Fish epigenetic markers for assessing the effects of climate change and their application to fisheries management

Francesc Piferrer

Institute of Marine Sciences (ICM), Spanish National Research Council (CSIC), Barcelona, Spain

Oceans are getting warmer due to anthropogenic climate change, resulting in effects at different scales, from molecular to ecosystem. Traditional demographic monitoring of affected species can track some of these changes; however, a complete mechanistic understanding of how species respond and adapt to rising temperatures is lacking. Here, we explore epigenetics as a key interface between the genome and the environment, which facilitates plastic responses to stressors like marine heatwaves. We outline the main epigenetic mechanisms present in fish, DNA methylation, histone modifications and non-coding RNAs, and their role in enabling acclimation and phenotypic plasticity. Specifically, we highlight the development of epigenetic markers to assess global warming, noting that early-life exposure to even small temperature increases can leave permanent signatures on the epigenome. Furthermore, we discuss the construction of piscine epigenetic clocks using machine learning models to provide accurate, non-invasive age determination for fisheries management. These clocks offer higher accuracy and precision than traditional otolith-based methods and can be implemented using fin clips samples. We also address the risks of epigenetic traps, i.e., epigenetic changes responsible for traits that can become maladaptive in unstable environments. Finally, we outline a roadmap for future implementation, focusing on standardization, the need for the development of ready-to-use kits and the creation of multi-species tools. Integrating these molecular tools into conservation protocols is essential for managing biodiversity and optimizing aquatic production in the face of the mounting challenges of the Anthropocene.