Biology subjects

Shin, Y.-J.

Publications and source records attributed to Shin, Y.-J..

8 recordsLinked to original sources

bioRxiv2026

Filling a metabolism data gap in marine fish reveals dual pace-of-life and reproductive strategy axes

Resting metabolic rate, the basal energy required for an organism's maintenance, is central to predicting the eco-evolutionary consequences of environmental and anthropogenic pressures on marine ectotherms. Yet, direct measurements remain extremely scarce, covering less than 1% of marine fish species. Building on the Pace Of Life Syndrome (POLS) hypothesis, which posits a positive correlation between metabolism and life-history speed, we inferred temperature- and mass-specific resting metabolic rate for 18,214 fish species (16,998 Teleostei and 1,216 Elasmobranchii). Estimates were derived from relationships with 15 functional traits and phylogeny using phylogenetic structural equation modelling, a novel approach combining phylogenetic comparative methods with structural equation models. Cross-validations indicated high predictive performance, although some clades require cautious interpretation due to limited empirical data. In line with expectations from life-history theory, ecological niche and morphology, species with the highest metabolic rates were small, narrow, shallow-bodied, and long-jawed pelagic fish with high mortality, short lifespan and rapid growth - traits typical of small epipelagics. The metabolic rate variation aligned with the slow-fast life-history continuum, supporting the POLS hypothesis, but was equally explained by reproductive strategy: highly fecund, fast species exhibited the highest metabolic rate independent of mass and temperature, whereas low-fecundity slow species had the lowest. By filling a critical physiological data gap, our dataset provides a foundation to test long-standing ecological and evolutionary hypotheses such as POLS, and offers a powerful resource to improve models of species and community responses to climate change and exploitation, ultimately supporting physiology-informed ecosystem management.

ecology↗

bioRxiv2026

Development and parameterisation of a size-structured multispecies bioeconomic model integrating consumer demand

A high proportion of the world's population relies on marine fisheries as a source of food and employment, highlighting the need for sustainable exploitation strategies. However, fisheries management commonly relies on single-species models that overlook ecological interactions and economic trade-offs, which may lead to stocks being exploited above sustainable levels. To address this gap, we developed a novel size-structured, multispecies bioeconomic module integrated within the spatially explicit, individual-based OSMOSE ecosystem model. OSMOSE represents exploited fish communities in which individuals interact through opportunistic, size-dependent predator-prey interactions which are explicitly incorporated into the bioeconomic framework. The bioeconomic model accounts for multiple species and size classes, allowing for size-dependent market prices. Fishing costs and profits are represented using an extension of the Gordon-Schaefer model to multiple interacting species, while consumer demand is modelled using a nested Dixit-Stiglitz utility function with three levels of constant elasticity of substitution for fish commodity, species and size classes. We present a method for estimating parameters for the bioeconomic module when empirical estimates are unavailable, using the North Sea OSMOSE configuration, which comprises 15 species. Our method successfully estimated the six bioeconomic parameters required to operationalise the model. Results indicate that differences in cost parameters were primarily associated with variability in species biomass rather than fishing gear, while fish prices were more strongly influenced by consumer's demand than by availability. This framework provides a basis for assessing the economic consequences of alternative climate change scenarios and supporting sustainable fisheries management.

ecology↗

bioRxiv2023

Future climate change impacts on anchoveta (Engraulis ringens) in the Northern Peru Current Ecosystem

The Northern Peru Current Ecosystem (NPCE) is the most productive ecosystem in terms of fish biomass and sustains the worlds largest small pelagic fishery, the Peruvian anchovy fishery. A cooling of this system has been observed during recent decades but the potential regional impacts of rising atmospheric CO2 concentrations on upwelling dynamics and productivity are still unknown. We used the ecosystem model OSMOSE to forecast the impacts of several scenarios of climate change on Peruvian anchovy in the NPCE. The OSMOSE model was forced by plankton production and climate drivers from the Earth System Models IPSL CM5A-LR and GFDL-ESM2M for the period 2009-2100. For each earth system model, representative concentration pathways (RCP) scenarios 2.6, 4.5, 6.0 and 8.5 were run. Our results showed that an optimistic trajectory for anchovy is a reduction of biomass at a rate of 14% per decade until mid-21st century, followed by a collapse and late recovery by the end of the 21st century, while no changes in the spatial distribution of the population were observed. The pessimistic trajectory for anchovy is a reduction of biomass of 22% per decade, with a collapse after 2020 and near extinction by 2060, with a spatial displacement of the population to the south and to more coastal areas. Further research is needed to include additional key environmental variables such as oxygen as well as more realistic fisheries management intervention scenarios to evaluate future options for the sustainability of anchovy resource and fisheries.

ecology↗

bioRxiv2023

Ev-OSMOSE: An eco-genetic marine ecosystem model

In the last decade, marine ecosystem models have been increasingly used to project interspecific biodiversity under various global change and management scenarios, considering ecological dynamics only. However, fish populations may also adapt to climate and fishing pressures, via evolutionary changes, leading to modifications in their life-history that could either mitigate or worsen, or even make irreversible, the impacts of these pressures. Building on the multispecies individual-based model Bioen-OSMOSE, an eco-evolutionary fish community model, Ev-Osmose, has been developed to account for evolutionary dynamics together with physiological and ecological dynamics in fish diversity projections. A gametic inheritance module describing the individuals genetic structure has been implemented. The genetic structure is defined by finite numbers of loci and alleles per locus that determine the genetic variability of growth, maturation and reproductive effort. Climate change and fishing activities will generate selection pressures on fish life-history traits that will respond through microevolution. This paper is an overview of the Ev-OSMOSE model. To illustrate the ability of the Ev-OSMOSE model to represent realistic fish community dynamics, genotypic and phenotypic traits mean and variance and consistent evolutionary patterns, we applied the model to the North Sea ecosystem. The simulated outputs are confronted to observed data of commercial catch, maturity ogives and length at age and to estimates of biomass for each modeled species. In addition to the evaluation of their mean value, the emerging traits variability is confronted to length-at-age and maturity data. To ensure the consistency of genetic inheritance and the resulting evolutionary patterns, we assessed the transmission of traits genotypic value across cohorts. Overall, the state of the modelled ecosystem was convincing at all these different biological levels. These results open perspectives for using Ev-OSMOSE in different marine regions to project the eco-evolutionary impact of various global change and management scenarios on different biological levels.

ecology↗

bioRxiv2023

Bioen-OSMOSE: A bioenergetic marine ecosystem model with physiological response to temperature and oxygen

O_LIMarine ecosystem models have been used to project the impacts of climate-induced changes in temperature and oxygen on biodiversity mainly through changes in species spatial distributions and primary production. However, fish populations may also respond to climatic pressures via physiological changes, leading to modifications in their life history that could either mitigate or worsen the consequences of climate change. C_LIO_LIBuilding on the individual-based multispecies ecosystem model OSMOSE, Bioen-OSMOSE has been developed to account for high trophic levels physiological responses to temperature and oxygen in future climate projections. This paper presents an overview of the Bioen-OSMOSE model, mainly detailing the new developments. These consist in the implementation of a bioenergetic sub-model that mechanistically describes somatic growth, sexual maturation and reproduction as they emerge from the energy fluxes sustained by food intake under the hypotheses of a biphasic growth model and plastic maturation age and size represented by a maturation reaction norm. These fluxes depend on temperature and oxygen concentration, thus allowing plastic physiological responses to climate change. C_LIO_LITo illustrate the capabilities of Bioen-OSMOSE to represent realistic ecosystem dynamics, the model is applied to the North Sea ecosystem. The model outputs are confronted with population biomass, catch, maturity ogive, mean size-at-age and diet data of each species of the fish community. A first exploration of current species spatial variability in response to temperature or oxygen is presented in this paper. The model succeeds in reproducing observations, with good performances for all indicators. C_LIO_LIThis new model development opens the scope for new fields of research such as the exploration of seasonal or spatial variation in life history in response to biotic and abiotic factors at the individual, population and community levels. Understanding such variability is crucial to improve our knowledge on potential climate change impacts on marine ecosystems and to make more reliable projections under climate change scenarios. C_LI

ecology↗

bioRxiv2021

Timescale of degradation-driven protein level fluctuation in the yeast Saccharomyces cerevisiae

Generating robust, predictable perturbations in cellular protein levels will advance our understanding of protein function and enable the control of physiological outcomes in biotechnology applications. Timed periodic changes in protein levels play a critical role in the cell division cycle, cellular stress response, and development. Here we report the generation of robust protein level oscillations by controlling the protein degradation rate in the yeast Saccharomyces cerevisiae. Using a photo-sensitive degron and red fluorescent proteins as reporters, we show that under constitutive transcriptional induction, repeated triangular protein level oscillations as fast as 5-10 minute-scale can be generated by modulating the protein degradation rate. Consistent with oscillations generated though transcriptional control, we observed a continuous decrease in the magnitude of oscillations as the input modulation frequency increased, indicating low-pass filtering of input perturbation. By using two red fluorescent proteins with distinct maturation times, we show that the oscillations in protein level is largely unaffected by delays originating from functional protein formation. Our study demonstrates the potential for repeated control of protein levels by controlling the protein degradation rate without altering the transcription rate.

bioengineering↗

bioRxiv2019

Catching the big picture of the Mediterranean Sea biodiversity with an end-to-end model of climate and fishing impacts

The Mediterranean Sea is among the main hotspots of marine biodiversity in the world. Under combined pressures of fishing activities and climate change it has also become a hotspot of global change, with increased concern about the worsening status of marine exploited species. More integrated modelling approaches are needed to anticipate global change impacts in the Mediterranean Sea, in order to help decision makers prioritizing management actions and strategies, mitigating impacts and adapting to changes. Our challenge was to develop a holistic model of the marine biodiversity in the Mediterranean Sea with an explicit representation of the spatial multispecies dynamics of exploited resources under the combined influence of climate variability and fishing pressure. An individual-based ecosystem model OSMOSE (Object-oriented Simulator of Marine ecOSystEms), including 100 marine species (fish, cephalopods and crustaceans) and representing about 95 % of the total declared catches, has been implemented for the first time at a high spatial resolution (400 km2) and at a large spatial scale (whole Mediterranean basin). The coupling of OSMOSE to the NEMOMED 12 physical model, and to the Eco3M-S biogeochemical and low trophic level model has been achieved to build the OSMOSE-MED end-to-end model. We fitted OSMOSE-MED to observed and estimated data of biomass and commercial catches using a likelihood approach and an evolutionary optimization algorithm. The outputs of OSMOSE-MED were then verified against observed biomass and catches, and confronted to independent datasets (MEDITS data, diet compositions and trophic levels). Although some improvements are suggested for future developments, the model results at different hierarchical levels, from individuals up to the ecosystem scale, were consistent with current knowledge and observations on the structure, the functioning and the dynamics of the ecosystems in the Mediterranean Sea. All the modelling steps, from the comprehensive representation of key ecological processes and feedbacks, the careful parameterization of the model, the confrontation to observed data, and the positive outcome from the validation process, allowed to strengthen the degree of realism of OSMOSE-MED and its relevance as an impact model to explore the futures of marine biodiversity under scenarios of global change, and as a tool to support the implementation of ecosystem-based fisheries management in the Mediterranean Sea.

ecology↗

bioRxiv2018

Ensemble projections of global ocean animal biomass with climate change

Climate change is shifting the abundance and distribution of marine species with consequences for ecosystem functioning, seafood supply, management and conservation. Several approaches for future projection exist but these have never been compared systematically to assess their variability. We conducted standardized ensemble projections including 6 global fisheries and marine ecosystem models, forced with 2 Earth-system models and 4 emission scenarios in a fished and unfished ocean, to derive average trends and associated uncertainties. Without fishing, mean global animal biomass decreased by 5% ({+/-}4%) under low and 17% ({+/-}11%) under high emissions by 2100, primarily driven by increasing temperature and decreasing primary production. These climate-change effects were slightly weaker for larger animals and in a fished ocean. Considerable regional variation ranged from strong biomass increases in high latitudes to strong decreases in mid-low latitudes, with good model agreement on the direction of change but variable magnitude. Uncertainties due to differences among ecosystem or Earth-system models were similar, suggesting equal need for model improvement. Our ensemble projections provide the most comprehensive outlook on potential climate-driven ecological changes in the ocean to date. Realized future trends will largely depend on how fisheries and management adapt to these changes in a changing climate.

ecology↗