Biology subjects

Chavarie, L.

Publications and source records attributed to Chavarie, L..

7 recordsLinked to original sources

bioRxiv2026

No-take zone effectiveness in linear coastal systems depends on spatially heterogeneous placement and larval dispersal directionality

Marine protected areas (MPAs) are widely implemented to protect and/or rebuild exploited populations, yet their population-level effectiveness remains highly variable. Key unresolved knowledge gaps include how the size and the spatial placement of no-take zones interacts with larval dispersal directionality, particularly in linear coastal systems where connectivity is asymmetric. For sedentary species with planktonic larvae, such as European lobster, it is unclear under which dispersal regimes spatial configuration of protection critically determines positive demographic outcomes. Here, we address this gap using a spatially explicit individual-based model parameterized for the European lobster. We ask (i) whether no-take zones consistently enhance abundance and size structure relative to fished areas, and (ii) whether the positioning of no-take and open areas affects spatial protection while holding total protected area constant and (iii) how the alignment between larval dispersal direction and the positioning of no-take areas influences protection outcome. We contrast local, symmetric long-distance, and strongly unidirectional larval dispersal across alternative MPA layouts with equal total protected area but with different spacing. We show that no-take zones reliably increase abundance and the prevalence of large individuals. However, when larval dispersal is strongly unidirectional, population recovery depends on reserve placement: downstream no-take zones benefit from both larval import and local retention, whereas upstream reserves primarily export reproductive output and show limited local recovery. These results indicate that reserve performance cannot be evaluated independently of connectivity structure and identify dispersal directionality as a key determinant of when and where spatial configuration matters for MPA effectiveness in linear coastal systems.

ecology↗

bioRxiv2026

Resampling-based validation of a SNP panel for hybrid detection across generations: a case study in European lobster

Accurate detection of hybridization and introgression is critical for both evolutionary research and applied conservation. In many systems, however, hybrid ancestry is difficult to detect beyond the F1 generation, especially when based on limited genetic markers. In European waters, hybridization between the native Homarus gammarus and the invasive H. americanus poses a direct risk to the integrity of native stocks and effective fishery management, yet detection methods are often limited to morphological traits or first-generation hybrids. A set of 79 SNPs previously developed to distinguish species between American and European lobsters and F1 individuals has shown promise, but its capacity to resolve later-generation backcrosses remains untested. Here, we present a resampling-based evaluation of this panels performance under realistic introgression scenarios, using individual-based population genetic models informed by empirical data. We show that the panel retains discriminatory power across multiple hybrid classes, with diminishing accuracy in second-generation backcrosses. These findings validate the panels utility for applied monitoring and highlight the broader potential of resumpling-anchored frameworks to benchmark hybrid detection tools in a wide range of species. Article summaryThis study tests how well a reduced panel of genetic markers can detect hybridization across multiple generations. Using empirical genetic data of a 79-SNP panel from European and American lobsters, the authors generated individuals with known ancestry proportions through a resampling framework that preserves observed genetic variation. These data were analysed using model-based genetic assignment and ordination. The results show that the marker panel reliably identifies pure species and first-generation hybrids, but has reduced power to distinguish later backcross generations, mainly between adjacent hybrid classes. The study provides a practical benchmark for evaluating reduced marker panels used in applied monitoring and conservation genetics.

genomics↗

bioRxiv2025

Investigating the dynamics of the aquatic community in Oslofjord through time series analysis of eDNA

Understanding temporal dynamics of marine communities is critical for assessing ecosystem health and guiding conservation efforts. Here, we conducted a survey using environmental DNA (eDNA) metabarcoding with two primer sets, MiFish and Elas02, to investigate seasonal and interannual changes in the fish community of Oslofjord (Norway) over two consecutive years. Using the MitoFish reference database through the GBIF querying tool, we identified 61 fish species and found significant changes in the dominant taxa between seasons and years. Clupea harengus (Atlantic herring) consistently peaked in early spring, while Scomber scombrus (Atlantic mackerel) dominated winter months in the second year. The MiFish primer set showed increased species richness in the second year, whereas the Elas02 primer set showed stable richness despite compositional turnover. Non-metric multidimensional scaling (NMDS) revealed distinct community separation between years in presence/absence data, driven by species turnover rather than abundance read changes. Our findings support the use of eDNA metabarcoding to capture fine-scale temporal dynamics and emphasise the importance of multi-year datasets for distinguishing ecological trends from stochastic changes. This strategy improves monitoring practices for marine ecosystems under anthropogenic stressors.

ecology↗

bioRxiv2021

The benefits of merging passive and active tracking approaches: new insights into riverine migration by salmonid smolts

The process of smolting is a critical phase in the life-cycle of anadromous salmonids and it has been associated with substantial rates of mortality. Survival during freshwater and marine migration is known to have population level effects, thus an understanding of the patterns of mortality has the potential to yield important insights into population bottlenecks. Despite important advancements in tracking techniques, the specifics of mortality events in anadromous salmonids during their initial migration to sea remains somewhat elusive. Here, we develop a framework combining spatial and temporal detections of smolt riverine migration from two tracking techniques, which enable inferences to be made about mortality locations, causes, and rates. In this study, we demonstrate that during their initial riverine transitional phase, smolts were particularly vulnerable to predators. Specifically, avian predation appeared to be the main cause of mortality (42%), although piscine predation events were not trivial (14%). Our results suggested some direct and indirect tagging-induced mortality (e.g., through increased predation vulnerability), which highlights the importance of determining tagging mortality in a telemetry study to ensure adequate interpretation of migration success. Overall, by estimating migration loss and its variability, our study framework should help to guide management actions to mitigate the widespread population declines these species are currently facing.

ecology↗

bioRxiv2020

Temporal instability of lake charr phenotypes: synchronicity of growth rates and morphology linked to environmental variables?

Pathways through which phenotypic variation arises among individuals arise can be complex. One assumption often made in relation to intraspecific diversity is that the stability or predictability of the environment will interact with expression of the underlying phenotypic variation. To address biological complexity below the species level, we investigated variability across years in morphology and annual growth increments between and within two sympatric lake charr ecotypes in Rush Lake, USA. We found a rapid phenotypic shift in body and head shape within a decade. The magnitude and direction of the observed phenotypic change was consistent in both ecotypes, which suggests similar pathways caused the temporal variation over time. Over the same time period, annual growth increments declined for both lake charr ecotypes and corresponded with a consistent phenotypic shift of each ecotype. Despite ecotype-specific annual growth changes in response to winter conditions, the observed annual growth shift for both ecotypes was linked, to some degree, with variation in the environment. Particularly, a declining trend in regional cloud cover was associated with an increase of early stage (age 1-3) annual growth for lake charr of Rush Lake. Underlying mechanisms causing reduced growth rates and constrained morphological modulation are not fully understood. An improved knowledge of the biology hidden within the expression of phenotypic variation promises to clarify our understanding of temporal morphological diversity and instability.

evolutionary biology↗

bioRxiv2020

How will cold water fish respond to climate change: rapid and high magnitude phenotypic responses in Arctic charr.

Phenotypic plasticity, the ability of an organism to express multiple phenotypes in response to the prevailing environmental conditions without genetic change, may occur as a response to anthropogenic environmental change. Arguably, the most significant future anthropogenic environment change is contemporary climate change. Given that increasing climate variability is predicted to pose a greater risk than directional climate change, we tested the effect of a water temperature differential of 4 {o}C on the Arctic charr phenotypic response within a generation. We demonstrate that Arctic charr phenotype can respond rapidly and markedly to an environmental cue. The plastic response to different temperature regimes comprised a shift in the mean phenotype coupled with a reduction in the between-individual phenotypic variation in the expressed head shape. The magnitude of shape difference was cumulative over time but the rate of divergence diminished as fish became larger. Individuals raised in the elevated temperature treatment expressed a phenotype analogous to a benthivorous ecotype of this species rather than that of the parental pelagic feeding form. The response of cold-water freshwater species to temperature change is likely to be an interaction between the capacity of the organism for phenotypic plasticity, the speed of mean change in the environment (e.g., temperature), and the degree of short interval variation in the environment.

evolutionary biology↗

bioRxiv2019

Dietary vs non-dietary fatty acid profiles of lake trout morphs from Lake Superior and Great Bear Lake: Are fish really what they eat?

Fatty acids are well-established biomarkers used to characterize trophic ecology, food-web linkages, and the ecological niche of many different taxa. Most often, fatty acids that are examined include only those previously identified as "dietary" or "extended dietary" biomarkers. Fatty acids considered as non-dietary biomarkers, however, represent numerous fatty acids that can be extracted. Some studies may include non-dietary fatty acids (i.e., combined with dietary fatty acids), but do not specifically assess them, whereas in other studies, these data are discarded. In this study, we explored whether non-dietary biomarkers fatty acids can provide worthwhile information by assessing their ability to discriminate intraspecific diversity within and between lakes. Non-dietary fatty acids used as biomarkers delineated variation among regions, among locations within a lake, and among ecotypes within a species. Physiological differences that arise from differences in energy processing can be adaptive and linked to habitat use by a species ecotypes, and likely explains why non-dietary fatty acids biomarkers can be a relevant tool to delineate intraspecific diversity. Little is known about the non-dietary-mediated differences in fatty acid composition, but our results showed that non-dietary fatty acids biomarkers can be useful tool in identifying variation.

ecology↗