| 1. |
- Arnoldi, Jean-Francois, et al.
(författare)
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Invasions of ecological communities : Hints of impacts in the invaders growth rate
- 2022
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Ingår i: Methods in Ecology and Evolution. - : Wiley. - 2041-210X. ; 13:1, s. 167-182
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Tidskriftsartikel (refereegranskat)abstract
- 1. Theory in ecology and evolution often relies on the analysis of invasion processes, and general approaches exist to understand the early stages of an invasion. However, predicting the long-term transformations of communities following an invasion remains a challenging endeavour. 2. We propose a general analytical method that uses both resident community and invader dynamical features to predict whether an invasion causes large long-term impacts on the invaded community. 3. This approach reveals a direction in which classic invasion analysis, based on initial invasion growth rate, can be extended. Indeed, we explain how the density dependence of invasion growth, if properly defined, synthetically encodes the long-term biotic transformations caused by an invasion, and therefore predicts its ultimate outcome. This approach further clarifies how the density dependence of the invasion growth rate is as much a property of the invading population as it is one of the invaded community. 4. Our theory applies to any stable community model, and directs us towards new questions that may enrich the toolset of invasion analysis, and suggests that indirect interactions and dynamical stability are key determinants of invasion outcomes.
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| 2. |
- Bartoszek, Krzysztof, et al.
(författare)
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Fast mvSLOUCH: Multivariate Ornstein-Uhlenbeck-based models of trait evolution on large phylogenies
- 2024
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Ingår i: Methods in Ecology and Evolution. - : WILEY. - 2041-210X.
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Tidskriftsartikel (refereegranskat)abstract
- <ol><li>The PCMBase R package is a powerful computational tool that enables efficient calculations of likelihoods for a wide range of phylogenetic Gaussian models.</li><li>Taking advantage of it, we redesigned the R package mvSLOUCH.</li><li>Here, we demonstrate how the new version of the package can be used to thoroughly examine the evolution and adaptation of traits in a large dataset of 1252 vascular plants through the use of multivariate Ornstein-Uhlenbeck processes.</li><li>The results of our analysis demonstrate the ability of the modelling framework to distinguish between various alternative hypotheses regarding the evolution of functional traits in angiosperms.</li> </ol>
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| 3. |
- Cirtwill, Alyssa, et al.
(författare)
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A quantitative framework for investigating the reliability of empirical network construction
- 2019
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Ingår i: Methods in Ecology and Evolution. - : WILEY. - 2041-210X. ; 10:6, s. 902-911
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Tidskriftsartikel (refereegranskat)abstract
- Descriptions of ecological networks typically assume that the same interspecific interactions occur each time a community is observed. This contrasts with the known stochasticity of ecological communities: community composition, species abundances and link structure all vary in space and time. Moreover, finite sampling generates variation in the set of interactions actually observed. For interactions that have not been observed, most datasets will not contain enough information for the ecologist to be confident that unobserved interactions truly did not occur. Here, we develop the conceptual and analytical tools needed to capture uncertainty in the estimation of pairwise interactions. To define the problem, we identify the different contributions to the uncertainty of an interaction. We then outline a framework to quantify the uncertainty around each interaction by combining data on observed co-occurrences with prior knowledge. We illustrate this framework using perhaps the most extensively sampled network to date. We found significant uncertainty in estimates for the probability of most pairwise interactions. This uncertainty can, however, be constrained with informative priors. This uncertainty scaled up to summary measures of network structure such as connectance and nestedness. Even with informative priors, we are likely to miss many interactions that may occur rarely or under different local conditions. Overall, we demonstrate the importance of acknowledging the uncertainty inherent in network studies, and the utility of treating interactions as probabilities in pinpointing areas where more study is needed. Most importantly, we stress that networks are best thought of as systems constructed from random variables, the stochastic nature of which must be acknowledged for an accurate representation. Doing so will fundamentally change network analyses and yield greater realism.
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| 4. |
- Eklöf, Anna, 1976-, et al.
(författare)
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Secondary extinctions in food webs : a Bayesian network approach
- 2013
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Ingår i: Methods in Ecology and Evolution. - : Wiley-Blackwell. - 2041-210X. ; 4:8, s. 760-770
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Tidskriftsartikel (refereegranskat)abstract
- Ecological communities are composed of populations connected in tangled networks of ecological interactions. Therefore, the extinction of a species can reverberate through the network and cause other (possibly distantly connected) species to go extinct as well. The study of these secondary extinctions is a fertile area of research in ecological network theory.However, to facilitate practical applications, several improvements to the current analytical approaches are needed. In particular, we need to consider that (i) species have different ‘a priori’ probabilities of extinction, (ii) disturbances can simultaneously affect several species, and (iii) extinction risk of consumers likely grows with resource loss. All these points can be included in dynamical models, which are, however, difficult to parameterize.Here we advance the study of secondary extinctions with Bayesian networks. We show how this approach can account for different extinction responses using binary – where each resource has the same importance – and quantitative data – where resources are weighted by their importance. We simulate ecological networks using a popular dynamical model (the Allometric Trophic Network model) and use it to test our method.We find that the Bayesian network model captures the majority of the secondary extinctions produced by the dynamical model and that consumers’ responses to species loss are best modelled using a nonlinear sigmoid function. We also show that an approach based exclusively on food web structure loses power when species at higher trophic levels are preferentially lost. Because the loss of apex predators is unfortunately widespread, the results highlight a serious limitation of studies on network robustness.
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| 5. |
- Farage, Carmel, et al.
(författare)
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Identifying flow modules in ecological networks using Infomap
- 2021
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Ingår i: Methods in Ecology and Evolution. - London : British Ecology Society. - 2041-210X. ; 12:5, s. 778-786
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Tidskriftsartikel (refereegranskat)abstract
- Analysing how species interact in modules is a fundamental problem in network ecology. Theory shows that a modular network structure can reveal underlying dynamic ecological and evolutionary processes, influence dynamics that operate on the network and affect the stability of the ecological system. Although many ecological networks describe flows, such as biomass flows in food webs or disease transmission, most modularity analyses have ignored network flows, which can hinder our understanding of the interplay between structure and dynamics. Here we present Infomap, an established method based on network flows to the field of ecological networks. Infomap is a flexible tool that can identify modules in virtually any type of ecological network and is particularly useful for directed, weighted and multilayer networks. We illustrate how Infomap works on all these network types. We also provide a fully documented repository with additional ecological examples. Finally, to help researchers to analyse their networks with Infomap, we introduce the open-source R package infomapecology. Analysing flow-based modularity is useful across ecology and transcends to other biological and non-biological disciplines. A dynamic approach for detecting modular structure has strong potential to provide new insights into the organisation of ecological networks.
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| 6. |
- Lindström, Tom, et al.
(författare)
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A spectral and Bayesian approach for analysis of fluctuations and synchrony in ecological datasets
- 2012
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Ingår i: Methods in Ecology and Evolution. - : Wiley-Blackwell. - 2041-210X. ; 3:6, s. 1019-1027
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Tidskriftsartikel (refereegranskat)abstract
- Autocorrelation within ecological time series and synchrony between them may provide insight into the main drivers of observed dynamics. We here present methods that analyse autocorrelation and synchrony in ecological datasets using a spectral approach combined with Bayesian inference. To exemplify, we implement the method on dendrochronological data of the pedunculate oak (Quercus robur). The data consist of 110 years of growth of 10 live trees and seven trees that died during a synchronized oak death in Sweden in c. 2002-2007. We find that the highest posterior density is found for a noise colour of tree growth of gamma approximate to 0.95 (i.e. pink noise) with little difference between trees, suggesting climatic variation as a driving factor. This is further supported by the presence of synchrony, which we estimate based on phase-shift analysis. We conclude that the synchrony is time-scale dependent with higher synchrony at larger time-scales. We further show that there is no difference between the growth patterns of the alive and dead tree groups. This suggests that the trees were driven by the same factors prior to the synchronized death. We argue that this method is a promising approach for linking theoretical models with empirical data.
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