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55 results for “landscape context”
Blue Crab Densities in a Landscape Context on the Virginia Coast, Summer 2019
Table 1 Crab Data : Blue crab (Callinectes sapidus) abundance was sampled at twenty-four sites in Spider Crab Bay, Cobb Bay, and South Bay (comprising two large seagrass meadows: "South Bay" for the northern portion and "Ship Shoal" for the southern portion) as part of a study to evaluate the drivers of blue crab spatial patterns across restored seagrass meadows in the coastal bays of Virginia, USA. The four meadows are representative of seagrass meadows in the region that have recovered after experiencing large declines due to wasting disease and storms (Orth et al., 2006). Each meadow contained six fixed sampling sites. Each captured crab's morphological and demographic characteristics were evaluated; as such, data are presented at the individual level. Table 2 Landscape Data: Landscape measurements were taken for twenty-four sites in Spider Crab Bay, Cobb Bay, and South Bay (comprising two large seagrass meadows: "South Bay" for the northern portion and "Ship Shoal" for the southern portion) as part of a study to evaluate the drivers of blue crab spatial patterns across restored seagrass meadows in the coastal bays of Virginia, USA. The four meadows are representative of seagrass meadows in the region that have recovered after experiencing large declines due to wasting disease and storms (Orth et al. 2006). Each meadow contained six fixed sampling sites. All landscape measurements were made using QGIS 3.14.0 (QGIS.org 2020). Seagrass landscape measurements were calculated using maps developed from aerial imagery by Orth et al. (2019). Oyster reefs polygons were mapped by Ross and Luckenbach (2009). Salt marsh polygons were mapped by Berman et al. (2011) and modified based on imagery from Planet Team (2019). Mean seagrass shoot density measurements were based on a VCR-wide 2019 sampling effort led by McGlathery (2018).
Data from: Context matters: the landscape matrix determines the population genetic structure of temperate forest herbs across Europe
<p>Context. Plant populations in agricultural landscapes are mostly fragmented and their functional connectivity often depends on seed and pollen dispersal by animals. However, little is known about how the interactions of seed and pollen dispersers with the agricultural matrix translate into gene flow among plant populations.</p> <p>Objectives. We aimed to identify effects of the landscape structure on the genetic diversity within, and the genetic differentiation among, spatially isolated populations of three temperate forest herbs. We asked, whether different arable crops have different effects, and whether the orientation of linear landscape elements relative to the gene dispersal direction matters.</p> <p>Methods. We analysed the species' population genetic structures in seven agricultural landscapes across temperate Europe using microsatellite markers. These were modelled as a function of landscape composition and configuration, which we quantified in buffer zones around, and in rectangular landscape strips between, plant populations.</p> <p>Results. Landscape effects were diverse and often contrasting between species, reflecting their association with different pollen- or seed dispersal vectors. Differentiating crop types rather than lumping them together yielded higher proportions of explained variation. Some linear landscape elements had both a channelling and hampering effect on gene flow, depending on their orientation.</p> <p>Conclusions. Landscape structure is a more important determinant of the species' population genetic structure than habitat loss and fragmentation <i>per se</i>. Landscape planning with the aim to enhance the functional connectivity among spatially isolated plant populations should consider that even species of the same ecological guild might show distinct responses to the landscape structure.</p>
Data from: "Landscape context and behavioral clustering contribute to flexible habitat selection strategies in a large mammal"
<p>Processed datasets used for analysis in "Landscape context and behavioral clustering contribute to flexible habitat selection strategies in a large mammal" by Hooven et al. published in <em>Mammal Research</em>. R scripts used to process and analyze these data are available from: <a href="https://github.com/nhooven/elk-individual-habitat">https://github.com/nhooven/elk-individual-habitat</a></p> <p>WS_sampled.csv, SU_sampled.csv, UA_sampled.csv, AW_sampled.csv - Processed telemetry datasets (with relocation data removed), resultant files from script "01 - Pre-processing.R".</p> <p>WS_HRs.csv, SU_HRs.csv, UA_HRs.csv, AW_HRs.csv - Home range areas (derived from autocorrelated kernel density estimators) and associated variables, by individual. </p> <p>WS_groups.csv, UA_groups.csv, AW_groups.csv - Home range areas (derived from autocorrelated kernel density estimators) and associated variables, by groups. </p> <p>Note: Raw telemetry data and home range polygons are not available due to the sensitive nature of providing animal locations publicly. Please direct any questions or concerns to the corresponding author (nathan.d.hooven@gmail.com). </p>
Fig. 6 in Role of landscape context in Toxoplasma gondii infection of invasive definitive and intermediate hosts on a World Heritage Island
Fig. 6. Relative density of black rats in different land-use types, as expressed by the capture rate by traps, i.e., number of individuals captured per 100 trapdays. Numerals above the bars indicate total trap-days.
Fig. 5 in Role of landscape context in Toxoplasma gondii infection of invasive definitive and intermediate hosts on a World Heritage Island
Fig. 5. Anti-Toxoplasma gondii seroprevalence and OD values of black rats as a function of the number of cattle barns within 1 ha or individual body weight. Gray areas indicate 95% confidence intervals. Dots represent individuals. The color becomes darker with increasing sample size.
Fig. 4 in Role of landscape context in Toxoplasma gondii infection of invasive definitive and intermediate hosts on a World Heritage Island
Fig. 4. Model averaged coefficients of variables (GLM) explaining seroprevalence and OD values of black rats. Bars indicate 95% confidence intervals.
Fig. 2 in Role of landscape context in Toxoplasma gondii infection of invasive definitive and intermediate hosts on a World Heritage Island
Fig. 2. Model averaged coefficients of variables (GLM) explaining seroprevalence and OD values of cats. Bars indicate 95% confidence intervals.
Fig. 3 in Role of landscape context in Toxoplasma gondii infection of invasive definitive and intermediate hosts on a World Heritage Island
Fig. 3. Anti-Toxoplasma gondii seroprevalence and OD values of cats as a function of the number of cattle barns within 1 ha or individual body weight. Gray areas indicate 95% confidence intervals. Dots represent individuals. The color becomes darker with increasing sample size.
Fig. 1 in Role of landscape context in Toxoplasma gondii infection of invasive definitive and intermediate hosts on a World Heritage Island
Fig. 1. Map showing the study area. Open circles and black triangles in the map indicate, respectively, capture sites of cats and black rats.
Data from: Landscape context modulates the effect of local canopy cover on forest multidiversity across elevations
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Data from: Context matters: the landscape matrix determines the population genetic structure of temperate forest herbs across Europe
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Data from: Vegetation biomass and landscape context shape web-building spider dietary niche breadth in urban vacant lots
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Data from: Pest control potential of adjacent agri-environment schemes varies with crop type and is shaped by landscape context and within-field position
<ol> <li>Increasing natural pest control in agricultural fields is an important aim of ecological intensification. Combined effects of landscape context and local placement of agri-environmental schemes on natural pest control and within field distance functions of natural pest control agents have rarely been addressed but might affect the distribution of biocontrol providers. Importantly, it is currently unknown whether ecosystem services provided by adjacent agri-environmental schemes (AES) are consistent for different crop types during crop rotation.</li> <li>In this study, we assessed whether crop rotation from oilseed rape to cereals altered within-field distance functions of ground dwelling predators from adjacent agri-environmental fields along a gradient in landscape context. Additionally we recorded crop pests, predation rates, parasitoids as well as crop yields on a total of 30 study sites.</li> <li>Distance functions varied between trophic levels: Carabid richness decreased while densities of carabid beetles, staphylinid beetles as well as crop yields increased towards the field centres. Distance functions of parasitoids and pests were modulated by the amount of semi-natural habitat in the surrounding landscape, while the effects of adjacent AES were limited.</li> <li>Distance decay functions found for ground dwelling predators in oilseed rape in the previous year were not always present in cereals. Increasing distance to the field edge also increased effects of crop rotation on carabid beetle assemblages, indicating a source habitat function of field edges.</li> <li>Synthesis and applications<i>.</i> Distance functions of natural pest control are not universal and the effects of agri-environmental schemes (AES) in different adjacent crops during crop rotation vary and depends on ecological contrasts. A network of semi-natural habitats and spatially optimised AES habitats can benefit pest control in agricultural landscapes, but constraints as a result of crop type need to be addressed by annually targeted, spatially shifting AES schemes for different crops.</li> </ol> <div> </div>
Landscape context affects patch habitat contributions to biodiversity in agroecosystems
<p>Effective conservation schemes are needed to advance dual objectives of biodiversity conservation and agronomic production in agricultural landscapes. Understanding how plant and arthropod taxa respond to both local habitat patch characteristics and landscape complexity is crucial for planning effective agri-environment schemes. This study investigated the relative effects of local (≤ 100 m from patch habitat center) and landscape (≤ 5 km from patch habitat center) variables on diversity of plants and arthropods within non-crop habitat patches (i) at different spatial extents ranging from 0.1 km to 5 km, while (ii) quantifying differential effects of local and landscape variables on unique components of diversity (i.e. species richness and abundance), and accounting for (iii) unique components of landscape extent (0.1, 0.5, 1, 2 and 5 km radii) and complexity (i.e. landscape composition and configuration). Landscape variables were significantly correlated with local plant and arthropod species richness and abundance at all spatial extents. Biodiversity responses to landscape variables were largely scale-dependent, as pairwise comparisons were significantly different between all spatial extents except between 1-km and 2-km extents, and correlations were lowest at the 5-km extent. Partial R-squared values for predicting local biodiversity were highest when both local and landscape variables were included as predictors of species richness and abundance, underscoring the importance of considering both local and landscape effects on local diversity. Landscape configuration variables accounted for more variation in plant and arthropod species richness than composition variables. However, models performed best when composition and configuration were considered together rather than alone, suggesting that both components of landscape complexity should be considered for identifying and managing conservation areas in crop fields. Conservation schemes that incentivize farmers to create or conserve small patch habitat within crop fields may be more effective when combined with landscape-scale designs that enhance landscape complexity across the Northern Great Plains. Local conservation efforts should be coordinated with landscape-level efforts to ultimately enhance biodiversity and desired ecosystem service outcomes across agricultural landscapes.</p>
Data from: Landscape context and substrate characteristics shape fungal communities of dead spruce in urban and semi-natural forests
<p>Data from:</p> <p>Korhonen, A., Miettinen, O., Kotze, D.J., & Hamberg, L. (2022). Landscape context and substrate characteristics shape fungal communities of dead spruce in urban and semi-natural forests. Environmental Microbiology. DOI: 10.1111/1462-2920.15903</p> <p>This dataset contains occurrence data of 475 fungal ITS2 sequence clusters (OTUs) across 360 sequenced samples originating from dead wood of Norway spruce (<em>Picea abies</em>). Wood samples were collected from 90 downed spruce trunks, at four points from each trunk. Trunks were at intermediate stages of decay and located in spruce-dominated stands in 24 urban forests (66 trunks) and in 8 rural semi-natural forests (24 trunks) in southern Finland. The data consists of an OTU table (sequence read counts in each sample) and sample metadata (locality information, trunk characteristics and environmental variables).</p>
Bird predation and landscape context shape arthropod communities on broccoli
<p>Birds increase crop yields via consumption of pests in some contexts but disrupt pest control via intraguild predation in others. Landscape complexity acts as an inconsistent mediator, sometimes increasing, decreasing, or not impacting pest control. Here, we examined how landscape context and seasonal variation mediate the impact of birds on arthropod pests and natural enemies, leaf damage, and yields of broccoli (<em>Brassica oleracea</em>) on highly diversified farms that spanned the USA West Coast. Our study had two complementary components: a bird exclusion experiment and molecular diet analysis of 357 fecal samples collected from the most commonly captured bird species that also foraged in Brassica fields (American Goldfinch, <em>Spinus tristis</em>; American Robin, <em>Turdus migratorius</em>; Savannah Sparrow, <em>Passerculus sandwichensis</em>; Song Sparrow, <em>Melospiza</em> <em>melodia</em>; and White-crowned Sparrow, <em>Zonotrichia leucophrys</em>).</p> <p>Bird access yielded higher, rather than lower, numbers of pest aphids and increased their parasitism, while no other arthropods examined were consistently impacted. Independent of bird presence, percent natural cover in the landscape sometimes increased and sometimes decreased densities of arthropods in the mid-growth period, with diminishing impacts in the late-growth period. Herbivore feeding damage to broccoli leaves decreased with increasing amounts of natural land cover and in the late-growth period. Molecular diet analysis revealed that Brassica pests and predatory arthropods were relatively uncommon prey for birds. Landscape context did not alter the prey items found in bird diets. Altogether, our bird-exclusion experiment and molecular diet analysis suggested that birds have relatively modest impacts on the arthropods associated with broccoli plantings. More broadly, the limited support in our study for net natural pest control services suggests that financial incentives may be required to encourage the adoption of bird friendly farming practices in certain cropping systems.</p>
Data from: Ecological requirements drive the variable responses of wheat pests and natural enemies to the landscape context
<p>1. Semi-natural habitats (SNH) are considered essential for pest suppressive landscapes, but their influence on crop pests and natural enemies can be highly variable. Instead of SNH per se, the availability of resources, such as pollen and nectar, may be more relevant for supporting pest control.</p> <p>2. Here, we assessed the spatio-temporal variation of multiple insect pests (cereal leaf beetles and aphids) and natural enemies (predators and aphid parasitoids) in wheat fields and their responses to landscape context and flower availability. We combined detailed information on pollen use by natural enemies with the specific distribution of pollen-providing plants across a gradient of landscape composition and configuration.</p> <p>3. The abundance of wheat pests was tightly linked to wheat development stage. Syrphids colonised the fields early in the season, while the abundance of other enemies increased later in the season. The responses of pests to landscape structure were variable and, while some pests had low abundances in landscapes with high edge density and SNH cover, <em>Sitobion avenae</em> abundance was positively associated with SNH cover. Lacewings, syrphids and cereal leaf beetles were abundant in landscapes with diverse and abundant flower resources, whereas the abundance of parasitoids and Nabis sp. was driven by aphid abundance. We detected no significant indirect effects of landscape on pests via natural enemies.</p> <p>4. Synthesis and applications. Our findings highlight the need for conservation biological control to go beyond "one size fits all" and consider the specific ecology of the involved organisms. Landscapes with high edge density and flowering woody plants may support natural enemies, in particular syrphids, which colonised the fields early in the season. Incentives for pest-suppressive landscapes should focus on tailored strategies that disfavour pests and simultaneously enhance natural enemies according to their ecological requirements.</p>
Fitness landscapes reveal context-dependent benefits of oviposition behaviour
<p><span>Resource choice behaviour has enormous fitness consequences and can drive niche expansion. However, individual behavioural choices are often mediated by context, determined by past experience. Do such context-dependent behaviours reflect maladaptive variation, or are they locally adaptive? Using Tribolium castaneum (the red flour beetle), we demonstrate that context-dependent oviposition behaviour reflects distinct, context-specific local fitness peaks. We measured offspring fitness to generate fitness landscapes as a function of all possible oviposition behaviours (i.e., combinations of fecundity and resource preference) in a habitat containing optimal and suboptimal resource patches. We did this by experimentally manipulating female egg allocation across patches, which allowed us to assess behaviours not typically observed in the laboratory. We found that females from different age and competition contexts exhibit distinct behaviours which optimize different fitness components, linked in a tradeoff. With prior exposure to strong competition and increasing age, females produce few but fast-developing offspring that are advantageous under high resource competition. In contrast, young naïve females produce significantly more (but slower-developing) offspring, which is beneficial under weak competition. Systematically mapping complete context-dependent fitness landscapes is thus critical to infer behavioural optimality and offers predictive power in novel contexts. </span></p>
Mapping the epigenomic landscape of human monocytes following innate immune activation reveals context-specific mechanisms driving endotoxin tolerance
<p><strong>Processed datasets for publication at <em>BMC Genomics</em>.</strong></p> <p>We exposed human primary monocytes from healthy donors (n=6) to interferon-γ or differing combinations of endotoxin (lipopolysaccharide), including acute response (2hr LPS; LPS2) and two models of endotoxin tolerance: repeated stimulations (6+6hr; LPS6:6) and prolonged exposure to endotoxin (24hr LPS; LPS24). Another subset of monocytes was left untreated (naïve; UT). We performed total RNA-seq and ATAC-seq for monocytes across these treatment conditions.</p> <p>The following processed datasets include the raw and normalised count data for each gene or ATAC peak, and the bedGraph and bigWig format for genome-wide signal data. [ bigWig files for RNA-seq (monocytes_*_mean.bw); bigWig files for ATAC-seq (Monocyte_ATAC_*_mean_normalised.by.1/size.factor.bw); bedgraph files for eRNA visualization (*RPKM_FR.bedgraph.gz); raw and normalised count files for ATAC-seq and RNA-seq data (Monocyte.featureCounts_RNAseq.txt.gz; Monocyte_filtered_log2.normalized_RNAseq_counts.txt.gz; Meta.file.txt.gz; Monocyte_raw.counts_ATACseq.txt.gz.).]</p> <p><strong>Data curator:</strong></p> <p>Ping Zhang</p> <p> </p>
Data from: Landscape context shifts the balance of costs and benefits from wildflower borders on multiple ecosystem services
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