Biology subjects

Guarini, J.-M.

Publications and source records attributed to Guarini, J.-M..

4 recordsLinked to original sources

bioRxiv2022

A new simulation framework to evaluate the suitability of eDNA for marine and aquatic Environmental Impact Assessments

This study evaluates how eDNA information could be used within Environmental Impact Assessment (EIA). We developed an original model to simulate the conditions for which an eDNA signal detects, or does not detect, an impact on a targeted (receptor) species in a given project area. The simulation has four consecutive steps. First, a deterministic model simulated the dynamics of the receptor population and their eDNA fragment concentrations in the environment. Second, random distributions of receptor organisms and eDNA fragment quantities at steady-state were simulated within the project area. Then Simple Random Samplings were performed for both the receptor and eDNA. Third, post-sampling processes (eDNA extraction, amplification, analysis) were simulated to estimate the detection probability of the species from sample plan characteristics (size of sampling unit, number of samples collected). Fourth, we simulated an impact by modifying the growth, mortality and mobility (null, passive and active) parameters of the receptor species, then determined if an impact was detected. Detection probability curves were estimated for a range of sample volumes fitted with a Weibull cumulative distribution function. An F-like statistic compared detection curves before and after impact. Twelve scenarios were simulated. A statistically significant impact was detected with eDNA when receptor species growth rate was halved, but only in cases of null or passive mobility. When the receptor experienced both reduced growth and increased mortality rates, an impact was detected in all three mobility cases (null, passive and active). Our results suggest that an impact could be detected using eDNA if both the population dynamics of the receptor and the dynamics of DNA shed into the environment are known. These results indicate that caution should be exercised with eDNA data for EIA, but the proposed framework provides a valuable starting point to improve interpretation of indirect observation methods such as eDNA.

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bioRxiv2020

Interactions between discrete events and continuous dynamics in the regulation of scallops valve opening: insights from a biophysical model

This study constitutes a first attempt to quantify processes that govern valve gape dynamics in bivalves. We elected to focus on the scallop, Pecten maximus, not only because of its economic importance but also because it has a complex behaviour and high sensitivity to stress, which can be inferred from valve gape dynamics. The adductor muscle is the primary organ implicated in valve movements. Scallops, as other bivalves, move their valves sharply to ensure basic physiological functions or to respond to stressing conditions; these sharp events can be perceived as discrete events within a continuous dynamic. A biophysical model, originally designed for human muscles, was first selected to simulate the adductor muscle contraction, countering the passive valve opening by the umbo ligament. However, to maintain the possibility of rapid valve movements, described as typical of bivalves behaviour, it was necessary to modify the model and propose an original formulation. The resulting hybrid modelling simulates how valve opening tends to converge continuously toward a stable steady-state angle, while being interspersed with discrete, sharp closing events, deviating values from this equilibrium. The parameters of the new model were estimated by optimization using Hall-Effect Sensor valvometry data recorded in controlled conditions. Equilibrium of the continuous regime (when fiber activation equals deactivation) was estimated for a gape angle close to ca. 15 degrees, which is ca. 45% of the maximum opening angle, hence implying a constant effort produced by the adductor muscle. The distribution of time intervals between two successive discrete events did not differ significantly from a random process, but the peak amplitudes deviated from randomness, suggesting they are regulated physiologically. These results suggest that discrete events interact with continuous dynamic regimes, regulating valve opening to minimize physiological efforts and conserve energy. However, because the overall physiological state of the scallop organism conditions the activity of the adductor muscle, a complete understanding of the physiology of bivalves will require linking a more comprehensive model of valve gape dynamics with experimental observations of physiological energy consumption under different conditions.

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bioRxiv2020

Calibrating Hall-Effect valvometers accounting for electromagnetic properties of the sensor and dynamic geometry of the bivalves shell

Hall-Effect valvometry (HES) is being used to describe bivalve valve gape variations and infer environmental perturbations in a variety of aquatic environments. Surprisingly, the published calibrations in ecological literature ignore both the electromagnetic properties of HES and that the valves rotate around their hinge when they move. The high sensitivity of HES suggests these features should be accounted for explicitly to estimate measurement accurately. To address these issues, two calibration functions were developed based on the electromagnetic properties of the HES: one assumes that the HES and magnet are maintained on the same linear axis, and the second model accounts for the geometric properties of the system (i.e. variations of the angle between HES and the magnet during shell rotation). The great scallop (Pecten maximus) was used as biological model because of its large range of valve openings. HES were installed on the flat valve and magnets installed on the opposing rounded valve; 12 individuals of similar size (10 {+/-} 1(SD) cm), were equipped and placed in controlled experimental conditions. A calibration was done for each individual once time series recordings were completed. The variability of parameter estimates was calculated with a bootstrap method. The second model (with rotatation) improves valve gape distance estimates for larger openings despite the decrease of sensor sensitivity. To infer valve gape dynamics, the reciprocal calculation of the calibration function was formalized and applied to the Hall voltage time series. Our analysis suggests that under controlled laboratory conditions, scallops are partially open most of the time (inter-valve distance equal ca. 27 mm on average, or 45 % of the average maximum opening distance). Interspersed in this continuous regime, individual scallops performed closing events at a frequency of ca. 2.5 closings per hour. A closing event is a movement that is fast enough relative to the recording frequency (10 Hz) to qualify as discrete. We find that the inversed calibration model without rotation allows negative value estimates, which indicates that this calibration function is incorrect. In contrast, the inversed calibration model with valve rotation around the hinge constrains gape distance values in their domain of definition which automatically excludes sensor readings that produce negative values from estimated gape time series.

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bioRxiv2017

Estimating Muricid abundances from trapping methods used in Mediterranean Tyrian Purple industry

A new statistical method based on a stochastic dynamic model is proposed to assess population abundances of murcid species at scales relevant to both Ancient and Modern artisanal, coastal fisheries. Motivated by the long-term goal of reconstructing the dynamics of exploited murex populations during Antiquity, the objective was to quantify the population density of the banded-dye murex, Hexaplex trunculus (Linnaeus, 1758) from successive captures with baited traps, using a method similar to the technique employed in the Mediterranean purple dye industry. A stochastic model simulating cumulative captures while taking into account high variability was developed and calibrated with data acquired during a field experiment conducted on Crete Island, near Heraklion. Sampling devices were deployed in two shallow water habitats. The traps catchability and the Effective Area of Attraction were estimated using the individual speed and behavioural response toward the bait observed during independent laboratory experiments. The average density of H. trunculus was estimated at 2.2 {+/-} 1.4 SE individuals per square meter, with no significant differences between seagrass and rocky habitats, respectively. The clearing time (the time to catch all individuals within reach of the trap) of the successive experiments was 84 {+/-} 6 SE hours, on average. This means that clearing ca. 0.4 ha of subtidal area would be necessary to produce ca. 1.0 g of pure dye pigment. While the method is discussed here with respect to a particular historical context, it is generalizable to making population abundance estimates for other species such as whelks, in modern fisheries.

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