The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control.

BACKGROUND: The stable fly, Stomoxys calcitrans, is a major blood-feeding pest of livestock that has near worldwide distribution, causing an annual cost of over $2 billion for control and product loss in the USA alone. Control of these flies has been limited to increased sanitary management practices and insecticide application for suppressing larval stages. Few genetic and molecular resources are available to help in developing novel methods for controlling stable flies. RESULTS: This study examines stable fly biology by utilizing a combination of high-quality genome sequencing and RNA-Seq analyses targeting multiple developmental stages and tissues. In conjunction, 1600 genes were manually curated to characterize genetic features related to stable fly reproduction, vector host interactions, host-microbe dynamics, and putative targets for control. Most notable was characterization of genes associated with reproduction and identification of expanded gene families with functional associations to vision, chemosensation, immunity, and metabolic detoxification pathways. CONCLUSIONS: The combined sequencing, assembly, and curation of the male stable fly genome followed by RNA-Seq and downstream analyses provide insights necessary to understand the biology of this important pest. These resources and new data will provide the groundwork for expanding the tools available to control stable fly infestations. The close relationship of Stomoxys to other blood-feeding (horn flies and Glossina) and non-blood-feeding flies (house flies, medflies, Drosophila) will facilitate understanding of the evolutionary processes associated with development of blood feeding among the Cyclorrhapha.

Patterns of genomic and allochronic strain divergence in the fall armyworm, Spodoptera frugiperda (J.E. Smith).

Speciation is the process through which reproductive isolation develops between distinct populations. Because this process takes time, speciation studies often necessarily examine populations within a species that are at various stages of divergence. The fall armyworm, Spodoptera frugiperda (J.E. Smith), is comprised of two strains (R = Rice & C = Corn) that serve as a novel system to explore population divergence in sympatry. Here, we use ddRADSeq data to show that fall armyworm strains in the field are largely genetically distinct, but some interstrain hybridization occurs. Although we detected F1 hybrids of both R- and C-strain maternal origin, only hybrids with R-strain mtDNA were found to contribute to subsequent generations, possibly indicating a unidirectional barrier to gene flow. Although these strains have been previously defined as "host plant-associated," we recovered an equal proportion of R- and C-strain moths in fields dominated by C-strain host plants. As an alternative to host-associated divergence, we tested the hypothesis that differences in nightly activity patterns could account for reproductive isolation by genotyping temporally collected moths. Our data indicates that strains exhibit a significant shift in the timing of their nightly activities in the field. This divergence in phenology creates a prezygotic reproductive barrier that likely maintains the genetic isolation between strains. Thus, we conclude that it may be ecologically inaccurate to refer to the C- and R- strain as "host-associated" and they should more appropriately be considered "allochronic strains."

Potential Distribution of Wild Host Plants of the Boll Weevil (Anthonomus grandis) in the United States and Mexico

The boll weevil (Anthonomus grandis Boheman) reproduces on a reported 13 species of wild host plants in North America, two in the United States and 12 in Mexico. The distributions of these plants are of economic importance to pest management and provide insight into the evolutionary history and origin of the BW. However, detailed information regarding the distributions of many of these species is lacking. In this article, we present distribution models for all of the reported significant BW host plants from Mexico and the United States using spatial distribution modelling software. Host plant distributions were divided into two groups: "eastern" and "western." In Mexico, Hampea nutricia along the Gulf Coast was the most important of the eastern group, and the wild cottons, Gossypium aridum and Gossypium thurberi were most important in the western group. Other species of Hampea, Gossypium, and Cienfuegosia rosei have relatively restricted distributions and are of apparent minimal economic importance. Cienfuegosia drummondii is the only truly wild host in the southern United States, east of New Mexico. Factors determining potential distributions were variable and indicated that species were present in five vegetation types. Ecological and economic considerations of host plant distributions are discussed, as well as threats to host plant conservation.

Population genomics and phylogeography of the boll weevil, Anthonomus grandis Boheman (Coleoptera: Curculionidae), in the United States, northern Mexico, and Argentina.

The boll weevil, Anthonomus grandis Boheman (Coleoptera: Curculionidae), is an important pest of commercial cotton across the Americas. In the United States, eradication of this species is complicated by re-infestations of areas where eradication has been previously successful and by the existence of morphologically similar variants that can confound identification efforts. 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. We used double digest restriction site-associated DNA sequencing (ddRADseq) to resolve the population genomic structure of the boll weevil in the southern United States, northern Mexico, and Argentina. Additionally, we assembled the first complete mitochondrial genome for this species and generated a preliminary whole genome assembly, both of which were used to improve the identification of informative loci. Downstream analyses revealed two main 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-were revealed, and both were sub-structured. Population geographic structure was consistent with the isolation by distance model, indicating that geogrpahic distance is likely a primary mechanism driving divergence in this species. Boll weevil populations from Argentina were found to be more closely related to the eastern lineage, suggesting a recent colonization of South America by the eastern lineage, but additional sampling across Mexico, Central America and South America is needed to further clarify their origin. Finally, we uncovered an instance of population turnover or replacement, highlighting the temporal instability of population structure.

Genome-wide markers reveal temporal instability of local population genetic structure in the cotton fleahopper, Pseudatomoscelis seriatus (Hemiptera: Miridae).

BACKGROUND: The cotton fleahopper, Pseudatomoscelis seriatus (Reuter) (Hemiptera: Miridae), is a pest of upland cotton, Gossypium hirsutum L. (Malvales: Malvaceae), that attacks pre-floral buds (squares), leading to abscission and yield losses. In the Brazos Valley cotton production area of Texas (USA), P. seriatus exhibits a seasonal pattern of host use. In spring, eggs hatch from stems of the overwintering host, woolly croton, Croton capitatus Michx. (Malpighiales: Euphorbiaceae). During the growing season, individuals feed on a variety of host plants, including cotton. Adults return to woolly croton at season end to oviposit. We investigated if genetic differentiation exists between populations infesting cotton and those infesting alternative hosts, and whether woolly croton serves as a year-end site of admixture that could be suitable as a natural refuge for the purposes of insect resistance management. We combined high-throughput DNA sequencing with fine-scale spatio-temporal sampling to test (i) whether a population genomic approach would recover patterns of genetic variation consistent with earlier studies and (ii) if local genetic population structure was robust to seasonal changes in local habitat over time. RESULTS: We found high gene flow among populations of P. seriatus collected from different host plants in the Brazos Valley. We also identified temporal instability of the local population genetic structure, including the near complete loss of a genotypic group that had been previously abundant. CONCLUSION: We support the status of woolly croton as a natural refuge that promotes year-end gene flow between genotypes infesting cotton and those infesting alternative hosts. © 2019 Society of Chemical Industry.