Landscape transcriptomics reveals ecological constraints on fish under anthropogenic coastal change

Abstract Urban zones are rapidly expanding worldwide, exposing organisms to complex and multidimensional stressors. However, linking organismal responses to environmental change at ecologically relevant scales remains a major challenge. To investigate the constraints imposed on fish living in coastal urban environments, we apply a landscape-scale framework to identify molecular signatures associated with human activities. Using transcriptomes from a common coral reef fish, Chrysiptera cyanea , sampled across 18 coastal sites in Okinawa, Japan, we implement scalable analytical and visualisation tools and identify coordinated shifts in metabolic, immune, and inflammatory pathways. By integrating field data with a fasting-feeding experiment, we find that transcriptomes of adult fish from urbanised sites resemble those of well-fed experimental fish, suggesting that these areas provide an energy-rich diet while imposing chronic stress. Our findings reveal how anthropogenic activities reshape organismal resilience and demonstrate the power of landscape transcriptomics as a link between molecular signatures and ecological outcomes across changing environments.