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93 results for “ecological dynamics”
Population ecology and dynamics of a remnant natural population of European yew (Taxus baccata) in a lowland temperate forest – implications for use in reforestation
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Social-ecological cascade effects of land-use on vertebrate pest dynamics in arid agricultural communities
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Regionalized dynamic climate series for ecological climate impact research in modern controlled environment facilities
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Data from: Detecting elusive aspects of wildlife ecology using drones: new insights on the mating dynamics and operational sex ratios of sea turtles
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Data from: Host and pathogen ecology drive the seasonal dynamics of a fungal disease, white-nose syndrome
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Data from: Cross-scale dynamics in community and disease ecology: relative timescales shape the community ecology of pathogens
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Data from: Keystone individuals alter ecological and evolutionary consumer-resource dynamics
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Data from: Explaining ecological shifts: the roles of temperature and primary production in the long-term dynamics of benthic faunal composition
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Data from: Linking topological structure and dynamics in ecological networks
Interaction networks are basic descriptions of ecological communities and are at the core of community dynamics models. Knowledge of their structure should enable us to understand dynamical properties of ecological communities. However, the relationships between dynamical properties of communities and qualitative descriptors of network structure remain unclear. To improve our understanding of such relationships, we develop a framework based on the concept of strongly connected components, which are key structural components of networks necessary to explain stability properties such as persistence and robustness. We illustrate this framework for the analysis of qualitative empirical food webs and plant-plant interaction networks. Both types of networks exhibit high persistence (on average, 99% and 80% of species, respectively, are expected to persist) and robustness (only 0.2% and 2% of species are expected to disappear following the extinction of a species). Each of the networks is structured as a large group of interconnected species accompanied by much smaller groups that most often consist of a single species. This low-modularity configuration can be explained by a negative modularity-stability relationship. Our results suggest that ecological communities are not typically structured in multispecies compartments and that compartmentalization decreases robustness.
Data from: Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with E. coli
Closely related organisms usually occupy similar ecological niches, leading to intense competition and even extinction. Such competition also can promote rapid phenotypic evolution and ecological divergence. This process may end with the stable occupation of distinct niches or, alternatively, may entail repeated bouts of evolution. Here we examine two Escherichia coli lineages, called L and S, that coexisted for more than 30,000 generations after diverging from a common ancestor. Both lineages underwent sustained phenotypic evolution based on global transcription and resource utilization profiles, with L seeming to encroach over time on the catabolic profile of S. Reciprocal invasion experiments with L and S clones from the same or different generations revealed evolutionary changes in their interaction, including an asymmetry that confirmed the encroachment by L on the niche of the S lineage. In general, L and S clones from the same generation showed negative frequency-dependent effects, consistent with stable coexistence. However, L clones could invade S clones from both earlier and later generations, whereas S clones could invade only L clones from earlier generations. In this system, the long-term coexistence of competing lineages evidently depended on successive rounds of evolution, rather than on initial divergence followed by a static equilibrium.
Data from: Ecological speciation in dynamic landscapes
Although verbal theories of speciation consider landscape changes, ecological speciation is usually modeled in a fixed geographical arrangement. Yet landscape changes occur, at different spatio-temporal scales, due to geological, climatic or ecological processes, and these changes result in repeated divisions and reconnections of populations. We examine the effect of such landscape dynamics on speciation. We use a stochastic, sexual population model with polygenic inheritance, embedded in a landscape dynamics model (allopatry-sympatry oscillations). We show that, under stabilizing selection, allopatry easily generates diversity, but species coexistence is evolutionarily unsustainable. Allopatry produces refuges whose persistence depends on the characteristic time scales of the landscape dynamics. Under disruptive selection, assuming that sympatric speciation is impossible due to Mendelian inheritance, allopatry is necessary for ecological differentiation. The completion of reproductive isolation, by reinforcement, then requires several sympatric phases. These results demonstrate that the succession of past, current and future geographical arrangements considerably influence the speciation process.
Data from: Ecological constraints coupled with deep-time habitat dynamics predict the latitudinal diversity gradient in reef fishes
We develop a spatially explicit model of diversification based on paleohabitat to explore the predictions of four major hypotheses potentially explaining the latitudinal diversity gradient (LDG), namely, the 'time-area', 'tropical niche conservatism', 'ecological limits' and 'evolutionary speed' hypotheses. We compare simulation outputs to observed diversity gradients in the global reef fish fauna. Our simulations show that these hypotheses are non-mutually exclusive and that their relative influence depends on the time scale considered. Indeed, simulations suggest that reef habitat dynamics produced the LDG during deep geological time, while ecological constraints shaped the modern LDG, with a strong influence of the reduction in the latitudinal extent of tropical reefs during the Neogene. Overall, this study illustrates how mechanistic models in ecology and evolution can provide a temporal and spatial understanding of the role of speciation, extinction and dispersal in generating contemporary biodiversity patterns.
Data from: The rate of environmental fluctuations shapes ecological dynamics in a two-species microbial system
Species interactions change when the external conditions change. How these changes affect microbial community properties is an open question. We address this question using a two-species consortium in which species interactions change from exploitation to competition depending on the carbon source provided. We built a mathematical model and calibrated it using single-species growth measurements. This model predicted that low frequencies of change between carbon sources lead to species loss, while intermediate and high frequencies of change maintained both species. We experimentally confirmed these predictions by growing co-cultures in fluctuating environments. These findings complement more established concepts of a diversity peak at intermediate disturbance frequencies. They also provide a mechanistic understanding for how the dynamics at the community level emerges from single-species behaviors and interspecific interactions. Our findings suggest that changes in species interactions can profoundly impact the ecological dynamics and properties of microbial systems.
Data from: Inference of Japanese encephalitis virus ecological and evolutionary dynamics from passive and active virus surveillance
A comprehensive monitoring strategy is vital for tracking the spread of mosquito-borne Japanese encephalitis virus (JEV), the leading cause of viral encephalitis in Asia. Virus detection consists of passive surveillance of primarily humans and swine, and/or active surveillance in mosquitoes, which may be a valuable proxy in providing insights into ecological processes underlying the spread and persistence of JEV. However, it has not been well characterized whether passive surveillance alone can capture the circulating genetic diversity to make reasonable inferences. Here, we develop phylogenetic models to infer JEV host changes, spatial diffusion patterns, and evolutionary dynamics from data collected through active and passive surveillance. We evaluate the feasibility of using JEV sequence data collected from mosquitoes to estimate the migration histories of genotypes GI and GIII. We show that divergence times estimated from this dataset were comparable to estimates from all available data. Increasing the amount of data collected from active surveillance improved time of most recent common ancestor estimates and reduced uncertainty. Phylogenetic estimates using all available data and only mosquito data from active surveillance produced similar results, showing that GI epidemics were widespread and diffused significantly faster between regions than GIII. In contrast, GIII outbreaks were highly structured and unlinked suggesting localized, unsampled infectious sources. Our results show that active surveillance of mosquitoes can sufficiently capture circulating genetic diversity of JEV to confidently estimate spatial and evolutionary patterns. While surveillance of other hosts could contribute to more detailed disease tracking and evaluation, comprehensive JEV surveillance programs should include systematic surveillance in mosquitoes to infer the most complete patterns for epidemiology, and risk assessment.
Data from: Eco-evolutionary dynamics in metacommunities: ecological inheritance, helping within species, and harming between species
Understanding selection on intra- and inter-specific interactions that take place in dispersal-limited communities is a challenge for ecology and evolutionary biology. The problem is that local demographic stochasticity generates eco-evolutionary dynamics that are generally too complicated to make tractable analytical investigations. Here, we circumvent this problem by approximating the selection gradient on a quantitative trait that influences local community dynamics, assuming that such dynamics are deterministic with a stable fixed point. We nonetheless incorporate unavoidable kin selection effects arising from demographic stochasticity. Our approximation reveals that selection depends on how an individual expressing a trait-change influences: (1) its own fitness and the fitness of its current relatives; and (2) the fitness of its downstream relatives through modifications of local ecological conditions (i.e., through ecological inheritance). Mathematically, the effects of ecological inheritance on selection are captured by dispersal-limited versions of press-perturbations of community ecology. We use our approximation to investigate the evolution of helping within- and harming between-species when these behaviours influence demography. We find that altruistic helping evolves more readily when intra-specific competition is for material resources rather than for space because in this case, the costs of kin competition tend to paid by downstream relatives. Similarly, altruistic harming between species evolves when it alleviates downstream relatives from inter-specific competition. Beyond these examples, our approximation can help better understand the influence of ecological inheritance on a variety of eco-evolutionary dynamics in metacommunities, from consumer-resource and predator-prey coevolution to selection on mating systems with demographic feedbacks.
Data from: Linking intra-specific trait variation to community abundance dynamics improves ecological predictability by revealing a growth-defence trade-off
1.Intraspecific trait change, including altered behaviour or morphology, can drive temporal variation in inter-specific interactions and population dynamics. In turn, variation in species' interactions and densities can alter the strength and direction of trait change. The resulting feedback between species′ traits and abundance permits a wide range of community dynamics that would not be expected from ecological theories purely based on species abundances. Despite the theoretical importance of these interrelated processes, unambiguous experimental evidence of how intraspecific trait variation modifies species interactions and population dynamics and how this feeds back to influence trait variation is currently required. 2.We investigate the role of trait-mediated demography in determining community dynamics and examine how ecological interactions influence trait change. We concurrently monitored the dynamics of community abundances and individual traits in an experimental microbial predator-prey-resource system. Using this data, we parameterized a trait dependent community model to identify key ecologically relevant traits and to link trait dynamics with those of species abundances. 3.Our results provide clear evidence of a feedback between trait change, demographic rates and species dynamics. The inclusion of trait-abundance feedbacks into our population model improved the predictability of ecological dynamics from r-squared of 34% to 57% and confirmed theoretical expectations of density dependent population growth and species interactions in the system. 4.Additionally, our model revealed that the feedbacks were underpinned by a trade-off between population growth and anti-predatory defence. High predator abundance was linked to a reduction in prey body size. This prey size decrease was associated with a reduction in its rate of consumption by predators and a decrease in its resource consumption. 5.Modelling trait-abundance feedbacks allowed us to pinpoint the underlying life history trade-off which links trait and abundance dynamics. These results show that accounting for trait-abundance feedbacks has the potential to improve understanding and predictability of ecological dynamics.
Figure 7 from: Capela N, Duan X, Ziółkowska EM, Topping CJ (2024) Modelling foraging strategies of honey bees as agents in a dynamic landscape representation. Food and Ecological Systems Modelling Journal 5: e99103. https://doi.org/10.3897/fmj.5.99103
Figure 7 Results of implementing different scouting and foraging strategies on the performance of model colonies in pollen collection. Three different foraging strategies (i.e. distance, quality or random) were tested for each scouting strategy (i.e. distance, quantity and random). The total amount of collected pollen, the mean number of daily foraging flights, the number of foraging flights and their success were evaluated for all combinations of scouting and foraging strategies.
Figure 5 from: Capela N, Duan X, Ziółkowska EM, Topping CJ (2024) Modelling foraging strategies of honey bees as agents in a dynamic landscape representation. Food and Ecological Systems Modelling Journal 5: e99103. https://doi.org/10.3897/fmj.5.99103
Figure 5 Scout, recruit and foragers behaviour rules. Without private and social information, model bees become scout bees. When there is no private information because they never performed a foraging flight or because the flight was unsuccessful, model bees become recruits and will search for social information. If model bees have private information, they are considered forager bees even if no social information is available in the colony. In the presence of social information, scout and forager bees can change foraging locations (50% chance).
Figure 4 from: Capela N, Duan X, Ziółkowska EM, Topping CJ (2024) Modelling foraging strategies of honey bees as agents in a dynamic landscape representation. Food and Ecological Systems Modelling Journal 5: e99103. https://doi.org/10.3897/fmj.5.99103
Figure 4 Available foraging hours and weather variables (temperature and solar radiation) for each simulation day throughout the year. Rain and wind variables are not shown, but were used to calculate the number of available foraging hours.
Figure 3 from: Capela N, Duan X, Ziółkowska EM, Topping CJ (2024) Modelling foraging strategies of honey bees as agents in a dynamic landscape representation. Food and Ecological Systems Modelling Journal 5: e99103. https://doi.org/10.3897/fmj.5.99103
Figure 3 Example of nectar (in yellow on the left side) and pollen (in blue on the right side) spatial and temporal distribution through the season. In each snapshot, a brighter colour indicates a higher amount of the resource in the polygon. A total of 12 snapshots were taken every 30 days, starting on day 15 of the simulation.
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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.