Resolution of inter and intra-species relationships of the West Indian fruit fly Anastrepha obliqua.

•Limits on most Anastrepha species are in agreement with morphological data except for A. fraterculus.•Strong support in concatenated nuclear data set for interspecific relationships of Anastrepha species.•Evidence for shared ancestral polymorphism or mitochondrial introgression between A. obliqua and A. fraterculus species.