javascript:void(0) The boll weevil, Anthonomus grandis grandis Boheman, and thurberia weevil, Anthonomus grandis thurberiae Pierce (Coleoptera: Curculionidae), together comprise a species complex that ranges throughout Mexico, the southwestern regions of the United States, and South America. The boll weevil is a historically damaging and contemporaneously threatening pest to commercial Upland cotton, Gossypium hirsutum L. (Malvales: Malvaceae), whereas the thurberia weevil is regarded as an innocuous non-pest subspecies that is mostly found on non-cultivated Gossypium species, e.g. Thurber’s or Arizona cotton, G. thurberi, throughout its native range in western parts of Mexico and the southwestern US. Recent independent analyses using mitochondrial COI and whole genome ddRADseq have suggested the independent evolution of these lineages is largely attributable to geographic isolation and not to host plant preference. We furthered this investigation by employing comparative genomic, population genetic, and pangenome methodologies to identify large and small polymorphisms within this complex and described their role in demography and adaptation. We also leveraged genetic differences to identify nearly 40,000 diagnostic loci between the subspecies, find genes under selection, and model the subspecies’ shared and unique evolutionary history. Interestingly, structural variations capture a large proportion of genes at the population level and demographic reconstruction suggests a split between these subspecies that coincides with cotton cultivation in the southern U.S. in the late 1800s. Observed polymorphisms are enriched for reproductive, regulatory, and metabolic genes which may be attributed to the boll weevil’s rapid expansion onto commercial cotton.

Structural variations (SVs) have been associated with genetic diversity and adaptation in diverse taxa. Despite these observations, it is not yet clear what their relative importance is for microevolution, especially with respect to known drivers of diversity, e.g., nucleotide substitutions, in rapidly adapting species. Here we examine the significance of SVs in pesticide resistance evolution of the agricultural super-pest, the Colorado potato beetle, Leptinotarsa decemlineata. By employing a trio-binning procedure, we develop near chromosomal reference genomes to characterize structural variation within this species. These updated assemblies represent >100-fold improvement of contiguity and include derived pest and ancestral non-pest individuals. We identify >200,000 SVs, which appear to be non-randomly distributed across the genome as they co-occur with transposable elements. SVs intersect exons for genes associated with insecticide resistance, development, and transcription, most notably cytochrome P450 (CYP) genes. To understand the role that SVs might play in adaptation, we incorporate an additional 66 genomes among pest and non-pest populations of North America into the SV graph. Single nucleotide polymorphisms (SNPs) and SVs have a similar proportion in coding and non-coding regions of the genome, but there is a deficit of SNPs in SVs, suggesting SVs may be under selection. Using multiple lines of evidence, we identify 28 positively selected genes that include 337 SVs and 442 outlier SNPs. Among these, there are four associated with insecticide resistance. Two of these genes (CYP4g15 and glycosyltransferase-13) are physically linked by a structural variant and have previously been shown to be co-induced during insecticide exposure.