Filogenômica das moscas-das-frutas do gênero Anastrepha do complexo fraterculus (Wiedemann) (Diptera, Tephritidae)

Abstract

The challenge of defining taxonomic relationships among cryptic species is still an open question and can result in biased and imprecise classifications. This is because these species show little phenotypic variation despite significant evolutionary divergence. Phylogenomic analysis of cryptic species, with particular emphasis on fruit flies, plays a crucial role within the taxonomic and evolutionary scope, in addition to serving as a tool of significant relevance in the context of pest management. Fruit flies (Diptera: Tephritidae) of the genus Anastrepha are economically important species in tropical and subtropical regions, causing extensive fruit crops losses due to their polyphagy and easy adaptation to different hosts. The family Tephritidae is among the largest families of Diptera and includes approximately 4,000 species across 500 genera, with around 1,500 species of fruit flies associated to annual losses. Due to the remarkable morphological similarities between the species in question, their identification is intrinsically linked to the use of morphometric studies, which, to date, are still in the initial stages of investigation for defining taxonomic groups and lineages. Species delimitation has proven to be a complex challenge within this group, resulting in the formation of imprecise clades and short branches, especially in the case of the specific entity of A. fraterculus, whose morphotypes continue to pose phylogenetic uncertainties. Through a comprehensive analysis of a large set of orthologous genes, we used several strategies to seek efficient subsets of select loci that are still able of accurately infer phylogenetic trees and identify different lineages of Anastrepha. By analyzing evolutionary rates, diversity indices, hypotheses of incomplete lineage classification, as well as the phenomena of introgression and gene flow between species, we aim to better understand the historical events that have made the differentiation of lineages and species within the genus Anastrepha a challenging, despite the extensive set of available data. In this context, we adopted an approach that uses several bioinformatics tools to identify regions in the genome that can provide additional insights into the divergences observed in the phylogenetic trees of Anastrepha.