Genetic barriers to gene flow separate divergent substitution rates across a butterfly hybrid zone

Abstract

AbstractSubstitution rate defines the fundamental timescale of molecular evolution which often varies in a species-specific manner. However, it is unknown under what conditions lineage-specific rates can be preserved between natural populations with frequent hybridization. Here, we show in a hybrid zone between two butterflies Papilio syfanius and Papilio maackii that genome-wide barriers to gene flow can effectively separate different rates of molecular evolution in linked regions. The increased substitution rate in the lowland lineage can be largely explained by temperature-induced changes to the spontaneous mutation rate. A novel method based on entropy is developed to test for the existence of barrier loci using a minimal number of samples from the hybrid zone, a robust framework when system complexity far exceeds sample information. Overall, our results suggest that during the process of speciation, the separation of substitution rates can occur locally in the genome in parallel to the separation of gene pools.