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Fig. 3 a in Phylogenetic and functional diversity of African muroid rodents at different spatial scales
Fig. 3 a Pairwise results of partition of phylogenetic and functional β diversity into its nestedness (above diagonal) and turnover (below diagonal) components wherein higher values are indicated in red. b Phylogenetic and functional dendrograms obtained by using UPGMA
FIG. 4 in Phenotypic Variation in Brook Trout Salvelinus fontinalis (Mitchill) at Broad Spatial Scales Makes Morphology an Insufficient Basis for Taxonomic Reclassification of the Species
FIG. 4. The number of vertebrae (A) and basihyal teeth (B) reported by Stauffer (2020) for Cosby (CS; yellow), Indian Camp (ICC; blue), and Greenbrier (GB; green) Creeks. Vertebrae counts from peer-reviewed literature are also shown (see the supplement for sources), and, where appropriate, mean (triangle), mode (circle), and/or range (line) are indicated. The dashed line in panel B reflects values that were reported for basihyal tooth count from Cosby Creek in Stauffer (2020) but which were inconsistent with the requested data.
FIG. 1 in Phenotypic Variation in Brook Trout Salvelinus fontinalis (Mitchill) at Broad Spatial Scales Makes Morphology an Insufficient Basis for Taxonomic Reclassification of the Species
FIG. 1. Native distribution of Brook Trout (shaded gray area) in the United States and Canada, with Brook Trout used in our comparative analyses originating from survey locations located in panels A and B. The three streams in Long Island, NY, surveyed by Stauffer and King (2014) are shown in panel A. Panel B shows streams from the Great Smoky Mountains National Park (GSMNP) surveyed by Weathers et al. (2019; circles) and Stauffer (2020; diamonds), with the three streams included in both studies symbolized with matching colors (Cosby Creek: yellow; Greenbrier Creek: green; Indian Camp Creek: blue). Streams included in Weathers et al. (2019) but not included in Stauffer (2020) are shown in gray circles.
FIG. 2 in Phenotypic Variation in Brook Trout Salvelinus fontinalis (Mitchill) at Broad Spatial Scales Makes Morphology an Insufficient Basis for Taxonomic Reclassification of the Species
FIG. 2. First two dimensions of principal components analysis (PCA) of ten meristic traits for five populations of SaLVELinUS. The populations analyzed included the three surveyed by Stauffer (2020) and Weathers et al. (2019) from Cosby (yellow), Greenbrier (green), and Indian Camp (blue) Creeks, collections from Weathers et al. (2019) for 35 additional streams in the Great Smoky Mountains National Park (GSMNP; gray), and three populations from Long Island, NY described by Stauffer and King (2014; red). Ellipses envelop 95% of variation for each population, and population centroids are indicated by a triangle.
Example dataset and expected outcomes of Spatially resolved in situ profiling of mRNA life cycle at transcriptome scale in intact cells and tissues
<p>Here are the example datasets and expected outcomes included in "<strong>Spatially resolved in situ profiling of mRNA life cycle at transcriptome scale in intact cells and tissues</strong>" from Ren et al. Please refer to the README.txt file for more detailed information. Corresponding computational tools are available at <a href="https://github.com/wanglab-broad/starfinder">https://github.com/wanglab-broad/starfinder.</a></p>
Data and code for "Assessing the spatial scale of synchrony in forest tree population dynamics"
<p>The data sets and code provided here facilitate reproduction of our results from this paper on synchrony of forest tree population dynamics. </p> <h3>Description of the data and file structure</h3> <p>The analyses in the paper were conducted at three scales, and each involves its own data files:</p> <ul> <li>Local scale: The relevant data files are named, e.g., "BCI1-7,L=250m,dbh=100mm.Rdata", where "BCI1-7" indicates the ForestGEO site name ("BCI") and census intervals (1 to 7 for BCI), "L=250m" indicates the quadrat size, and "dbh=100mm" indicates the diameter-at-breast height (DBH) threshold used. There are 12 such files (two ForestGEO plots--BCI and Pasoh--times three quadrat sizes times two DBH thresholds). Each file contains a single list "N_all", whose length is equal to the number of quadrats at the given grain. Each element in the list is a data frame containing mean census times (in days), tree species' population sizes and number of survivors across the two censuses for the corresponding quadrat.</li> <li>Regional scale: The relevant data files are "Marena_data,dbh=100mm,spp_anonymised.Rdata" and "Marena_data,dbh=100mm,spp_anonymised.Rdata". Each file contains three objects: "dists" is a matrix giving the distances between all pairs of sites; "N_all1" is a list with one element for each plot, and each element being a data frame with (anonymised) species ids in the first column and abundances in the remaining columns (column names give mean census dates in days); "S_all1" has a similar structure to "N_all1" except that the data give numbers of survivors from any given census to any subsequent census (column headings indicate the two census numbers).</li> <li>Global scale: The relevant data files are "global_data,dbh=10mm,spp_anonymised.Rdata" and "global_data,dbh=100mm,spp_anonymised.Rdata". The data in the files have the same structure as in the regional-scale files.</li> </ul>
Data from: Functional traits and environmental conditions predict community isotopic niches and energy pathways across spatial scales
1. Despite ongoing research in food web ecology and functional biogeography, the links between food-web structure, functional traits and environmental conditions across spatial scales remain poorly understood. Trophic niches, defined as the amount of energy and elemental space occupied by species and food webs, may help bridge this divide. 2. Here, we ask how the functional traits of species, the environmental conditions of habitats and the spatial scale of analysis jointly determine the characteristics of trophic niches. We used isotopic niches as a proxy of trophic niches, and conducted analyses at spatial scales ranging from local food webs and metacommunities to geographically distant sites. 3. We sampled aquatic macroinvertebrates from 104 tank bromeliads distributed across five sites from Central to South America, and compiled the macroinvertebrates' functional traits and stable isotope values (δ15N and δ13C). We assessed how isotopic niches within each bromeliad were influenced by the functional trait composition of their associated invertebrates and environmental conditions (i.e., habitat size, canopy cover, and detrital concentration). We then evaluated whether the diet of dominant predators and, consequently, energy pathways within food webs, reflected functional and environmental changes among bromeliads across sites. Finally, we determined the extent to which the isotopic niches of macroinvertebrates within each bromeliad contributed to the metacommunity isotopic niches within each site, and compared these metacommunity-level niches over biogeographic scales. 4. At the bromeliad level, isotopic niches increased with the functional richness of species in the food web and the detrital concentration in the bromeliad. The diet of top predators tracked shifts in prey biomass along gradients of canopy cover and detrital concentration. Bromeliads that grew under heterogeneous canopy cover displayed less trophic redundancy and therefore combined to form larger metacommunity isotopic niches. Finally, the size of metacommunity niches depended on within-site heterogeneity in canopy cover. 5. Our results suggest that the trophic niches occupied by food webs can predictably scale from local food webs to metacommunities to biogeographic regions. This scaling process is determined by both the functional traits of species and heterogeneity in environmental conditions.
Data from: The effects of spatial scale and isoscape on consumer isotopic niche width
1. The mean and variance of ecological variables are dependent on sampling attributes such as the coverage of environmental heterogeneity (sampling extent) and spatial scale. Trophic niche width is often approximated by bulk tissue stable isotopes of C and N, i.e. the population isotopic niche. However, recent studies suggest that environmental heterogeneity (experienced by individuals) may be more important in defining the isotopic niche width than trophic variability. We hypothesised that isotopic niche width will increase monotonically with spatial scale, largely produced by environmental variation, e.g. nutrient source. 2. To refine this hypothesis, by describing the shapes of isotope scaling curves, we explored a previously published dataset describing three Chilean intertidal species representing different feeding guilds (grazing snails, suspension feeding mussel). We tested these hypotheses on a new, larger dataset describing three functionally-analogous intertidal species from Northern Ireland. We generated isotopic variance-area curves from a spatially-explicit bootstrap and investigated the scale-dependency of environment-isotope relationships, including wave exposure and sub-habitat heterogeneity. 3. Spatial scale explained 50% of the variance in population isotopic niche widths (bivariate C-N ellipse area) by simple, non-linear relationships. Finer scales (< 1 to 10 km lag) accounted for most variance. Scale dependence was strong for ẟ15N variance, of which > 40% was explained by modelling linear coefficients. A ẟ15N baseline gradient, or isoscape, dominated ẟ15N variance scaling patterns, from sheltered, terrestrially-influenced embayments to exposed, pelagic-dominated coastline. Consumer ẟ13C variance had a weaker scale-dependence, plateauing at mesoscales (> 20 km lag). 4. We show that isotopic niche width is strongly dependent on sampling spatial extent, which controls the environmental heterogeneity experienced by individual consumers. Environmental heterogeneity must be accounted for before isotopic niche width can be considered to accurately represent trophic niche width. Studies conducted at different spatial scales are likely to identify different environment-isotope relationships. 5. We recommend that spatial scale should be incorporated into sampling designs explicitly, easiest by maintaining a consistent lag distance or area within which populations are sampled. Identified isoscapes can be de-trended, where necessary.
Data from: Differences in epiphyte biomass and community composition along landscape and within-crown spatial scales
<p>Vascular epiphytes contribute to the structural, compositional, and functional complexity of tropical montane cloud forests because of their high biomass, diversity, and ability to intercept and retain water and nutrients from atmospheric sources. However, human-caused climate change and forest-to-pasture conversion are rapidly altering tropical montane cloud forests. Epiphyte communities may be particularly vulnerable to these changes because of their dependence on direct atmospheric inputs and host trees for survival. In Monteverde, Costa Rica, we measured vascular epiphyte biomass, community composition, and richness at two spatial scales: (1) along an elevation gradient spanning premontane forests to montane cloud forests; and (2) within trees along branches from inner to outer crown positions. We also compared epiphyte biomass and distribution at these scales between two different land-cover types, comparing trees in closed canopy forest to isolated trees in pastures. An ordination of epiphyte communities at the level of trees grouped forested sites above versus below the cloud base, and separated forest versus pasture trees. Species richness increased with increasing elevation and decreased from inner to outer branch positions. Although richness did not differ between land-cover types, there were significant differences in community composition. The variability in epiphyte community organization between the two spatial scales and between land-cover types underscores the potential complexity of epiphyte responses to climate and land-cover changes.</p>
Data from: Population genetic structure of the tree-hole tick Ixodes arboricola (Acari: Ixodidae) at different spatial scales
The endophilic tick Ixodes arboricola infests cavity-nesting birds, and its dispersal strongly depends on the movements of its host. Population genetic structure of I. arboricola was studied with seven polymorphic microsatellite markers. We collected 268 ticks from 76 nest boxes in four woodlots near Antwerp, Belgium. These nest boxes are mainly used by the principal hosts of I. arboricola, the great tit Parus major and the blue tit Cyanistes caeruleus. As these birds typically return to the same cavity for roosting or breeding, ticks within nest boxes were expected to be highly related, and tick populations were expected to be spatially structured among woodlots and among nest boxes within woodlots. In line with the expectations, genetic population structure was found among woodlots and among nest boxes within woodlots. Surprisingly, there was considerable genetic variation among ticks within nest boxes. This could be explained by continuous gene flow from ticks from nearby tree holes, yet this remains to be tested. A pairwise relatedness analysis conducted for all pairs of ticks within nest boxes showed that relatedness among larvae was much higher than among later instars, which suggests that larvae are the most important instar for tick dispersal. Overall, tick populations at the studied spatial scale are not as differentiated as predicted, which may influence the scale at which host–parasite evolution occurs.
Urbanization reduces genetic connectivity in bobcats (Lynx rufus) at both intra- and inter-population spatial scales
<p>Urbanization is a major factor driving habitat fragmentation and connectivity loss in wildlife. However, the impacts of urbanization on connectivity can vary among species and even populations due to differences in local landscape characteristics, and our ability to detect these relationships may depend on the spatial scale at which they are measured. Bobcats (<i>Lynx rufus</i>) are relatively sensitive to urbanization and the status of bobcat populations is an important indicator of connectivity in urban coastal southern California. We genotyped 271 bobcats at 13,520 SNP loci to conduct a replicated landscape resistance analysis in five genetically distinct populations. We tested urban and natural factors potentially influencing individual connectivity in each population separately, as well as study-wide. Overall, landscape genomic effects were most frequently detected at the study-wide spatial scale, with urban land cover (measured as impervious surface) having negative effects and topographic roughness having positive effects on gene flow. The negative effect of urban land cover on connectivity was also evident when populations were analyzed separately despite varying substantially in spatial area and the proportion of urban development, confirming a pervasive impact of urbanization largely independent of spatial scale. The effect of urban development was strongest in one population where stream habitat had been lost to development, suggesting that riparian corridors may help mitigate reduced connectivity in urbanizing areas. Our results demonstrate the importance of replicating landscape genetic analyses across populations and considering how landscape genetic effects may vary with spatial scale and local landscape structure.</p>
Data from: Oscillayers: a dataset for the study of climatic oscillations over Plio-Pleistocene time scales at high spatial-temporal resolution
Motivation: In order to understand how species evolutionarily responded to Plio-Pleistocene climate oscillations (e.g. in terms of speciation, extinction, migration and adaptation), it is first important to have a good understanding of those past climate changes per se. This, however, is currently limited due to the lack of global-scale climatic datasets with high temporal resolution spanning the Plio-Pleistocene. To fill this gap, I here present Oscillayers, a global-scale and region-specific bioclim dataset, facilitating the study of climatic oscillations during the last 5.4 million years at high spatial (2.5 arc-minutes) and temporal (10 kyr time periods) resolution. This data set builds upon interpolated anomalies (Δ layers) between bioclim layers of the present and the Last Glacial Maximum (LGM) that are scaled relative to the Plio-Pleistocene global mean temperature curve, derived from benthic stable oxygen isotope ratios, to generate bioclim variables for 539 time periods. Evaluation of the scaled, interpolated estimates of palaeo-climates generated for the Holocene, Last Interglacial and Pliocene showed good agreement with independent General Circulation Models (GCMs) for respective time periods in terms of pattern correlation and absolute differences. Oscillayers thus provides a new tool for studying spatial-temporal patterns of evolutionary and ecological processes at high temporal and spatial resolution. Main types of variable contained: 19 bioclim variables for time periods throughout the Plio-Pleistocene. Input data and R script to recreate all 19 bioclim variables. Spatial location and grain: Global at 2.5 arc-minutes (4.65 x 4.65 = 21.62 km2 at the equator). Time period and grain: The last 5.4 million years. The grain is 10 kyr (= 539 time periods). Level of measurement: Data are for terrestrial climates (excluding Antarctica) taking sea level changes into account. Software format: All data are available as ASCII (ESRI) grid files.
Figure 5 in Dissecting copepod diversity at different spatial scales in southern European groundwater
Figure 5. Plots of γ -diversity (regional species richness) versus (A) mean α-diversity (mean species richness of local units: black dots; mean species richness of habitats: grey dots; standard error bars shown), and (B) β -diversity (average dissimilarity of local units: black dots; average dissimilarity of habitats: grey dots).
Figure 3 in Dissecting copepod diversity at different spatial scales in southern European groundwater
Figure 3. (A) Multidimensional Scaling plots of centroids of the habitats (region acronyms as in Figure 1; K, karstic aquifers; P, porous aquifers); (B) Magnitude of the different spatial scale contributions to α-diversity and β -diversity variation.
Figure 1 in Dissecting copepod diversity at different spatial scales in southern European groundwater
Figure 1. Map of distribution of the four regions analysed in Southern Europe (CAN, Cantabria; JUR, Jura Massif; LES, Lessinian Massif; KRI, Krim Massif).
Figure 2 in Dissecting copepod diversity at different spatial scales in southern European groundwater
Figure 2. Multidimensional Scaling plots of the local units using presence/absence multivariate data; aggregation at the aquifer type-level and at the regional level is highlighted; labels of units include the region acronyms (as in Figure 1), habitat (Ku, unsaturated karst; Ks, saturated karst; Ph, hyporheic habitat; Ps, saturated porous), and codes of the four replicates (basins A, B, C, D). Each point representing a local unit is the centroid of 12 sampling sites.
Data from: Fine-scale spatial associations between functional traits and tree growth
<p>This data set relates to a 40x60 m2 stem-mapped plot that was established in a temperate rainforest of southern Chile. It contains data for each individual stem located within the plot. Each individual is characterized by a species code, diameter at breast height (dbh, 1.35 m), diameter at coring height (dch, ca. 30 cm), x and y coordinates, basal area index of the last 10 years (bai, cm2), and growth efficiency (ge, cm2/cm2).</p>
Spatial scale-dependent dilution effects of biodiversity on plant diseases in grasslands
<p>This study was conducted at the Gansu Gannan Grassland Ecosystem National Observation and Research Station of Lanzhou University (33°40'N, 101°52'E, 3540 m a.s.l.), which is located on the eastern edge of the Qinghai-Tibetan Plateau. </p>
Data to reproduce the results presented in Lake et al. 2023. Science of The Total Environment, https://doi.org/10.1016/j.scitotenv.2023.162332 ("Use of a submersible spectrophotometer probe to fingerprint spatial suspended sediment sources at catchment scale")
<p>This repository contains the absorbance data measured on the water samples collected in all sampling sites, for the three campaigns, as described in Lake et al., 2023. </p> <p>Data consists of:</p> <p>- Absorbance data compensated for measured concentration and compensated for absorbance measured on filtered water </p> <p>- Absorbance data compensated for measured concentration</p> <p>Shown files are the input files for the MixSIAR modelling exercise as described in Lake et al., 2023.</p>
Micro-scale spatial preference and temporal cyclicity linked to foraging in harbour porpoises
<p><span>Habitat heterogeneity is a crucial driver for species distribution across scales</span><span>. Harbour porpoise <em>Phocoena phocoena</em> basin-wide distribution is linked to prey availability, and small-scale (kilometres to tens of kilometres) differences in distribution are prevalent. However, information on porpoise distribution and foraging-behaviour variations on a micro-scale (hundred meters to kilometres) is limited. To monitor harbour porpoise distribution and foraging activity on a micro-scale we deployed passive acoustic dataloggers, logging porpoise acoustic activity at six sites in a small, high porpoise-density area in southern Sweden. Data were collected for almost a year, giving detailed time series on porpoise activity. The time series were analysed using dynamic time warping to compare activity patterns between sites.</span><span> La</span><span>rge </span><span>differences were found between sites separated by only a few hundred meters, indicating micro-scale spatial preference. Spectral analysis for temporal cyclicity in activity revealed a dominant peak for 24-hour cycles with higher activity during the night for all sites. All sites also had a second peak for 29.5 days, linked to the lunar cycle with higher activity during the full moon. Activity was overall highest during autumn and winter (September–December). Spatial and temporal patterns were linked to foraging, showing a positive correlation between porpoise presence and the percent of time present with detected foraging. The study demonstrates that harbour porpoise spatial distribution on a micro-scale should be considered in e.g. behavioural, management, and conservation studies and actions. In addition, we show that </span><span>time series statistical methodology, such as dynamic time warping and spectral analysis, are informative and appropriate for analysis of acoustic temporal data. </span></p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.