Everything but the lab sink: Using 1,000 phylogenomically informative markers to resolve historically messy species groups in Anastrepha fruit flies (Diptera: Tephritidae)

Everything but the lab sink: Using 1,000 phylogenomically informative markers to resolve historically messy species groups in Anastrepha fruit flies (Diptera: Tephritidae)

The genus Anastrepha (Diptera: Tephritidae) is long overdue for a major taxonomic revision. Of the 22 recognized species groups within Anastrepha, only ~5 are well supported clades. Molecular methods, such as traditionally used mitochondrial DNA markers, have been unsuccessful at elucidating relationships amongst Anastrepha species; therefore, a more robust phylogenomic tool is likely necessary. To accomplish this, we used Highly Multiplexed Amplicon-based Phylogenomics (HiMAP) to identify 1,000 phylogenomically informative nuclear markers. Post sequencing, we obtained data for 500+ amplicons for 90 Anastrepha spp. belonging to 18 Anastrepha species groups. Our findings agree with some aspects of the most recently published Anastrepha phylogeny, but discrepancies exist and may be the result of intensive patterns of introgression among Anastrepha species groups. These data shed light on the potential for using genomic data to delimit unresolved taxa, especially in groups currently considered to be paraphyletic.