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358 results for “fine-scale”
Accounting for behaviour in fine-scale habitat selection: a case study highlighting methodological intricacies
<p>Data for the article “Accounting for behaviour in fine-scale habitat selection: a case study highlighting methodological intricacies”</p> <p>By LT Beumer, NMS Schmidt, J Pohle, J Signer, M Chimienti, JP Desforges, LH Hansen, SH Pedersen, DA Rudd, M Stelvig, FM van Beest</p> <p>The data set includes five files: A readme file describing the data files, and four data files accompanying the above publication.</p> <p>For further queries please contact Larissa T. Beumer: ltbeumer@gmail.com</p> <p> </p>
Environmental DNA reveals fine-scale habitat associations for sedentary and resident marine species across a coastal mosaic of soft and hard-bottom habitats
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Beneath the Antarctic sea-ice: Fine-scale analysis of Weddell seal (Leptonychotes weddellii) behaviour and predator-prey interactions, using micro-sonar data in Terre Adélie
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Fine-scale variation in soil properties promotes local taxonomic diversity of hybridizing oak species (Quercus spp.)
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Broad-scale patterns of geographic avoidance between species emerge in the absence of fine-scale mechanisms of coexistence
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Data from: Defaunation increases clustering and fine-scale spatial genetic structure in a small-seeded palm despite remaining small-bodied frugivores
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Fine-scale changes in speed and altitude suggest protean movements in homing pigeon flights
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Data from: Fine-scale reconstruction of pelagic fish migration by iso-logging of eye lens
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Large differences in herbivore performance emerge from simple herbivore behaviors and fine-scale spatial heterogeneity in phytochemistry
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Data from: Foundation species promote local adaptation and fine-scale distribution of herbaceous plants
<p><span><span><span>1) Interactions among neighbors can alter demography and traits of commingled species via adaptation or plasticity in phenotypic expression and understanding these two mechanisms in diverse communities is important for determining the ecological and evolutionary consequences of plant–plant interactions. </span></span></span></p> <p><span><span><span>2) We reciprocally transplanted perennial species (<i>Arenaria armerina</i> and <i>Festuca indigesta</i>) among patches of two foundation shrub species and open ground to assess whether origin microsite (defined as the spatially distinct abiotic and biotic conditions associated with the two shrubs and open ground) determines germination, recruitment and growth that, in turn, promotes fine-scale distribution of species among microsites. In addition, we tested the effect of origin microsite on traits, competitive ability, drought tolerance and outlier loci to assess whether origin microsite conditions drove differences in traits, strategies and adaptive loci.</span></span></span></p> <p><span><span><span>3) Germination was consistently greater for seeds planted back into their origin microsite relative to seeds sourced from foreign microsites, although this effect was weakened for recruitment. Plant growth was best in open sites regardless of origin microsite. In the greenhouse, <i>A.</i> <i>armerina</i> had conserved traits within origin microsite but distinct trait values among microsite conditions, specifically for plants originating from the most productive microsite (e.g. sufficient light and high nutrients and water availability). <i>Festuca indigesta</i> had conserved trait responses among microsites while within microsite, individuals had significant trait plasticity to different environmental conditions. The combined field and greenhouse results suggest that fine-scale distributions are supported by local adaptation among microsites of <i>A.</i> <i>armerina </i>and phenotypic plasticity of <i>F.</i> <i>indigesta</i>.</span></span></span></p> <p><span><span><span><i>Synthesis </i>Adaptation or plasticity in phenotypic expression have different implications for demographic rate and persistence of species in changing environments. Local adaptation to neighbors suggests that reductions in foundation species diversity could concomitantly lead to reduced genetic diversity of commingled species while a plastic response indicates a more robust and broad response to changing climatic and biotic conditions.</span></span></span></p>
Fine-scale habitat heterogeneity influences browsing damage by elephant and giraffe
Effects of large mammalian herbivores on woody vegetation tend to be heterogeneous in space and time, but the factors that drive such heterogeneity are poorly understood. We examined the influence of fine-scale habitat heterogeneity on the distribution and browsing effects of two of the largest African terrestrial mammals, the elephant and giraffe. We conducted this study within a 120-ha (500 x 2400 m) ForestGEO long-term vegetation monitoring plot located at Mpala Research Center, Kenya. The plot traverses three distinct topographic habitats ('plateau', 'steep slopes', and 'valley') with contrasting elevation, slope, soil properties, and vegetation composition. To quantify browsing damage, we focused on Acacia mellifera, a palatable tree species that occurs across the three habitat categories. Overall tree density, species richness, and diversity was highest on the steep slopes and lowest on the plateau. Acacia mellifera trees were tallest and had the lowest number of stems per tree on the steep slopes. Both elephant and giraffe avoided the steep slopes and their activity was higher during the wet season than during the dry season. Browsing damage on Acacia mellifera was lowest on the steep slopes. Elephant browsing damage was highest in the valley whereas giraffe browsing damage was highest on the plateau. Our findings suggest that fine-scale habitat heterogeneity is an important factor in predicting the distribution of large herbivores and their effects on vegetation and may interact with other drivers such as edaphic variations to influence local variation in vegetation structure and composition.
Data from: Genome-wide diversity and habitat underlie fine-scale phenotypic differentiation in the rainbow darter (Etheostoma caeruleum)
<p>Adaptation to environmental change requires that populations harbor the necessary genetic variation to respond to selection. However, dispersal-limited species with fragmented populations and reduced genetic diversity may lack this variation and are at an increased risk of local extinction. In freshwater fish species, environmental change in the form of increased stream temperatures places many cold-water species at-risk. We present a study of rainbow darters (<i>Etheostoma caeruleum</i>) in which we evaluated the importance of genetic variation on adaptive potential and determined responses to extreme thermal stress. We compared fine-scale patterns of morphological and thermal tolerance differentiation across eight sites, including a unique lake habitat. We also inferred contemporary population structure using genomic data and characterized the relationship between individual genetic diversity and stress tolerance. We found site-specific variation in thermal tolerance that generally matched local conditions and morphological differences associated with lake-stream divergence. We detected patterns of population structure on a highly local spatial scale that could not be explained by isolation by distance or stream connectivity. Finally, we showed that individual thermal tolerance was positively correlated with genetic variation, suggesting that sites with increased genetic diversity may be better at tolerating novel stress. Our results highlight the importance of considering intraspecific variation in understanding population vulnerability and stress response.</p>
Fine-scale empirical data on niche divergence and homeolog expression patterns in an allopolyploid and its diploid progenitor species
<ul> <li>Polyploidization is pervasive in plants, but little is known about the niche divergence of wild allopolyploids (species that harbor polyploid genomes originating from different diploid species) relative to their diploid progenitor species and the gene expression patterns that may underlie such ecological divergence. We conducted a fine-scale empirical study on habitat and gene expression of an allopolyploid and its diploid progenitors.</li> <li> We quantified soil properties and light availability of habitats of an allotetraploid <i>Cardamine flexuosa</i> and its diploid progenitors <i>C. amara</i> and <i>C. hirsuta</i> in two seasons. We analyzed expression patterns of genes and homeologs (homeologous gene copies in allopolyploids) using RNA-seq.</li> <li>We detected niche divergence between the allopolyploid and its diploid progenitors along water availability gradient at a fine scale: the diploids in opposite extremes and the allopolyploid in a broader range between diploids, with limited overlap with diploids at both ends. Most of the genes whose homeolog expression ratio changed among habitats in <i>C. flexuosa</i> varied spatially and temporally. </li> <li>These findings provide empirical evidence for niche divergence between an allopolyploid and its diploid progenitor species at a fine scale and suggest that divergent expression patterns of homeologs in an allopolyploid may underlie its persistence in diverse habitats.</li> </ul>
Fine-scale habitat heterogeneity favours the coexistence of supergene-controlled social forms in Formica selysi
<p><b>Background:</b> Social insects vary widely in social organization, yet the genetical and ecological factors influencing this variation remain poorly known. In particular, whether spatially varying selection influences the maintenance of social polymorphisms in ants has been rarely investigated. To fill this gap, we examined whether fine-scale habitat heterogeneity contributes to the co-existence of alternative forms of social organization within populations. Single-queen colonies (monogyne social form) are generally associated with better colonization abilities, whereas multiple-queen colonies (polygyne social form) are predicted to be better competitors and monopolize saturated habitats. We hypothesize that each social form colonizes and thrives in distinct local habitats, as a result of their alternative dispersal and colony founding strategies. Here, we test this hypothesis in the Alpine silver ant, in which a supergene controls polymorphic social organization.</p> <p><b>Results:</b> Monogyne and polygyne colonies predominate in distinct habitats of the same population. The analysis of 59 sampling plots distributed across six habitats revealed that single-queen colonies mostly occupy unconnected habitats that were most likely reached by flight. This includes young habitats isolated by water and old habitats isolated by vegetation. In contrast, multiple-queen colonies were abundant in young, continuous and saturated habitats. Hence, alternative social forms colonize and monopolize distinct niches at a very local scale.</p> <p><b>Conclusions:</b> Alternative social forms colonized and monopolized different local habitats, in accordance with differences in colonization and competition abilities. The monogyne social form displays a colonizer phenotype, by efficiently occupying empty habitats, while the polygyne social form exhibits a competitor phenotype, thriving in saturated habitats. The combination of the two phenotypes, coupled with fine-scale habitat heterogeneity, may allow the coexistence of alternative social forms within populations. Overall, these results suggest that spatially varying selection may be one of the mechanisms contributing to the maintenance of genetic polymorphisms in social organization.</p>
Data from: Fine-scale genetic structure due to adaptive divergence among microhabitats
It has been suggested that adaptive evolution on ecological timescales shapes communities. However, adaptation among environments relies on isolation or large selection coefficients that exceed migration effects. This reliance is tempered if adaptation is polygenic—does not depend on one allele completely replacing another but instead requires small allele frequency changes at many loci. Thus, whether individuals can evolve adaptation to fine-scale habitat variation (for example, microhabitats) is not resolved. Here we analyze the genetic divergence of the teleost fish, Fundulus heteroclitus, among microhabitats that are <200 m apart in three separate saltmarshes using 4741 single-nucleotide polymorphisms (SNPs). Among these SNPs, 1.3–2.3% have large and highly significant differences among microhabitats (mean FST=0.15; false discovery rate less than or equal to1%). The divergence among microhabitats for these outlier SNPs is larger than that among populations, exceeds neutral expectation and indicates surprising population structure among microhabitats. Thus, we suggest that polygenic selection is surprisingly effective in altering allele frequencies among many different SNPs that share similar biological functions in response to environmental and ecological differences over very small geographic distances. We acknowledge the evolutionary difficulty of large genetic divergence among well-connected habitats. Therefore, these studies are only the first step to discern whether natural selection is responsible and capable of effecting genetic divergence on such a fine scale.
Data from: Ecological differentiation facilitates fine-scale coexistence of sexual and asexual Boechera
Premise of the study: Ecological differentiation (ED) between sexual and asexual organisms may permit the maintenance of reproductive polymorphism. Several studies of sexual/asexual ED in plants have shown that the geographic ranges of asexuals extend beyond those of sexuals, often in areas of higher latitude or elevation. But very little is known about ED at fine scales, wherein coexistence of sexuals and asexuals may be permitted by differential niche occupation. Methods: We used 149 populations of sexual and apomictic lineages in the genus Boechera (rock cress) collected across a portion of this mustard's vast range. We characterized reproductive mode, ploidy, and species identity or hybrid parentage of each individual, and then used a multi-pronged statistical approach to 1) identify ED between sexuals and asexuals; 2) investigate the impacts of two confounding factors, polyploidy and hybridization, on ED; and 3) determine the environmental variables underlying ED. Key results: We found that sexuals and asexuals are significantly ecologically differentiated across the landscape, despite fine-scale interdigitation of these two reproductive forms. Asexual reproduction was strongly associated with greater disturbance, reduced slope, and greater environmental variability. Although ploidy had little effect on the patterns observed, hybridization has a unique impact on the relationships between asexual reproduction and specific environmental variables. Conclusions: Ecological differentiation along the axes of disturbance, slope, and climatic variability, as well as the effects of heterozygosity, may contribute to the maintenance of sexuality and asexuality across the landscape, ultimately impacting the establishment and spread of asexual lineages.
Data from: Habitat structure modifies microclimate: an approach for mapping fine-scale thermal refuge
1. Contemporary techniques predicting habitat suitability under climate change projections often underestimate availability of thermal refuges. Habitat structure contributes to thermal heterogeneity at a variety of spatial scales, but quantifying microclimates at organism‐relevant resolutions remains a challenge. Landscapes that appear homogeneous at large scales may offer patchily distributed thermal refuges at finer scales. 2. We quantified the relationship between vegetation structure and the thermal environment at a scale relevant to small, terrestrial animals using a new approach for mapping fine‐scale thermal heterogeneity. We expected that vegetation would create attenuated microclimates and that the influence of vegetation structure would vary seasonally. We measured shrub volume, horizontal cover, and operative temperature (Te) in a sagebrush‐steppe habitat in Idaho, USA, at 534 microsites across two study sites of approximately 1 km2 each. We modeled relationships between habitat structure and both mean daily maximum temperature (urn:x-wiley:2041210X:media:mee313008:mee313008-math-0001max) and mean diurnal temperature range (urn:x-wiley:2041210X:media:mee313008:mee313008-math-0002) for each study site during summer and winter. Aerial imagery from unmanned aerial systems was used to estimate shrub volume and canopy cover at 1‐m resolution, and we applied the best fit model to map thermal heterogeneity across broader extents. 3. Increasing shrub volume and cover was associated with lower urn:x-wiley:2041210X:media:mee313008:mee313008-math-0003max and (urn:x-wiley:2041210X:media:mee313008:mee313008-math-0004, but strengths of the relationships differed between study sites. There was considerable heterogeneity in availability of thermal refuges across sagebrush‐steppe rangelands that have traditionally been considered relatively homogeneous. 4. This technique can help ecologists and land managers identify critical thermal refuges that large‐scale climate modelling can overlook and thus contribute to an understanding of animal‐habitat relationships under changing climates and land uses.
Australian Frog Atlas: Fine-scale species distribution maps informed by the FrogID dataset
<p>This is version three of the Australian Frog Atlas: shapefiles and KML files of the most up to date, accurate and detailed set of Australian frog species distribution maps available, and both a shapefile and detailed PDF map of Australian frog species richness. All of these are available as a free resource under the Creative Commons Attribution (CC-BY) 4.0 License. When using any material from the Australian Frog Atlas, please refer to and cite Cutajar et al. (2022), outlined in full below, which introduces the dataset and describes it in detail.</p> <p>Cutajar. T. P., Portway, C. D., Gillard, G. L., and Rowley, J. J. L. (2022) Australian Frog Atlas: Fine-scale species distribution maps informed by the FrogID dataset. <em>Technical Reports of the Australian Museum Online</em>. 36: 1-48. <a href="https://doi.org/10.3853/j.1835-4211.36.2022.1789">https://doi.org/10.3853/j.1835-4211.36.2022.1789</a></p> <p><strong>Caveat:</strong> The occurrence data used in the development of these maps are from a range of sources. Every effort has been made to ensure accuracy and completeness, including vetting of data using published literature. However, no guarantee is given, nor responsibility taken by the authors or their institutions for errors or omissions, nor in respect of any information or advice given in relation to, or as a consequence of, the maps and data provided herein. These maps are indicative only and aim to capture the known and presumed distributions of individual frog species and frog species richness within Australia. A taxonomic revision of Australo-Papuan tree frogs published in June 2025 proposes the reclassification of more than 120 Australian tree frog species (in the genera <em>Litoria</em> and <em>Cyclorana</em>) into 22 genera. This proposed change has not been adopted in this version of the Australian Frog Atlas. </p> <p> </p> <p> </p>
VCF files and regression analyses for: Assessing fine-scale pondscape connectivity with amphibian eyes: an integrative approach using genomic and capture-mark-recapture data
<p><span>In the face of habitat loss, preserving functional connectivity is essential to maintain genetic diversity and the demographic dynamics required for the viability of biotic communities. This requires knowledge of the dispersal behavior of target species, which can be modeled as kernels, or probability density functions of dispersal distances at increasing geographic distances. We present an integrative approach to investigate the relationships between genetic connectivity and demographic parameters in organisms with low vagility focusing on five syntopic pond-breeding amphibians. We genotyped 1,056 individuals of two anuran and three urodele species (1,732–3,913 SNPs per species) from populations located in a landscape comprising 64 ponds to characterize fine-scale genetic structure in a comparative framework and combined this genetic data with information obtained in a previous two-year capture-mark-recapture (CMR) study. Specifically, we contrasted graphs reconstructed from genomic data with connectivity graphs based on dispersal kernels and demographic information obtained from CMR data from previous studies and assessed the effects of population size, population density, geographical distances, inverse movement probabilities and the presence of habitat patches potentially functioning as stepping stones on genetic differentiation. Our results suggest a significant influence of local population sizes on patterns of genetic connectivity at small spatial scales. In addition, m</span><span>ovement records and cluster-derived kernels provide robust inferences on most likely dispersal paths that are consistent with </span><span>genomic inferences on genetic connectivity. The integration of genetic and CMR data holds great potential for understanding genetic connectivity at spatial scales relevant to individual organisms, with applications for the implementation of management actions at the landscape level. </span></p>
Proximity-sensors on GPS collars reveal fine-scale predator-prey behavior during a predation event: A case study from Scandinavia
<p>Although the advent of high-resolution GPS tracking technology has helped increase our understanding of individual and multi-species behavior in wildlife systems, detecting and recording direct interactions between free-ranging animals remains difficult. In 2023, we deployed GPS collars equipped with proximity sensors (GPS proximity collars) on brown bears (<em>Ursus</em> <em>arctos</em>) and moose (<em>Alces</em> <em>alces</em>) as part of a multi-species interaction study in central Sweden. On 6 June, 2023, a collar on an adult female moose and a collar on an adult male bear triggered on each other's UHF signal and started collecting fine-scale GPS positioning data. The moose collar collected positions every 2 minutes for 89 minutes and the bear collar collected positions every 1 minute for 41 minutes. On 8 June, field personnel visited the site and found a female neonate moose carcass with clear indications of bear bite marks on the head and neck. During the predation event, the bear remained at the carcass while the moose moved back and forth, moving towards the carcass site about 5 times. The moose was observed via drone with 2 calves on 24 May and with only one remaining calf on 9 June. This case study describes, to the best of our knowledge, the first instance of a predation event between two free-ranging, wild species recorded by GPS proximity collars. Both collars successfully triggered and switched to finer-scaled GPS fix rates when the individuals were in close proximity producing detailed movement data for both predator and prey during and after a predation event. We suggest that, combined with standard field methodology, GPS proximity collars placed on free-ranging animals offer the ability for researchers to observe direct interactions between multiple individuals and species in the wild without the need for direct visual observation.</p>
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.