A Comprehensive Exome Scan for Signatures of Rapid Fisheries-Induced Evolution

It has become evident that fisheries can inflict evolutionary changes in the exploited populations. Yet, so far almost nothing is known about the underlying genomic basis for the widespread changes in life history traits observed across the world’s fish stocks: What types of genetic variation does fisheries-selection act on, how extensively does it impact the genome, and how reversible are the changes once fishing stops? To address these questions, we have returned to a seminal experiment that demonstrated substantial evolution in growth rates in response to size-selective fishing over just five generations in the Atlantic silverside. We use low coverage whole genome sequencing of 900 individually barcoded fish to track allele frequency changes in different experimental populations at >800,000 SNPs covering ~80% of the exome. We have identified strong differentiation between large- and small-selected populations at 1,118 SNPs and nearly fixed differences in 17 genes, including bone morphogenic proteins and macrophage stimulating factors, previously linked to growth. However, selected genes maintain high overall levels of diversity, indicating that selection has primarily acted as ‘soft' sweeps on old alleles. These findings improve our mechanistic understanding of fisheries-induced evolution and provide an important baseline for assessing genomic changes in wild fish populations.