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143 results for “urban landscape”
Raw data and code for: Drivers of nocturnal and diurnal pollinating insect declines in urban landscapes
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Data from: Urban landscapes can change virus gene flow and evolution in a fragmentation-sensitive carnivore
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Data from: Fine-scale variation in microclimate across an urban landscape shapes variation in mosquito population dynamics and the potential of Aedes albopictus to transmit arboviral disease
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Functional diversity of farmland bees across rural-urban landscapes in a tropical megacity
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Variety is the spice of life: flying-foxes exploit a variety of native and exotic food plants in an urban landscape mosaic
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Data from: Bee-mediated pollen transport across five urban landscape features: Buildings are important barriers
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Multiple ecosystem service synergies and landscape-mediation of biodiversity within urban agroecosystems
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Datasets and analysis for: Microclimatic buffering in forest, agricultural and urban landscapes through the lens of a grass-feeding insect
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Shifts in host-parasitoid networks across community garden management and urban landscape gradients
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Mycorrhizae in an experimental urban landscaped site in central Arizona-Phoenix
The primary objective of this project is to study Mycorrhizal relationships at an experimental xeric urban landscaped site . One study quantified the local diversity and spatial patterns of arbuscular mycorrhizal fungal (AMF) species. AMF species at 25 points in a 9.2 x 9.2 m regular grid pattern were identified using trap cultures. A total of twelve species were detected, with seven species detected in one plot and eleven in the other. Sampling effort curves and jackknife estimates indicate that a limited number of species was still undetected. No single species was dominant at either plot, and a rank-frequency plot for the site revealed a log-normal species distribution. The number of AMF species was not correlated with proximity to plants. Despite the patchiness of plants in the plots, the number of species detected per point exhibited spatial structuring only at the smallest sampling scale in a single plot, and only a single species in each plot was non-randomly distributed.The results indicate that there is a diverse AMF propagule bank at the site and/or there has been significant in-migration from the surrounding metacommunity. The second study examined the effects of three shoot pruning techniques (shearing every 6 weeks, heading back every 6 months and renewal pruning every year) on root length density, biomass, AMF colonization and soil respiration in two woody shrubs, Nerium oleander (oleander) and Leucophyllum frutescens (Texas sage). Roots were sampled at the base of plants by soil coring to depths of 0-20 cm and 20-40 cm in February, after the shearing and heading back treatments had been imposed, but prior to the first renewal pruning, and in May, after all treatments had been imposed. Shearing stimulated root biomass in Nerium in February, but shearing and renewal pruning reduced biomass compared to unpruned plants in both species in May. Nerium colonization was stimulated by shearing and heading back in February and by shearing and renewal pruning in
Water, energy and carbon fluxes and ancillary meteorological measurements of four different urban landscapes in Phoenix, AZ during 2015
<p>Water, energy and carbon fluxes and ancillary meteorological measurements of four different urban landscapes in Phoenix, AZ during 2015. The measurements were done in three temporal not continuous deployment and in a permanent site as a reference. The urban landscape sites consisted in:</p> <ul> <li>A xeric landscape (XL), with measurements from 01/20/2015 to 03/13/2015.</li> <li>A parking lot (PL), with measurements from 05/19/2015 to 06/30/2015.</li> <li>A mesic landscape (ML), with measurements from 07/08/2015 to 09/18/2015.</li> <li>A reference suburban neighbourhood (REF), with measurements from 01/01/2015 to 12/13/2015.</li> </ul> <p>Water energy and carbon fluxes were processed using the software EdiRe. If additional data or information is needed, please contact the authors.</p> <p>The use of the datasets requires the citation of the next papers:</p> <p>- Templeton, N.P., Vivoni, E.R., Wang, Z-H., and Schreiner-McGraw, A.P. 2018. Quantifying Water and Energy Fluxes over Different Urban Land Covers in Phoenix, Arizona. Journal of Geophysical Research - Atmospheres. 123(4): 2111-2128.</p> <p>-Pérez-Ruiz, E. R., Vivoni, E. R. and Templeton, N. P. 2020. Urban land cover type determines the sensitivity of carbon dioxide fluxes to precipitation in Phoenix, Arizona. PLoS ONE 15(2): e0228537. https://doi.org/10.1371/journal.pone.0228537</p>
Code and Data from Bhakti et al. on landscape permeability of urban landscape, v. 1.0
<p>This repository shares the code and data from the paper Bhakti et al. (in review), on integrating land cover, animal behavior, and master plan regulations to assess urban landscape permeability for birds. The paper is under review on Landscape and Urban Planning.</p> <p>Bhakti, T.; Pena, J.C.; Niebuhr, B.B.; Sampaio, J.; Goulart, F.F.; Azevedo, C.S.; Ribeiro, M.C., and Antonini, Y. Combining land cover, animal behavior, and master plan regulations to assess landscape permeability for birds. In review.</p>
Data from: Impacts of habitat on butterfly dispersal in tropical forests, parks and grassland patches embedded in an urban landscape
<p>Dispersal distances of 17 species of butterflies in tropical Singapore were significantly greater in forest than in urban habitat. Butterflies in urban plots frequently moved within suitable habitat (park/grassland) patches but rarely crossed non-habitat patches suggesting potential isolation and a need for urban corridors.</p>
Data from: Functional diversity of phyllostomid bats in an urban-rural landscape: a scale-dependent analysis
<p>Urbanization is one of the most pervasive landscape transformational processes responsible for novel selection agents promoting functional community homogenization. Bats may persist in those human environments, but the mechanisms responsible for their adaptability and the spatial scales in which landscape imposes environmental filtering remain poorly studied in the Neotropics. We tested the hypothesis that landscape composition interacts with the spatial scale to affect the functional diversity of phyllostomids in an urban-rural gradient. Based on functional traits, we calculated indices of functional richness, divergence, evenness, community-weighted means of morphological traits, and classified species into functional groups. We evaluated the changes of those variables in response to forest, grassland, and urbanized areas at 0.5, 1.25 and, 2 km scales. The number of functional groups, functional richness, and functional evenness tended to be higher in areas far from cities and with higher forest cover, whereas functional divergence increased in more urbanized areas. Our results show that the mean value of wing loading in the assemblage was negatively associated to landscape transformation at several spatial scales. However, environmental filtering driven by grass cover was particularly robust at the 500 m scale, affecting big-sized species with long pointed wings. Retaining natural forest in cattle ranging systems at ~12 km<sup>2</sup> appears to favor bat abundance evenness among functional types in the urban-rural landscape. Recognizing the scale of the effect on phyllostomid functional responses appears to be a fundamental issue for elucidating the spatial extent to which phyllostomid conservation planning in urban-rural landscapes should be addressed.</p>
Data from: Are house sparrow populations limited by the lack of cavities in urbanized landscapes? an experimental test.
Current urban policies are associated with deep changes in urban structures, which may impoverish urban biodiversity. A major concern is the disappearance of nesting sites for wild vertebrate species living in urban areas. New urban structures without any cracks or cavities may especially preclude cavity nesters from breeding in cities and they may cause population declines. In that context, we experimentally investigated this question in an urban exploiter bird species (the house sparrow, Passer domesticus), which is dramatically declining in most European cities. To test if the lack of cavities is limiting house sparrow populations in urban areas, we equipped 11 sites along an urbanization gradient with nest boxes and we then evaluated the rate of occupancy of these nest-boxes. This urbanization gradient was characterized by very rural places (isolated farms) and moderately urbanized areas (town of medium size, i.e. 60 000 inhabitants). Surprisingly, rural nest boxes were more occupied than urban ones, suggesting that cavity availability is probably more constraining in rural areas relative to urban ones. Therefore, our study suggests that urban house sparrow populations are probably not constrained by a lack of nesting sites in medium size cities with urban designs similar to our city of interest (Niort, Western France). This hypothesis definitely needs now to be tested in further urban landscapes (e.g. large cities and urban landscapes with other architecture and management policies).
Data from: A 454 survey reveals the community composition and core microbiome of the common bed bug (Cimex lectularius) across an urban landscape
Elucidating the spatial dynamic and core constituents of the microbial communities found in association with arthropod hosts is of crucial importance for insects that may vector human or agricultural pathogens. The hematophagous Cimex lectularius (Hemiptera: Cimicidae), known as the human bed bug, has made a recent resurgence in North America, as well as worldwide, potentially owing to increased travel, climate change and resistance to insecticides. A comprehensive survey of the bed bug microbiome has not been performed to date, nor has an assessment of the spatial dynamics of its microbiome. Here we present a survey of internal and external bed bug microbial communities by amplifying the V4–V6 hypervariable region of the 16S rDNA gene region followed by 454 Titanium sequencing using 31 individuals from eight distinct collection locations obtained from residences in Cincinnati, OH. Across all samples, 97% of the microbial community is made up of two dominant OTUs, previously identified as the α-proteobacterium Wolbachia and an unnamed γ-proteobacterium from the Enterobacteriaceae. Microbial communities varied among host locations for measures of community diversity and exhibited structure according to collection location. This broad survey represents the most in-depth assessment, to date, of the microbes that associate with bed bugs.
Data from: Nest suitability, fine-scale population structure and male-mediated dispersal of a solitary ground nesting bee in an urban landscape
Bees are the primary pollinators of flowering plants in almost all ecosystems. Worldwide declines in bee populations have raised awareness about the importance of their ecological role in maintaining ecosystem functioning. The naturally strong philopatric behavior that some bee species show can be detrimental to population viability through increased probability of inbreeding. Furthermore, bee populations found in human-altered landscapes, such as urban areas, can experience lower levels of gene flow and effective population sizes, increasing potential for inbreeding depression in wild bee populations. In this study, we investigated the fine-scale population structure of the solitary bee Colletes inaequalis in an urbanized landscape. First, we developed a predictive spatial model to detect suitable nesting habitat for this ground nesting bee and to inform our field search for nests. We genotyped 18 microsatellites in 548 female individuals collected from nest aggregations throughout the study area. Genetic relatedness estimates revealed that genetic similarity among individuals was slightly greater within nest aggregations than among randomly chosen individuals. However, genetic structure among nest aggregations was low (Nei's GST = 0.011). Reconstruction of parental genotypes revealed greater genetic relatedness among females than among males within nest aggregations, suggesting male-mediated dispersal as a potentially important mechanism of population connectivity and inbreeding avoidance. Size of nesting patch was positively correlated with effective population size, but not with other estimators of genetic diversity. We detected a positive trend between geographic distance and genetic differentiation between nest aggregations. Our landscape genetic models suggest that increased urbanization is likely associated with higher levels of inbreeding. Overall, these findings emphasize the importance of density and distribution of suitable nesting patches for enhancing bee population abundance and connectivity in human dominated habitats and highlights the critical contribution of landscape genetic studies for enhanced conservation and management of native pollinators.
Data from: Local and landscape metrics identify opportunities for conserving cavity-nesting birds in a rapidly urbanizing ecoregion
Urban centers are rapidly expanding globally, resulting in regional forest-cover transformations that shift from temperate forest biomes to a heterogeneous mix of urban development, forest patches, and agriculture. Data on habitat use within remaining forest patches embedded across land use types, particularly in urban land use, are needed to optimize conservation strategies as urban growth continues. In the rapidly urbanizing southern Piedmont, USA, small pine patches have become more frequent across the landscape and are found embedded within second-growth forest, agricultural, and urban land use matrices. We used point-count surveys and N-mixture models to determine the effect of patch- and landscape-scale drivers on cavity-nesting bird abundance, including the threatened Brown-headed Nuthatch (Sitta pusilla), in pine forest patches. Model-averaged estimates suggest Brown-headed Nuthatches are more abundant in large patches in a heterogeneous matrix that includes urban residential development. Three other cavity-nesting species declined in abundance as a function of reduced canopy cover. White-breasted Nuthatches increased and Tufted Titmice decreased in abundance in response to patch area. By identifying factors that predict abundance at local and landscape scales for ecologically sensitive and generalist species, we can more effectively contribute to regional conservation efforts in urban ecosystems, extending conservation in practice beyond protected areas.
Data from: Human activities and landscape features interact to closely define the distribution and dispersal of an urban commensal.
The rock pigeon, Columba livia, is a cosmopolitan human commensal, domesticated thousands of years ago. However, the human-mediated factors governing its distribution and dispersal are not well understood. In this study, we performed (1) hierarchical distance sampling on ~400 island-wide point transects, (2) a population genomic inquiry based on ~7000 SNPs from almost 150 individuals, and (3) landscape-genomic analyses on the basis of extensive ecological and social-economic databases to characterize the distribution and dispersal patterns of rock pigeons across Singapore. Our distance sampling results indicated that the volume of intentional 'mercy feeding' and availability of high-rise buildings are the most reliable predictors of high pigeon densities in Singapore. Genomic analyses demonstrated that rock pigeons in Singapore form a single population possibly derived from rapid expansion from a genetically homogenous group of founder individuals. Specifically, rock pigeons in Singapore lack sex-biased dispersal and are clustered with a genetic patch size of ~3km. Landscape genomic analyses of great precision pointed to the presence of dense trees as agents of resistance to dispersal whereas a high road density reduces this resistance. By pinpointing a range of ecological and socio-economic variables determining the distribution and dispersal of pigeons, our study provides urban planners with the tools for optimal management of this human commensal, such as a curtailment of the practice of mercy feeding and modifications to the urban landscape to reduce pigeon density and to lower the likelihood of repopulation by dispersal.
Local and landscape scale variables shape insect diversity in an urban biodiversity hotspot.
<p>Local community structure is shaped by processes acting at local and landscape scales. The relative importance of drivers operating across different spatial scales are difficult to test without observations across regional or latitudinal gradients. Cities exhibit strong but predictable environmental gradients overlaying a mosaic of highly variable but repeated habitat types within a constrained area. Thus, cities present a unique opportunity to explore how both local and landscape factors influence local biotic communities. We used insect communities to examine the interactions among local environmental variables (such as temperature and relative humidity), local habitat characteristics (such as plant community composition), and broad-scale patterns of urbanization (including biophysical, human-built, and socio-economic variables) on local insect abundance, species richness, and species composition in Los Angeles, a hot, dry, near-desert city. After accounting for seasonal trends, insect species richness and abundance were highest in drier and hotter sites, but the magnitude of local environmental effects varied with the degree of urbanization. In contrast, insect species composition was best predicted by broad-scale urbanization trends, with the more native communities occurring in less urbanized sites and more cosmopolitan insects occurring in highly urbanized sites. However, insect species richness and abundance were >30% higher and insect composition was similar across sites that hosted either native or drought-tolerant plants, regardless of the degree of urbanization. These results demonstrate that urban insect biodiversity is a product of interacting mechanisms working at both local and landscape scales. However, local scale changes to urban habitats, such as cultivating plants that are adapted to the natural environment nearest the city, can positively impact urban biodiversity regardless of location.</p>
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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.