A Universal Genomic Approach to Detect Hybridization Using MIPs: Insights From a Case Study on Pike

ABSTRACT Interspecific hybridization poses a major challenge to biodiversity conservation, as genetic introgression can threaten the persistence of native species. This phenomenon occurs when individuals from distinct species interbreed, producing hybrids with a combination of genetic traits from both parents. The implications are especially concerning when these hybrids are fertile and able to backcross with the parental species, potentially leading to the permanent integration of foreign genetic material into native populations. Human‐mediated translocations further increase hybridization risk by bringing reproductively compatible species into contact. Detecting introgression in individuals that cannot be reliably distinguished morphologically is therefore crucial for conservation planning. In this study, we investigate hybridization between the southern pike ( Esox flaviae ) and northern pike ( Esox lucius ) in Italy and Central Europe. We evaluate multilocus intron polymorphisms (MIPs) as a molecular tool for species identification and hybrid detection by analysing pike samples using a combination of previously available MIP loci and newly isolated pike‐specific MIPs. Our results show that MIP loci successfully reproduce patterns previously identified with microsatellites, confirming their suitability for detecting hybridization and interspecific genetic structure. We also developed a panel of diagnostic loci enabling rapid species/hybrids identification for routine applications. This is the first study demonstrating the effectiveness of MIPs for accurate species assignment and assessment of genetic diversity in pike, particularly in the context of hybridization and its conservation implications. Overall, our findings highlight the value of MIPs as complementary molecular markers for biodiversity studies, providing practical diagnostic tools for species monitoring and management in conservation programmes.