All detectable ancient whole-genome duplications involve hybridization

Abstract

Whole-genome duplication (WGD), or polyploidy, is a major evolutionary force throughout the tree of life. Ancient WGDs are commonly inferred from the distribution of synonymous substitutions per synonymous site (Ks) between duplicated genes. Here, we argue that the standard interpretation of these distributions is incomplete. Using haplotype-phased genome assemblies spanning canonical autopolyploid and allopolyploid systems, we find that Ks accumulates primarily between gene copies on non-recombining chromosomes. Thus, Ks-based WGD detection depends not simply on WGD, but on whether duplicated copies evolve independently. This distinction reframes many inferences of ancient WGD as signatures of hybridization and the evolution of meiotic isolation and alters how we interpret the origin, detectability, and evolutionary consequences of polyploidy across the tree of life.