An ecological-economic model of land-use decisions, agricultural production and biocontrol.

The regulation of agricultural pests by their natural enemies is a key step in the agroecological transition. The level of biocontrol seems, however, to highly depend on the agronomic and ecological context. It is thus important to identify the conditions under which this ecosystem service is efficient as well as the magnitude of its effects. An actual reduction of pesticide use depends on a change in farmers' decisions, calling for the consideration of economic dimensions. We develop a dynamic agroecological-economic model representing land-use and agricultural intensity decisions as well as the dynamics of a crop pest and a natural enemy. Biocontrol is assessed considering both private benefits (increase in farmers' profit) and public benefits (reduction of pesticide use) with respect to a situation without a natural enemy. We provide a theoretical assessment of the magnitude of biocontrol over a wide range of agronomic contexts (spatially explicit maps of agricultural production potential, with heterogeneous distribution and control of spatial fragmentation) and ecological contexts, described through various parameter values of a reaction-diffusion model. The contexts in which biocontrol plays a significant role are identified, and the role of key parameters is discussed. Our open-access model offers a tool to investigate alternative specifications.

Parameter Estimation in a PDE Model for the Spatial Spread of Cocoa Black Pod Disease.

In this paper, we develop an epidemiological model with both environmental (primary infection from the environmental spores reservoir) and direct transmission (secondary infection from an infected host to a susceptible pod). This model simulates the spatiotemporal evolution of cocoa black pod disease caused by Phytophthora megakarya. Since reliable parameter estimation is a central issue for modeling realistic biological systems, we used a mechanistic-statistical approach to estimate model parameters from real observations of a specific cocoa plot. In addition, to refine numerical simulations of the pathosystem, data describing the shade intensity all over the plot were exploited and led to increased model predictions accuracy and also highlighted a higher number of infected pods located in areas of the plot with higher shading intensity. Recommendations in terms of promoting cocoa farming in systems with low shading intensity may be evident if these results are confirmed. Our results also highlight the importance of the environmental spore reservoir in black pod disease dynamics.

Emerging strains of watermelon mosaic virus in Southeastern France: model-based estimation of the dates and places of introduction.

Where and when alien organisms are successfully introduced are central questions to elucidate biotic and abiotic conditions favorable to the introduction, establishment and spread of invasive species. We propose a modelling framework to analyze multiple introductions by several invasive genotypes or genetic variants, in competition with a resident population, when observations provide knowledge on the relative proportions of each variant at some dates and places. This framework is based on a mechanistic-statistical model coupling a reaction-diffusion model with a probabilistic observation model. We apply it to a spatio-temporal dataset reporting the relative proportions of five genetic variants of watermelon mosaic virus (WMV, genus Potyvirus, family Potyviridae) in infections of commercial cucurbit fields. Despite the parsimonious nature of the model, it succeeds in fitting the data well and provides an estimation of the dates and places of successful introduction of each emerging variant as well as a reconstruction of the dynamics of each variant since its introduction.

A parsimonious approach for spatial transmission and heterogeneity in the COVID-19 propagation.

Raw data on the number of deaths at a country level generally indicate a spatially variable distribution of COVID-19 incidence. An important issue is whether this pattern is a consequence of environmental heterogeneities, such as the climatic conditions, during the course of the outbreak. Another fundamental issue is to understand the spatial spreading of COVID-19. To address these questions, we consider four candidate epidemiological models with varying complexity in terms of initial conditions, contact rates and non-local transmissions, and we fit them to French mortality data with a mixed probabilistic-ODE approach. Using statistical criteria, we select the model with non-local transmission corresponding to a diffusion on the graph of counties that depends on the geographic proximity, with time-dependent contact rate and spatially constant parameters. This suggests that in a geographically middle size centralized country such as France, once the epidemic is established, the effect of global processes such as restriction policies and sanitary measures overwhelms the effect of local factors. Additionally, this approach reveals the latent epidemiological dynamics including the local level of immunity, and allows us to evaluate the role of non-local interactions on the future spread of the disease.

When sinks become sources: Adaptive colonization in asexuals.

The establishment of a population into a new empty habitat outside of its initial niche is a phenomenon akin to evolutionary rescue in the presence of immigration. It underlies a wide range of processes, such as biological invasions by alien organisms, host shifts in pathogens, or the emergence of resistance to pesticides or antibiotics from untreated areas. We derive an analytically tractable framework to describe the evolutionary and demographic dynamics of asexual populations in a source-sink system. We analyze the influence of several factors on the establishment success in the sink, and on the time until establishment. To this aim, we use a classic phenotype-fitness landscape (Fisher's geometrical model in n dimensions) where the source and sink habitats have different phenotypic optima. In case of successful establishment, the mean fitness in the sink follows a typical four-phases trajectory. The waiting time to establishment is independent of the immigration rate and has a "U-shaped" dependence on the mutation rate, until some threshold where lethal mutagenesis impedes establishment and the sink population remains so. We use these results to get some insight into possible effects of several management strategies.

Using genetic data to estimate diffusion rates in heterogeneous landscapes.

Having a precise knowledge of the dispersal ability of a population in a heterogeneous environment is of critical importance in agroecology and conservation biology as it can provide management tools to limit the effects of pests or to increase the survival of endangered species. In this paper, we propose a mechanistic-statistical method to estimate space-dependent diffusion parameters of spatially-explicit models based on stochastic differential equations, using genetic data. Dividing the total population into subpopulations corresponding to different habitat patches with known allele frequencies, the expected proportions of individuals from each subpopulation at each position is computed by solving a system of reaction-diffusion equations. Modelling the capture and genotyping of the individuals with a statistical approach, we derive a numerically tractable formula for the likelihood function associated with the diffusion parameters. In a simulated environment made of three types of regions, each associated with a different diffusion coefficient, we successfully estimate the diffusion parameters with a maximum-likelihood approach. Although higher genetic differentiation among subpopulations leads to more accurate estimations, once a certain level of differentiation has been reached, the finite size of the genotyped population becomes the limiting factor for accurate estimation.

The effect of competition on the neutral intraspecific diversity of invasive species.

This paper deals with the effect of interspecific competition on the dynamics of neutral genetic diversity in a range-expanding population. The spread of an invasive species in an environment already hosting a resident competitor is described by a traveling wave solution with minimal speed, u(t,x) = U(x - c ∗ t), of a diffusive Lotka-Volterra competition model. The description of the dynamics of neutral genetic fractions in this wave is based on a decomposition of the wave into several components, as proposed by Roques et al. (Proc Natl Acad Sci USA 109(23):8828-8833, 2012). Our analytical results reveal that the wave can be either the pulled type, corresponding to strong erosion of the diversity, or the pushed type, corresponding to maintenance of the initial diversity. The pulled/pushed nature of the wave depends on the linear or nonlinear nature of the speed c *. Our results show that, for sufficiently strong competition, the speed is nonlinear, and therefore all of the genetic diversity in the invasive population is maintained. Conversely, in the absence of competition, or when competition is mild, the speed is linear, which means that only the furthest forward fraction in the initial invasive population eventually remains in the colonization front. Our numerical results also show that the sufficient conditions of Lewis et al. (J Math Biol 45(3):219-233, 2002) and Huang (J Dyn Differ Equ 22(2):285-297, 2010) for the linearity of the speed c * can still be improved, and they show that nonlinear speeds occur across a wide region of the parameter space, providing a counterpoint to recent analytical results suggesting that nonlinear speeds only occur in certain limiting cases.

Recolonisation by diffusion can generate increasing rates of spread.

Diffusion is one of the most frequently used assumptions to explain dispersal. Diffusion models and in particular reaction-diffusion equations usually lead to solutions moving at constant speeds, too slow compared to observations. As early as 1899, Reid had found that the rate of spread of tree species migrating to northern environments at the beginning of the Holocene was too fast to be explained by diffusive dispersal. Rapid spreading is generally explained using long distance dispersal events, modelled through integro-differential equations (IDEs) with exponentially unbounded (EU) kernels, i.e. decaying slower than any exponential. We show here that classical reaction-diffusion models of the Fisher-Kolmogorov-Petrovsky-Piskunov type can produce patterns of colonisation very similar to those of IDEs, if the initial population is EU at the beginning of the considered colonisation event. Many similarities between reaction-diffusion models with EU initial data and IDEs with EU kernels are found; in particular comparable accelerating rates of spread and flattening of the solutions. There was previously no systematic mathematical theory for such reaction-diffusion models with EU initial data. Yet, EU initial data can easily be understood as consequences of colonisation-retraction events and lead to fast spreading and accelerating rates of spread without the long distance hypothesis.