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262 results for “indirect effects”
Data from: Direct and indirect effects of nitrogen enrichment on soil organisms and carbon and nitrogen mineralization in a semi‐arid grassland
1. Semi-arid grasslands on the Mongolian Plateau are expected to experience high inputs of anthropogenic reactive nitrogen in this century. It remains unclear, however, how soil organisms and nutrient cycling are directly affected by N enrichment (i.e., without mediation by plant input to soil) vs. indirectly affected via changes in plant-related inputs to soils resulting from N enrichment. 2. To test the direct and indirect effects of N enrichment on soil organisms (bacteria, fungi, and nematodes) and their associated C and N mineralization, in 2010 we designated two subplots (with plants and without plants) in every plot of a six-level N-enrichment experiment established in 1999 in a semi-arid grassland. 3. In 2014, 4 years after subplots with and without plant were established, N enrichment had substantially altered the soil bacterial, fungal, and nematode community structures due to declines in biomass or abundance whether plants had been removed or not. N enrichment also reduced the diversity of these groups (except for fungi) and the soil C mineralization rate and induced a hump-shaped response of soil N mineralization. As expected, plant removal decreased the biomass or abundance of soil organisms and C and N mineralization rates due to declines in soil substrates or food resources. 4. Analyses of plant removal-induced changes (ratios of without- to with-plant subplots) showed that microorganisms and C and N mineralization rates were not enhanced as N enrichment increased but that nematodes were enhanced as N enrichment increased, indicating that the effects of plant removal on soil organisms and mineralization depended on trophic level and nutrient status.5. Surprisingly, there was no statistical interaction between N enrichment and plant removal for most variables, indicating that plant-related inputs did not qualitatively change the effects of N enrichment on soil organisms or mineralization. Structural equation modeling confirmed that changes in soil communities and mineralization rates were more affected by the direct effects of N enrichment (via soil acidification and increased N availability) than by plant-related indirect effects. Our results provide insight into how future changes in N-deposition and vegetation may modify below-ground communities and processes in grassland ecosystems.
Data from: Fatiguing effects of indirect vibration stimulation in upper limb muscles- post and during isometric contractions superimposed on upper limb vibration
Whole body vibration and upper limb vibration (ULV), continues to gain popularity as exercise intervention for rehabilitation and sports applications. However, the fatiguing effects of indirect vibration stimulation are not yet fully understood. We investigated the effects of ULV stimulation superimposed on fatiguing isometric contractions using a purpose developed upper limb stimulation device. Thirteen healthy volunteers were exposed to both ULV superimposed to fatiguing isometric contractions (V) and isometric contractions alone- Control (C). Both Vibration (V) and Control (C) exercises were performed at 80% of the maximum voluntary contractions. The stimulation used was 30 Hz frequency of 0.4 mm amplitude. Surface-electromyographic (EMG) activity of the Biceps Brachii, Triceps Brachii, and Flexor Carpi Radialis were measured. EMG amplitude (EMGrms) and mean frequency (MEF) were computed to quantify muscle activity and fatigue levels. All muscles displayed significantly higher reduction in MEFs and corresponding significant increase in EMGrms with the V than the Control, during fatiguing contractions (P < 0.05). Post vibration, all muscles showed higher levels of MEFs after recovery compared to the control. Our results show that near maximal isometric fatiguing contractions superimposed on vibration stimulation lead to a higher rate of fatigue development compared to the isometric contraction alone in the upper limb muscles. Results also show higher manifestation of mechanical fatigue post treatment with vibration compared to the control. Vibration superimposed on isometric contraction not only seems to alter the neuromuscular function during fatiguing efforts by inducing higher neuromuscular load but also post vibration treatment.
Data from: Indirect genetic effects and the genetic bases of social dominance: evidence from cattle
Genetic studies of social behaviour have currently received new impetus from models including indirect genetic effects (IGEs) of social partners. This study aimed at investigating the contribution of conspecifics in social dominance, considered as response of dyadic interaction that is, winning (dominant individual) or losing (subordinate). A genetic correlation of −1 is expected between the attitude to win and the attitude to loose, and because a population always accounts for half winners and half losers, the heritability of the dominant status should be close to zero. Specifically, social dominance was studied in Aosta Chestnut and Aosta Black Pied (Bos taurus) breeds, alpine rustic cattle famous for traditional tournaments where pairs of cows assess dominant status in bloodless fights. The outcomes of 25 590 dyadic interactions performed by 8159 individuals in 11 years were analysed by applying a classical quantitative model and models including indirect effects. Data were analysed via Bayesian approach on a threshold trait. The assessment of variances revealed a genetic correlation of −0.976 between direct and indirect genetic components. The heritability measured on a liability scale was 0.122 for direct phenotype, but decreased to 0.014 when the total heritable variance (TBV) was considered. The trend of estimated breeding values showed that the total TBV was constant over the years, even though its direct component increased and the indirect part decreased. This result confirms the relevance of IGEs on social behaviour and the assumption that the mean individual social dominance cannot evolve within a population, due to the evolutionary constraints imposed by the 'social environment'.
Data from: Direct and indirect genetic and fine-scale location effects on breeding date in song sparrows
Quantifying direct and indirect genetic effects of interacting females and males on variation in jointly expressed life-history traits is central to predicting microevolutionary dynamics. However, accurately estimating sex-specific additive genetic variances in such traits remains difficult in wild populations, especially if related individuals inhabit similar fine-scale environments. Breeding date is a key life-history trait that responds to environmental phenology and mediates individual and population responses to environmental change. However, no studies have estimated female (direct) and male (indirect) additive genetic and inbreeding effects on breeding date, and estimated the cross-sex genetic correlation, while simultaneously accounting for fine-scale environmental effects of breeding locations, impeding prediction of microevolutionary dynamics. We fitted animal models to 38 years of song sparrow (Melospiza melodia) phenology and pedigree data to estimate sex-specific additive genetic variances in breeding date, and the cross-sex genetic correlation, thereby estimating the total additive genetic variance while simultaneously estimating sex-specific inbreeding depression. We further fitted three forms of spatial animal model to explicitly estimate variance in breeding date attributable to breeding location, overlap among breeding locations and spatial autocorrelation. We thereby quantified fine-scale location variances in breeding date and quantified the degree to which estimating such variances affected the estimated additive genetic variances. The non-spatial animal model estimated nonzero female and male additive genetic variances in breeding date (sex-specific heritabilities: 0·07 and 0·02, respectively) and a strong, positive cross-sex genetic correlation (0·99), creating substantial total additive genetic variance (0·18). Breeding date varied with female, but not male inbreeding coefficient, revealing direct, but not indirect, inbreeding depression. All three spatial animal models estimated small location variance in breeding date, but because relatedness and breeding location were virtually uncorrelated, modelling location variance did not alter the estimated additive genetic variances. Our results show that sex-specific additive genetic effects on breeding date can be strongly positively correlated, which would affect any predicted rates of microevolutionary change in response to sexually antagonistic or congruent selection. Further, we show that inbreeding effects on breeding date can also be sex specific and that genetic effects can exceed phenotypic variation stemming from fine-scale location-based variation within a wild population.
Data from: Indirect genetic effects underlie oxygen-limited thermal tolerance within a coastal population of chinook salmon
With global temperatures projected to surpass the limits of thermal tolerance for many species, evaluating the heritable variation underlying thermal tolerance is critical for understanding the potential for adaptation to climate change. We examined the evolutionary potential of thermal tolerance within a population of chinook salmon (Oncorhynchus tshawytscha) by conducting a full-factorial breeding design and measuring the thermal performance of cardiac function and the critical thermal maximum (CTmax) of offspring from each family. Additive genetic variation in offspring phenotype was mostly negligible, although these direct genetic effects explained 53% of the variation in resting heart rate (fH). Conversely, maternal effects had a significant influence on resting fH, scope for fH, cardiac arrhythmia temperature and CTmax. These maternal effects were associated with egg size, as indicated by strong relationships between the mean egg diameter of mothers and offspring thermal tolerance. Because egg size can be highly heritable in chinook salmon, our finding indicates that the maternal effects of egg size constitute an indirect genetic effect contributing to thermal tolerance. Such indirect genetic effects could accelerate evolutionary responses to the selection imposed by rising temperatures and could contribute to the population-specific thermal tolerance that has recently been uncovered among Pacific salmon populations.
Data from: Hemiparasites can transmit indirect effects from their host plants to herbivores
Parasitic plants can serve as critical intermediaries between their hosts and other organisms; however these relationships are not well understood. To investigate the relative importance of plant traits in such interactions, we studied the role of the root hemiparasite, Castilleja levisecta (Orobanchaceae), as a mediator of interactions between the host plants it parasitizes and the lepidopteran herbivore Euphydryas editha (Nymphalidae), whose caterpillars feed on Castilleja and sequester iridoid glycosides from it. We tested whether the hemiparasite's size, leaf N concentration, and iridoid glycoside concentrations were influenced by the identity of its host plant, and then whether these traits influenced outcomes for the herbivore. We found that the hemiparasite's size and leaf N depended on the host it parasitized, and these traits in turn affected outcomes for E. editha. Specifically, Euphydryas editha survival increased with hemiparasite size and caterpillar mass increased with leaf N; caterpillars with greater mass were more likely to survive during diapause. We also found preliminary evidence that host identity influenced iridoid glycoside sequestration by the herbivore. Mean iridoid glycoside concentrations in caterpillars ranged from 1-12% depending on the host being parasitized by Castilleja. This study demonstrates that root parasitism can result in strong indirect effects on higher trophic levels, influencing organisms' survival, growth, and chemical interactions.
Data from: Modelling the co-evolution of indirect genetic effects and inherited variability
When individuals interact, their phenotypes may be affected by genes in their social partners, a phenomenon known as Indirect Genetic Effects (IGEs). In aquaculture species and some plants, competition not only affects trait levels of individuals, but also inflates variation of trait values among individuals. Variability of trait values has been studied as a quantitative trait in itself, and is often referred to as inherited variability. Although the observed phenotypic relationship between competition and variability suggests an underlying genetic relationship, models of IGE and inherited variability do not allow for such relationship. Models of trait levels show IGEs may considerably change heritable variation in trait values. Currently, we lack the tools to investigate whether this result extends to inherited variability. Here we present a model that integrates IGEs and inherited variability. In this model, the target phenotype, say growth rate, is a function of genetic and environmental effects of the focal individual and of the difference in trait values between the social partner and the focal individual, multiplied by a regression coefficient. The regression coefficient is a genetic trait which is measure of cooperation; a negative value indicates competition, a positive value cooperation, and an increasing value due to selection indicates the evolution of cooperation. Our simulations show that the model results in increased variability of body weight with increase of competition. When competition decreases, variability becomes significantly smaller. Our findings suggest we may have been overlooking an entire level of genetic variation in variability, the one due to IGEs.
Data from: Direct and indirect ecosystem effects of evolutionary adaptation in the Trinidadian guppy (Poecilia reticulata)
Ecological and evolutionary processes may interact on the same timescale, but we are just beginning to understand how. Several studies have examined the net effects of adaptive evolution on ecosystem properties. However, we do not know if the these effects are confined to direct interactions or if they propagate further through indirect ecological pathways. Even less well understood is how the combination of direct and indirect ecological effects of the phenotype promotes or inhibits evolutionary change. We coupled mesocosm experiments and ecosystem modeling to evaluate the ecological effects of local adaptation in Trinidadian guppies (Poecilia reticulata). The experiments show that guppies adapted to life with and without predators alter the ecosystem directly through differences in diet. The ecosystem model reveals that the small total indirect effect of the phenotype observed in the experiments is likely a combination of several large indirect effects which act in opposing directions. The model further suggests that these indirect effects can reverse the direction of selection that direct effects alone exert back on phenotypic variation. We conclude that phenotypic divergence can have major effects deep in the web of indirect ecological interactions and even small total indirect effects can radically change the dynamics of adaptation.
Data from: Direct and indirect effects of early-life environment on lifetime fitness of bighorn ewes
Cohort effects, when a common environment affects long-term performance, can have a major impact on population dynamics. Very few studies of wild animals have obtained the necessary data to study the mechanisms leading to cohort effects. We exploited 42 years of individual-based data on bighorn sheep to test for causal links between birth density, body mass, age at first reproduction, longevity, and lifetime reproductive success using path analysis. Specifically, we investigated whether the effect of early-life environment on lifetime fitness was the result of indirect effects through body mass or direct effects of early-life environment on fitness. Additionally, we evaluated whether the effects of early-life environment where dependant on the environment experienced during adulthood. Contrary to expectation, the effect on lifetime reproductive success mediated through body mass was weak compared to the effects found via a delay in age at first reproduction, reduced longevity, and the direct effect of birth density. Birth density also had an important indirect effect on lifetime reproductive success through reduced longevity, but only when adult density was high. Our results show that the potential long-term consequences of a harsh early-life environment on fitness are likely to be underestimated if investigations are limited to body mass instead of fitness at several life stages, or if the interactions between past and present environment is ignored.
Post-processing codes for AC for Aerosol Indirect Effects
<p>This file contains the necessary codes to process the AC model output to get the profiles of various micro-, macrophysical and radiative properties of the simulated APPRAISE and MC3E clouds. With the help of given MatLAB scripts, corresponding profiles for all these properties can be obtained for the 'control', 'no SIP' and 'no time dependent INP freezing' runs, simulated for the present-day and pre-industrial solid aerosol conditions.</p>
Data from: Quantifying direct vs. indirect effects of nectar robbers on male and female components of plant fitness
1. Plants interact simultaneously with both mutualists and antagonists. While webs of plant-animal interactions in natural systems can be highly complex, most interactions can be simplified into those that are either direct (mediated through pairwise interactions) or indirect (mediated through third-party species). Mechanistic studies of the direct and indirect pathways by which foliar herbivores affect plants have been well explored; however, mechanistic explorations of how floral herbivores, such as nectar robbers, affect total plant fitness via direct vs. indirect pathways have received less attention. 2. The goal of this study was to assess the importance of direct vs. pollinator-mediated indirect effects of a floral antagonist on female and male components of plant fitness. We focused on the hummingbird-pollinated plant scarlet gilia, Ipomopsis aggregata, which is nectar-robbed by the bumble bee Bombus occidentalis. Prior studies have found evidence for pollinator-mediated indirect effects of robbing on female and male components of I. aggregata fitness, but the mechanisms by which these indirect effects occur, and experimental evidence supporting or refuting direct effects of robbing, have been lacking. 3. We found no evidence for direct effects of robbing on plant fitness. Robbers did not act as pollinators of I. aggregata nor did they directly affect seed production by making nectar-robber holes or removing nectar in hand-pollinated flowers. Moreover, robbing had no direct effect on pollen production per flower or the ability of pollen from robbed flowers to sire seeds in hand-pollinations. 4. However, nectar robbing had indirect effects on plant reproduction mediated through per-visit pollinator effectiveness at depositing pollen in robbed vs. unrobbed flowers. A simple model of a plant-robber-pollinator system suggested that robbing effects in general may occur through more indirect mechanisms when nectar removal by robbers is high relative to nectar replenishment, and that compensation for robbing is then more profitable through the production of additional flowers. 5. Synthesis. Our results highlight the importance of indirect effects in mediating the fitness consequences of species interactions.
Data from: Direct and indirect effects of pine silviculture on the larval occupancy and breeding of declining amphibian species
1. Plantation silviculture is increasing globally and is particularly intensive in temperate coniferous forests, where densely planting trees requires practices common to non-conifer systems that can alter forest floor microhabitat, and potentially threaten amphibian persistence. Most declining amphibian species depend on specific forest microhabitats as terrestrial refugia, but amphibian extirpation associated with tree harvest alone appears unlikely, suggesting that impacts of planting forests on groundcover might better predict recent declines in amphibian occupancy. 2. We repeatedly sampled larval presence or absence of 10 amphibian species native to temperate coniferous forest in the Southeastern United States for one year at 62 isolated wetlands located in either naturally regenerating or planted forest (plantation) to assess three direct ways that planted forests might reduce amphibian breeding site occupancy by: 1) increasing conifer densities, 2) decreasing groundcover, and 3) an indirect pathway, whereby increased tree densities at plantations might reduce groundcover and thus amphibian site occupancy. 3. After controlling for wetland traits and accounting for differences in detection, breeding site occupancy for 8/10 amphibian species was dependent upon whether forests were planted surrounding wetlands (within 300 m). Herbaceous groundcover, not canopy, most commonly influenced occupancy and increased occupancy for declining surface active or fossorial amphibians. 4. Path analyses showed that, by directly and indirectly reducing groundcover (via conifer densities), plantations had significantly lower occupancy of two declining surface active or fossorial frog species, whereas two common aquatic frog species were tolerant to planting conifers. Among declining species, salamanders showed a greater reduction in occupancy than anurans, likely because of greater vulnerability to the drier forest floor conditions of plantation than naturally regenerating forests. 5. Synthesis and applications: Direct negative impacts of coniferous plantation on amphibians can be addressed by limiting groundcover and soil impacts, including switching from high intensity practices, such as mechanical chopping vegetation or bedding soil, to lower intensity site preparation treatments that are less likely to significantly disturb groundcover. Indirect negative effects of dense canopy cover at planted forests could be lowered by periodically thinning canopies prior to final harvest, thus increasing intact forest groundcover and the conservation of both common and declining amphibians.
Data from: Grazers affect selection on inflorescence height both directly and indirectly and effects change over time
Selection mediated by one biotic agent will often be modified by the presence of other biotic interactions, and the importance of such indirect effects might change over time. We conducted an 11-year field experiment to test the prediction that large grazers affect selection on floral display of the dimorphic herb Primula farinosa not only directly through differential grazing damage, but also indirectly by affecting vegetation height and thereby selection mediated by pollinators and seed predators. Exclusion of large grazers increased vegetation height and the strength of pollinator-mediated selection for tall inflorescences and seed predator-mediated selection for short inflorescences. The direct effect of grazers on selection resulting from differential grazing damage to the two scape morphs showed no temporal trend. By contrast, the increase in vegetation height in exclosures over time was associated with an increase in selection mediated by pollinators and seed predators. In the early years of the experiment, the indirect effects of grazers on selection mediated by pollinators and seed predators were weak, whereas at the end of the experiment, the indirect effects were of similar magnitude as the direct effect due to differential grazing damage. The results demonstrate that the indirect effects of a selective agent can be as strong as its direct effects, and that the relative importance of direct vs. indirect effects on selection can change over time. A full understanding of the ecological processes governing variation in selection thus requires that both direct and indirect effects of biotic interactions are assessed.
Data from: Behavior and nutritional condition buffer a large-bodied endotherm against direct and indirect effects of climate
Temporal changes in net energy balance of animals strongly influence fitness; consequently, natural selection should favor behaviors that increase net energy balance by buffering individuals against negative effects of environmental variation. The relative importance of behavioral responses to climate-induced variation in costs versus supplies of energy, however, is uncertain, as is the degree to which such responses are mediated by current stores of energy. We evaluated relationships among behavior, nutritional condition (i.e., energetic state), and spatiotemporal variation in costs versus supplies of energy available to a large-bodied endotherm, the North American elk (Cervus elaphus), occupying two ecosystems with contrasting climates; 1) a temperate, montane forest; and 2) an arid, high-elevation desert. We hypothesized that during spring through autumn, behavioral responses to the energetic landscape would be both context-dependent (i.e., would vary as a function of the environmental conditions experienced by elk in the forest versus the desert), and state-dependent (i.e., would vary as a function of the energetic state of an individual). We tested several predictions derived from that hypothesis by combining output from a biophysical model of the thermal environment with data on forage quality, animal locations, and nutritional condition of individuals. At the population level, elk in the desert selected areas that reduced costs of thermoregulation over those that provided the highest quality forage. In the forest, however, costs imposed by the thermal environment were less pronounced, and elk selected areas that increased access to high quality forage over those that reduced costs of thermoregulation. At the individual level, nutritional condition did not influence strength of selection for low-cost areas or high quality forage among elk in the forest. In the desert, however, strength of selection for low-cost areas (but not forage quality) was state-dependent - individuals in the poorest condition at the end of winter showed the strongest selection for areas that reduced costs of thermoregulation during spring and summer, and also expended the least amount of energy on locomotion. Our results highlight the importance of understanding the roles of behavior and nutritional condition in buffering endotherms against direct and indirect effects of climate on fitness.
Disentangling the direct and indirect effects of canopy and understory vegetation on the foraging habitat selection of the brown bear Ursus arctos
<p>Elucidating the factors affecting the foraging habitat selection of wildlife can further our understanding of the animal– habitat relationships and inform wildlife conservation and management. Canopy and understory vegetation may directly or indirectly affect the foraging habitat selection of carnivores through changes in habitat structure and prey availability, respectively; however, the relative importance of these two effects remains largely unknown. Dwarf bamboo Sasa kurilensis is a predominant understory plant that suppresses regeneration in the forests of northern Japan. The purpose of this study was to disentangle the direct and indirect effects of canopy forest type Larix kaempferi plantation versus natural mixed forest) and dwarf bamboo on foraging habitat selection of a large carnivore, the brown bear Ursus arctos. In the Shiretoko World Heritage, brown bears dig for cicada nymphs during summer. We evaluated the frequency of brown bear foraging on cicadas by investigating traces of digging for cicada nymphs. A structural equation model was used to statistically disentangle the direct and indirect effects of vegetation. Our results demonstrated that canopy and understory vegetation directly and indirectly affected foraging habitat selection of brown bears. Dwarf bamboo negatively affected cicada nymph density, which positively affected brown bear digging. This suggests that dwarf bamboo also had indirect negative effects on brown bears. Forest type had significant direct and indirect effects via change in cicada nymph density on foraging behavior in brown bears. Forestry managers in northern Japan, including the study site, try to remove dwarf bamboo for assisting natural regeneration. Removal of dwarf bamboo by scarification might not only promote natural regeneration, but also provide a beneficial foraging habitat for bears.</p>
Supplementary material 5 from: Scheunemann N, Russell DJ (2023) Hydrological regime and forest development have indirect effects on soil fauna feeding activity in Central European hardwood floodplain forests. Nature Conservation 53: 257-278. https://doi.org/10.3897/natureconservation.53.106260
Soil fauna feeding activity of single sites in forest development gradient
Supplementary material 4 from: Scheunemann N, Russell DJ (2023) Hydrological regime and forest development have indirect effects on soil fauna feeding activity in Central European hardwood floodplain forests. Nature Conservation 53: 257-278. https://doi.org/10.3897/natureconservation.53.106260
Soil fauna feeding activity of single sites in hydrology gradient
Supplementary material 3 from: Scheunemann N, Russell DJ (2023) Hydrological regime and forest development have indirect effects on soil fauna feeding activity in Central European hardwood floodplain forests. Nature Conservation 53: 257-278. https://doi.org/10.3897/natureconservation.53.106260
PCA of ecological site parameters of all sites in the forest development gradient
Supplementary material 2 from: Scheunemann N, Russell DJ (2023) Hydrological regime and forest development have indirect effects on soil fauna feeding activity in Central European hardwood floodplain forests. Nature Conservation 53: 257-278. https://doi.org/10.3897/natureconservation.53.106260
PCA plot of sites and environmental parameters of the hydrology gradient
Supplementary material 1 from: Scheunemann N, Russell DJ (2023) Hydrological regime and forest development have indirect effects on soil fauna feeding activity in Central European hardwood floodplain forests. Nature Conservation 53: 257-278. https://doi.org/10.3897/natureconservation.53.106260
Soil parameters of all study sites
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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.
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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
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