Patterns of divergence and speciation on islands have long been of interest in the broader study of evolution. Hawaiʻi’s endemic Kamehameha butterfly (Vanessa tameamea) is experiencing population decline, but because of its high vagility and assumed genetic homogeneity as a species, its population structure has not been investigated. To evaluate V. tameamea genetic variation across the Hawaiian Islands, we assembled a reference quality genome assembly for the species using HiFi and HiC reads and performed range-wide population genetic analyses using ddRAD sequencing data. A discriminant analysis of principal components (DAPC) revealed that, contrary to prior assumptions, V. tameamea populations appear to be diverging based on geography, in a pattern similar to other native Hawaiian terrestrial arthropods. Specifically, through demographic history analyses, we find that the distinct population on Kauai is likely to be ancestral, the central islands of Maui, Molokai, and Oahu comprise another population, and Hawaii Island forms a third population, with likely more gene exchange with the central islands. Finally, we investigate the SNPs driving differences between groups and find that many are associated with genes that may be relevant to local adaptation to environmental chemicals such as host plant defenses or chemicals introduced by human activity, notably to do with metabolism and detoxification. While much field work remains to investigate any cryptic or phenotypic patterns as well as quantify effective migration, we hope that this work will inform refinement of conservation plans for one of Hawaiʻi’s two native butterflies.

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.

The rusty patched bumble bee, Bombus affinis, is an important pollinator in North America and a federally listed endangered species. Due to habitat loss and large declines in population size, B. affinis is facing imminent extinction unless human intervention and recovery efforts are implemented. To better understand B. affinis biology and population genetic and genomic landscapes, we sequenced and assembled the B. affinis genome from a single male. Whole genome HiFi sequencing on PacBio coupled with HiC sequencing resulted in a complete and highly contiguous contig assembly that was scaffolded into a chromosomal context, resolving 18 chromosomes for this species. All material for both HiFi and HiC sequencing was derived from a single abdominal tissue segment from the one male. These assembly results, coupled with the minimal amount of tissue destructively sampled, demonstrates methods for generating contiguous and complete genomic resources for a rare and endangered species with limited material available and highlights the importance of sample preservation. Precise methods and applications of these methods are presented for potential applications in other species with similar limitations in specimen availability and curation considerations.