitoring is not feasible.</p>
Data from: Landscape composition and life-history traits influence bat movement and space use: analysis of 30 years of published telemetry data
<p><span><b>Aim: </b>Animal movement determines home range patterns, which in turn affect individual fitness, population dynamics and ecosystem functioning. Using temperate bats, a group of particular conservation concern, we investigated how morphological traits, habitat specialization and environmental variables affect home range sizes and daily foraging movements, using a compilation of 30 years of published bat telemetry data.</span></p> <p><span><b>Location</b>: Northern America and Europe.</span></p> <p><span><b>Time period</b>: 1988 – 2016.</span></p> <p><span><b>Major taxa studied</b>: Bats.</span></p> <p><span><b>Methods</b>: We compiled data on home range size and mean daily distance between roosts and foraging areas at both colony and individual levels from 166 studies of 3,129 radiotracked individuals of 49 bat species. We calculated multi-scale habitat composition and configuration in the surrounding landscapes of the 165 studied roosts. Using mixed models, we examined the effects of habitat availability and spatial arrangement on bat movements, while accounting for body mass, aspect ratio, wing loading and habitat specialization.</span></p> <p><span><b>Results:</b><i> </i>We found a significant effect of landscape composition on home range size and mean daily distance at both colony and individual levels. On average, home ranges were up to 42% smaller in the most habitat-diversified landscapes while mean daily distances were up to 30% shorter in the most forested landscapes. Bat home range size significantly increased with body mass, wing aspect ratio and wing loading, and decreased with habitat specialization.</span></p> <p><span><b>Main conclusions: </b>Promoting bat movements through the landscape surrounding roosts at large spatial scales is crucial for bat conservation. Forest loss and overall landscape homogenization lead temperate bats to fly farther to meet their ecological requirements, by increasing home range sizes and daily foraging distances. Both processes might be more detrimental for smaller, habitat-specialized bats, less able to travel increasingly longer distances to meet their diverse needs.</span></p>
Model and data for: Economical defense of resources structures territorial space use in a cooperative carnivore
<p>Manuscript Abstract: Ecologists have long sought to understand space use and mechanisms underlying patterns observed in nature. We developed an optimality landscape and mechanistic territory model to understand mechanisms driving space use and compared model predictions to empirical reality. We demonstrate our approach using gray wolves (<i>Canis lupus</i>). In the model, simulated animals selected territories to economically acquire resources by selecting patches with greatest value, accounting for benefits, costs, and tradeoffs of defending and using space on the optimality landscape. Our approach successfully predicted and explained first- and second-order space use of wolves, including the population's distribution, territories of individual packs, and influences of prey density, competitor density, human-caused mortality risk, and seasonality. It accomplished this using simple behavioral rules and limited data to inform the optimality landscape. Results contribute evidence that economical territory selection is a mechanistic bridge between space use and animal distribution on the landscape. This approach and resulting gains in knowledge enable predicting effects of a wide range of environmental conditions, contributing to both basic ecological understanding of natural systems and conservation. We expect this approach will demonstrate applicability across diverse habitats and species, and that its foundation can help continue to advance understanding of spatial behavior.</p> <p>Model & Data Abstract: In support of the above manuscript, all model files and data to re-create the analyses for the manuscript are included on Dryad. The model can be run in NetLogo (installation file included), using the associated input files to build the Montana landscape for wolves. Expertise in NetLogo is strongly recommended for using this model. Output files are likewise included along with code to create each plot in the manuscript and SI. Software files for the model and code to create each plot in the manuscript are located at Zenodo: https://doi.org/10.5281/zenodo.5802243.</p>
Data and analysis scripts for "Impact of grid spacing, convective parameterization and cloud microphysics in ICON simulations of a warm conveyor belt"
<p>The data relates to the analysis of "Impact of grid spacing, convective parameterization and cloud microphysics in ICON simulations of a warm conveyor belt" and is in support and reference to the work titled as the same for a research article authored by Choudhary and Voigt. The file 'data.zip' contains different directories named as per the computations related to particular analysis as mentioned below:</p> <table> <tbody> <tr> <td> <p>Directory names and content inside 'data.zip'</p> </td> </tr> <tr> <td> <p>Name of directory</p> </td> <td> <p>Content</p> </td> </tr> <tr> <td> <p>trajectories </p> </td> <td> <p>Output from run of LAGRANTO tool on regridded ICON simulations<strong><sup>*</sup></strong> (the input data is not provided here). The output contains computations of 'warm conveyor belt (WCB)' trajectories and different variables traced along them which are stored in different files named as outtrace1.nc and so on. The subdirectories are named as per the resolution, convection and cloud microphysics parametrization used in model setup, for e.g. '0.025convon/1m' corresponds to 2.5 km resolution with parametrized convection and 1-moment cloud microphysics. The file with name ending with 'box' corresponds to different subclasses of trajectory as described in the work. </p> </td> </tr> <tr> <td> <p>dhr</p> </td> <td> <p>diabatic heating rate, traced along WCB and binned in pressure levels (for 1-moment cloud microphysics)</p> </td> </tr> <tr> <td> <p>dynamical variables</p> </td> <td> <p>av- absolute vorticity, pv- potential vorticity and w- vertical wind traced along WCB and binned in pressure levels (for 1-moment cloud microphysics)</p> </td> </tr> <tr> <td> <p>statistics</p> </td> <td> <p>statistics (different statistical computation of WCB parcels ascent for 1- and 2- moment cloud microphysics, details described in work)</p> </td> </tr> <tr> <td> <p>theta_e</p> </td> <td> <p>equivalent potential temperature for 2.5 km explicit convection simulation (.pkl file) for 2016.09.22 12UTC, 2016.09.23 12UTC and 2016.09.24 12UTC in files numbered 1, 2 and 3 respectively.</p> </td> </tr> <tr> <td> <p>ipv</p> </td> <td> <p>same as above but for isentropic potential vorticity</p> </td> </tr> <tr> <td> <p>mslp</p> </td> <td> <p>mslp.nc- same as above but for mean sea level pressure field </p> </td> </tr> <tr> <td> <p>cyclone_track</p> </td> <td> <p>File name with convention 'nawdexnwp-5km-mis-0001_vladiana_cyclonepressure.nc' corresponds to file containing central mean sea level pressure of cyclone Vladiana during the simulation period for 5 km resolution with parametrized convection and 1-moment cloud microphysics. </p> <p>coord_1m.npy- the coordinate/ location of cyclone Vladiana based on central mean sea level pressure </p> </td> </tr> <tr> <td> <p>pte</p> </td> <td> <p>Pressure tendency equation (PTE) analysis. Subdirectories are named after different resolutions of simulation with 1-moment cloud microphysics and parametrized convection (except for 10, 5 and 2.5 km where convection is explicit).</p> <p>Further, the .npy files are named as per the different vertically integrated tendency terms of PTE equation they represent, as mentioned below:</p> <p>dp_dt: surface pressure</p> <p>dfi_dt: geopotential (upper boundary of integral)</p> <p>i_diab_res: diabatic heating (including residual)</p> <p>i_itt: virtual temperature</p> <p>i_tadv: temperature advection</p> <p>i_vmt: vertical motions</p> </td> </tr> </tbody> </table> <p> </p> <p><strong>*</strong>Note: The original ICON simulations which are not part of this dataset were carried out by Prof. Aiko Voigt (University of Vienna) at the Mistral High Performance Computing system of the German Climate Computing Center (DKRZ) in Hamburg, Germany. The primary data of the ICON simulations (run scripts, namelists, scripts for lateral boundary data) are published at KITopen of Karlsruhe Institute of Technology, https://doi.org/10.5445/IR/1000123695. Note that the KITopen dataset includes all simulations of \cite{svchd20}, from which a subset is analyzed here.</p> <p> </p> <p>The file 'scripts.zip' contains two directories which is related with analysis presented in the work:</p> <p>'plotting_scripts' includes script for creating different plots/ figures showcased in the work </p> <p>'processing_scripts' includes computations for producing different quantities/ data that are named as described above in the table for 'data.zip'</p> <p> </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.