Temperature reorganises developmental time during thyroid hormone-driven fish metamorphosis

The development of organisms with complex life cycles relies on precise endocrine coordination to link environmental cues with morphogenetic programs. In teleost fish, thyroid hormones (TH) play a central role in post-embryonic development by orchestrating the onset, pacing, and consistency of metamorphosis. The influence of climate change-induced warming on developmental coordination in fish remains poorly understood. Here, we investigated how elevated temperature reshapes TH-driven developmental trajectories during fish metamorphosis using a transcriptomic time series spanning six developmental stages in the false clownfish Amphiprion ocellaris. By combining timeseries analyses, dynamic time warping, and endocrine network reconstruction at the gene level, we show that warming profoundly altered the TH signalling pathway. Elevated temperature induced an earlier stimulation of TH synthesis and modified the temporal trajectory of tissue-level transcriptional responses to TH. This led to an altered timing of TH-responsive developmental programs at the gene expression level. While cellular proliferation and shifts in energy metabolism associated with readiness for metamorphosis occurred earlier, multiple TH-dependent pathways, including cellular differentiation, neuronal maturation, and sensory system development, exhibited delayed and attenuated expression. Developmental progression under elevated temperature became temporally uncoupled, with accelerated initiation but impaired coordination of key TH-mediated morphogenetic modules. Our results demonstrate that thermal stress disrupts fine-scale endocrine timing mechanisms that ensure orderly developmental transitions, revealing how environmental warming can generate developmentally accelerated yet functionally mismatched phenotypes. This study establishes TH signalling as a critical and previously overlooked mediator of temperature-sensitive developmental timing and provides a mechanistic framework for understanding how climate-driven thermal changes interfere with post-embryonic development in vertebrates.