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262 results for “indirect effects”
Terrestrial herbivory drives adaptive evolution in an aquatic community via indirect effects
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Data from: Direct and indirect effect of cannibalism and intraguild predation in the two sibling Harmonia ladybird beetles
<p>In this study, we focused on the direct (i.e. predation) and indirect (i.e. potential threat from coexisting with a larger individual) effects of cannibalism and intraguild predation (IGP) during larval stages of two sibling ladybird beetles. These effects play an important role in the coexistence of the generalist–common Harmonia axyridis and specialist–rare H. yedoensis (Coleoptera: Coccinellidae). Direct predation effect of cannibalism and IGP were asymmetric in the two sibling ladybird beetles; the fourth instar larvae of H. axyridis were better intraguild predators than cannibals, while the reverse was true in the larvae of H. yedoensis. Neither cannibalism nor IGP significantly affected female body weight in either species. Larval H. axyridis surviving exposure to cannibalism or IGP had a reduced number of ovarioles as adults, whereas adult H. yedoensis ovarioles were not affected. For the indirect effects, longer developmental times in males and females and a lower total number of ovarioles in females were detected in H. axyridis. In H. yedoensis, shorter developmental time of males, lighter adult weight and fewer total ovarioles in females were observed. Olfactometer choice experiments clarified that the fourth instar larvae of H. axyridis avoided the first instar conspecific larvae, while those of H. yedoensis were attracted to the odours from H. axyridis and conspecifics. Thus, H. axyridis has an avoidance mechanism only for cannibalism but not for IGP, whereas H. yedoensis does not have any avoidance mechanism. These different behaviours in the direct and indirect effects of cannibalism and IGP observed in the laboratory may play important roles in the coexistence of generalist–common H. axyridis and specialist–rare H. yedoensis in natural conditions, compensating for the large handicap of H. yedoensis at reproductive interference from H. axyridis.</p>
Data from: Understanding the social dynamics of breeding phenology: indirect genetic effects and assortative mating in a long distance migrant
Phenological traits, such as the timing of reproduction, are often influenced by social interactions between paired individuals. Such partner effects may occur when pair members affect each other's pre-breeding environment. Partner effects can be environmentally and/or genetically determined, and quantifying direct and indirect genetic effects is important for understanding the evolutionary dynamics of phenological traits. Here, using 26 years of data from a pedigreed population of a migratory seabird, the common tern ( Sterna hirundo ), we investigate male and female effects on female laying date. We find that female laying date harbors both genetic and environmental variation, and is additionally influenced by the environmental, and, to a lower extent, genetic, component of her mate. We demonstrate this partner effect to be largely explained by male arrival date. Interestingly, analyses of mating patterns with respect to arrival date show mating to be strongly assortative and, using simulations, we show that this assortative mating for arrival date leads to overestimation of partner effects. Our study provides evidence for partner effects on breeding phenology in a long distance migrant, while uncovering the potential causal pathways underlying the observed effects and raising awareness for confounding effects due to assortative mating or other common environmental effects.
Data from: Comparing the indirect effects between exploiters in predator-prey and host-pathogen systems
DataS1 <p>These files are Maple and Matlab scripts for analyzing the predator-prey and host-pathogen models in "Comparing the indirect effects between exploiters in predator-prey and host-pathogen systems" and generating the figures in that study. </p>
Effects of soil salinity on the expression of direct and indirect defences in wild cotton (Gossypium hirsutum)
<p>Previous studies have reported effects of abiotic factors on herbivore-induced plant defences based on effects on single plant traits. However, plants commonly express multiple defences simultaneously and these traits are often correlated. Thus, a fuller understanding of abiotic-context dependency in plant defence requires measuring multiple traits and addressing their patterns of correlated expression.</p> <p>We evaluated the effects of soil salinity on the induction of direct (phenolic compounds, gossypol gland density) and indirect (volatile organic compounds, extrafloral nectar) defensive traits in wild cotton (Gossypium hirsutum). We asked whether soil salinity affects the induction of these traits, and whether it shapes trait correlations potentially underlying salinity effects on trait induction. We conducted a factorial experiment with 16 cotton genotypes where we manipulated soil salinity and defence induction by applying artificial leaf damage (25% mechanical damage and caterpillar oral secretions) and measured defence levels at different time points post-damage.</p> <p>Leaf damage induced most traits except gossypol gland density, whereas salinity did not have a mean effect (across constitutive and induced levels) on any of the measured traits. Nonetheless, salinity prevented the induction of phenolic compounds (condensed and hydrolysable tannins), and also affected trait correlations. Specifically, phenolic compounds were negatively associated with nectar production only under salinized conditions, an apparent trade-off that presumably affects the induced levels of phenolic compounds. In addition, positive correlations between phenolic compounds and gland density and root biomass observed under control conditions were lost under salinized conditions.</p> <p>By investigating the effects of soil salinity on the expression of multiple direct and indirect defensive traits and their underlying correlations, these findings build toward a better understanding of how abiotic context-dependency shapes plant allocation to and expression of multiple defensive traits.</p>
Indirect parental effects on offspring fitness by egg-derived fluids in an external fertiliser
<p>The capacity for parents to influence offspring phenotypes via nongenetic inheritance is currently a major area of focus in evolutionary biology. Intriguing recent evidence suggests that sexual interactions among males and females, both before and during mating, are important mediators of such effects. Sexual interactions typically extend beyond gamete release, involving both sperm and eggs, and their associated fluids. However, the potential for gamete-level interactions to induce transgenerational parental effects remains under-investigated. Here, we test for such effects using an emerging model system for studying gamete interactions, the external fertiliser Mytilus galloprovincialis. We employed a split-ejaculate design to test whether exposing sperm to egg-derived chemicals (ECs) from one female would affect fertilisation rate and offspring survival when those sperm were used to fertilise a different female's eggs. We found significant and separate effects of ECs from non-fertilising females on both fertilisation rate and offspring survival. The offspring survival effect indicates that EC-driven interactions can have transgenerational implications for offspring fitness independent of the genotypes inherited by those offspring. These findings provide a rare test of indirect parental effects driven exclusively by gamete-level interactions, and to our knowledge the first evidence that such effects occur via the gametic fluids of females.</p>
Experimental shifts in exotic flowering phenology produce strong indirect effects on native plant reproductive success
<ol> <li>By causing phenological shifts that vary among species, climate change is altering time envelopes for species interactions, often with unexpected demographic consequences. Indirect interactions, like apparent competition and apparent facilitation, are especially likely to change in duration because they involve multiple interactors, increasing the likelihood of asynchronous phenological shifts by at least one interactor. Thus, we might observe ecological surprises if intermediaries of indirectly interacting species change their mediating behavior.</li> <li>We explored this possibility in a plant-pollinator community that is likely to experience asynchronous phenological shifts. We advanced and delayed the flowering phenology of two ubiquitous exotic plants of western Washington prairies, <i>Hypochaeris radicata</i> and <i>Cytisus scoparius,</i> relative to seven native perennial forb species whose phenologies remained unmanipulated. These species interact indirectly through shared pollinators, whose foraging behavior influences plant reproductive success. We quantified impacts of experimental phenological shifts on seedset, pollinator visitation rates, and visiting pollinator composition relative to an unmanipulated control. We first verified that unmanipulated indirect interactions between native and exotic plants were strong, ranging from facilitative to competitive.</li> <li>Seedset of native plants was strongly affected by changes in exotic flowering phenology, but the magnitude and direction of effects were not predicted by the nature of the original indirect interaction (facilitative vs. neutral vs. competitive) or the change in interaction duration. The relationship between pollinator visitation and seedset changed for most species, though changes in pollinator visitation rate and pollinator composition were not as widespread as effects on native seedset.</li> <li> <b>Synthesis. </b>Changes in pollinator foraging behavior in response to changes in available floral resources are probably responsible for the unexpected effects we observed. Asynchronous phenological shifts have the potential to produce large and unexpected effects on reproductive success via indirect interactions.</li> </ol>
Data from: Indirect legacy effects of an extreme climactic event on a marine megafaunal community
While extreme climactic events (ECEs) are predicted to become more frequent, reliably predicting their impacts on consumers remains challenging– particularly for large consumers in marine environments. Many studies that do evaluate ECE effects focus primarily on direct effects, though indirect effects can be equally or more important. Here, we investigate the indirect impacts of the 2011 "Ningaloo Niño" marine heatwave ECE on a diverse megafauna community in Shark Bay, Western Australia. We use an 18 year community level dataset before (1998-2010) and after (2012-2015) the heatwave to assess the effects of seagrass loss on the abundance of seven consumer groups: sharks, sea snakes (multiple species), Indo-pacific bottlenose dolphins (Tursiops aduncus), dugongs (Dugong dugon), green turtles (Chelonia mydas), loggerhead turtles (Caretta caretta), and pied cormorants (Phalacrocorax spp.). We then assess whether seagrass loss influences patterns of habitat use by the latter five groups, which are under risk of shark predation. Sharks catch rates were dominated by the generalist tiger shark (Galeocerdo cuvier) and changed little, resulting in constant apex predator density despite heavy seagrass degradation. Abundances of most other consumers declined markedly as food and refuge resources vanished, with the exception of generalist loggerhead turtles. Several consumer groups significantly modified their habitat use patterns in response to the die-off, but only bottlenose dolphins did so in a manner suggestive of a change in risk-taking behavior. We show that ECEs can have strong indirect effects on megafauna populations and habitat use patterns in the marine environment, even when direct effects are minimal. Our results also show that indirect impacts are not uniform across taxa or trophic levels and suggest that generalist marine consumers are less susceptible to indirect effects of ECEs than specialists. Such non-uniform changes in populations and habitat use patterns have implications for community dynamics, such as the relative strength of direct predation and predation risk. Attempts to predict ecological impacts of ECEs should recognize that direct and indirect effects often operate through different pathways and that taxa can be strongly impacted by one even if resilient to the other.
Data from: Climatic variation modulates the indirect effects of large herbivores on small-mammal habitat use
Large mammalian herbivores (LMH) strongly shape the composition and architecture of plant communities. A growing literature shows that negative direct effects of LMH on vegetation frequently propagate to suppress the abundance of smaller consumers. Indirect effects of LMH on the behaviour of these consumers, however, have received comparatively little attention despite their potential ecological significance. We sought to understand (i) how LMH indirectly shape small-mammal habitat use by altering the density and distribution of understorey plants; (ii) how these effects vary with climatic context (here, seasonality in rainfall); and (iii) the extent to which behavioural responses of small mammals are contingent upon small-mammal density. We tested the effects of a diverse LMH community on small-mammal habitat use using 4 years of spatially explicit small-mammal trapping and vegetation data from the UHURU Experiment, a replicated set of LMH exclosures in semi-arid Kenyan savanna. Small-mammal habitat use was positively associated with tree density and negatively associated with bare (unvegetated) patches in all plots and seasons. In the presence of LMH, and especially during the dry season, small mammals consistently selected tree cover and avoided bare patches. In contrast, when LMH were excluded, small mammals were weakly associated with tree cover and did not avoid bare patches as strongly. These behavioural responses of small mammals were largely unaffected by changes in small-mammal density associated with LMH exclusion. Our results show that LMH indirectly affect small-mammal behaviour, and that these effects are influenced by climate and can arise via density-independent mechanisms. This raises the possibility that anthropogenic LMH declines might interact with changing patterns of rainfall to alter small-mammal distribution and behaviour, independent of numerical responses by small mammals to these perturbations. For example, increased rainfall in East Africa (as predicted in many recent climate-model simulations) may relax constraints on small-mammal distribution where LMH are rare or absent, whereas increased aridity and/or drought frequency may tighten them.
Data and code for: The role of indirect interspecific effects in the stochastic dynamics of a simple trophic system
<p>Understanding indirect interspecific effects (IIEs) on population dynamics is key for predicting community dynamics. Yet, empirically teasing apart IIEs from other interactions and population drivers is data-demanding. We used stochastic population models parameterized with long-term vital rate time series to simulate population trajectories and examine IIEs in a high-arctic vertebrate trophic chain: Svalbard reindeer, its scavenger (Arctic fox), and a migratory fox prey (barnacle goose). Reindeer carcass supply shaped fox abundance fluctuations, subsequently affecting goose fluctuations. Yet reindeer and goose population growth rates were only weakly correlated, probably due to stochasticity, density dependence, and life history traits. However, by isolating the effects of individual processes within our simulation model, we demonstrate the presence of strong IIEs on goose population fluctuations and extinction probability. Thus, we highlight the long-term impact of species interactions, including IIEs, on species coexistence and communities, beyond immediate effects and short-term fluctuations.</p>
Trophic rewilding benefits a tropical community through direct and indirect network effects
Species reintroductions can be used as a conservation strategy to restore ecological interactions and the functionality of impoverished ecosystems. The ecological effects of reintroductions go beyond restoring pairwise interactions, because reintroductions can change how extant species are indirectly linked to each other in an ecological community. These indirect pathways, in turn, may shape a myriad of ecological and evolutionary processes operating in ecological systems. Here, we investigated how reintroductions may affect the direct and indirect pathways connecting species in ecological networks. We modeled the potential effects of the reintroduction of four frugivore species (channel-billed toucans, red-humped agoutis, brown howler monkeys and yellow-footed tortoises) to the local seed dispersal network in an Atlantic Forest site, the Tijuca National Park (Tijuca, Brazil). We used a seed dispersal interaction dataset together with data on species occurrences in Tijuca to build network models. Then, we calculated how network structure and the total amount of indirect effects varied across simulated networks with and without the reintroduced species. Using random reintroduction simulations, we tested if the observed network changes were expected merely from the increase in species richness. The reintroduction of the frugivore species increased network connectance, nestedness, robustness, number of pathways and total amount of indirect effects in all simulated networks. The increase in number of pathways with the addition of the four reintroduced species was greater than the sum of isolated effects for each species, as some interaction pathways contained several reintroduced species. These changes in network metrics were significantly greater than if a randomly chosen set of four species were reintroduced. Furthermore, our results indicate that multiple reintroductions in the same area, known as refaunation, may have an even greater restoration effect than single species reintroductions through increased indirect connections in the network.
Disturbance and indirect effects of climate warming support a plant invader in mountains
<p><strong>ABSTRACT </strong>from the connected paper [Haider, S., Palm, S., Bruelheide, H., de Villemereuil, Menzel, A. & Lachmuth, S. (2022): Disturbance and indirect effects of climate warming support a plant invader in mountains. Oikos, https://doi.org/10.1111/oik.08783]:</p> <p>Climate warming and increased disturbance (resulting from intensified land use) are expected to enhance the invasibility of plant communities and the performance of exotic species also at high elevations, and thus pose additional threats to mountain ecosystems. The invasion success of introduced genotypes will also depend on their degree of pre-adaption to high elevation climatic conditions, which may vary intra-specifically across source populations. For populations currently spreading in the lowlands, climate warming might reduce the climatic distance to high-elevation sites and thus remove a barrier to upwards spread.</p> <p>Here, we investigated the various facets of mountain invasions in a single, integrative experimental study. We applied a community transplant approach between high- and low-elevation sites in the European Alps to address effects of climate warming and disturbance through land use on community invasibility and the performance of the exotic species <em>Senecio inaequidens</em>, a potential future plant invader in the Alps. Additionally, the transplant sites served as common gardens to test the influence of climatic pre-adaptation to current (high site) and future (low site) climatic conditions on the performance of <em>S. inaequidens</em> in the transplanted communities. The 16 invasive Central and Western European <em>S. inaequidens</em> source population locations covered a wide geographic range, and thus a wide amplitude of climatic distances and presumed pre-adaptation to our gardens.</p> <p>Our results attest to a strong effect of disturbance, which increased community invasibility, and promoted the performance of the exotic species. Contrary to our expectation, experimentally induced climate warming did not increase community invasibility. However, the performance of the <em>S. inaequidens</em> populations was positively related to their pre-adaptation to the climatic conditions of our common gardens. Climate warming might thus promote the invasion of exotic species by reducing the climatic distance between mountain ranges and locations of potential source populations.</p> <p><strong>DESCRIPTION </strong>of the data can be found in the Material and methods section of the paper, and in the meta-data sheet included in each data file.</p>
Grazing changes the direction of direct effect of shrubs on nematode communities but suppresses indirect effects through microbial pathways
<p>It is well established that dominant plants shape belowground communities, which in turn influence ecosystem functioning. Similarly, herbivores affect belowground communities through physical disturbance and redistribution of organic inputs, but also through their interactions with the plants themselves. However, we know little about how grazing moderates effects of dominant plants on belowground organisms. We established a three-year removal experiment in a grazed and an ungrazed alpine meadow on the Qinghai-Tibet plateau to explore how grazing mediates the effects of the dominant shrub, <em>Dosiphora fruticosa</em>, on nematode communities. We applied structural equation modelling to assess how grazing moderates the effects of <em>D. fruticosa</em> on nematode communities both directly and indirectly via changes in soil physicochemical properties<span>, root biomass and microbial communities</span>. We found that 1) grazing changed the direction of the direct effect of shrub on nematode communities as indicated by the shift from a negative to a positive path coefficient; 2) shrub affected nematode richness mainly through microbial richness. Accordingly, nematode community composition was more closely related to microbial community composition in the ungrazed alpine meadow, while edaphic properties were stronger predictors of nematode community composition responses to shrubs in the grazed meadow; and 3) grazing suppressed the indirect effects of shrub on nematode communities via microbial communities. Our study shows that grazing plays an important role in regulating dominant plant's effects on belowground community composition and interactions in alpine meadows.</p>
Direct and indirect effects of fire on microbial communities in a pyrodiverse dry-sclerophyll forest
<p>Fire is one of the predominant drivers of the structural and functional dynamics of forest ecosystems. In recent years, novel fire regimes have posed a major challenge to the management of pyrodiverse forests. While previous research efforts have focused on quantifying the impacts of fire on above-ground forest biodiversity, how microbial communities respond to fire is less understood, despite their functional significance.</p> <p>Here, we describe the effects of time since fire, fire frequency and their interaction on soil and leaf litter fungal and bacterial communities from the pyrodiverse, <em>Eucalyptus pilularis</em> forests of south-eastern Australia. Using structural equation models, we also elucidate how fire can influence these communities both directly and indirectly through biotic-abiotic interactions.</p> <p>Our results demonstrate that fire is a key driver of litter and soil bacterial and fungal communities, with effects most pronounced for soil fungal communities. Notably, recently burnt forest hosted lower abundances of symbiotic ectomycorrhizal fungi and Acidobacteria in the soil, and basidiomycetous fungi and Actinobacteriota in the litter. Compared with low fire frequencies, high fire frequency increased soil fungal plant pathogens, but reduced Actinobacteriota. The majority of fire effects on microbial communities were mediated by fire-induced changes in litter and soil abiotic properties. For instance, recent and more frequent fire was associated with reduced soil sulphur, which led to an increase in soil fungal plant pathogens and saprotrophic fungi in these sites. Pathogenic fungi also increased in recently burnt forests that had a low fire frequency, mediated by a decline in litter carbon and an increase in soil pH in these sites.</p> <p><em>Synthesis</em>. Our findings indicate that predicted increases in the frequency of fire <span>may select for specific microbial communities directly and indirectly through ecological interactions, which may have functional implications</span> for plants (increase in pathogens, decrease in symbionts), decomposition rates (declines in Actinobacteriota and Acidobacteriota) and carbon storage (decrease in ectomycorrhizal fungi). In the face of predicted shifts in wildfire regimes, which may exacerbate fire-induced changes in microbial communities, adaptive fire-management and monitoring is required to address the potential functional implications of fire-altered microbial communities<span>.</span></p>
Data from: Disentangling direct from indirect effects of habitat disturbance on multiple components of biodiversity
<p><span>Human habitat disturbance affects both species diversity and intraspecific genetic diversity, leading to correlations between these two components of biodiversity</span><span> </span><span>(termed species - genetic diversity correlation, SGDC). However, whether</span><span> </span><span>SGDC predictions extend to host-associated communities, such as the intestinal parasite and gut microbial diversity, remains largely unexplored.</span><span> </span><span>Additionally, the role of dominant generalist species is often neglected despite their importance in shaping the environment experienced by other members of the ecological community, and their role as source, reservoir and vector of zoonotic diseases. New analytical approaches (e.g., structural equation modelling, SEM) can be used to assess SGDC relationships and distinguish among direct and indirect effects of habitat characteristics and disturbance on the various components of biodiversity</span><span>.</span></p> <p><span>With six concrete and biologically sound models in mind, we collected habitat characteristics of 22 study sites from four distinct landscapes located</span><span> </span><span>in central Panama. Each landscape differed in the degree of human disturbance and fragmentation measured by several quantitative variables, such as canopy cover, canopy height and understory density.</span><span> </span><span>In terms of biodiversity, we estimated on the one hand, 1) small mammal species diversity, and, on the other hand, 2) genome-wide diversity, 3) intestinal parasite diversity and 4) gut microbial heterogeneity of the most dominant generalist species (Tome's spiny rat, <em>Proechimys semispinosus</em>). We used</span><span> </span><span>SEMs to assess the links between habitat characteristics and biological diversity measures.</span></p> <p><span>The best supported SEM suggested that habitat characteristics directly and positively affect the richness of small mammals, the genetic diversity of <em>P. semispinosus</em> and its gut microbial heterogeneity. Habitat characteristics did not, however, directly impact intestinal parasite diversity.</span><span> </span><span>We</span><span> also </span><span>detected indirect, positive effects of habitat characteristics on both host-associated assemblages via small mammal richness. For microbes, this is likely linked to cross species transmission, particularly in shared and/or anthropogenically altered habitats, whereas host diversity mitigates parasite infections. The SEM revealed an additional indirect but negative effect on </span><span>intestinal</span><span> parasite diversity via host genetic diversity.</span></p> <p><span>Our study </span><span>showcases that habitat alterations not only affect species diversity and host genetic diversity in parallel, but also species diversity of host-associated assemblages. The impacts from </span><span>human disturbance are therefore expected to ripple through entire ecosystems with far reaching effects felt even by generalist species.</span></p>
Dataset for: Stronger Response to the Aerosol Indirect Effect due to Cooling in Remote Regions
<p>Data and Python scripts for generating the figures in Huusko, L., Modak, A., & Mauritsen, T. (2022): Stronger Response to the Aerosol Indirect Effect due to Cooling in Remote Regions. <em>Geophysical Research Letters</em>, 49, e2022GL101184. <a href="https://doi.org/10.1029/2022GL101184">https://doi.org/10.1029/2022GL101184</a></p>
Data for: Direct and indirect effects of management and landscape on biological pest control and crop pest infestation in apple orchards
<p>Biological pest control, relying on naturally occurring predator-prey dynamics, is considered a key element to achieve more sustainable farming systems. However, the combined effects of local management and landscape factors on communities of natural enemies as well as the cascading effects on pest infestations are rarely addressed, especially in perennial crops. Here, we used Piecewise Structural Equation Modelling (PSEM) to test direct and indirect effects of landscape composition, landscape configuration and local management practices on natural enemy communities, the pest control services they provide and ultimately on pest infestation and pest-related yield damage in apple crops. To this end, we surveyed 12 organic and 12 Integrated Pest Management (IPM) orchards during three consecutive years, and we also established a semi-natural benchmark to quantify the extent to which predator communities in the orchards were degraded. Natural enemies had a different community composition and were more abundant in organic orchards compared to IPM orchards. This had a small and positive effect on sentinel egg predation rates in organic orchards, but overall had very little impact on actual apple pest infestation. On the contrary, apple pest infestation levels were directly and positively affected by organic management practices and by increasing semi-natural habitat cover and landscape edge density. Compared to a semi-natural benchmark, both agricultural management systems showed degraded predator communities, which translated into an impaired delivery of biological control services. Synthesis and applications. Our results indicate that organic management and habitat conservation can enhance natural enemies and stimulate pest control, but also show that these factors can enhance pest infestations and can even lead to an overall increase in pest-related crop damage. Our study thus highlights the complex interplay of ecosystem services and disservices provided by biodiversity, which should be taken into account when advising farmers, policy makers and land managers on effective and sustainable strategies to control pest species and safeguard crop production.</p>
Chromophore-driven optical path reduction as an indirect inner filter effect correction strategy in fluorescence microplate assays - experimental data
<p>Experimental data for the paper entitled <em>Chromophore-driven optical path reduction as an indirect inner filter effect mitigation strategy in fluorescence microplate assays</em> (<a title="Persistent link using digital object identifier" href="https://doi.org/10.1016/j.saa.2025.127049" target="_blank" rel="noreferrer noopener"><span><span>https://doi.org/10.1016/j.saa.2025.127049</span></span></a>). </p> <p>An Excel file with multiple worksheets is provided for the following:</p> <p>1. Fluorescence data:</p> <p>The worksheets contain fluorescence values measured in tetraplicates using two microplate readers (Tecan Spark M10, Tecan, Austria and SpectraMax iD3, Molecular Devices, USA), with baseline values recorded in octuplicates. The results were averaged and baseline-corrected. Detailed notes on the titration experiments are included in the manuscript. Data include both IFE-uncorrected fluorescence and fluorescence corrected (fully or partially) by the addition of an absorbing chromophore.</p> <p>2. Absorbance data:</p> <p>All measured absorbance values obtained using the Tecan Spark M10 microplate reader with UV-Vis transparent microplates are included. The absorbance values at specific wavelengths suitable for the Lakowicz IFE correction method or for determining the concentration of the compound are given separately.</p> <p>3. Fluorescein spectra:</p> <p>UV-Vis and fluorescence excitation/emission spectra for highly dilute fluorescein concentrations where the inner filter effect (IFE) is negligible are reported. These measurements were performed to obtain “true” excitation and emission spectra without the influence of IFE quenching effects.</p> <p>4. ZINFE/NINFE IFE corrections:</p> <p>The dataset contains the results of ZINFE/NINFE IFE corrections (<a href="https://doi.org/10.1021/acs.analchem.2c01031">https://doi.org/10.1021/acs.analchem.2c01031</a>) applied to the fluorescence data and processed using the web service available at <a href="https://ninfe.science">https://ninfe.science</a>.</p> <p>The notation of the fluorophores and microplates is the same as in the manuscript. For reasons of visual clarity, the numerical titration indices are not in subscript.</p> <p> </p>
New Zealand native forest plant cover data for Popovic et al. MEE (2019), Untangling direct species associations from indirect mediator species effects with graphical models.
<p>Forest cover measurements were collected at 1246 native forest sites that form part of a network of permanent 20 x 20 m plots spread throughout New Zealand. A total of 1831 plant species were present in these plots, with the most common being herbs, graminoids, ferns, shrubs and trees. Plant cover (in ordinal categories) was assessed for each species in several tiers at different heights. The cover data we analysed (<em>NZ_native_forest_cover.csv) </em>were the maximum cover recorded over all the tiers at the 964 sites identified as native forests, containing 1311 species with at least one presence. <em>NZ_native_forest_species.csv</em> contains species data including species name, exotic/native, and plant type (tree, shrub, etc.), corresponding to the plant species in the columns of <em>NZ_native_forest_cover.csv</em>.</p> <p>We acknowledge the use of data drawn from the Natural Forest plot data collected between January 2002 and March 2007 by the LUCAS programme for the Ministry for the Environment, New Zealand.</p> <p> </p>
Data from: Direct and indirect effects of landscape and field management intensity on carabids through trophic resources and weeds
<p>Carabids are important biological control agents of weeds and other pests in agricultural fields. The carabid community is built upon direct and indirect ecological effects of landscape complexity, field management intensity and biotic components that in interaction make any prediction of community size and composition challenging.</p> <p>We analyse a large-scale sample of 60 European cereal fields using Structural Equation Modelling to quantify the direct effects of field management intensity and the surrounding landscape, and their indirect effect via biotic components, on carabid diversity.</p> <p>Our results highlight that direct and indirect effects of increasing landscape complexity, mediated by trophic resources, mainly affect carabids positively. Field management intensity only ever affects carabids through indirect effects that are generally negative, by suppressing standing weeds and weed seeds.</p> <p>Indirect effects on granivore carabid species depended on weed seed availability whereas omnivores depended on the availability of both weed seeds and animal prey.</p> <p><i>Synthesis and applications</i><span>: A consideration of both the direct and indirect effects of landscape and field management is necessary for predicting carabid communities and with interactions. These effects, mediated via trophic resources, supports the diversity and abundance of carabid communities and their provision of ecosystem services. Our results show that promoting crop diversity and connectivity to semi-natural habitats will directly enhance carabid communities in farmland by manipulating their migration from source habitats. A reduction in field management intensity will preserve local standing weeds and weed seeds, and indirectly support carabid communities. These local and landscape modifications could contribute to improve the natural regulation of pests and weeds by carabids.</span></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.