Data from: A new phylogeny of Anastrepha (Diptera: Tephritidae) based on nuclear loci obtained by phylogenomic methods

<p>Phylogenetic alignments, datasets, and tree files from anchored hybrid enrichment (AHE) from Norrbom et al. for <em>Anastrepha</em> true fruit flies (Diptera: Tephritidae). The data sets include sequences from 293 (DS1) and 1110 (DS2) aligned orthologous loci sampled for 735 sampled specimens, with 728 identified as representatives of 237 species. Multiple sequence alignments were inferred using the program MAFFT. Phylogenetic data sets are formatted for use in IQTree2 and were used to reconstruct phylogenetic trees depicted in Figures 1 and 2, S1, S2 ,and S3 in the manuscript. This study presents a comprehensive phylogenetic analysis of the genus <em>Anastrepha</em>, utilizing anchored hybrid enrichment to sample hundreds of nuclear genes from a global collection of their diversity. Our results provide a robust and novel reconstruction of the evolutionary history of this group, allowing a better resolution of their lineages and a revised classification in species groups.</p>