Comparative Genomics and Phylogenomics of Anastrepha fruit flies, with emphasis on the fraterculus group

Abstract

Fruit flies of the genus Anastrepha are endemic to South America and harbor several important agricultural pest species, particularly those belonging to the fraterculus group. Despite their economic importance, and the several articles that has provided relevant genetic and morphological information about species in this group, and in the genus, there are still several important unresolved issues, particularly about the phylogenetic relationships among Anastrepha species and their evolutionary history, particularly in the fraterculus group, which has several closely related, and even cryptic species. The goals of this proposal are to help identify evolutionary lineages among Anastrepha species distributed in Brazil, with a special focus on species of the economically important fraterculus group. Using genomic and transcriptomic data from several species of Anastrepha and Bactrocera and bioinformatics tools, we will select 2000 gene regions that will be sequenced from over 1000 samples collected from several species across various parts of Brazil using a strategy to capture target regions and sequence them on a Illumina MiSeq platform. This strategy will produce continuous fragments of about 500 bp-long for each chosen genomic region from individual samples, allowing for their gametic phase to be directly established. These data will be used for populational and coalescent analyses not only to determine evolutionary forces affecting such regions, but also to estimate divergence levels among Anastrepha populations and species, in particular of the fraterculus group, using several modern species delimitation strategies. These studies will help establish evolutionary lineages and investigate historical and recurrent gene flow among different lineages, which will be paramount to help determine species taxonomic statuses, and understand genetic changes that occurred during speciation processes across this important genus, particularly among species of the fraterculus group. In so doing, this project may enable the identification of species-specific genetic markers for several of the most economically important species of this genus which, despite considerable efforts, has still been elusive, thereby facilitating the establishment of better conditions for the control of these important agricultural pests. (AU)