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Oceans are vast, dynamic, and complex ecosystems characterized by fluctuations in environmental parameters like sea surface temperature (SST), salinity, oxygen availability, and productivity. Environmental variability acts as the driver of organismal evolution and speciation as organisms strive to cope with the challenges. We investigated the evolutionary consequences of heterogeneous environmental conditions on the mitogenome of a widely distributed small pelagic fish of Indian ocean, Indian oil sardine,  Sardinella longiceps . Sardines were collected from different eco-regions of the Indian Ocean and selection patterns analyzed in coding and non-coding regions. Signals of diversifying selection were observed in key functional regions involved in OXPHOS indicating OXPHOS gene regulation as the critical factor to meet enhanced energetic demands. A characteristic control region with 38–40 bp tandem repeat units under strong selective pressure as evidenced by sequence conservation and low free energy values was also observed. These changes were prevalent in fishes from the South Eastern Arabian Sea (SEAS) followed by the Northern Arabian Sea (NAS) and rare in Bay of Bengal (BoB) populations. Fishes belonging to SEAS exhibited accelerated substitution rate mainly due to the selective pressures to survive in a highly variable oceanic environment characterized by seasonal hypoxia, variable SST, and food availability.

Signals of selection in the mitogenome provide insights into adaptation mechanisms in heterogeneous habitats in a widely distributed pelagic fish