Cryptic diversification proceeds despite historical and contemporary hybridization in Patagonian ants

Understanding how independently evolving lineages arise despite ongoing gene flow remains a central question in evolutionary biology. Although genomic studies increasingly suggest that hybridization can accompany diversification, empirical evidence from ecologically dominant insect groups remains limited. Here, we present the first population-scale phylogenomic analysis of Patagonian ants, sampling Dorymyrmex across approximately 450,000 km2. Using genome-wide SNPs, coalescent phylogenetics, phylogenetic networks, demographic modelling, species delimitation, and genome scans, we reconstruct the evolutionary history of this widespread genus. We discovered extensive cryptic diversity with strong genomic differentiation and detected both recent and historical hybridization, demonstrating that substantial genomic divergence accumulated despite recurrent gene flow events. Genome scans further identify candidate loci associated with adaptation to Patagonias contrasting environments, suggesting that ecological divergence contributed to lineage diversification. Our results show that cryptic diversification can proceed despite recurrent gene flow, supporting hybridization as an integral component of the diversification process. More broadly, this study illustrates how genome-scale data can reveal hidden biodiversity and the evolutionary processes shaping it in ecologically important but genomically understudied taxa.