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 fundamental goal of evolutionary biology. For speciation to occur, gene flow between populations must be reduced or restricted, allowing for the accumulation of reproductive barriers and ultimately resulting in complete isolation. Hybrid zones, regions where genetically distinct populations interbreed, serve as powerful “natural laboratories” for studying the genomic mechanisms of species divergence and revealing how genetic barriers form and persist. Here, we examine a hybrid zone between the introduced fire ants Solenopsis invicta and S. richteri in the southeastern United States. Although the two species overlap in their native South American range, previous studies found no evidence of successful hybridization. Using reduced representation sequencing (RADSeq) and genomic cline models, we identified nearly 1,500 SNP loci that exhibited impeded introgression (i.e., signatures of reduced gene flow) within hybrid genomic backgrounds. Notably, most of the SNP loci were co-localized in narrow regions across eleven different chromosomes. Comparisons of genetic differentiation (F_ST), linkage disequilibrium (LD), and SNP association tests indicate that chromosomal inversions, rearrangements in which DNA segments are reversed 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.