Large-effect loci in a duplicated genomic region modulate reproductive phenology in salmon

Abstract

AbstractWhole genome duplication (WGD) provides evolutionary opportunities to increase biological complexity and phenotypic diversity by selective retention of duplicated genes. We identify a small genomic region in salmon that governs complex life history variation and has diversified across four WGDs to fine-tune trait expression. Within this region, three large-effect loci on three chromosomes modulate migration timing across four species - a critical trait optimizing fitness by synchronizing reproduction and environmental conditions. Life history and genome resequencing data support intraspecific evolution of polymorphisms related to early- and late-reproducing phenotypes. We demonstrate that the repeated evolution of loci underlying reproductive timing carries the signature of WGD-facilitated adaptive evolution. This adaptation is driven by the subsequent subfunctionalization of genes within the highly conserved HPG axis, which regulates vertebrate reproduction.