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238 results for “spatial dynamics”
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: Significant genetic boundaries and spatial dynamics of giant pandas occupying fragmented habitat across southwest China
Understanding population history and genetic structure are key drivers of ecological research. Here we studied two highly fragmented and isolated populations (Xiaoxiangling and Daxiangling) of giant pandas (Ailuropoda melanoleuca) at the extreme southwestern edge of their distribution. This area also contains the Dadu River, national road 108 and various human infrastructure and development, providing an ideal region in which we can identify the effects of different barriers on animal movements. We used partial mitochondrial control region (mtDNA) and nine microsatellite loci (nuclear DNA) data derived from 192 fecal and one blood sample collected from the wild. We found 136 genotypes corresponding to 53 unique multilocus genotypes and eight unique control region haplotypes (653 bp). Significant genetic boundaries correlated spatially with the Dadu River (K=2). We estimate that a major divergence took place between these populations 26 000 YBP, at around the similar time the rock surface of valley bottom formed in Dadu River. The national road has resulted in further recent population differentiation (Pairwise FS on mtDNA and nuclear DNA) so that in effect, four smaller sub-populations now exist. Promisingly, we identified two possible first generation migrants and their migration paths, and recommended the immediate construction of a number of corridors. Fortunately, the Chinese government has accepted our advice and is now planning corridor construction.
Data from: Impact of the spatial uncertainty of seed dispersal on tree colonization dynamics in a temperate forest
An aggregated distribution of dispersed seeds may influence the colonization process in tree communities via inflated spatial uncertainty. To evaluate this possibility, we studied 10 tree species in a temperate forest: one primarily barochorous, six anemochorous and two endozoochorous species. A statistical model was developed by combining an empirical seed dispersal kernel with a gamma distribution of seedfall density, with parameters that vary with distance. In the probability density, the fitted models showed that seeds of Fagaceae (primarily barochorous) and Betulaceae (anemochorous) were disseminated locally (i.e., within 60 m of a mother tree), whereas seeds of Acer (anemochorous) and endozoochorous species were transported farther. Greater fecundity compensated for the lower probability of seed dispersal over long distances for some species. Spatial uncertainty in seedfall density was much greater within 60 m of a mother tree than farther away, irrespective of dispersal mode, suggesting that seed dispersal is particularly aggregated in the vicinity of mother trees. Simulation results suggested that such seed dispersal patterns could lead to sites in the vicinity of a tree being occupied by other species that disperse seeds from far away. We speculate that this process could promote coexistence by making the colonization rates of the species more similar on average and equalizing species fitness in this temperate forest community.
Data from: Spatially explicit models of dynamic histories: examination of the genetic consequences of Pleistocene glaciation and recent climate change on the American Pika.
A central goal of phylogeography is to identify and characterize the processes underlying divergence. One of the biggest impediments currently faced is how to capture the spatiotemporal dynamic under which a species evolved. Here we described an approach that couples species distribution models (SDMs), demographic and genetic models in a spatiotemporally explicit manner. Analyses of American Pika (Ochotona priniceps) from the sky islands of the central Rocky Mountains of North America are used to provide insights into key questions about integrative approaches in landscape genetics, population genetics and phylogeography. This includes (i) general issues surrounding the conversion of time-specific SDMs into simple continuous, dynamic landscapes from past to current, and (ii) the utility of SDMs to inform demographic models with deme-specific carrying capacities and migration potentials, as well as (iii) the contribution of the temporal dynamic of colonization history in shaping genetic patterns of contemporary populations. Our results support that the inclusion of a spatiotemporal dynamic is an important factor when studying the impact of distributional shifts on patterns of genetic data. Our results also demonstrate the utility of SDMs to generate species-specific predictions about patterns of genetic variation that account for varying degrees of habitat specialization and life-history characteristics of taxa. Nevertheless, the results highlight some key issues when converting SDMs for use in demographic models. Because the transformations have direct affects on the genetic consequence of population expansion by prescribing how habitat heterogeneity and spatiotemporal variation is related to the species-specific demographic model, it is important to consider alternative transformations when studying the genetic consequences of distributional shifts.
Data from: Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next generation sequencing
The Atlantic bluefin tuna is a highly migratory species emblematic of the challenges associated with shared fisheries management. In an effort to resolve the species' stock dynamics, a genome-wide search for spatially informative single nucleotide polymorphisms (SNPs) was undertaken, by way of sequencing reduced representation libraries. An allele frequency approach to SNP discovery was used, combining the data of 555 larvae and young-of-the-year (LYOY) into pools representing major geographical areas and mapping against a newly assembled genomic reference. From a set of 184,895 candidate loci, 384 were selected for validation using 167 LYOY. A highly discriminatory genotyping panel of 95 SNPs was ultimately developed by selecting loci with the most pronounced differences between western Atlantic and Mediterranean Sea LYOY. The panel was evaluated by genotyping a different set of LYOY (n= 326) and from these 77.8% and 82.1% were correctly assigned to western Atlantic and Mediterranean Sea origins, respectively. The panel revealed temporally persistent differentiation among LYOY from the western Atlantic and Mediterranean Sea (FST = 0.008, p=0.034). The composition of six mixed feeding aggregations in the Atlantic Ocean and Mediterranean Sea was characterized using genotypes from medium (n = 184) and large (n = 48) adults, applying population assignment and mixture analyses. The results provide evidence of persistent population structuring across broad geographic areas and extensive mixing in the Atlantic Ocean, particularly in the mid-Atlantic Bight and Gulf of St. Lawrence. The genomic reference and genotyping tools presented here constitute novel resources useful for future research and conservation efforts.
Figure 4 in Spatial and temporal dynamics of exuberant colour polymorphism in the southern cricket frog
Figure 4. Green (a) and brown (b) dorsal colour morphs of the southern cricket frogs (Acris gryllus). c) Frequency of dorsal colour morphs at two study locations in Georgia, USA (N = 61, Site A; N = 82, Site B). Site A had significantly more green morphs that site B. Both sites had proportionally more brown morphs than green morphs.
Figure 3. a in Spatial and temporal dynamics of exuberant colour polymorphism in the southern cricket frog
Figure 3. a) Principal components loadings from a logistical principal components analysis for each polymorphic trait measured in Acris gryllus using logistical principal components. Points are labelled with each trait, where DPBE = dark patch behind eye, LLUE = light line under eye, DPBF = dark patch behind forelimb, LLIH = light limb inside of hindlimb, 3BUH = presence of three blotches on upper hindlimb, 3BLH = presence of three blotches on lower hindlimb, BlShape = shape of blotch on hindlimbs. b) Principal component scores of principal components 1 and 2, which explained 64.8% of the variance in morph frequency among individuals. Points represent individuals, with colour corresponding to the collecting locality for that individual.
Figure 2. a in Spatial and temporal dynamics of exuberant colour polymorphism in the southern cricket frog
Figure 2. a) The southern cricket frog (Acris gryllus). Frequency of individuals with b) a light line under the eye, c) a light line inside of the hindlimb, d) a circular hindlimb blotch, e) dark patch behind the eye, f) dark patch behind the forelimb, g) three blotches on the upper hindlimb, and h) three blotches on the lower hindlimb across 90 museum specimens. All traits varied significantly among populations except for the light line inside of the hindlimb.
Figure 1 in Spatial and temporal dynamics of exuberant colour polymorphism in the southern cricket frog
Figure 1. Morphological traits that were scored from specimens in a natural history collection. a) upper hindlimb blotches, b) lower hindlimb blotches, c) dark patch behind eye, d) light line under eye, e) dark patch behind the forelimb. The light line inside of the hindlimb is not pictured.
Spatial–temporal dynamics of gesture–speech integration: a simultaneous EEG-fMRI study
<p>The semantic integration between gesture and speech (GSI) is mediated by the left posterior temporal sulcus/middle temporal gyrus (pSTS/MTG) and the left inferior frontal gyrus (IFG). Evidence from electroencephalography (EEG) suggests that oscillations in the alpha and beta bands may support processes at different stages of GSI. In the present study, we investigated the relationship between electrophysiological oscillations and blood-oxygen-level-dependent (BOLD) activity during GSI. In a simultaneous EEG-fMRI study, German participants (n = 19) were presented with videos of an actor either performing meaningful gestures in the context of a comprehensible German (GG) or incomprehensible Russian sentence (GR), or just speaking a German sentence (SG). EEG results revealed reduced alpha and beta power for the GG vs. SG conditions, while fMRI analyses showed BOLD increase in the left pSTS/MTG for GG > GR ∩ GG > SG. In time-window-based EEG-informed fMRI analyses, we further found a positive correlation between single-trial alpha power and BOLD signal in the left pSTS/MTG, the left IFG, and several sub-cortical regions. Moreover, the alpha-pSTS/MTG correlation was observed in an earlier time window in comparison to the alpha-IFG correlation, thus supporting a two-stage processing model of GSI. Our study shows that EEG-informed fMRI implies multiple roles of alpha oscillations during GSI, and that the method is a best candidate for multidimensional investigations on complex cognitive functions such as GSI.</p>
Knowledge-intensive firms, connectivity and spatial restructuring: dynamics and differences in Germany and Switzerland
<p>This dataset is based on the interlocking network model developed by the Globalization and World Cities Study Group (GaWC) at Loughborough University (Taylor 2004). It provides one specific way to address the question how inter‐city relations can be empirically measured despite the chronic lack of data on inter‐city information flows. The model uses a proxy – intra‐firm networks of multi‐branch, multi‐location enterprises – to estimate potential flows of knowledge‐creating information between cities and towns. The method was originally developed to measure the connectivity between global cities based on multi‐branch advanced producer services (APS) firms as they organize business activities across their offices worldwide. In this dataset, the model is adapted to measure relations between functional urban areas (FUAs) within and beyond the German and Swiss space economy, for both APS and High-Tech firms. In contrast to the original methodology, in this dataset the company locations were localized by the exact, georeferenced address, not only on the level of FUAs.</p> <p>The present dataset is created as part of the SNF research project “Knowledge-intensive firms, connectivity<br> and spatial restructuring: dynamics and differences in Germany and Switzerland”.</p>
Spatial structure and dispersal dynamics in a house sparrow metapopulation
<p>1. The effects of spatial structure on metapopulation dynamics depend upon the interaction between local population dynamics and dispersal, and how this relationship is affected by the geographical isolation and spatial heterogeneity in habitat characteristics.</p> <p>2. Our aim is to examine how emigration and immigration of house sparrows, <i>Passer domesticus</i>, in a Norwegian archipelagic metapopulation are affected by key factors predicted by classic metapopulation models to affect dispersal: spatial and temporal variation in population size, inter-island distance, local demography and habitat characteristics.</p> <p>3. This metapopulation can be divided into two major habitat types: (1) islands closer to the mainland where sparrows breed in colonies on farms, and (2) islands without farms, situated farther away from the mainland where sparrows are exposed to harsher environmental conditions.</p> <p>4. Dispersal was spatially structured within the metapopulation; there was proportionally and numerically less emigration and immigration involving farm islands, as compared to non-farm islands. Furthermore, emigration and immigration occurred mostly between nearby islands. Moreover, emigration in response to spatial differences in mean population size differed between the habitat types, but populations with large mean received more immigrants in both habitat types. The number of emigrants and immigrants was negatively related to long-term recruit production, which was not the case in non-farm islands. The proportion and number of emigrants was positively related to temporal increases in recruit production on farm islands, however, not on non-farm islands.</p> <p>5. Our results demonstrate that spatial heterogeneity in environmental conditions influences how spatial variation in long-term mean population size, and temporal and spatial variation in recruit production, affects dispersal dynamics. The spatial structure of this metapopulation is therefore best described by a spatially explicit model in which the exchange of individuals within each habitat type is strongly affected by the degree of geographical isolation, population size and recruit production. However, these relationships differed between the two habitat types, with the non-farm islands showing similarities to a mainland-island model type of structure, whereas dispersal on the farm islands showed features more associated with source-sink or balanced dispersal models. Such differential dispersal dynamics between habitat types is expected to have important consequences for the ecological and evolutionary dynamics within this metapopulation.</p>
Divergent patterns and spatial heterogeneity of soil nutrients in a complex and dynamic savanna landscape
<p>Many grassy ecosystems around the world are experiencing woody encroachment. These woody encroachers often cause nutrient enrichment in the plant-soil environment, potentially facilitating their growth and reproduction. However, studies of encroachment effects on nutrient distributions have been confined to a few major elements (<i>e.g.,</i> N, and P) and limited in spatial extent. We analyzed 19 elements in dominant plants and in georeferenced soils across a subtropical savanna landscape experiencing woody encroachment to quantify their spatial patterns and elucidate drivers responsible for these patterns. We found divergent patterns of spatial heterogeneity of these elements in surface soils across this complex landscape. Nutrient accumulation underneath woody canopies and redistribution by woody plants occurred in a subset of elements (<i>i.e.</i>, N, P, S, Ca, Cu, and Sr). Though some of these elements are not necessarily growth-limiting, they do occur in higher concentrations in woody compared to herbaceous plants. Distributions of the other elements were closely related to spatial variation in soil pH, clay content, and slope rather than to woody encroachment. Our nuanced spatial sampling approach and analysis reveal significant variation in nutrient distributions in response to woody encroachment, and illustrate the role of landscape patterns in mediating ecosystem processes. These changes in the concentrations and distributions of key essential nutrients broaden our understanding of the biogeochemical consequences of woody encroachment, and provide new insights regarding the significance of long-term vegetation dynamics in dryland ecosystems.</p>
Data for: Spatial heterogeneity and infection patterns on epidemic transmission disclosed by a combined contact-dependent dynamics and compartmental model
<p>Epidemics, such as COVID-19, have caused significant harm to human society worldwide. A better understanding of epidemic transmission dynamics can contribute to more efficient prevention and control measures. Compartmental models, which assume homogeneous mixing of the population, have been widely used in the study of epidemic transmission dynamics, while agent-based models rely on a network definition for individuals. In this study, we developed a real-scale contact-dependent dynamic (CDD) model and combined it with the traditional susceptible-exposed-infectious-recovered (SEIR) compartment model. </p>
EMBEDWATCH: Dynamic Root Cause Detection of Spatial Memory Errors in Embedded Systems
<p>Dataset of firmwares used for the experiments of the paper <em>EMBEDWATCH: Dynamic Root Cause Detection of Spatial Memory Errors in Embedded Systems</em></p>
Research data supporting "Dynamic Local Structure in Caesium Lead Iodide: Spatial Correlation and Transient Domains"
<p>This is research data associated with "Dynamic Local Structure in Caesium Lead Iodide: Spatial Correlation and Transient Domains", accepted to Small. </p> <p>The repository contains the trajectories which support the conclusions of the paper, the MLIP parameters, and some additional visualizations.</p>
Spatial and Dynamic Characterization of Brain Activity for Language and Posture (Verticality) During Normal Aging. Magnetoencephalography (MEG) Study (MEG-AGING)
ClinicalTrials.gov study NCT04036162. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Data from: Impact of the spatial uncertainty of seed dispersal on tree colonization dynamics in a temperate forest
Open the record for dataset details and reuse information.
Data from: Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next generation sequencing
Open the record for dataset details and reuse information.
Data from: Seasonal and spatial dynamics of gas ebullition in a temperate water-storage reservoir
Open the record for dataset details and reuse information.
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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.