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.

Despite the success of the United States (US) Boll Weevil Eradication Program, the boll weevil, Anthonomus grandis Boheman (Coleoptera: Curculionidae), remains a threat to cotton production in the southern US and is arguably the most important cotton pest in Central and South America. Management of this species is complicated by the existence of morphologically similar variants and re-infestations of areas where eradication had been successful. To date, no study has applied a high-throughput sequencing approach to better understand the population genetic structure of the boll weevil. Furthermore, only a single study has investigated genetic relationships between populations in North and South America. Here, we used double digest restriction site-associated DNA sequencing (ddRADseq) to resolve the population genomic structure of the boll weevil in the southern US, northern Mexico, and Argentina, test the two-form and three-form hypotheses of boll weevil variation in North America using a phylogeographic approach, and determine the relationship of the South American populations to the North. Our results supported the two-form hypothesis of boll weevil variation in North America wherein there are two major genetic lineages – one consisting of populations found geographically west of the Sierra Madre Occidental mountain range and the second consisting of populations found to the east – both are highly sub-structured across space and time. Boll weevil populations from Argentina were more closely related to the eastern lineage, suggesting a range expansion by the eastern lineage, but additional sampling across Central and South America is needed to determine a probable origin.