Phylogenomic approach reveals intense signatures of introgression in the rapid radiation of Neotropical true fruit flies (Anastrepha: Tephritidae)

3811 alignments and gene trees of Anatrepha fraterculus group lineages and A. bistrigata as outgroup; 2498 alignments and gene trees of Anatrepha lineages and C. capitata as outgroup; mtDNA alignment and partition scheme; and ITS1 alignment including data from Sutton et al. (2015) and Prezotto et al. (2019). These datasets were used to perform a phylogenomic analysis of Neotropical true fruit flies.