Population Structuring and Phylogenetic Inference in a Species of Tropical Fly Using Double Digest Rad Markers

Blepharoneura (Diptera: Tephritidae) is a highly diverse, Neotropical genus of fruit flies that feed on cucurbit (Cucurbitaceae) host plants. Like most plant-feeding insects, Blepharoneura are highly specialized, with most species utilizing only a single part of one host species. Due to this extreme specialization and close, life-long associations with their host plants, shifts and subsequent adaptation to new hosts would be expected to drive divergence and diversification within the genus. However, sister species of Blepharoneura occupy extremely overlapping niches – they frequently share host plants and often utilize the same plant tissues. To investigate what role, if any, host use plays in driving divergence, we use double-digest restriction- associated sequencing (ddRAD-seq) to examine population structure and phylogenetic relationships between individuals of Blepharoneura species 10, which uses multiple host plants and parts throughout its range. Our findings show that, although the majority of divergence is linked to geographic location, host use may also contribute to differentiation.