Genomic analyses of hybrids indicate chromosomal inversions reinforce structural genomic differences between fire ant species Solenopsis invicta and S. richteri

Understanding the genetic basis of speciation is a central goal in evolutionary biology. For speciation to occur, gene flow between populations must be reduced, allowing reproductive barriers to accumulate and ultimately lead to complete isolation. However, empirically studying this process remains challenging. Hybrid zones - geographical regions where two distinct populations interbreed - serve as "natural laboratories" for investigating speciation. These zones provide valuable opportunities to study reproductive isolation at the genomic level using next-generation sequencing, offering insights into the architecture and maintenance of species boundaries. Here, we investigate a hybrid zone between two invasive fire ants, Solenopsis invicta and S. richteri, in the southeastern United States. Previous genetic studies found no evidence of hybridization in overlapping areas of their native range in South America. By using reduced-representation sequencing and genomic cline analyses, we identified nearly 7,000 SNPs with signatures of reduced introgression, indicating limited gene flow, within hybrid genomes. Notably, these SNPs were not randomly distributed but instead clustered in narrow regions on at least eight chromosomes. Further analysis of genetic differentiation (FST), linkage disequilibrium, and SNP associations suggests that chromosomal inversions - rearrangements where DNA segments are flipped within a chromosome - likely contribute to the maintenance of species differences between S. invicta and S. richteri. Our study highlights the role of genomic rearrangements in shaping species divergence, as well as the interaction between genome architecture and reproductive isolation in two natively parapatric species that are known to successfully hybridize only in their invaded range.