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495 results for “spatial scale”
Urbanisation lowers great tit (Parus major) breeding success at multiple spatial scales
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Data from: Differential divergence in autosomes and sex chromosomes is associated with intra-island diversification at a very small spatial scale in a songbird lineage
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The limited spatial scale of dispersal in soil arthropods revealed with whole-community haplotype-level metabarcoding
<p>Soil mesofauna communities are hyperdiverse and critical for ecosystem functioning. However, our knowledge on spatial structure and underlying processes of community assembly for soil arthropods is scarce, hampered by limited empirical data on species diversity and turnover. We implement a high-throughput-sequencing approach to generate comparative data for thousands of arthropods at three hierarchical levels: genetic, species and supra-specific lineages. A joint analysis of the spatial arrangement across these levels can reveal the predominant processes driving the variation in biological assemblages at the local scale. This multi-hierarchical approach was performed using <span>haplotype-level-COI metabarcoding</span> of entire communities of mites, springtails and beetles from three Iberian mountain regions. Tens of thousands of specimens were extracted from deep and superficial soil layers and produced comparative phylogeographic data for >1000 co-distributed species and nearly 3000 haplotypes. Local assemblages were highly distinctive between grasslands and forests, and within each of them showed strong spatial structures and high endemicity at the scale of a few kilometres or less. The local distance-decay patterns were self-similar for the haplotypes and higher hierarchical entities, and this fractal structure was very similar in all three regions, pointing to a significant role of dispersal limitation driving the local-scale community assembly. Our results from whole-community metabarcoding provide insight into how dispersal limitations constrain mesofauna community structure within local spatial settings over evolutionary timescales. If generalized across wider areas, the high turnover and endemicity in the soil locally may indicate extremely high richness globally, challenging our current estimations of total arthropod-diversity on Earth.</p>
Anuran accents: Continental-scale citizen science data reveal spatial and temporal patterns of call variability
<p>Data and code associated with the 2020 publication in Ecology and Evolution (doi:10.1002/ece3.6833).</p>
The diversification and evolution of niche breadth across spatial scales in western North American monkeyflowers
<p><span>Species show remarkable variation in ecological niche breadth, but the directionality of niche breadth evolution remains a question for niche axes across spatial scales. Testing the association between niche breadth evolution and the process of diversification could shed light on the role of ecology in the formation and maintenance of biodiversity. Here we applied Cladogenetic State change Speciation and Extinction models in western North American monkeyflowers (</span><em>Mimulus</em><span> sensu lato), with two states of niche breadth (generalist and specialist). We aimed to estimate the effects of niche breadth along broad-scale bioclimatic and local-scale microhabitat axes on diversification rate, and the evolutionary trend and mode of niche breadth. We found opposite patterns across spatial scales, with higher speciation rates detected for generalists along broad-scale bioclimatic axes and for specialists along local-scale microhabitat axes. Furthermore, we found weak trends towards specialization for bioclimatic niche breadth, but generalization for microhabitat niche breadth. Both cladogenetic and anagenetic changes were comparable and thus important in the evolution of niche breadth in this group. Together, these findings suggest that the underlying mechanisms of niche breadth evolution might differ across spatial scales, and that change in niche breadth could be tightly associated with the diversification process.</span></p>
Climate drives community-wide divergence within species over a limited spatial scale: evidence from an oceanic island
<p><span>Geographic isolation substantially contributes to species endemism on oceanic islands when speciation involves the colonisation of a new island. However, less is understood about the drivers of speciation within islands. What is lacking is a general understanding of the geographic scale of gene flow limitation within islands, and thus the geographic scale and drivers of geographical speciation within insular contexts. Using a community of beetle species, we show that when dispersal ability and climate tolerance are restricted, microclimatic variation over distances of only a few kilometres can maintain strong geographic isolation and drive incipient speciation. Further to this, we demonstrate congruent diversification with gene flow across species, mediated by Quaternary climate oscillations that have facilitated a dynamic of isolation and secondary contact. The unprecedented scale of parallel species responses to a common environmental driver for evolutionary change has profound consequences for understanding past and future species responses to climate variation.</span></p>
Trait-similarity and trait-hierarchy jointly determine fine-scale spatial associations of resident and invasive ant species
<p>Interspecific competition, a dominant process structuring ecological communities, is influenced by species' phenotypic differences. Limiting similarity theory holds that species with similar traits should compete intensely ("trait-similarity"). In contrast, competing theories including modern coexistence theory emphasize that species with traits conferring competitive advantages should outcompete others ("trait-hierarchy"). Either or both of these mechanisms may drive competitive exclusion, but their relative importance and interacting effects are rarely studied. Here, we explore empirically whether trait-similarity and trait-hierarchy can explain fine-scale spatial associations observed between invasive and native ant species in a tropical assemblage. We find that pairwise co-occurrences between the invasive red imported fire ant Solenopsis invicta and 28 other species across relatively homogenous grasslands can be explained largely by an interaction of trait-similarity and trait-hierarchy in a single morphological trait, relative pronotum width. Specifically, higher trait-hierarchy values are associated with negative co-occurrences; however, these effects are counteracted when species are increasingly dissimilar in their trait ranges. These findings are consistent with the notion that limiting similarity and competitive hierarchies are interactive rather than discrete mechanisms driving competitive exclusion.</p>
Data from: Metacommunity structure of stream insects across three hierarchical spatial scales
<p>A major challenge in community ecology is to understand the underlying factors driving metacommunity (i.e. a set of local communities connected through species dispersal) dynamics. However, little is known about the effects of varying spatial scale on the relative importance of environmental and spatial (i.e. dispersal related) factors in shaping metacommunities and on the relevance of different dispersal pathways. Using a hierarchy of insect metacommunities at three spatial scales (a small, within-stream scale, intermediate, among-stream scale, and large, among-sub-basin scale), we assessed whether the relative importance of environmental and spatial factors shaping metacommunity structure varies predictably across spatial scales, and tested how the importance of different dispersal routes vary across spatial scales. We also studied if different dispersal ability groups differ in the balance between environmental and spatial control. Variation partitioning showed that environmental factors relative to spatial factors were more important for community composition at the within-stream scale. In contrast, spatial factors (i.e. eigenvectors from Moran's eigenvector maps) relative to environmental factors were more important at the among-sub-basin scale. These results indicate that environmental filtering is likely to be more important at the smallest scale with highest connectivity, while dispersal limitation seems to be more important at the largest scale with lowest connectivity. Community variation at the among-stream and among-sub-basin scales were strongly explained by geographical and topographical distances, indicating that overland pathways might be the main dispersal route at the larger scales among more isolated sites. The relative effect of environmental and spatial factors on insect communities varied between low and high dispersal ability groups; this variation was inconsistent among three hierarchical scales. In sum, our study indicates that spatial scale, connectivity and dispersal ability jointly shape stream metacommunities.</p>
Data from: Revised time scales of RNA virus evolution based on spatial information
The time scales of pathogen evolution are of major concern in the context of public and veterinary health, epidemiology and evolutionary biology. Dating the emergence of a pathogen often relies on estimates of evolutionary rates derived from nucleotide sequence data. For many viruses, this has yielded estimates of evolutionary origins only a few hundred years in the past. Here we demonstrate through the incorporation of geographic information from virus sampling that evolutionary age estimates of two European hantaviruses are severely underestimated because of pervasive mutational saturation of nucleotide sequences. We detected very strong relationships between spatial distance and genetic divergence for both Puumala and Tula hantavirus – irrespective whether nucleotide or derived amino acid sequences were analyzed. Extrapolations from these relationships dated the emergence of these viruses most conservatively to at least 3,700 and 2,500 years ago, respectively. Our minimum estimates for the age of these hantaviruses are ten to a hundred times older than results from current non-spatial methods and in much better accordance with the biogeography of these viruses and their respective hosts. Spatial information can thus provide valuable insights on the deeper time scales of pathogen evolution and improve our understanding of disease emergence.
Data from: The challenges that spatial context present for synthesizing community ecology across scales
Accurately characterizing spatial patterns on landscapes is necessary to understand the processes that generate biodiversity, a problem that has applications in ecological theory, conservation planning, ecosystem restoration, and ecosystem management. However, the measurement of biodiversity patterns and the ecological and evolutionary processes that underlie those patterns is highly dependent on the study unit size, boundary placement, and number of observations. These issues, together known as the modifiable areal unit problem, are well known in geography. These factors limit the degree to which results from different metacommunity and macro-ecological studies can be compared to draw new inferences, and yet these types of comparisons are widespread in community ecology. Using aquatic community datasets, we demonstrate that spatial context drives analytical results when landscapes are sub-divided. Next, we present a framework for using resampling and neighborhood smoothing to standardize datasets to allow for inferential comparisons. We then provide examples for how addressing these issues enhances our ability to understand the processes shaping ecological communities at landscape scales and allows for informative meta-analytical synthesis. We conclude by calling for greater recognition of issues derived from the modifiable areal unit problem in community ecology, discuss implications of the problem for interpreting the existing literature, and identify tools and approaches for future research.
Data from: Morphological variability in propagules of a desert annual as a function of rainfall patterns at different temporal and spatial scales
1.Organisms living in highly variable environments have to display integrated strategies to deal with both systematic and random variation occurring at different temporal and spatial scales. Two predictions were tested by analysing geographic-scale patterns of seed size and seed retention (serotiny) in Chorizanthe rigida, a strict winter desert annual that delays seed dispersal and releases propagules after rainfall events: (a) Adaptation to systematic environmental cues occurs by means of changes in morphology, and (b) within-individual variation in seed size allows a differential response to rainfall cues: while some seeds germinate rapidly others are retained for future rainfall events. 2.We quantified morphological variation and performed germination experiments on C. rigida propagules (involucres + achenes) from six populations distributed throughout the Mojave and Sonoran deserts covering: (a) a systematic, west-to-east, winter-to-bi-seasonal (summer and winter) precipitation gradient, and (b) a winter-rain unpredictability gradient inferred from long-term climatic data. 3.The propagule retention structure (i.e., base area of the pedicel) of C. rigida individuals experiencing bi-seasonal rainfall are double the size of those that have evolved under a strict winter rainfall regime, showing that populations living in bi-seasonal environments have higher seed retention which allows them to avoid releasing seeds to a summer rainfall cue. 4.Within-individual variance of propagule size varied significantly between populations and was correlated with winter rainfall variability in each site. 5.Germination varied as a function of propagule size; smaller seeds germinated more readily than larger seeds. Increased variability in propagule size might result in a more variable germination response. 6.Under common experimental conditions germination varied significantly among sites and was negatively correlated with mean winter effective precipitation, suggesting that propagules from populations in drier sites have lower germination moisture thresholds. 7.Synthesis. C. rigida propagules have larger bases in deserts with biseasonal rainfall, which allows them to avoid seed release during summer rainfall cues, and display within-individual seed variance associated to rainfall unpredictability, a trait often interpreted as a bet-hedging strategy. Our study provides empirical evidence of an integrated strategy that allows to cope with both random and systematic rainfall variation.
At what spatial scale(s) do mammals respond to urbanization?
<p>Spatial scale is fundamental in understanding species-landscape relationships because species' responses to landscape characteristics typically vary across scales. Nonetheless, such scales are often unidentified or unreliably predicted by theory. Many landscapes worldwide are urbanizing, yet the spatial scaling of species' responses to urbanization is poorly understood. We investigated the spatial scaling of urbanization effects on a community of 15 mammal species using ~ 60,000 wildlife detections collected from a constellation of 207 camera traps across an extensive urban park system. We embedded a bivariate Gaussian kernel in hierarchical multi-species models to determine two scales of effect (a scale of maximal effect and a broader scale of cumulative landscape effect) for two biological responses (occupancy and site visit frequency) across two seasons (winter and summer) for each species. We then assessed whether scales of effect varied according to theoretical predictions associated with biological responses and species traits (body size and mobility). Scales of effect ranged from < 50 m to > 9,000 m and varied among species, but not as predicted by theory. Species' occupancy generally showed a weak response to urbanization and the scale of this effect was both highly uncertain and consistent across species. We did not detect any relationship between scales of effect and species' body size or mobility, nor was there any evident pattern of scaling across biological response or seasons. These results imply that 1) urbanization effects on mammals manifest across a very broad spectrum of spatial scales, and 2) current theories that a priori predict the scale at which urbanization affects mammals may be of limited use within a given system. Overall, this study suggests that developing general theory regarding the scaling of species-landscape relationships requires additional empirical work conducted across multiple species, systems, and timescales.</p>
Data from: Identifying biases at different spatial and temporal scales of diversification: a case study in the Neotropical parrotlet genus Forpus
The temporal origins of the extraordinary biodiversity of the Neotropical region are highly debated. Recent empirical work has found support for alternative models on the tempo of speciation in Neotropical species further fuelling the debate. However, relationships within many Neotropical lineages are poorly understood and it is unclear how this uncertainty impacts inferences on the evolution of taxa in the region. We examined the robustness of diversification patterns in the avian genus Forpus by testing whether the use of different units of biodiversity (i.e. biological species and statistically inferred species) impacted diversification rates and inferences regarding important biogeographic breaks in the genus. We found that the best-fit model of diversification for the biological species data set was a declining rate of diversification; whereas a model of constant diversification was the best-fit model for statistically inferred species or subspecies. Moreover, the relative importance of different landscape features in delimiting genetic structure across the landscape varied across data sets with differing units of biodiversity. Patterns based on divergence times among biological species indicated old speciation events across major geographic and river barriers, in contrast, data sets more inclusive of the diversity in Forpus illustrate the role of both old divergence across major landscape features as well as more recent divergences that are possibly attributed to Pleistocene climatic changes. Overall, these results indicate that conflicting models on the temporal origins of Neotropical birds may be attributable to sampling biases.
Data from: Shape up or ship out: migratory behaviour predicts morphology across spatial scale in a freshwater fish
1. Migration is a widespread phenomenon, with powerful ecological and evolutionary consequences. Morphological adaptations to reduce the energetic costs associated with migratory transport are commonly documented for migratory species. However, few studies have investigated whether variation in body morphology can be explained by variation in migratory strategy within a species. 2. We address this question in roach Rutilus rutilus, a partially migratory freshwater fish that migrates from lakes into streams during winter. We both compare body shape between populations that differ in migratory opportunity (open vs. closed lakes), and between individuals from a single population that vary in migratory propensity (migrants and residents from a partially migratory population). Following hydrodynamic theory, we posit that migrants should have a more shallow body depth, to reduce the costs associated with migrating into streams with higher flow conditions than the lakes the residents occupy all year round. 3. We find evidence both across and within populations to support our prediction, with individuals from open lakes and migrants from the partially migratory population having a more slender, shallow-bodied morphology than fish from closed lakes and all-year residents. 4. Our data suggest that a shallow body morphology is beneficial to migratory individuals and our study is one of the first to link migratory strategy and intraspecific variation in body shape.
Data from: Stable coexistence of genetically divergent Atlantic cod ecotypes at multiple spatial scales
Coexistence in the same habitat of closely related yet genetically different populations is a phenomenon that challenges our understanding of local population structure and adaptation. Identifying the underlying mechanisms for such coexistence can yield new insight into adaptive evolution, diversification, and the potential for organisms to adapt and persist in response to a changing environment. Recent studies have documented cryptic, sympatric populations of Atlantic cod (Gadus morhua) in coastal areas. We analyzed genetic origin of 6483 individual cod sampled annually over 14 years from 125 locations along the Norwegian Skagerrak coast and document stable coexistence of two genetically divergent Atlantic cod ecotypes throughout the study area and study period. A 'fjord' ecotype dominated in numbers deep inside fjords while a 'North Sea' ecotype was the only type found in offshore North Sea. Both ecotypes coexisted in similar proportions throughout coastal habitats at all spatial scales. The size-at-age of the North Sea ecotype on average exceeded that of the fjord ecotype by 20% in length and 80% in weight across all habitats. Different growth and size among individuals of the two types might be one of several ecologically significant variables that allow for stable coexistence of closely related populations within the same habitat. Management plans, biodiversity initiatives, and other mitigation strategies that do not account for the mixture of species ecotypes are unlikely to meet objectives related to the sustainability of fish and fisheries.
Data from: Large-scale functional networks identified from resting-state EEG using spatial ICA
Several methods have been applied to EEG or MEG signals to detect functional networks. In recent works using MEG/EEG and fMRI data, temporal ICA analysis has been used to extract spatial maps of resting-state networks with or without an atlas-based parcellation of the cortex. Since the links between the fMRI signal and the electromagnetic signals are not fully established, and to avoid any bias, we examined whether EEG alone was able to derive the spatial distribution and temporal characteristics of functional networks. To do so, we propose a two-step original method: 1) An individual multi-frequency data analysis including EEG-based source localisation and spatial independent component analysis, which allowed us to characterize the resting-state networks. 2) A group-level analysis involving a hierarchical clustering procedure to identify reproducible large-scale networks across the population. Compared with large-scale resting-state networks obtained with fMRI, the proposed EEG-based analysis revealed smaller independent networks thanks to the high temporal resolution of EEG, hence hierarchical organization of networks. The comparison showed a substantial overlap between EEG and fMRI networks in motor, premotor, sensory, frontal, and parietal areas. However, there were mismatches between EEG-based and fMRI-based networks in temporal areas, presumably resulting from a poor sensitivity of fMRI in these regions or artefacts in the EEG signals. The proposed method opens the way for studying the high temporal dynamics of networks at the source level thanks to the high temporal resolution of EEG. It would then become possible to study detailed measures of the dynamics of connectivity.
Data from: The Urban Heat Island and its spatial scale dependent impact on survival and development in butterflies of different thermal sensitivity
Climate alteration is one of the most cited ecological consequences of urbanization. However, the magnitude of this impact is likely to vary with spatial scale. We investigated how this alteration affects the biological fitness of insects, which are especially sensitive to ambient conditions and well-suited organisms to study urbanization-related changes in phenotypic traits. We monitored temperature and relative air humidity in wooded sites characterized by different levels of urbanization in the surroundings. Using a split-brood design experiment, we investigated the effect of urbanization at the local (i.e., 200 × 200 m) and landscape (i.e., 3 × 3 km) scale on two key traits of biological fitness in two closely related butterfly species that differ in thermal sensitivity. In line with the Urban Heat Island concept, urbanization led to a 1°C increase in daytime temperature and an 8% decrease in daytime relative humidity at the local scale. The thermophilous species Lasiommata megera responded at the local scale: larval survival increased twofold in urban compared to rural sites. Urbanized sites tended to produce bigger adults, although this was the case for males only. In the woodland species Pararge aegeria, which has recently expanded its ecological niche, we did not observe such a response, neither at the local, nor at the landscape scale. These results demonstrate interspecific differences in urbanization-related phenotypic plasticity and larval survival. We discuss larval pre-adaptations in species of different ecological profiles to urban conditions. Our results also highlight the significance of considering fine-grained spatial scales in urban ecology.
Data from: Local biotic environment shapes the spatial scale of bacteriophage adaptation to bacteria
The ecological, epidemiological, and evolutionary consequences of host-parasite interactions are critically shaped by the spatial scale at which parasites adapt to hosts. The scale of interaction between hyperparasites and their parasites is likely to be influenced by the host of the parasite and potentially likely to differ among within-host environments. Here we examine the scale at which bacteriophages adapt to their host bacteria by studying natural isolates from the surface or interior of horse chestnut leaves. We find that phages are more infective to bacteria from the same tree relative to those from other trees but do not differ in infectivity to bacteria from different leaves within the same tree. The results suggest that phages target common bacterial species, including an important plant pathogen, within plant host tissues; this result has important implications for therapeutic phage epidemiology. Furthermore, we show that phages from the leaf interior are more infective to their local hosts than phages from the leaf surface are to theirs, suggesting either increased resistance of bacteria on the leaf surface or increased phage adaptation within the leaf. These results highlight that biotic environment can play a key role in shaping the spatial scale of parasite adaptation and influencing the outcome of coevolutionary interactions.
Data from: Changeable camouflage: how well can flounder resemble the colour and spatial scale of substrates in their natural habitats?
Flounder change colour and pattern for camouflage. We used a spectrometer to measure reflectance spectra and a digital camera to capture body patterns of two flounder species camouflaged on four natural backgrounds of different spatial scale (sand, small gravel, large gravel and rocks). We quantified the degree of spectral match between flounder and background relative to the situation of perfect camouflage in which flounder and background were assumed to have identical spectral distribution. Computations were carried out for three biologically relevant observers: monochromatic squid, dichromatic crab and trichromatic guitarfish. Our computations present a new approach to analysing datasets with multiple spectra that have large variance. Furthermore, to investigate the spatial match between flounder and background, images of flounder patterns were analysed using a custom program originally developed to study cuttlefish camouflage. Our results show that all flounder and background spectra fall within the same colour gamut and that, in terms of different observer visual systems, flounder matched most substrates in luminance and colour contrast. Flounder matched the spatial scales of all substrates except for rocks. We discuss findings in terms of flounder biology; furthermore, we discuss our methodology in light of hyperspectral technologies that combine high-resolution spectral and spatial imaging.
Data from: Life history determines biogeographical patterns of soil bacterial communities over multiple spatial scales
The extent to which the distribution of soil bacteria is controlled by local environment versus spatial factors (e.g., dispersal, colonisation limitation, evolutionary events) is poorly understood and widely debated. Our understanding of biogeographic controls in microbial communities is likely hampered by the enormous environmental variability encountered across spatial scales and the broad diversity of microbial life histories. Here we constrained environmental factors (soil chemistry, climate, above-ground plant community) to investigate the specific influence of space, by fitting all other variables first, on bacterial communities in soils over distances from m to 102 km. We found strong evidence for a spatial component to bacterial community structure that varies with scale and organism life history (dispersal and survival ability). Geographic distance had no influence over community structure for organisms known to have survival stages, but the converse was true for organisms thought to be less hardy. Community function (substrate utilisation) was also shown to be highly correlated to community structure, but not to abiotic factors, suggesting non-stochastic determinants of community structure are important Our results support the view that bacterial soil communities are constrained by both edaphic factors and geographic distance, and further show that the relative importance of such constraints depends critically on the taxonomic resolution used to evaluate spatio-temporal patterns of microbial diversity, as well as life-history of the groups being investigated, much as is the case for macro-organisms.
ScienceDex guides
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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.