Abstract

Summary Marine microalgae demonstrate a notable capacity to adapt to high CO 2 and warming in the context of global change. However, the dynamics of their evolutionary processes under simultaneous high CO₂ and warming conditions remain poorly understood. Here, we analyze the dynamics of evolution in experimental populations of a model marine diatom Phaeodactylum tricornutum . We conducted whole‐genome resequencing of populations under ambient, high‐CO 2 , warming and high CO 2 + warming at 2‐yr intervals over a 4‐yr adaptation period. The common genes selected between 2‐ and 4‐yr adaptation were found to be involved in protein ubiquitination and degradation and the tricarboxylic acid (TCA) cycle, and were consistently selected regardless of the experimental conditions or adaptation duration. The unique genes selected only by 4‐yr adaptation function in respiration, fatty acid, and amino acid metabolism, facilitating adaptation to prolonged high CO 2 with warming conditions. Corresponding changes at the metabolomic level, with significant alterations in metabolites abundances involved in these pathways, support the genomic findings. Our study, integrating genomic and metabolomic data, demonstrates that long‐term adaptation of microalgae to high CO 2 and/or warming can be characterized by a complex and dynamic genetic process and may advance our understanding of microalgae adaptation to global change.