Genomic Traces of the Fruit Fly Anastrepha obliqua Associated with Its Polyphagous Nature

SIMPLE SUMMARY: Individuals of a polyphagous species, such as Anastrepha obliqua, that plague different host plants, present differences at the genome level; these differences are associated with adaptive processes related to the exploitation of the resource and can lead to speciation in sympatry, first with the formation of host races. In this studio, we used pooled RAD-seq to assess genomic differentiation and population structure in sympatric populations of Anastepha obliqua that infest three different host plants. The results obtained support the effect of host plants on genomic differentiation in populations of the species A. obliqua. We identified a small group of candidate genes that could be under divergent selection, a product of the selective pressure mediated by the host plants. ABSTRACT: Anastrepha obliqua (Macquart) (Diptera: Tephritidae) is an important pest in the neotropical region. It is considered a polyphagous insect, meaning it infests plants of different taxonomic families and readily colonizes new host plants. The change to new hosts can lead to diversification and the formation of host races. Previous studies investigating the effect of host plants on population structure and selection in Anastrepha obliqua have focused on the use of data from the mitochondrial DNA sequence and microsatellite markers of nuclear DNA, and there are no analyses at the genomic level. To better understand this issue, we used a pooled restriction site-associated DNA sequencing (pooled RAD-seq) approach to assess genomic differentiation and population structure across sympatric populations of Anastrepha obliqua that infest three host plants—Spondias purpurea (red mombin), Mangifera indica (mango) of the family Anacardiaceae and Averrhoa carambola (carambola) of the family Oxalidaceae—in sympatric populations of the species Anastrepha obliqua of Inter-Andean Valley of the Cauca River in southwestern Colombia. Our results show genomic differentiation of populations from carambola compared to mango and red mombin populations, but the genetic structure was mainly established by geography rather than by the host plant. On the other hand, we identified 54 SNPs in 23 sequences significantly associated with the use of the host plant. Of these 23 sequences, we identified 17 candidate genes and nine protein families, of which four protein families are involved in the nutrition of these flies. Future studies should investigate the adaptive processes undergone by phytophagous insects in the Neotropics, using fruit flies as a model and state-of-the-art molecular tools.