Genomic Adaptation of Marine Medaka (Oryzias melastigma) Under Artificial Life-History Selection

Size-selective harvesting imposes indirect selection on life-history traits and has profound evolutionary and ecological implications for fish populations, influencing traits such as body size, reproductive success, hatchability, and driving significant genetic shifts. Here, we investigated the long-term effects of three harvesting strategies, large-harvested (LH), small-harvested (SH), and random-harvested (RH), on marine medaka (Oryzias melastigma) populations over five generations. We observed declines in body length and weight in the LH group, whereas these traits increased in the SH group, with the RH group remaining relatively stable. In terms of hatchability, SH surpassed LH but remained below RH. Genome-wide analyses identified key selective regions on chromosomes 8, 13, and 21, which were associated with growth and reproductive fitness. Genome-wide association studies (GWAS) identified significant loci on chromosome 13 linked to genes such as fat3a, kcnj13, and gucy1a2, which are strongly correlated with body weight. These findings suggest a close link between selective harvesting and life-history evolution, indicating that fishing behaviour may drive genetic shifts within populations. Furthermore, our results imply that selective pressures could influence phenotypic traits and allele frequencies, potentially leading to long-term or even irreversible genetic changes that might affect growth and survival, traits important for population sustainability.