An approximation approach to spatial connectivity for a data-limited endangered species with implications for habitat restoration

Among numerous concerns, restoration ecologists are routinely plagued with the problem of where to implement conservation efforts to best maintain spatial connectivity and population structure. Knowledge about connectivity within a metapopulation could offer valuable insight to address this issue and could help with the allocation of limited resources more effectively. However, direct estimation of dispersal is challenging because species can disperse widely within a landscape. Here, we developed a novel hierarchical Bayesian model to estimate spatial connectivity from occurrence data of an endangered stream fish, Topeka shiner (Notropis topeka). Our goal was to identify dispersal corridors that are centrally connected to the metapopulation that could be beneficial in decision making about future habitat restorations aimed at maintaining population structure. Connectivity modeling is data intensive and resource managers may not have the necessary data requirements; thus, we also examined the usefulness of graph theory (i.e. network centrality) as a proxy for connectivity. Model selection identified an upstream biased asymmetric dispersal pattern for the species. We were able to quantify and map connectivity and identified over 68 km of stream reaches as highly connected to the metapopulation. Probability of occurrence in dispersal corridors (i.e. streams) increased with connectivity and decreased with drainage area, highlighting the importance of conserving dispersal corridors and preferred habitat patches. Restorations in connected locations would provide critical habitat near important dispersal corridors. Betweenness centrality was positively correlated with connectivity and occurrence in restored habitat. Modeling of metapopulation connectivity and its correlation with graph theory demonstrated the usefulness of these techniques to guide conservation actions, especially in countries where data collection efforts are not common and conservation funding is limited.This article is published as Wahl, Charles F., Nika Galic, Richard Brain, Maxime Vaugeois, Michael Weber, Kevin J. Roe, Timothy Stewart et al. "An approximation approach to spatial connectivity for a data-limited endangered species with implications for habitat restoration." Biological Conservation 291 (2024): 110470. doi:10.1016/j.biocon.2024.110470. Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted

Modelling of the appendicularian life cycle : assessment of the ecological consequences of the uniqueness of its energy acquisition process

Dans cette thèse, nous nous sommes intéressés aux appendiculaires, et plus particulièrement à l'espèce Oikopleura dioica, qui appartiennent au groupe du mésozooplancton. Toutes leurs particularités découlent principalement de leurs caractéristiques anatomiques et physiologiques : ils sécrètent une extra-structure, appelée logette, dans laquelle ils vivent dont ils contrôlent le contenu qualitatif et quantitatif en nourriture. Nous avons développé un modèle détaillant les processus liés à l'acquisition d'énergie chez Oikopleura dioica, à savoir la filtration, l'ingestion et l'assimilation. Le modèle proposé reproduit plusieurs données de la littérature, et notamment l'accumulation de nourriture dans la logette, tout en proposant une formulation originale de l'ingestion et de l'assimilation. Les résultats suggèrent qu'à de faibles valeurs de concentration alimentaire la taille des pelotes fécales n'ait pas la même proportionnalité par rapport à la taille de l'organisme qu'à des valeurs de concentration plus importantes. Egalement, il apparaît que la logette constitue une structure pouvant retarder d'une heure et demie le début de la perception d'une période de rupture alimentaire du milieu par l'organisme. En utilisant la théorie des budgets dynamiques d'énergie (DEB), nous avons élaboré un modèle standard ne représentant pas explicitement les logettes ni leurs effets sur les processus d'acquisition de l'énergie. Nous avons ensuite, sur la base de ce premier modèle sans logette, décliné une seconde version du modèle représentant explicitement les logettes ainsi que leurs effets sur les processus d'acquisition de l'énergie.In this thesis, we studied the appendicularian, specifically the species Oikopleura dioica, which are members of the mesozooplankton group. Their particular features are due to their anatomical and physiological characteristics: they secrete an extra-corporal structure, called house, where they live and use as food reservoir. As such, they control its qualitative and quantitative content. We developed a model detailing the processes of filtration, ingestion and assimilation. We formulated an original mathematical representation of the physiology of this organism which integrates the current knowledge about the above-mentioned processes. The simulations results were used to investigate the mechanisms involved in the production of fecal pellets. The results suggest that the proportionality between fecal pellet size and organism size is not the same for low and high values of environmental food concentration. Moreover the house could delay of about one and half hours the organism perception of the beginning of an alimentary interruption.Using the Dynamic Energy Budget (DEB) theory, we developed a standard model which does not take into account the house production nor its impacts on energy acquisition processes. We then proposed a second version of the model which explicitly represents the houses and their effects on energy acquisition process. The results about sizes simulations are significantly different between the two model versions

A Mechanistic Individual-Based Model of the Feeding Processes for Oikopleura dioica

International audienceA mechanistic physiological model of the appendicularian Oikopleura dioica has been built to represent its three feeding processes (filtration, ingestion and assimilation). The mathematical formulation of these processes is based on laboratory observations from the literature, and tests different hypotheses. This model accounts for house formation dynamics, the food storage capacity of the house and the gut throughput dynamics. The half-saturation coefficient for ingestion resulting from model simulations is approximately 28 mgCl-1 and is independent of the weight of the organism. The maximum food intake for ingestion is also a property of the model and depends on the weight of the organism. Both are in accordance with data from the literature. The model also provides a realistic representation of carbon accumulation within the house. The modelled half-saturation coefficient for assimilation is approximately 15 mgC l-1 and is also independent of the weight of the organism. Modelled gut throughput dynamics are based on faecal pellet formation by gut compaction. Model outputs showed that below a food concentration of 30 mgCl-1, the faecal pellet weight should represent a lower proportion of the body weight of the organism, meaning that the faecal pellet formation is not driven by gut filling. Simulations using fluctuating environmental food availability show that food depletion is not immediately experienced by the organism but that it occurs after a lag time because of house and gut buffering abilities. This lag time duration lasts at least 30 minutes and can reach more than 2 hours, depending on when the food depletion occurs during the house lifespan

Modelling effects of temperature and oxygen on the population dynamics of the European sturgeon using dynamic energy budget theory

European sturgeon (Acipenser sturio) is an anadromous fish that breeds in rivers and which was previously found on most coasts of Europe. The last population of this species, nowadays listed as critically endangered, is reproducing in the Garonne basin near Bordeaux, south-west of France. In order to avoid extinction, the applied strategy since 1985 has been to release young fish into natural environment. These young individuals resulted from the assisted reproduction of wild and/or captive mature individuals. Recently recorded data in the Garonne basin show that in some sectors, where juveniles are likely to growth, summer temperatures have reached very high levels and water column has been hypoxic. Therefore, the combined influence of these factors on the young developmental stages needs to be assessed. The main goal of our project is to provide key information for improving the management of young fish release, especially age at release and release sites that maximize the fish survival. In this purpose, we will first calibrate a standard DEB model, based on the large dataset provided by the long term ex-situ stock breeding in our research institute. This model will firstly be used to evaluate the effect of temperature and oxygen on the survival rate of the first developmental stages. Other aspects of the life cycle will also be investigated, such as the link between maturity and the migration dynamics of the species and the impact of environmental conditions on eggs quality. The last part of our project will consist in the implementation of the standard DEB model within a pre-existing Individual Based Model (IBM) of the sturgeon population dynamics in the Garonne basin. This methodology will allow us to identify which individual traits are determinant in order to maximize the reinforcement of the sturgeon population in this basin

Modélisation des effets de la température et de l'oxygène sur la dynamique de la population de l'esturgeon européen utilisant la théorie du budget énergétique dynamique

International audienceEuropean sturgeon (Acipenser sturio) is an anadromous fish that breeds in rivers and which was previously found on most coasts of Europe. The last population of this species, nowadays listed as critically endangered, is reproducing in the Garonne basin near Bordeaux, south-west of France. In order to avoid extinction, the applied strategy since 1985 has been to release young fish into natural environment. These young individuals resulted from the assisted reproduction of wild and/or captive mature individuals. Recently recorded data in the Garonne basin show that in some sectors, where juveniles are likely to growth, summer temperatures have reached very high levels and water column has been hypoxic. Therefore, the combined influence of these factors on the young developmental stages needs to be assessed. The main goal of our project is to provide key information for improving the management of young fish release, especially age at release and release sites that maximize the fish survival. In this purpose, we will first calibrate a standard DEB model, based on the large dataset provided by the long term ex-situ stock breeding in our research institute. This model will firstly be used to evaluate the effect of temperature and oxygen on the survival rate of the first developmental stages. Other aspects of the life cycle will also be investigated, such as the link between maturity and the migration dynamics of the species and the impact of environmental conditions on eggs quality. The last part of our project will consist in the implementation of the standard DEB model within a pre-existing Individual Based Model (IBM) of the sturgeon population dynamics in the Garonne basin. This methodology will allow us to identify which individual traits are determinant in order to maximize the reinforcement of the sturgeon population in this basin

Physiological variables in machine learning QSARs allow for both cross-chemical and cross-species predictions

A major challenge in ecological risk assessment is estimating chemical-induced effects across taxa without species-specific testing. Where ecotoxicological data may be more challenging to gather, information on species physiology is more available for a broad range of taxa. Physiology is known to drive species sensitivity but understanding about the relative contribution of specific underlying processes is still elusive. Consequently, there remains a need to understand which physiological processes lead to differences in species sensitivity. The objective of our study was to utilize existing knowledge about organismal physiology to both understand and predict differences in species sensitivity. Machine learning models were trained to predict chemical- and species-specific endpoints as a function of both chemical fingerprints/descriptors and physiological properties represented by dynamic energy budget (DEB) parameters. We found that random forest models were able to predict chemical- and species-specific endpoints, and that DEB parameters were relatively important in the models, particularly for invertebrates. Our approach illuminates how physiological properties may drive species sensitivity, which will allow more realistic predictions of effects across species without the need for additional animal testing

Model outputs (lines) versus experimental data (points) used for parameter estimation.

<p>Modelled filtration, ingestion and assimilation rates versus data from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078255#pone.0078255-Lombard3" target="_blank">[35]</a> (a); modelled faecal pellet rate production versus data from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078255#pone.0078255-Selander1" target="_blank">[29]</a> (b); modelled assimilation efficiency versus data from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078255#pone.0078255-Lombard3" target="_blank">[35]</a> (c); modelled ingestion efficiency data from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078255#pone.0078255-Acua1" target="_blank">[27]</a> (d).</p

The time required to empty a compartment as function of the moment when alimentary interruption starts during the house lifetime.

<p>Times required to empty the gut (a) and the house (b). Simulations with an initial food concentration of 100 and a temperature of 15°C, and during which alimentary interruptions occurred at different moments of a house lifespan.</p

Simulated carbon accumulation rate within a house as function of the environmental food concentration (from 0 to 800 ).

<p>Simulations for an organism weight of 1 (solid line), and an organism weight of 3.97 (dashed line) versus experimental data from Acuña <i>et al. </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0078255#pone.0078255-Acua1" target="_blank">[27]</a> (empty circles).</p

Fluxes and state variables dynamics during simulation at constant food concentration.

<p>Rates of filtration (F), ingestion (I) and assimilation (A) in (a); carbon mass of the house contents (HOU) and carbon mass of the gut contents (GUT) (b) in . Run performed at a temperature of 15°C and a food concentration of 100 over four house cycles for an individual organism of 1 .</p