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7,081 results for “Habitats”
Restored off-channel pond habitats create thermal regime diversity and refuges within a Mediterranean-climate watershed
<p>Cool-water habitats provide increasingly vital refuges for cold-water fish living on the margins of their historical ranges; consequently, efforts to enhance or create cool-water habitat are becoming a major focus of river restoration practices. However, the effectiveness of restoration projects for providing thermal refuge and creating diverse temperature regimes at the watershed scale remains unclear. In the Klamath River in Northern California, the Karuk Tribe Fisheries Program, the Mid-Klamath Watershed Council, and the U.S. Forest Service constructed a series of off-channel ponds that recreate floodplain habitat and support juvenile coho salmon (<em>Oncorhynchus kisutch</em>) and steelhead (<em>Oncorhynchus mykiss</em>) along the Klamath River and its tributaries. We instrumented these ponds and applied multivariate auto-regressive time series models of fine-scale temperature data from ponds, tributaries, and the mainstem Klamath River to assess how off-channel ponds contributed to thermal regime diversity and thermal refuge habitat in the Klamath riverscape. Our analysis demonstrated that ponds provide diverse thermal habitats that are significantly cooler than creek or mainstem river habitats, even during severe drought. Wavelet analysis of long-term (10 years) temperature data indicated that thermal buffering (i.e. dampening of diel variation) increased over time but was disrupted by drought conditions in 2021. Our analysis demonstrates that in certain situations, human-made off-channel ponds can increase thermal diversity in modified riverscapes even during drought conditions, potentially benefiting floodplain-dependent cold-water species. Restoration actions that create and maintain thermal regime diversity and thermal refuges will become an essential tool to conserve biodiversity in climate-sensitive watersheds. </p>
Data from: Digging deeper: habitat selection within the home ranges of a threatened marsupial
<p>While resource selection varies according to the scale and context of study, gathering data representative of multiple scales and contexts can be challenging especially when a species is small, elusive, and threatened. We explore resource selection in a small, nocturnal, threatened species—the greater bilby (<em>Macrotis lagotis</em>)—to test <strong>(a)</strong> which resources best predict bilby occupancy, and <strong>(b) </strong>whether responses are sex-specific and/or vary over time. We tracked a total of 20 bilbies and examined within home range resource selection over multiple seasons in a large (110ha) fenced sanctuary in temperate Australia. We tested a set of plausible models for bilby resource selection, showing that food biomass (terrestrial and subterranean invertebrates, and subterranean plants) and soil textures (% sand, clay and silt) best predicted bilby resource selection for all sampling periods. Selection was also sex-specific; female resource use, relative to males, was more closely linked to the location of high-quality resources (sandier soils, and terrestrial invertebrate biomass). Bilby selection for roads was independent of season but varied over time with females selecting for areas closer to roads when plants increased in density off roads. Our findings demonstrate the importance of considering resource selection over multiple contexts and highlight a method to collect such data on a difficult to study, threatened species. Collecting such data is critical to understanding the habitat required by species.</p>
Data from: Mean landscape-scale incidence of species in discrete habitats is patch size dependent
<p>Contains data and code for the manuscript 'Mean landscape-scale incidence of species in discrete habitats is patch size dependent'.</p> <p>Raw data consist of 202 published datasets collated from primary and secondary (e.g., government technical reports) sources. These sources summarise metacommunity structure for different taxonomic groups (birds, invertebrates, non-avian vertebrates or plants) in different types of discrete metacommunities including 'true' islands (i.e., inland, continental or oceanic archipelagos), habitat islands (e.g., ponds, wetlands, sky islands) and fragments (e.g., forest/woodland or grass/shrubland habitat remnants). </p> <p>The aim of the study was to test whether the size of a habitat patch influences the mean incidences of species within it, relative to the incidence of all species across the landscape. In other words, whether high-incidence (widespread) or low-incidence (narrow-range) species are found more often than expected in smaller or larger patches. To achieve this, a new standardized effect size metric was developed that quantifies the mean observed incidence of all species present in every patch (the geometric mean of the number of patches in which all species were observed) and compares this with an expectation based on re-sampling the incidences of all species in all patches. Meta-regression of the 202 datasets was used to test the relationship between this metric, the 'mean species landscape-scale incidences per patch' (MSLIP), and the size of habitat patches, and for differences in response among metacommunity types and taxonomic groups. </p>
Energy input, habitat heterogeneity, and host specificity on avian haemosporidian diversity at continental scales
<p>The correct identification of biotic and abiotic drivers affecting parasite diversity and assemblage composition at different spatial scales is crucial for understanding how pathogen distribution responds to anthropogenic disturbance and climate change. Here, we used a database of avian haemosporidian parasites to identify such drivers and their effect on the taxonomic and phylogenetic diversity of genera Plasmodium, Haemoproteus, and Leucocytozoon from three zoogeographic regions. We explored how parasite diversity is related to energy input (i.e., temperature, precipitation, and potential evapotranspiration [PET]), to habitat heterogeneity (i.e., climatic seasonality, vegetation density, ecosystem heterogeneity, human disturbance, and host richness), and to a novel assemblage-level metric related to parasite niche overlap (degree of generalism). We found that the relative importance of the predictors differed between the three studied parasite genera and across diversity metrics. Among the most consistent predictors, host richness was positively related to the taxonomic diversity of the three genera. Energy input and human footprint explained the phylogenetic diversity of Haemoproteus. Finally, the degree of generalism explained the diversity of Plasmodium and Leucocytozoon. Our results suggest that different dimensions of haemosporidian diversity are shaped by energy input, host heterogeneity, and assembly processes related to parasite resource use within local parasite assemblages.</p>
Overcoming confusion and stigma in habitat fragmentation research - supplementary data and R code
<p>Data and code necessary to produce results and figures for the manuscript:</p> <p>Riva, Koper and Fahrig (2024). "Overcoming confusion and stigma in habitat fragmentation research". Biol Rev. Accepted conditional on minor revisions. </p>
Major changes in fish thermal habitat diversity in Canada's Arctic lakes due to climate change
<p>Climate warming is a major disruptor of fish community structure globally. We use large-scale geospatial analyses of 447,077 Canadian Arctic lakes to predict how climate change would impact lake thermal habitat diversity across the Arctic landscape. Increases in maximum surface temperature (+2.4–6.7 °C), ice-free period (+14–38 days), and thermal stratification presence (+4.2–18.9%) occur under all climate scenarios. Lakes, currently fishless due to deep winter ice, open up; many thermally uniform lakes become thermally diverse. Resilient coldwater habitat supply is predicted; however, thermally diverse lakes shift from providing almost exclusively coldwater habitat to providing substantial coolwater habitat and previously absent warmwater habitat. Across terrestrial ecozones, most lakes exhibit major shifts in thermal habitat. The prevalence of thermally diverse lakes more than doubles, providing refuge for coldwater taxa. Ecozone-specific differences in the distribution of thermally diverse and thermally uniform lakes require different management strategies for adapting fish resource use to climate change.</p>
Sexual dimorphism in subterranean amphipod crustaceans covaries with subterranean habitat type: data and R code
<p>The data and R code used for data analyses in the manuscript titled "Sexual dimorphism in <em>Niphargus </em>amphipods is predicted by surface-subterranean environmental gradient". The collection contains:</p> <ol> <li>A zipped folder "videos", where raw videos used in the study are stored.</li> <li>A zipped folder "tracking_results", where video-tracking results obtained from the raw videos are stored, along with supporting files and R code (Rscript_extract_behavior.Rmd) with custom functions (Behavior_custom_functions.Rmd) needed to analyze tracking results and retrieve final behavioral data.</li> <li>A README file with details on how the data and code is organized.</li> <li>Supplementary Material file including all raw data used in the main data analysis (SupplementaryMaterial.xlsx)</li> <li>A supporting file with data from another study used in the main data analysis (sex_ratio.xlsx, results from https://onlinelibrary.wiley.com/doi/full/10.1111/jeb.13917; https://zenodo.org/records/5175861)</li> <li>Two files containing phylogenetic trees: one complete phylogenetic tree of<em> Niphargus </em>(consensus_tree)<em> </em>and 100 randomly drawn phylogenetic trees from the stationary phase of the Bayesian analysis, pruned to focal species (100_pruned_trees), which were used in the main data analysis.</li> <li>The Rcode containing the code of the main data analysis to reproduce the reported results (RScript_data_analysis.Rmd), as well as some additional analyses not included in the manuscript.</li> </ol>
Environmental DNA metabarcoding differentiates between micro-habitats within the rocky intertidal
<p>While the utility of environmental DNA (eDNA) metabarcoding surveys for biodiversity monitoring continues to be demonstrated, the spatial and temporal variability of eDNA, and thus the limits of the differentiability of an eDNA signal, remains under-characterized. In this study, we collected eDNA samples from distinct micro-habitats (~40 m apart) in a rocky intertidal ecosystem over their exposure period in a tidal cycle. During this period, the micro-habitats transitioned from being interconnected, to physically isolated, to interconnected again. Using a well-established eukaryotic (cytochrome oxidase subunit I) metabarcoding assay, we detected 415 species across 28 phyla. Across a variety of univariate and multivariate analyses, using exclusively taxonomically assigned data as well as all detected amplicon sequence variants (ASVs), we identified unique eDNA signals from the different micro-habitats sampled. This difference paralleled expected ecological gradients and increased as the sites became more physically disconnected. Our results demonstrate that eDNA biomonitoring can differentiate micro-habitats in the rocky intertidal only 40 m apart, that these differences reflect known ecology in the area, and that physical connectivity informs the degree of differentiation possible. These findings showcase the potential power of eDNA biomonitoring to increase the spatial and temporal resolution of marine biodiversity data, aiding research, conservation, and management efforts.</p>
Maintaining habitat diversity at small scales benefits wild bees and pollination services in mountain apple orchards
<p>In 2021, we conducted our study in apple orchards in South Tyrol, an Alpine region in Italy, using pan-traps, direct observations of visitation frequency, and a pollinator exclusion experiment. We investigated the scale-dependent effects of landscape heterogeneity and other parameters on wild bee assemblages and the related pollination service they provide at five spatial scales (radius 100 – 2,000 m).</p>
Reproducibility code and data - Understanding cetacean habitats in the Eastern Caribbean: a study combining data from multiple sources
<p>This R project reproduces the analyses carried out in the article entitled “Modelling cetacean habitats in the Eastern Caribbean: a study combining data from multiple sources” submitted to PCI Ecology. Analyses involve two steps (modelling 1: exploratory; and modelling 2: inferential).</p>
Concrete habitat: Impervious surface in nest vicinity is associated with avian fitness decline in two urban adapters
<p>The conversion of natural habitats to impervious surfaces in cities affects biotic and abiotic attributes of urban ecosystems. Detailed information on the gradual influence of impervious surfaces on reproductive success, however, is lacking. Using five years of nestbox-breeding great tit and blue tit breeding data collected across various habitat types within and outside a Central-Eastern European capital city, we quantified the impact of impervious surfaces on avian reproductive success. Impervious surfaces strongly and negatively covaried with the number of fledged young in both species: a 50% increase in impervious surface resulted in 2.93 (95% CI: -4.27; -1.58) fewer blue tit offspring fledging the nest, and 3.51 (95% CI: -4.79; -2.23) fewer great tit offspring fledging the nest, thus halving the reproductive output of two widespread urban species. These results provide benchmark values of avian productivity for ecologists and urban policy makers, and for the management of urban areas.</p>
Fig. 2 in Carabid beetle (Coleoptera: Carabidae) diversity in agricultural and post-agricultural areas in relation to the surrounding habitats
Fig. 2. Ordination plot based on correspondence analysis (CA) of carabid species (triangles) and study sites (circles).
Fig. 2 in Carabid beetle (Coleoptera: Carabidae) distribution in a rural landscape based on habitat diversity and habitat characteristics
Fig. 2. Cluster analysis of the results (individual years separated) based on Euclidian distance as distance measure and agglomeration according to Ward. Numbers indicate the percentage of replicates where each node is still supported (Hammer 2012)
Fig. 3 in Carabid beetle (Coleoptera: Carabidae) distribution in a rural landscape based on habitat diversity and habitat characteristics
Fig. 3. Ordination plot based on correspondence analysis (CA) of the results (individual years separated) for study sites (open circles) and species (open triangles)
Fig. 5 in Carabid beetle (Coleoptera: Carabidae) distribution in a rural landscape based on habitat diversity and habitat characteristics
Fig. 5. Ordination plot based on correspondence analysis (CA) of the results (years for the study sites pooled) for study sites (open circles) and species (open triangles)
Fig. 1 in Carabid beetle (Coleoptera: Carabidae) distribution in a rural landscape based on habitat diversity and habitat characteristics
Fig. 1. Scheme of the research object "Krzywda" (a) and location of the study sites (1-6) (b) (After Bùaszkiewicz & Schwerk (2013), modified).
Fig. 4 in Carabid beetle (Coleoptera: Carabidae) distribution in a rural landscape based on habitat diversity and habitat characteristics
Fig. 4. Cluster analysis of the results (years for the study sites pooled) based on Euclidian distance as distance measure and agglomeration according to Ward. Numbers indicate the percentage of replicates where each node is still supported (Hammer 2012)
FIGURE 3 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry
FIGURE 3 Salmo trutta fry abundances from the four sites in which three pass removals were conducted in July through October 2018 and associations with D50 and presence of wood. The trendline shows the relationship between S. trutta fry abundance and D50 in the three sites in which wood was absent () Wood () No Wood
FIGURE 5 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry
FIGURE 5 Oncorhynchus mykiss fry abundances from the four sites in which three pass removals were conducted in July through October 2018 and associations with (a) velocity and (b) depth. A trendline shows the relationship between each habitat variable and the fry abundance data for both the sites that were stocked (dotted line) and not stocked (solid line) () Not Stocked () Stocked
FIGURE 1 in Habitat associations of rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta fry
FIGURE 1 Fry site locations used to obtain abundance estimates or single-pass counts for Salmo trutta and Oncorhynchus mykiss in the upper Colorado River study section in Grand County, Colorado, downstream of Windy Gap Reservoir. The 20 15.2 m sites, sampled five times from July through October 2018, included one abundance estimation and four single-pass sites at the Sheriff Ranch, four single-pass sites at Kinney Creek, two abundance estimation and five single-pass sites in the Red Barn area and one abundance estimation and three single-pass sites at Hitching Post
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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.