Timothée Poisot

Timothée Poisot
Université du Québec à Rimouski UQAR | uqar

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123
Publications
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3,115
Citations

Publications

Publications (123)
Preprint
Pathogen evolution is one of the least predictable components of disease emergence, particularly in nature. Here, building on principles established by the geographic mosaic theory of coevolution, we develop a quantitative, spatially-explicit framework for mapping the evolutionary risk of viral emergence. Driven by interest in diseases like SARS, M...
Article
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Despite having established its usefulness in the last ten years, the decomposition of ecological networks in components allowing to measure their β-diversity retains some methodological ambiguities. Notably, how to quantify the relative effect of mechanisms tied to interaction rewiring vs. species turnover has been interpreted differently by differ...
Article
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Data that catalogue viral diversity on Earth have been fragmented across sources, disciplines, formats, and various degrees of open sharing, posing challenges for research on macroecology, evolution, and public health. Here, we solve this problem by establishing a dynamically maintained database of vertebrate-virus associations, called The Global V...
Article
Despite their importance in many ecological processes, collecting data and information on ecological interactions is an exceedingly challenging task. For this reason, large parts of the world have a data deficit when it comes to species interactions, and how the resulting networks are structured. As data collection alone is unlikely to be sufficien...
Article
Full-text available
Local contributions to beta diversity (LCBD) can be used to identify sites with high ecological uniqueness and exceptional species composition within a region of interest. Yet, these indices are typically used on local or regional scales with relatively few sites, as they require information on complete community compositions difficult to acquire o...
Preprint
Metawebs, i.e. networks of potential interactions within a species pool, are a powerful abstraction to understand how large-scales species interaction networks are structured.Because metawebs are typically expressed at large spatial and taxonomic scales, assembling them is a tedious and costly process; predictive methods can help circumvent the lim...
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Despite the global investment in One Health disease surveillance, it remains difficult and costly to identify and monitor the wildlife reservoirs of novel zoonotic viruses. Statistical models can guide sampling target prioritisation, but the predictions from any given model might be highly uncertain; moreover, systematic model validation is rare, a...
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Better methods to predict and prevent the emergence of zoonotic viruses could support future efforts to reduce the risk of epidemics. We propose a network science framework for understanding and predicting human and animal susceptibility to viral infections. Related approaches have so far helped to identify basic biological rules that govern cross-...
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Networks of species interactions underpin numerous ecosystem processes, but comprehensively sampling these interactions is difficult. Interactions intrinsically vary across space and time, and given the number of species that compose ecological communities, it can be tough to distinguish between a true negative (where two species never interact) fr...
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Collecting well-resolved empirical trophic networks requires significant time, money and expertise, yet we are still lacking knowledge on how sampling effort and bias impact the estimation of network structure. Filling this gap is a critical first step towards creating accurate representations of ecological networks and for teasing apart the impact...
Preprint
NCBITaxonomy.jl is a package designed to facilitate the reconciliation and cleaning of taxonomic names, using a local copy of the NCBI taxonomic backbone (Federhen 2012, Schoch et al. 2020); The basic search functions are coupled with quality-of-life functions including case-insensitive search and custom fuzzy string matching to facilitate the amou...
Article
Ecological communities face a variety of environmental and anthropogenic stressors acting simultaneously. Stressor impacts can combine additively or can interact, causing synergistic or antagonistic effects. Our knowledge of when and how interactions arise is limited, as most models and experiments only consider the effect of a small number of non-...
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Full-text available
The fields of viral ecology and evolution are rapidly expanding, motivated in part by concerns around emerging zoonoses. One consequence is the proliferation of host–virus association data, which underpin viral macroecology and zoonotic risk prediction but remain fragmented across numerous data portals. In the present article, we propose that synth...
Preprint
Despite their importance in many ecological processes, collecting data and information on ecological interactions, and therefore species interaction networks, is an exceedingly challenging task. For this reason, large parts of the world have a deficit of data of which species interact, and what we can expect the network structure of these interacti...
Article
Full-text available
Quantifying the complexity of ecological networks has remained elusive. Primarily, complexity has been defined on the basis of the structural (or behavioural) complexity of the system. These definitions ignore the notion of “physical complexity,” which can measure the amount of information contained in an ecological network, and how difficult it wo...
Article
Full-text available
If we want to protect our environment, we first need to know where animals and plants are. Are they hidden in the woods? Are they next to cities? Which woods or which cities? Wandering all over the world to find where living things are might seem exciting at first. However, in the long run, it might get a little tiring, no? Thankfully, we do not ne...
Preprint
Full-text available
Aim: Local contributions to beta diversity (LCBD) can be used to identify sites with high ecological uniqueness and exceptional species composition within a region of interest. Yet, these indices are typically used on local or regional scales with relatively few sites, as they require information on complete community compositions difficult to acqu...
Article
Full-text available
Ecological networks are increasingly studied at large spatial scales, expanding their focus from a conceptual tool for community ecology into one that also addresses questions in biogeography and macroecology. This effort is supported by increased access to standardized information on ecological networks, in the form of openly accessible databases....
Article
The beta-diversity of interactions between communities does not necessarily correspond to the differences related to their species composition because interactions show greater variability than species co-occurrence. Additionally, the structure of species interaction networks can itself vary over spatial gradients, thereby adding constraints on the...
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Full-text available
• Observed biotic interactions between species, such as in pollination, predation, and competition, are determined by combinations of population densities, matching in functional traits and phenology among the organisms, and stochastic events (neutral effects). • We propose optimal transportation theory as a unified view for modeling species intera...
Preprint
Full-text available
Networks of species interactions can capture meaningful information on the structure and functioning of ecosystems. Yet the scarcity of existing data, and the difficulty associated with comprehensively sampling interactions between species, means that to describe the structure, variation, and change of ecological networks over time and space, we ne...
Article
The importance of climate, habitat structure, and higher trophic levels on microbial diversity is only beginning to be understood. Here, we examined the influence of climate variables, plant morphology, and the abundance of aquatic invertebrates on the microbial biodiversity of the northern pitcher plant Sarracenia purpurea. The plant's cup‐shaped...
Preprint
Quantifying the complexity of ecological networks has remained elusive. Primarily , complexity has been defined on the basis of the structural (or behavioural) complexity of the system. These definitions ignore the notion of 'physical com-plexity', which can measure the amount of information contained in an ecological network, and how difficult it...
Article
Full-text available
Predicting the number of interactions among species in a food web is an important task. These trophic interactions underlie many ecological and evolutionary processes, ranging from biomass fluxes, ecosystem stability, resilience to extinction, and resistance against novel species. We investigate and compare several ways to predict the number of int...
Preprint
Full-text available
In a rapidly changing world, the composition, diversity and structure of ecological communities face many threats. Biodiversity-Ecosystem Functioning (BEF) and community food-chain analyses have focused on investigating the consequences of these changes on ecosystem processes and the resulting functions. These different and diverging conceptual fra...
Preprint
Full-text available
Ecological networks are increasingly studied at large spatial scales, expanding their focus from a conceptual tool for community ecology into one that also adresses questions in biogeography and macroecology. This effort is supported by increased access to standardized information on ecological networks, in the form of openly accessible databases....
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Full-text available
The grand ambition of theorists studying ecology and evolution is to discover the logical and mathematical rules driving the world's biodiversity at every level from genetic diversity within species to differences between populations, communities, and ecosystems. This ambition has been difficult to realize in great part because of the complexity of...
Article
Full-text available
Networks are a convenient way to represent many interactions among ecological entities. The analysis of ecological networks is challenging for two reasons. First, there is a plethora of measures that can be applied (and some of them measure the same property). Second, the implementation of these measures is sometimes difficult. We present ’Ecologic...
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Full-text available
The structure of ecological interactions is commonly understood through analyses of interaction networks. However, these analyses may be sensitive to sampling biases with respect to both the interactors (the nodes of the network) and interactions (the links between nodes), because the detectability of species and their interactions is highly hetero...
Article
Full-text available
The productivity of marine ecosystems and the services they provide to humans are largely dependent on complex interactions between prey and predators. These are embedded in a diverse network of trophic interactions, resulting in a cascade of events following perturbations such as species extinction. The sheer scale of oceans, however, precludes th...
Article
Full-text available
Computational thinking is the integration of algorithms, software, and data, to solve general questions in a field. Computation ecology has the potential to transform the way ecologists think about the integration of data and models. As the practice is gaining prominence as a way to conduct ecological research, it is important to reflect on what it...
Article
Full-text available
Interactions among species is at the heart of ecology. Despite their importance, studying ecological interactions remains difficult due to the lack of standard information and the disparity of formats in which ecological interactions are stored (Poisot et al. 2015). Historically, ecologists have used matrices to store interactions, which tend to ea...
Article
Aim How do factors such as space, time, climate and other ecological drivers influence food web structure and dynamics? Collections of well‐studied food webs and replicate food webs from the same system that span biogeographical and ecological gradients now enable detailed, quantitative investigation of such questions and help integrate food web ec...
Article
Drawing upon the data deposited in publicly shared archives has the potential to transform the way we conduct ecological research. For this transformation to happen, we argue that data need to be more interoperable and easier to discover. One way to achieve these goals is to adopt domain-specific data representations.
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Full-text available
Aim Ecological communities are composed of both species and the biotic relationships (interactions or spatial associations) among them. Biotic homogenization in species composition (i.e., increased site‐to‐site similarity) is recognized as a common consequence of global change, but less is known about how the similarity of species relationships ch...
Article
Aim: Ecological communities are comprised of both species and the biotic relationships among them. Biotic homogenization in species composition (i.e. increased site-to-site similarity) is recognized as a common consequence of global change. Far less is known about how patterns of species relationships (interactions and/or spatial associations) chan...
Article
Biogeography has traditionally focused on the spatial distribution and abundance of species. Both are driven by the way species interact with one another, but only recently community ecologists realized the need to document their spatial and temporal variation. Here, we call for an integrated approach, adopting the view that community structure is...
Preprint
Full-text available
Computational thinking is the integration of algorithms, software, and data, to solve general questions in a field. Computation ecology has the potential to transform the way ecologists think about the integration of data and models. As the practice is gaining prominence as a way to conduct ecological research, it is important to reflect on what it...
Article
Full-text available
Although the structure of empirical food webs can differ between ecosystems, there is growing evidence of multiple ways in which they also exhibit common topological properties. To reconcile these contrasting observations, we postulate the existence of a backbone of interactions underlying all ecological networks-a common substructure within every...
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Full-text available
Network approaches to ecological questions have been increasingly used, particularly in recent decades. The abstraction of ecological systems – such as communities – through networks of interactions between their components indeed provides a way to summarize this information with single objects. The methodological framework derived from graph theor...
Preprint
Full-text available
The structure of ecological interactions is commonly understood through analyses of interaction networks. However, these analyses may be sensitive to sampling biases in both the interactors (the nodes of the network) and interactions (the links between nodes), because the detectability of species and their interactions is highly heterogeneous. Thes...
Article
Full-text available
Data are one of the primary outputs of science. Although certain subdisciplines of biology have pioneered efforts to ensure their long-term preservation and facilitate collaborations, data continue to disappear, owing mostly to technological, regulatory, and ideological hurdles. In this article, we describe the important steps toward proper data ma...
Preprint
Full-text available
Ecological communities are comprised of both species and the biotic relationships among them. Biotic homogenization in species composition (i.e. increased site-to-site similarity) is recognized a common consequence of global change, but less is known about how species relationships change over space and time. Does homogenization of species composit...
Article
Full-text available
Species interactions are a key component of ecosystems but we generally have an incomplete picture of who-eats-who in a given community. Different techniques have been devised to predict species interactions using theoretical models or abundances. Here, we explore the K nearest neighbour approach, with a special emphasis on recommendation, along wi...
Article
Full-text available
The structure of ecological interactions is commonly understood through analyses of interaction networks. However, these analyses may be sensitive to sampling biases in both the interactors (the nodes of the network) and interactions (the links between nodes). These issues may affect the accuracy of empirically constructed ecological networks. We e...
Article
Full-text available
The concordance of evolutionary histories and extant species interactions provides a useful metric for addressing questions of how the structure of ecological communities is influenced by macroevolutionary processes. 2.We introduce paco (v0.3.1), an R package to perform Procrustean Approach to Cophylogeny. This method assesses the phylogenetic cong...
Article
Both species and their interactions are affected by changes that occur at evolutionary time-scales, and shape both ecological communities and their phylogenetic structure. But because extent ecological community structure is contingent upon random chance, environmental filters, and local effects, it is unclear how much ecological signal local commu...
Article
Full-text available
Computer science offers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results, however computational science lags behind. In the best case, authors may provide their source code as a compressed archive and they may feel confident their research is reproducible. But this is not exactly true. Jam...
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Full-text available
Although there is a vast body of literature on the causes of variation in species composition in ecological communities, less effort has been invested in understanding how interactions between these species vary. Given that interactions are crucial to the structure and functioning of ecological communities, we need to develop a better understanding...
Article
Full-text available
Species interaction datasets, often represented as sparse matrices, are usually collected through observation studies targeted at identifying species interactions. Due to the extensive required sampling effort, species interaction datasets usually contain many false negatives, often leading to bias in derived descriptors. We show that a simple line...
Article
Full-text available
Networks provide one of the best representation for ecological communities, composed of many speecies with dense connections between them. Yet the methodological literature allowing one to analyse and extract meaning from ecological networks is dense, fragmented, and unwelcoming. We provide a general overview to the field, outlining both the intent...
Preprint
Full-text available
Species interactions are a key component of ecosystems but we generally have an incomplete picture of who-eats-who in a given community. Different techniques have been devised to predict species interactions using theoretical models or abundances. Here, we explore the K nearest neighbour approach, with a special emphasis on recommendation, along wi...
Preprint
Full-text available
Aim: Although there is a vast body of literature on the causes of variation in species composition in ecological communities, less effort has been invested in understanding how interactions between these species vary. Since interactions are crucial to the structure and functioning of ecological communities, we need to develop a better understanding...
Data
b) asymmetric superimposition c) symmetric superimposition a) original projection of distance matrices Figure S1: Diagrammatical representation of the alternative approaches to Procrustean superimposition in paco. In each panel (a–c), the shapes represent a phylogeny of pollinators (blue) and plants (orange) projected in multidimensional space. Das...
Data
Data on the Mendoza pollination network analysed with paco. Phylogenies of both plants and pollinators as well as their interaction network are included. There is also an R script for the analyses. Please note that the interaction network was originally published by Arroyo, M. T. K., Primack, R. B. & Armesto, J. J. (Community studies in pollination...
Article
Full-text available
Numerous theoretical and experimental studies have investigated antagonistic coevolution between parasites and their hosts. Although experimental tests of theory from a range of biological systems are largely concordant regarding the influence of several driving processes, we know little as to how mechanisms acting at the smallest scales (individua...
Preprint
Full-text available
Food webs are the backbone upon which biomass flows through ecosystems. Dynamical models of biomass can reveal how the structure of food webs is involved in many key ecosystem properties, such as persistence, stability, etc. In this contribution, we present BioEnergeticFoodWebs , an implementation of Yodzis & Innes (1992) bio-energetic model, in th...
Article
Full-text available
Data is the central currency of science, but the nature of scientific data has changed dramatically with the rapid pace of technology. This change has led to the development of a wide variety of data formats, dataset sizes, data complexity, data use cases, and data sharing practices. Improvements in high throughput DNA sequencing, sustained institu...
Preprint
Full-text available
Ecological networks represent the backbone of biodiversity. As species diversify over macro-evolutionary time-scales, the structure of these networks changes; this happens because species are gained and lost, and therefore add or remove interactions in their communities. The mechanisms underlying such dynamic changes in ecological network structure...
Preprint
Full-text available
Biogeography has traditionally focused on the spatial distribution and abundance of species. Both are driven by the way species interact with one another, but also by the way these interactions vary across time and space. Here, we call for an integrated approach, adopting the view that community structure is best represented as a network of ecologi...
Preprint
Data is the central currency of science, but the nature of scientific data has changed dramatically with the rapid pace of technology. This change has led to the development of a wide variety of data formats, dataset sizes, data complexity, data use cases, and data sharing practices. Improvements in high throughput DNA sequencing, sustained institu...
Preprint
Full-text available
Data is the central currency of science, but the nature of scientific data has changed dramatically with the rapid pace of technology. This change has led to the development of a wide variety of data formats, dataset sizes, data complexity, data use cases, and data sharing practices. Improvements in high throughput DNA sequencing, sustained institu...
Article
Full-text available
The study of ecological networks is severely limited by 1) the difficulty to access data, 2) the lack of a standardized way to link meta-data with interactions, and 3) the disparity of formats in which ecological networks themselves are stored and represented. To overcome these limitations, we have designed a data specifi cation for ecological netw...
Article
The increased availability of both open ecological data, and software to interact with it, allows the fast collection and integration of information at all spatial and taxonomic scales. This offers the opportunity to address macroecological questions in a cost-effective way. In this contribution, we illustrate this approach by forecasting the struc...
Article
Full-text available
Temperature is known to influence ecosystem processes through its direct effect on biological rates such as respiration and nutrient cycling. These changes can then indirectly affect ecologically processes by altering trophic dynamics, the persistence of a species in a given environment, and, consequently, its distribution. However, it is not known...