Transgene introgression into wild cotton populations generates long-term genetic and ecological effects in a center of origin

The environmental persistence of genetically modified (GM) traits beyond authorized cultivation areas remains poorly understood, particularly in centers of origin of crop species. Here, we evaluated the presence, genetic configuration, and ecological effects of transgenes introgressed into two sites of the Yucatan Peninsula Metapopulation of Gossypium hirsutum in Mexico. Using molecular detection of GM traits combined with field-based ecological sampling, we found that 47.2% of sampled individuals carried at least one transgene, with cp4-epsps being the most frequently detected modifications (20.8%), followed by cry genes (13.9%) and stacked events (12.5%). Notably, we detected the isolated presence of cry2Ab , suggesting post-introgression segregation and recombination of commercial events under natural conditions. We also assessed indirect ecological effects associated with transgenes by analyzing ant abundance and species richness on wild cotton plants. Ant abundance differed significantly between transgene-positive and transgene-negative plants, with consistent but non-significant trends for species richness, indicating that introgressed GM traits can modify biotic interactions with non-target organisms in natural environments. These effects were detected outside authorized release areas and years after initial commercial deployment of GM cotton. Our findings demonstrate that transgene introgression into wild cotton populations can generate genetically novel configurations and long-term ecological effects not accounted for in current biosafety and environmental risk assessment frameworks, which focus on event stability under controlled conditions and assume limited gene flow. We argue that risk assessments should incorporate post-release evolutionary dynamics and indirect ecological interactions to evaluate the long-term environmental consequences of GM crop cultivation in centers of origin.