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opencc-by-4.0Apr 2020View details →

Individual-based plant-pollinator networks are structured by phenotypic and microsite plant traits

Dataset associated with the manuscript "Individual-based plant-pollinator networks are structured by phenotypic and microsite plant traits" (Arroyo-Correa et al. 2020), including plant-pollinator interactions, individual plant attributes and the plant polygon map created with drone flights.

opencc-by-4.0Jun 2017View details →

Individual-based simulation model of annual movement paths for the Darwin's frog (R code and data)

Desprition of the R code I constructed an individual-based simulation model that describes the movement path of an individual Rhinoderma darwinii through 3-month displacement steps. This model was primarily developed to evaluate the age-specific movement behaviour of Darwin's frogs, however, I also used it to provide better estimates (i.e. alleviating for movement censoring) of age-specific annual displacements in the species. I developed several variations of this model through a combination of different random walk sub-models for juveniles and adults: uncorrelated non-stationary random walks (NRW), correlated non-stationary random walks (CRW), and stationary random walks (SRW). The NRW and CRW were modelled as a first-order Markovian process where the location of an individual i in time t depends on its spatial location in t - 1. The NRW is unbiased, i.e., there is no preferred direction in each movement step. In contrast, the CRW includes persistence in the directionality of movement, so there is a correlation between successive step orientations. Finally, the SRW assumes that individuals have an activity centre to which all their spatial locations are related. Related data are provided (y.txt, x.txt and age.txt)

opencc-zeroMar 2024View details →

Core individual-based model simulation script and landscape data

Habitat loss and isolation caused by landscape fragmentation represent a growing threat to global biodiversity. Existing theory suggests that the process will lead to a decline in metapopulation viability. However, since most metapopulation models are restricted to simple networks of discrete habitat patches, the effects of real landscape fragmentation, particularly in stochastic environments, are not well understood. To close this major gap in ecological theory, we developed a spatially explicit, individual-based model applicable to realistic landscape structures, bridging metapopulation ecology and landscape ecology. This model reproduced classical metapopulation dynamics under conventional model assumptions, but on fragmented landscapes, it uncovered general dynamics that are in stark contradiction to the prevailing views in the ecological and conservation literature. Notably, fragmentation can give rise to a series of dualities: a) positive and negative responses to environmental noise, b) relative slowdown and acceleration in density decline, and c) synchronization and desynchronization of local population dynamics. Furthermore, counter to common intuition, species that interact locally ("residents") were often more resilient to fragmentation than long-ranging "migrants". This set of findings signals a need to fundamentally reconsider our approach to ecosystem management in a noisy and fragmented world.

opencc-by-4.0Jan 2024View details →

Figure 2 in Adaptations in wild radish (Raphanus raphanistrum) flowering time, Part 1: Individual-based modeling of a polygenic trait

Figure 2. The relationship between the number of semidominant larger M1 alleles and days to first flower (DFF), needed to model the long-day selections. Note that six smallereffect M2 genes will add another 0 to 18 days to DFF. If each M1 allele added the same amount in the long-day selections, the relationship would be linear.

opencc-by-4.0Jan 2024View details →

Figure 1 in Adaptations in wild radish (Raphanus raphanistrum) flowering time, Part 1: Individual-based modeling of a polygenic trait

Figure 1. Goodness of fit of the modeled data (A) when compared with the recorded glasshouse data (B). Graphs show cumulative days to first flowering (DFF) adaptations in Raphanus raphanistrum populations as a result of repeated early and late days to flowering selection. In both graphs, the basal population is the black solid line in the center,the darker lines are the matched generations of early flowering (EF1, EF3, FE4,and EF5; colored orange), and late flowering (LF2 and LF3; colored purple), with and late flowering (LF2 and LF3),with the two unmatched generations (EF2 and LF2) shown in lighter tones.The far-left population (early flowering EF5) displays very little phenotypic variability, whereas the far-right population (late flowering 3) is very diverse.

opencc-by-sa-4.0Oct 2024View details →

Measuring them all: individual-based functional spatial patterns in mountain grasslands

Raw data, additional material and instructions for reproducibility for the article De Benedictis, L.L.M., Chelli, S., Canullo, R., Campetella, G., 2025. Measuring Them all: Individual-Based Functional Spatial Patterns in Mountain Grasslands. Journal of Vegetation Science 36, e70029. <a href="https://doi.org/10.1111/jvs.70029">https://doi.org/10.1111/jvs.70029</a>. Scripts are found in the linked repository.

publicMar 2024View details →

Core individual-based model simulation script and landscape data

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publicOct 2024View details →

An individual-based model trained on multiple data sources estimates population connectivity and facilitates aggregation of harvest management units

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publicAug 2024View details →

Data from: Evaluating the effects of wolf culling on livestock predation when considering wolf population dynamics in an individual-based model

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opencc-zeroAug 2020View details →

Code for individual-based simulations in "Environmental fluctuations can promote evolutionary rescue in high-extinction-risk scenarios"

Substantial environmental change can force a population onto a path towards extinction, but under some conditions, adaptation by natural selection can rescue the population and allow it to persist. This process, known as evolutionary rescue, is believed to be less likely to occur with greater magnitudes of random environmental fluctuations because environmental variation decreases expected population size, increases variance in population size, and increases evolutionary lag. However, previous studies of evolutionary rescue in fluctuating environments have only considered scenarios in which evolutionary rescue was likely to occur. We extend these studies to assess how baseline extinction risk (which we manipulated via changes in the initial population size, degree of environmental change, or mutation rate) influences the effects of environmental variation on evolutionary rescue following an abrupt environmental change. Using a combination of analytical models and stochastic simulations, we show that autocorrelated environmental variation hinders evolutionary rescue in low-extinction-risk scenarios but facilitates rescue in high-risk scenarios. In these high-risk cases, the chance of a run of good years counteracts the otherwise negative effects of environmental variation on evolutionary demography. These findings can inform the development of effective conservation practices that consider evolutionary responses to abrupt environmental changes.

opencc-zeroOct 2020View details →

SARS-CoV-2 transmission and control in a hospital setting: an individual-based modelling study

Background: Development of strategies for mitigating the severity of COVID-19 is now a top public health priority. We sought to assess strategies for mitigating the COVID-19 outbreak in a hospital setting via the use of non-pharmaceutical interventions. Methods: We developed an individual-based model for COVID-19 transmission in a hospital setting. We calibrated the model using data of a COVID-19 outbreak in a hospital unit in Wuhan. The calibrated model was used to simulate different intervention scenarios and estimate the impact of different interventions on outbreak size and workday loss. Findings: The use of high efficacy facial masks was shown to be able to reduce infection cases and workday loss by 80% (90% CrI: 73.1% - 85.7%) and 87% (CrI: 80.0% - 92.5%), respectively. The use of social distancing alone, through reduced contacts between healthcare workers, had a marginal impact on the outbreak. Our results also indicated that a quarantine policy should be coupled with other interventions to achieve its effect. The effectiveness of all these interventions was shown to increase with their early implementation. Conclusions: Our analysis shows that a COVID-19 outbreak in a hospital's non-COVID-19 unit can be controlled or mitigated by the use of existing non-pharmaceutical measures.

opencc-zeroMar 2024View details →

Long-term individual-based records of mountain goat mortality and terrain use in relation to avalanches in coastal Alaska during 2005-2022

Snow is a major, climate-sensitive feature of the Earth's surface and a catalyst of fundamentally important ecosystem processes. Understanding how snow influences sentinel species in rapidly changing mountain ecosystems is particularly critical. Whereas the effects of snow on food availability, energy expenditure, and predation are well documented, we report how avalanches exert major impacts on an ecologically significant mountain ungulate - the coastal Alaskan mountain goat (Oreamnos americanus). Using long-term GPS data and field observations across four populations (421 individuals over 17 years), we show that avalanches caused 23-65% of all mortality, depending on area. Deaths varied seasonally and were directly linked to spatial movement patterns and avalanche terrain use. Population-level avalanche mortality, 61% of which comprised reproductively important prime-aged individuals, averaged 8% annually and exceeded 22% when avalanche conditions were severe. Our findings reveal a widespread but previously undescribed pathway by which snow can elicit major population-level impacts and shape demographic characteristics of slow-growing populations of mountain-adapted animals.

opencc-zeroMar 2024View details →

Data from: Exploring the macroevolutionary impact of ecosystem engineers using an individual-based eco-evolutionary simulation

Ecosystem engineers can radically reshape ecosystems by modulating the availability of resources to other organisms through modifying either physical or biological aspects of the environment. The introduction or removal of ecosystem engineers from otherwise stable ecosystems can impact the diversity of co-occurring species, such as driving local extinctions of native taxa. While these impacts are well established over ecological timescales for a wealth of taxa, the macroevolutionary implications of the onset of ecosystem engineering behaviours are less clear. Despite this uncertainty, ecosystem engineering has been implicated in several major transitions in Earth's history including the appearance of extensive bioturbation during the Cambrian substrate revolution and associated Ediacaran-Cambrian turnover and the Great Oxygenation Event. Whether ecosystem engineers are frequently associated with turnover and extinction in deep time is not known. Here we investigate this with an eco-evolutionary simulation framework in which we assign lineages the ability to impact the fitness of co-occurring taxa through phenotype-environment feedback. We explore numerous conditions, including how frequently these feedbacks occur, and whether ecosystem engineers modify or create niches. We show that there is no general expected outcome from the introduction of ecosystem engineers. In a minority of runs, ecosystem engineering lineages completely dominate, rendering all others extinct, but in others, they persist (but do not dominate), or die out. We suggest that ecosystem engineers have complex impacts but possess the capacity to profoundly shape diversity, and it is appropriate to consider them alongside other exogenous extinction drivers in deep time.

opencc-zeroDec 2021View details →

The individual-based network structure of palm-seed dispersers is explained by a rainforest gradient

How species interactions change in space and time is a major question in ecology. In tropical forests, plant individuals share mutualistic partners (pollinators or seed dispersers), yet we have little understanding of the factors affecting these individual interaction patterns. We used a seed dispersal individual-based network describing interactions between individuals of a palm species with bird species to investigate how intrinsic and extrinsic characteristics of individual plants influence the network structure. In our work we evaluated if average canopy height, number of fruits, distance to forest gap, and habitat type influence the role of palm individuals in the network. From 102 palms, 62 individuals had their seeds dispersed at least once: 17 individual palms in the restinga, 15 in the lowland and 30 in the pre-montane habitat. Twelve bird species were recorded dispersing Euterpe edulis seeds in our study area.

zenodo36/100

Dataset for the manuscript: Modelling the within-host spread of SARS-CoV-2 infection, and the subsequent immune response, using a hybrid, multiscale, individual-based model. Part I: Macrophages.

Dataset for the manuscript: Modelling the within-host spread of SARS-CoV-2 infection, and the subsequent immune response, using a hybrid, multiscale, individual-based model. Part I: Macrophages. preprint, bioRxiv, 2022. DOI: 10.1101/2022.05.06.490883 Each zip file contains the raw computational data (as a gzip compressed tarball), YAML input files, as well as Python plotting scripts. The Python plotting scripts have dependencies on the packages: tarfile, multiprocessing, numpy, scipy, and matplotlib. Note that the Python plotting scripts plot directly from the gzip compressed tarballs. The corresponding code can be found on GitHub: https://github.com/Ruth-Bowness-Group/CAModel

opencc-by-4.0May 2022View details →

opencc-zeroJun 2022View details →

Data supporting: Drivers of individual-based, antagonistic interaction networks during plant range expansion

1. Range expansion in plant populations, especially at the colonization front, can be either limited by disproportionately large effects of antagonistic interactions or facilitated by their release. How the strength of antagonistic interactions changes along successional gradients during range expansion is still poorly documented, especially when diverse assemblages of plant antagonists (rodents, invertebrates, and birds) combine within interaction networks. 2. We study the changes in individual-based, predispersal seed-pulp predator networks along a colonization gradient in a rapidly-expanding Juniperus phoenicea population in Doñana National Park (SW Spain). Additionally, we analysed the role of individual plant traits and neighbourhood attributes in network configuration by using Exponential Random Graph Models. 3. Seven seed-pulp consumer animal species varied significantly in their frequency of interaction and prevalence. While invertebrate species were well established in old and intermediately mature stands, greenfinch (Chloris chloris) was dominant at the colonization front. Variable species roles and spread of interactions among individual plants generated changes in the configuration of interactions during plant expansion. 4. Individual plant traits strongly determined the topology of these networks, although with differences between stands. Increasing individual crop size and seeds per cone increased the interaction odds of individual plants, while seed viability showed the opposite effect. The network topology at the colonization front appeared less driven by individual traits, possibly because of the short interaction history of this recently established area. The disproportionately large effect of C. chloris in these recently established stands, potentially resulted in large seed losses during range expansion. 5. Synthesis. Turnover of antagonistic interactions, characterized the colonization front, resulting in more heterogeneous interaction strengths among individual plants. We found no evidence for a complete or sizeable antagonistic release of J. phoenicea at the colonization front promoting this rapid expansion. It becomes necessary to explore interactions with seed dispersers to understand how antagonistic and mutualistic plant-animal interactions balance during range expansion. Our study highlights the importance of an individual-based approach in understanding how interactions are structured and driven in natural changing landscapes.

opencc-zeroAug 2021View details →

Individual-based networks reveal the highly skewed interactions of a frugivore mutualist with individual plants in a diverse community

While plant-animal interactions occur fundamentally at the individual level, the bulk of research examining the mechanisms that drive interaction patterns has focused on the species or population level. In seed-dispersal mutualisms between frugivores and plants, little is known about the role of space and individual-level variation among plants in structuring patterns of frugivore foraging and, thus, seed dispersal in a plant community. Here we use an animal perspective to examine how space and variation between individual plants affect movement and visitation by frugivores foraging on individual fruiting plants. To do this, we used a spatially explicit network approach informed by observations of the movement and foraging of a frugivorous lemur species (Eulemur rubriventer) amongst individual plants in a diverse plant community in Madagascar. The resulting hierarchical networks, in which a few individual plants received the bulk of the interactions, demonstrated how a generalist frugivore species could act as an individual-plant specialist within a plant community. The few individual plants that dominated interactions with the lemurs shaped the modular spatial structure of frugivory interactions in the community and facilitated visitation to near neighbors. This interaction structure was primarily driven by extrinsic factors, as lemur movements among plants were significantly influenced by the individual plant's spatial position and the species richness of fruiting plants in its immediate neighborhood. Individual plants in central spatial locations, with a rich fruiting neighborhood and large fruit crops, received the most visits. The observed drastic inequality in the interactions of a generalist frugivore within a highly diverse plant community highlights the importance of considering individual-level variation for essential ecosystem processes, such as seed dispersal.