Evolution of freshwater reproduction in a marine fish: Evidence from genetics and otolith microchemistry

The evolution of distinct reproductive strategies within the same species can offer unique insights into adaptive divergence. Since the discovery of European flounder (Platichthys flesus) in the freshwater environment of the isolated Lake Pulmanki in the 1970s, the evolutionary origin and reproductive strategy of this euryhaline fish has remained a mystery. Using otolith chemistry and whole-genome resequencing, we tested the hypothesis that flounders in Lake Pulmanki constitute a freshwater-adapted lineage, distinct from their marine ancestors. Otoliths confirmed that most of the flounders caught in Lake Pulmanki were born and lived exclusively in freshwater, providing the first evidence for a fully freshwater confined life cycle in Platichthys. Unexpectedly, most individuals in nearby fjords were also born in freshwater. While the genome-wide differentiation among marine- and freshwater-born flounders was weak, 77 SNPs across 18 chromosomes were significantly associated with habitat-use type, mapping to 35 genes. Moreover, outlier loci show strong interchromosomal linkage disequilibrium (LD), suggesting divergent selection for allelic combinations associated with reproductive habitat use. This pattern is consistent with a genetic basis for early habitat use differences involving epistatic interactions among alleles in different chromosomes, pointing to a genetic adaptation for freshwater reproduction in Lake Pulmanki.