Christian E. Vincenot

Self-DNA inhibitory effects: Underlying mechanisms and ecological implications

ABSTRACT DNA is usually known as the molecule that carries the instructions necessary for cell functioning and genetic inheritance. A recent discovery reported a new functional role for extracellular DNA. After fragmentation, either by natural or artificial decomposition, small DNA molecules (between ∼50 and ∼2000 bp) exert a species specific inhibitory effect on individuals of the same species. Evidence shows that such effect occurs for a wide range of organisms, suggesting a general biological process. In this paper we explore the possible molecular mechanisms behind those findings and discuss the ecological implications, specifically those related to plant species coexistence.

Impact of the topology of metapopulations on the resurgence of epidemics rendered by a new multiscale hybrid modeling approach

Abstract Simulating epidemics in metapopulations is a challenging issue due to the large demographic and geographic scales to incorporate. Traditional epidemiologic models choose to simplify reality by ignoring both the spatial distribution of populations and possible intrapopulation heterogeneities, whereas more recent solutions based on Individual-Based Modeling (IBM) can achieve high precision but are costly to compute and analyze. We introduce here an original alternative to these two approaches, which relies on a novel hybrid modeling framework and incarnates a multiscale view of epidemics. The model relies on a technical fusion of two modeling paradigms: System Dynamics (SD) and Individual-Based Modeling. It features an aggregated representation of local outbreaks rendered in SD, and at the same time a spatially-explicit simulation of the spread between populations simulated in IBM. We first present the design of this deterministic model, show that it can reproduce the dynamics of real resurgent epidemics, and infer from the sensitivity of several spatial factors absent in compartmental models the importance of having large-scale epidemiological processes represented inside of an explicitly disaggregated metapopulation. After discussing the implications of results obtained from simulation runs and the applicability of this model, we conclude that SD–IB hybrid modeling can be an interesting choice to represent epidemics in a spatially-explicit way without necessarily taking into account individual heterogeneities, and therefore it can be considered as a valuable alternative to simple compartmental models suffering from detrimental effects of the well-mixed assumption.

Can we protect island flying foxes

Flying foxes play key ecological roles on tropical islands, yet face rising threats. Flying foxes provide critical ecosystem services by pollinating and disseminating diverse plant species. Yet, they face intensifying threats, particularly on islands. The situation is epitomized by the Indian Ocean island of Mauritius. In December 2016, the Mauritian government implemented the second mass cull of a threatened, endemic flying fox species, Pteropus niger (see the left photo), in 2 years. Government figures suggest that at least 45% of the overall P. niger population of just over 90,000 individuals were culled during the two campaigns; illegal killing and incidental mortality of pups during the culls raise likely losses to over 50%. The dire situation of island flying foxes worldwide calls for effective, science-based conservation strategies to prevent further loss of biodiversity and function.

Spatial Self-Organization of Vegetation Subject to Climatic Stress—Insights from a System Dynamics—Individual-Based Hybrid Model

In simulation models of populations or communities, individual plants have often been obfuscated in favor of aggregated vegetation. This simplification comes with a loss of biological detail and a smoothing out of the demographic noise engendered by stochastic individual-scale processes and heterogeneities, which is significant among others when studying the viability of small populations facing challenging fluctuating environmental conditions. This consideration has motivated the development of precise plant-centered models. The accuracy gained in the representation of plant biology has then, however, often been balanced by the disappearance in models of important plant-soil interactions (esp. water dynamics) due to the inability of most individual-based frameworks to simulate complex continuous processes. In this study, we used a hybrid modeling approach, namely integrated System Dynamics (SD)—Individual-based (IB), to illustrate the importance of individual plant dynamics to explain spatial self-organization of vegetation in arid environments. We analyzed the behavior of this model under different parameter sets either related to individual plant properties (such as seed dispersal distance and reproductive age) or the environment (such as intensity and yearly distribution of precipitation events). While the results of this work confirmed the prevailing theory on vegetation patterning, they also revealed the importance therein of plant-level processes that cannot be rendered by reaction-diffusion models. Initial spatial distribution of plants, reproductive age, and average seed dispersal distance, by impacting patch size and vegetation aggregation, affected pattern formation and population survival under climatic variations. Besides, changes in precipitation regime altered the demographic structure and spatial organization of vegetation patches by affecting plants differentially depending on their age and biomass. Water availability influenced non-linearly total biomass density. Remarkably, lower precipitation resulted in lower mean plant age yet higher mean individual biomass. Moreover, seasonal variations in rainfall greater than a threshold (here, ±0.45 mm from the 1.3 mm baseline) decreased mean total biomass and generated limit cycles, which, in the case of large variations, were preceded by chaotic demographic and spatial behavior. In some cases, peculiar spatial patterns (e.g., rings) were also engendered. On a technical note, the shortcomings of the present model and the benefit of hybrid modeling for virtual investigations in plant science are discussed.

Cell-Based Models in Plant Developmental Biology: Insights into Hybrid Approaches

Computer models are nowadays part of the biologists toolbox for studying biological dynamics and processes. Tissue development and functioning results from extremely complicated dynamics, that usual analysis does not come very far in terms of understanding the processes underlying those dynamics. In this context, mathematical and numerical models can help to disentangle complex interactions and to analyze non-intuitive dynamics that drives tissue development and functioning.Since these are multi-scale processes, both in time and space, there is the need to develop an appropriate modelling approach.The most promising one is hybrid modelling, that is a synthesis of the differential equation based reaction-diffusion approach at molecular and chemical continuous scales, and the Individual-Based modelling approach for simulating the mechanical and behavioural interactions of the cell ensemble constituting the tissue. Such an approach has been often used in developmental biology, both for plants and animals. In this paper, a brief history of hybrid modelling approaches and tools will be reviewed, and a simple example of its application to a current problem in plant developmental biology (the appearance of vascular patterning during plant growth) will be illustrated, showing the intuitiveness and the strength of such an approach.

Broader conservation strategies needed

Over the past 3 years, the Mauritian flying fox (Pteropus niger), a Mascarene endemic and threatened island fruit bat, has been culled to half its global population in attempts to increase fruit producers’ profits (1). As a result, its Red List status was recently reassessed from Vulnerable to Endangered (2). Culling of flying foxes has been shown to be ineffective in boosting profits of commercial fruit producers; lychee production dropped by some 70% (3) after the previous mass culling campaigns. Despite the risks, the lack of benefits, and the existence of effective alternatives (4), Mauritius is planning a new mass cull for 2018 (5). The fruit bat is the last survivor of three Pteropus species and of other large frugivores such as Dodos and giant tortoises that used to inhabit the island (6). By eating fruits and potentially disseminating seeds of about half of the native trees of the island’s forests (7), the species fulfills a keystone ecological role in Mauritius’s remnant native habitats. Only 5% of these habitats remain, and they harbor one of the most threatened biota worldwide (8). Mauritius’s biodiversity protection law was weakened in 2015 specifically to enable mass culls (9), which are supported by National Parks and Conservation Service resources that were originally intended to conserve the country’s threatened biodiversity (10). Events unfolding in Mauritius are exposing the limitations to the approach Edited by Jennifer Sills local and international conservationists and conservation organizations have used as they call for reasonable management. Evidence, appeals, petitions, articles (11), street protests, and the missions of international experts such as the International Union for Conservation of Nature (10) have been largely ignored. Conservationists should diversify and intensify their approaches for tangible results by incorporating litigation that stalls unnecessary biodiversity destruction (12). For example, the 2015 mass cull breached the law in place at the time and therefore may have been prevented by an injunction (9). In the longer term, conservationists should apply marketing persuasion principles to conservation. They should focus on educating the public, fruit producers, and ministry advisers and technicians about the ineffectiveness of culling and the nonlethal alternative solutions. Conservationists should also identify and address barriers to the implementation of evidence-based policy, including the focus on short-term goals driven by election cycles at the expense of long-term environmental interests (12). F. B. Vincent Florens* and Christian E. Vincenot University of Mauritius, Réduit, Mauritius. Department of Social Informatics, Kyoto University, Kyoto, Japan. *Corresponding author. Email: vin.florens@uom.ac.mu

How new concepts become universal scientific approaches: insights from citation network analysis of agent-based complex systems science

Progress in understanding and managing complex systems comprised of decision-making agents, such as cells, organisms, ecosystems or societies, is—like many scientific endeavours—limited by disciplinary boundaries. These boundaries, however, are moving and can actively be made porous or even disappear. To study this process, I advanced an original bibliometric approach based on network analysis to track and understand the development of the model-based science of agent-based complex systems (ACS). I analysed research citations between the two communities devoted to ACS research, namely agent-based (ABM) and individual-based modelling (IBM). Both terms refer to the same approach, yet the former is preferred in engineering and social sciences, while the latter prevails in natural sciences. This situation provided a unique case study for grasping how a new concept evolves distinctly across scientific domains and how to foster convergence into a universal scientific approach. The present analysis based on novel hetero-citation metrics revealed the historical development of ABM and IBM, confirmed their past disjointedness, and detected their progressive merger. The separation between these synonymous disciplines had silently opposed the free flow of knowledge among ACS practitioners and thereby hindered the transfer of methodological advances and the emergence of general systems theories. A surprisingly small number of key publications sparked the ongoing fusion between ABM and IBM research. Beside reviews raising awareness of broad-spectrum issues, generic protocols for model formulation and boundary-transcending inference strategies were critical means of science integration. Accessible broad-spectrum software similarly contributed to this change. From the modelling viewpoint, the discovery of the unification of ABM and IBM demonstrates that a wide variety of systems substantiate the premise of ACS research that microscale behaviours of agents and system-level dynamics are inseparably bound.

Long-term selection using a single trait criterion, non-destructive deformation, in White Leghorns: Effect over time on genetic parameters for traits related to egg production.

Although non-destructive deformation is relevant for assessing eggshell strength, few long-term selection experiments are documented which use non-destructive deformation as a selection criterion. This study used restricted maximum likelihood-based methods with a four-trait animal model to analyze the effect of non-destructive deformation on egg production, egg weight and sexual maturity in a two-way selection experiment involving 17 generations of White Leghorns. In the strong shell line, corresponding to the line selected for low non-destructive deformation values, the heritability estimates were 0.496 for non-destructive deformation, 0.253 for egg production, 0.660 for egg weight and 0.446 for sexual maturity. In the weak shell line, corresponding to the line selected for high non-destructive deformation values, the heritabilities were 0.372, 0.162, 0.703 and 0.404, respectively. An asymmetric response to selection was observed for non-destructive deformation, egg production and sexual maturity, whereas egg weight decreased for both lines. Using non-destructive deformation to select for stronger eggshell had a small negative effect on egg production and sexual maturity, suggesting the need for breeding programs to balance selection between eggshell traits and egg production traits. However, the analysis of the genetic correlation between non-destructive deformation and egg weight revealed that large eggs are not associated with poor eggshell quality.

Effect of Long-Term Selection for Non-Destructive Deformation on Egg Shape in White Leghorns

Several conventional traits, including eggshell thickness, are commonly being improved genetically as a means to increase eggshell strength. At the same time, researchers have come to recognize that factors related to egg geometry, such as egg shape, are important determinants of the variability remaining in eggshell strength, after conventional traits have been considered. Therefore, given that the value of the egg shape index –the eggs width to length ratio–depends highly on the hen strain, it is necessary to examine the relationship between eggshell strength and shape index more closely in a variety of breeds. From this perspective, by using REML methodology under a five-trait animal model, we analyzed a two-way selection experiment for non-destructive eggshell deformation in 31 generations of White Leghorns, to evaluate the effect of selection for eggshell strength on egg shape. In the strong line, which refers to the line that was selected for decreased non-destructive deformation value, the genetic correlation between eggshell breaking strength and shape index was 0.285±0.055, whereas that between non-destructive deformation and shape index was −0.021±0.063. In the weak line, these values were 0.244±0.055 and −0.093±0.060, respectively. The heritability estimates were 0.381±0.033 for non-destructive deformation, 0.349±0.029 for eggshell breaking strength, and 0.544 ±0.027 for shape index in the strong line, and 0.408±0.031, 0.468±0.032, and 0.484±0.028, respectively, in the weak line. The genetic correlation between eggshell breaking strength and shape index suggests that rounder eggs are somewhat more resistant to breakage than more elongated eggs. The moderately high heritability estimates for shape index indicate the potential to improve egg shape through genetic gain.