Coexistence of piRNA and KZFP defense systems: evolutionary dynamics of layered defense against transposable elements

Transposable elements (TEs) pose a persistent threat to genome stability, and host organisms have consequently evolved sophisticated defense mechanisms to restrain them. In animals, the most prominent systems include PIWI-interacting RNAs (piRNAs) and Krüppel-associated box zinc-finger proteins (KZFPs). Because both systems recognize TEs in a sequence-specific manner and induce epigenetic silencing, they appear functionally redundant at first glance. However, KZFPs are a relatively recent innovation that emerged and diversified in genomes where the piRNA pathway was already established. This raises an important question: under what conditions can a second, seemingly redundant defense system invade and persist? To address this, we constructed a mathematical model integrating the evolutionary dynamics of TEs, piRNAs, and KZFPs. Our approach focuses on a key mechanistic asymmetry between the two defense systems: whereas piRNA-mediated suppression is dependent on TE activity, KZFPs provide constitutive suppression that does not rely on ongoing TE activity. We show that these distinct modes of action generate interactions that extend beyond simple redundancy or additivity. We derive analytical conditions under which KZFPs can invade a pre-existing TE-piRNA equilibrium and characterize the evolutionary logic that enables stable coexistence of these multilayered defense strategies. Together, our results provide a theoretical framework for understanding how complex, layered genome defense systems can evolve and persist.