Genomic mechanisms underlying Bombay duck's rapid population surge

Abstract Bombay duck (Harpadon nehereus), once a minor by-catch in the East China Sea, has bloomed into a dominant species, altering marine ecosystems. This study explored the genomic basis of its mysterious recent success via chromosome-level genome assembly, comparative and population genomics. The genome assemblies of H. nehereus and its closely related outgroup species Saurida undosquamis were of good quality, showing a 96.7–96.8% Benchmarking Universal Single-Copy Orthologues completeness. Population resequencing supports a single panmictic population throughout the coast of China. Expanded gene families and genes under intensified and positive selection are related to osmoregulation, hypoxia tolerance, immune function and reproduction. Recent selective sweeps are mostly related to immune response. These molecular signatures are consistent with long-term adaptations to a hypoxic, polluted and fluctuating environment. These findings suggest that species genomically preadapted to environments affected by global change can suddenly become new native invaders.