Resampling-based validation of a SNP panel for hybrid detection across generations: a case study in European lobster

Abstract

Accurate detection of hybridization and introgression is critical for both evolutionary research and applied conservation. In many systems, however, hybrid ancestry is difficult to detect beyond the F1 generation, especially when based on limited genetic markers. In European waters, hybridization between the native Homarus gammarus and the invasive H. americanus poses a direct risk to the integrity of native stocks and effective fishery management, yet detection methods are often limited to morphological traits or first-generation hybrids. A set of 79 SNPs previously developed to distinguish species between American and European lobsters and F1 individuals has shown promise, but its capacity to resolve later-generation backcrosses remains untested. Here, we present a resampling-based evaluation of this panels performance under realistic introgression scenarios, using individual-based population genetic models informed by empirical data. We show that the panel retains discriminatory power across multiple hybrid classes, with diminishing accuracy in second-generation backcrosses. These findings validate the panels utility for applied monitoring and highlight the broader potential of resumpling-anchored frameworks to benchmark hybrid detection tools in a wide range of species. Article summaryThis study tests how well a reduced panel of genetic markers can detect hybridization across multiple generations. Using empirical genetic data of a 79-SNP panel from European and American lobsters, the authors generated individuals with known ancestry proportions through a resampling framework that preserves observed genetic variation. These data were analysed using model-based genetic assignment and ordination. The results show that the marker panel reliably identifies pure species and first-generation hybrids, but has reduced power to distinguish later backcross generations, mainly between adjacent hybrid classes. The study provides a practical benchmark for evaluating reduced marker panels used in applied monitoring and conservation genetics.