Recent Polygenic Adaptation in Heavily Fished Malawi Cichlids

Intense fishing pressure can drive rapid evolution in wild populations, yet the underlying genomic mechanisms often remain elusive. Here, we investigate the genomic consequences of five decades of intense harvesting on the cichlid fish Copadichromis mloto in Lake Malombe, Malawi. By comparing whole-genome data from almost 200 individuals from the heavily fished Lake Malombe with less-fished populations in Lake Malawi, we identified a widespread signal of recent, population-specific positive selection. This genomic footprint, spanning hundreds of loci, is consistent with a rapid, polygenic adaptive response. The candidate genes under selection were significantly enriched for high-level developmental processes, including neurogenesis and the formation of the heart and muscle, providing a plausible mechanistic link to the dramatic reduction in size and age at maturity observed in this population. Furthermore, our strongest candidate loci include genes with known roles in controlling somatic growth (zdhhc13, myh7, csrp3, gnb1l) and reproductive timing (mpped2a, kitlga, kat6a, stra6). We also found that candidate genes were nearly five-fold more likely to be differentially expressed in male gonad tissue, providing a strong link between selection and regulatory changes in a key reproductive organ. Our findings point towards a polygenic basis for fisheries-induced evolution in this tropical system and highlight how intense harvesting can rapidly reshape the genetic architecture of complex life-history traits, with important implications for the long-term resilience of exploited fish stocks.