Biology subjects

Edeline, E.

Publications and source records attributed to Edeline, E..

10 recordsLinked to original sources

bioRxiv2026

Invasive alien predators overturn the spatial-scaling laws of biocomplexity

The theory of island biogeography and its trophic extensions predict that both species richness and food-web complexity should increase with increasing ecosystem surface area. Accordingly, Species-Area Relationships (SARs) and Network-Area Relationships (NARs) are often observed to be positively-sloped, an observation that came to be considered as a law, and on which rest many area-based conservation plans for biodiversity. However, our mechanistic understanding of the driving mechanisms of SARs and NARs slopes remains limited, undermining our ability to predict how biodiversity will respond to habitat gain or loss. We show in 180 rural ponds sampled across five years that invasive alien predators reversed the SAR and NARs from positive in invader-free ponds, to negative in invaded ponds. Relationship reversal resulted from a higher prevalence of invasive alien predators driving magnified prey extinctions and simplified food webs in larger ponds. The ability of invasive alien predators to reverse SAR and NARs presumably reflected disproportionately high predation rates combined with a low sensitivity to prey extinction conferred by a wide trophic generalism. In a world where virtually all ecosystems face biological invasions, omnipresent invasive alien predators stress the pivotal role played by predation in shaping biocomplexity-area relationships, and highlight a growing need to preserve small ecosystems where invasive alien predators are less prevalent.

ecology↗

bioRxiv2026

Biological invasion drives ecosystem state and metabolism across tipping points

Abrupt regime shifts of complex ecosystems between alternative stable states are widespread in nature. Yet, our mechanistic understanding of disturbance-shift-ecosystem functioning relationships remains poor, and it is further unclear whether biotic disturbances can drive such shifts. Using a 5-year pond experiment, we demonstrate that invasion by the red swamp crayfish (Procambarus clarkii) drove a regime shift from a clear-water, macrophyte-dominated, to a turbid, phytoplankton-dominated state. The regime shift was associated with increased water temperature due to increased water turbidity enhanced light absorption, and with a seasonal switch of ecosystem metabolism from hetero-to autotrophy due to decreased respiration in summer, despite constant gross primary production. Reducing crayfish population densities by 44 % failed to move ecosystems back towards their initial state and functioning. Our results stress that biotic disturbances may have hardly-reversible consequences on the biophysical and biogeochemical processes that support ecosystem functioning.

ecology↗

bioRxiv2025

PlanktonFlow : hands-on deep-learning classification of plankton images for biologists

High throughput image-acquisition devices tremendously increase our capacity to observe biodiversity. However, for many biologists, the high-performance deep learning models that are needed to make biological sense out of very-large image sets remain difficult to implement. To fill this gap in biologists toolkit, we developed PlanktonFlow, a Python pipeline that streamlines the automation of plankton-image taxonomic assignment. PlanktonFlow makes it easy for inexperienced users to run a whole sequence of (i) automated image pre-processing and augmentation of rare classes, (ii) training up to four different high-performance convolution neural networks (CNNs: ResNet, DenseNet, EfficientNet, and YOLO), (iii) computing model classification-performance metrics so as to choose the best-performing model, and (iv) running inference on novel image sets. PlanktonFlow further includes routines to easily fine tune model hyper-parameters and optimize models performances. Using a tutorial style, we demonstrate the usage of PlanktonFlow to analyse freshwater-plankton images produced with the FlowCAM, comparing the relative classification performances of the four optimized CNN architectures. For a baseline comparison with a reference tool used by plankton biologists, we further assessed the classification performances of the EcoTaxa web-service when used without any eye validation in a pure-prediction mode. In line with a previous study on a benchmark plankton dataset, we found that EfficientNet-B5 achieved the highest macro-averaged F1 Score, outperforming other CNN models, which all surpassed EcoTaxa. Hyper-parameter optimization was key to improving model performances. To ease an appropriation and further developments by the community, PlanktonFlow is open source, comes with a detailed documentation, and has a modular structure. We foresee that future work could integrate new deep-learning architectures (e.g., vision transformers, semi-supervised learning), and test the pipeline on images produced by other devices or from other taxonomic groups.

ecology↗

bioRxiv2023

Habitat structural complexity increases age-class coexistence and productivity in fish populations

Structurally-complex habitats harbour more taxonomically-diverse and more productive communities, a phenomenon generally ascribed to habitat complexity relaxing the strength of inter-specific predation and competition. Here, we extend this classical, community-centred view by showing that positive complexity-diversity and complexity-productivity relationships may also emerge from between-age-class, intra-specific interactions at a single-population level. In the laboratory, we show that medaka fish (Oryzias latipes) are strongly cannibalistic in complexity-free habitats, and that cannibalism may occur over a wide range of victim/cannibal body size ratios. In replicated outdoor pond populations, we manipulated habitat structural complexity using floating artificial structures, which selectively hampered movements of large-bodied medaka. Habitat complexity relaxed the strength of cannibalism, resulting in (1) increased survival of age-0+ individuals, (2) elevated age-class diversity, (3) increased population growth rate, and (4) dampened negative density-dependence in the stock-recruitment relationship reflecting elevated habitat carrying capacity. The resultant higher population density in complex habitats was associated with increased competition for food among both age-0+ and age-1+ individuals. Our results highlight that positive complexity-diversity and complexity-productivity relationships may be considered as a generally-emergent property of size-structured populations and communities in which a larger body size brings a predation or interference advantage. Hence, enhancement of habitat structural complexity may be seen as a pivotal management strategy not only in favour of taxonomic diversity, but also to increase the productivity and resilience of exploited populations and to improve the conservation status of endangered species.

ecology↗

bioRxiv2023

Within-species variation in the gut microbiome of fish is driven by the interaction of light intensity and genetic background

Unravelling evolution-by-environment interactions on the gut microbiome is particularly relevant considering the unprecedented level of human-driven disruption of the ecological and evolutionary trajectories of species. Here, we aimed to evaluate whether an evolutionary response to size-selective mortality influences the gut microbiome of medaka (Oryzias latipes), how environmental conditions interact with the genetic background of medaka on their microbiota, and the association between microbiome diversity and medaka growth-related traits. To do so, we studied two lineages of medaka with known divergence in foraging efficiency and life history raised under antagonistic size-selective regimes for 10 generations (i.e. the largest or the smallest breeders were removed to mimic fishing-like or natural mortality). In pond mesocosms, the two lineages were subjected to contrasting population density and light intensity (used as proxies of resource availability). We observed significant differences in the gut microbiome composition and richness between the two lines, and this effect was mediated by light intensity. The bacterial richness of fishing-like medaka (small-breeder line) was reduced by 34% under low-light conditions compared to high-light conditions, while it remained unchanged in natural mortality-selected medaka (large-breeder line). However, the observed changes in bacterial richness did not correlate with changes in adult growth rate or body condition. Given the growing evidence about the gut microbiomes importance to host health, more in-depth studies are required to fully understand the role of the microbiome in size-selected organisms and the possible ecosystem-level consequences.

ecology↗

bioRxiv2022

Determinants of survival and dispersal along the range expansion of a biological invasion

Projecting and managing the future response of biological systems to global change requires a mechanistic understanding of how climate and ecology jointly drive species demography and range dynamics. Such knowledge is particularly crucial when it comes to invasive species, which expansion may have far-reaching consequences for recipient ecosystems. Here, we use mark recapture in replicated outdoor mesocosms to examine how survival and dispersal, two key drivers of population and range dynamics, respond to climate and ecology in the invasive red swamp crayfish (Procambarus clarkii) along an invasion gradient. We show that crayfish survival probability increased with (i) increasing body size at high (but not low) crayfish density and (ii) with warmer temperatures, and decreased (i) with increasing body condition and (ii) under higher crayfish density. Overland dispersal probability by crayfish increased with increasing (i) body-size, (ii) body condition and (iii) temperatures. In contrast, crayfish from range-edge and range-core habitats had similar survival and overland dispersal probabilities, suggesting no evolution of the crayfish expansion potential along the invasion gradient. Our results highlight that species population dynamics and range shifts in a changing world are driven by joint contributions from both climate and ecology. In P. clarkii, global warming will simultaneously promote both a demographic increase and a geographic range expansion, especially in populations dominated by large-bodied individuals. In already-invaded ecosystems, selective harvesting of large-bodied crayfish can potentially reduce the dispersal potential of populations and, after a few generations, might further induce an evolutionary decline in fitness traits that is desirable from a management perspective. Open research statementUpon acceptance of this manuscript, data and codes will be made publicly available online on the INRAE data repository (https://entrepot.recherche.data.gouv.fr/dataverse/inrae).

ecology↗

bioRxiv2020

Size-dependent eco-evolutionary feedback loops in exploited ecosystems

AO_SCPLOWBSTRACTC_SCPLOWHarvesting may drive body downsizing along with population declines and decreased harvesting yields. These changes are commonly construed as consequences of direct harvest selection, where small-bodied, early-reproducing individuals are immediately favoured. However, together with directly selecting against a large body size, harvesting and body downsizing alter many ecological features, such as competitive and trophic interactions, and thus also indirectly reshape natural selection acting back on body sizes through eco-evolutionary feedback loops (EEFLs). We sketch plausible scenarios of simple EEFLs in which one-dimensional, density-dependent natural selection acts either antagonistically or synergistically with direct harvest selection on body size. Antagonistic feedbacks favour body-size stasis but erode genetic variability and associated body-size evolvability, and may ultimately impair population persistence and recovery. In contrast, synergistic feedbacks drive fast evolution towards smaller body sizes and favour population resilience, but may have far-reaching bottom-up or top-down effects. We illustrate the further complexities resulting from multiple environmental feedbacks using a co-evolving predator-prey pair, in which case outcomes from EEFLs depend not only on population densities, but also on whether prey sit above or below the optimal predator/prey body-size ratio, and whether prey are more or less evolvable than their predators. EEFLs improve our ability to understand and predict natures response to harvesting, but their integration into the research agenda will require a full consideration of the effects and dynamics of natural selection.

ecology↗

bioRxiv2020

Unidirectional response to bidirectional selection on body size. II Quantitative genetics.

Anticipating the genetic and phenotypic changes induced by natural or artificial selection requires reliable estimates of trait evolvabilities (genetic variances and covariances). However, whether or not multivariate quantitative genetics models are able to predict precisely the evolution of traits of interest, especially fitness-related, life-history traits, remains an open empirical question. Here, we assessed to what extent the response to bivariate artificial selection on both body size and maturity in the medaka Oryzias latipes, a model fish species, fits the theoretical predictions. Three lines (Large, Small, and Control lines) were differentially selected for body length at 75 days of age, conditional on maturity. As maturity and body size were phenotypically correlated, this selection procedure generated a bi-dimensional selection pattern on two life history traits. After removal of non-heritable trends and noise with a random effect (animal) model, the observed selection response did not match the expected bidirectional response. For body size, Large and Control lines responded along selection gradients (larger body size and stasis, respectively), but, surprisingly, the Small did not evolve a smaller body length, and remained identical to the Control line throughout the experiment. The magnitude of the empirical response was smaller than the theoretical prediction in both selected directions. For maturity, the response was opposite to the expectation (the Large line evolved late maturity compared to the Control line, while the Small line evolved early maturity, while the opposite pattern was predicted due to the strong positive genetic correlation between both traits). The mismatch between predicted and observed response was substantial and could not be explained by usual sources of uncertainties (including sampling effects, genetic drift, and error in G matrix estimates).

evolutionary biology↗

bioRxiv2019

Density-dependent selection mediates harvest-induced evolution

Rapid life-history changes caused by size-selective harvesting are often interpreted as a response to direct harvest selection against a large body size. However, similar trait changes may result from a harvest-induced relaxation of natural selection for a large body size via density-dependent selection. Here, we show evidence of such density-dependent selection favouring large-bodied individuals at high population densities, in replicated pond populations of medaka fish. Harvesting, in contrast, selected medaka directly against large-bodied medaka and, in parallel, decreased medaka population densities. Five years of harvesting were enough for harvested and unharvested medaka populations to inherit the classically-predicted trait differences, whereby harvested medaka grew slower and matured earlier than unharvested medaka. We demonstrate that this life-history divergence was not driven by direct harvest selection for a smaller body size in harvested populations, but by density-dependent natural selection for a larger body size in unharvested populations.

evolutionary biology↗

bioRxiv2018

Anthropogenic selection along directions of most evolutionary resistance

Anthropogenic perturbations such as harvesting often select against a large body size and are predicted to induce rapid evolution towards smaller body sizes and earlier maturation. However, body-size evolvability and, hence, adaptability to anthropogenic perturbations remain seldom evaluated in wild populations. Here, we use a laboratory experiment over 6 generations to measure the ability of wild-caught medaka fish (Oryzias latipes) to evolve in response to bidirectional size-dependent selection mimicking opposite harvest regimes. Specifically, we imposed selection against a small body size (Large line), against a large body size (Small line) or random selection (Control line), and measured correlated responses across multiple phenotypic, life-history and endocrine traits. As expected, the Large line evolved faster somatic growth and delayed maturation, but also evolved smaller body sizes at hatch, with no change in average levels of pituitary gene expressions of luteinizing, folliclestimulating or growth (GH) hormones. In contrast, the Small medaka line was unable to evolve smaller body sizes or earlier maturation, but evolved smaller body sizes at hatch and showed marginally-significant signs of increased reproductive investment, including larger egg sizes and elevated pituitary GH production. Natural selection on medaka body size was too weak to significantly hinder the effect of artificial selection, indicating that the asymmetric body-size response to size-dependent selection reflected an asymmetry in body-size evolvability. Our results show that trait evolvability may be contingent upon the direction of selection, and that a detailed knowledge of trait evolutionary potential is needed to forecast population response to anthropogenic change.

evolutionary biology↗