Parallel genetic adaptation amidst a background of changing effective population sizes in divergent yellow perch (Perca flavescens) populations

Abstract

Aquatic ecosystems are highly dynamic environments vulnerable to a wide variety of natural and anthropogenic disturbances. High-economic value fisheries are one of many ecosystem services affected by these disturbances and it is critical to accurately characterize their genetic diversity and effective population sizes through time. We used genome-wide data to reconstruct the demographic histories of economically important yellow perch (Perca flavescens) populations. In two isolated and genetically divergent populations, we provide strong evidence for simultaneous increases in effective population sizes over both historic and contemporary time scales including negative genome-wide estimates of Tajima's D, 3.1 times more SNPs than adjacent populations, and effective population sizes that have increased 10- and 47-fold from their minimum. We also identified parallel, genetic adaptation to reduced visual clarity in the same two habitats. These results suggest that the synchrony of key ecological and evolutionary processes can drive parallel demographic and evolutionary trajectories across independent populations.