How do genetic diversity, gene flow, and divergent haplotypes drive population differentiation in the invasive red palm weevil (Rhynchophorus ferrugineus) in Qassim, Saudi Arabia? Evidence from COI and ITS markers

The red palm weevil, Rhynchophorus ferrugineus, is a pest that has become invasive on a global scale, particularly affecting date palms and ranking among the most damaging insect pests worldwide, leading to significant internal harm and considerable economic losses. Although it has been present in Saudi Arabia for a long time, there is a scarcity of regional studies focusing on its population structure and genetic connectivity. This research examines the factors of genetic diversity, gene flow, and divergent haplotypes that contribute to the population differentiation of R. ferrugineus in Qassim, utilizing mitochondrial COI and nuclear ITS markers. The analysis of ITS markers achieved a notably higher coverage (91.2%) compared to COI (35.1%), allowing for a more detailed resolution. The COI analysis indicated a high level of genetic homogeneity among local haplotypes (0.0000–0.0007) and demonstrated strong connectivity with populations from Egypt, Al-Ahsa, Pakistan, and the UAE, while also effectively distinguishing R. ferrugineus from closely related species (R. bilineatus and R. vulneratus; 4.4–5.8% interspecific divergence), thereby confirming its effectiveness for species-level identification and tracking of invasions. The ITS markers identified three biologically significant clusters: haplotypes that were identical to regional references, indicating ongoing gene flow; moderately divergent haplotypes (0.2–0.8%) that align with local evolution or multiple introductions; and highly divergent haplotypes (4–25%) that suggest the presence of cryptic lineages or novel strains. Importantly, two specimens exhibiting over 18% ITS divergence may indicate cryptic or non-R. ferrugineus lineages, which calls for a taxonomic revaluation. The coloration of the pronotum and the patterns of spots were found to correspond with the genetic clusters, implying possible adaptive differentiation. In summary, these results highlight the intricate genetic structure and invasion dynamics of R. ferrugineus in Qassim, offering a molecular basis for early detection, accurate monitoring, and region-specific IPM strategies aimed at preserving the sustainability of date palms.