In this study, we study the process of whole genome differentiation between sympatric strains in fall armyworms (Spodoptera frugiperda) based on population genomics approaches.

The process of speciation involves the differentiation of whole genome sequences. Gene flow between population impedes this process because recombination in hybrids homogenizes sequences. Accumulating empirical cases demonstrate that speciation indeed occurs in the presence of gene flow, and several speciation models have been proposed to explain the process of whole genome differentiation. In particular, the differentiation of whole genomes may involve physical linkage among targets of divergent selection, linkage disequilibrium among targets generated by the selection process, chromosomal rearrangement, and genome-wide reduction in migration rate due to many selectively targeted loci. Polymorphism patterns from a pair of very recently diverged taxa may provide insightful information to identify critical evolutionary forces enabling genomic differentiation. Lepidopteran Fall armyworm, Spodoptera frugiperda is observed as two sympatric strains, corn strains, and rice strains, named after their preferred host plants, throughout the entire range of habitats. Moreover, assortative mating between these two strains is reported as well. The difference in host-plant ranges suggests a possibility of ecological divergent selection. In this study, we analyzed resequencing data of these two strains from Mississippi to study initial steps toward genomic differentiation based on population genetics approaches and de novo genome assembling.