Bactrocera jarvisi is an endemic Australian fruit fly species (Diptera: Tephritidae). It occurs commonly across tropical and subtropical coastal Australia, from far-northern Western Australia, across the ‘Top End’ of the Northern Territory, and then down the Queensland east coast.  Across this range, its distribution crosses several well-documented biogeographic barriers.  In order to better understand factors leading to the divergence of Australian fruit fly lineages, we carried out a population genetic study of B. jarvisi from across its range using genome-wide SNP analysis, utilising adult specimens gained from trapping and fruit rearing.  Populations from the Northern Territory (NT) and Western Australia were genetically similar to each other but divergent from the genetically uniform east-coast (=Queensland, QLD) population. Phylogenetic analysis demonstrated that the NT population derived from the QLD population. We infer a role for the Carpentaria Basin as a biogeographic barrier restricting east-west gene flow.  The QLD populations were largely panmictic and recognised east-coast biogeographic barriers play no part in north-south population structuring.  While the NT and QLD populations were genetically distinct, there was evidence for the historically recent translocation of flies from each region to the other.  Flies reared from different host fruits collected in the same location showed no genetic divergence.  While a role for the Carpentaria Basin as a barrier to gene flow for Australian fruit flies agrees with existing work on the related B. tryoni, the reason(s) for population panmixia for B. jarvisi (and B. tryoni) over the entire Queensland east coast, a linear north-south distance of >2000km, remains unknown.

For DNA extractions, either the head and legs or the full body without the abdomen was used depending on the samples’ freshness and quality. DNA was extracted using QIAGEN DNeasy® Blood & Tissue Kit following the manufacturer’s protocol with only slight modifications (i.e., overnight incubation of the tissue with lysis buffer and proteinase K at 36 0C and eluting the genomic DNA into 30–50 µL of elution buffer for more concentrated DNA extraction. DNA samples were screened for quality and quantity, using both gel electrophoresis and Qubit assay, and then sent to Diversity Arrays Technology Pty Ltd, Canberra (DArT P/L), for DArTseq high-density genotyping. The restriction enzyme combination, PstI/SphI, was used by DArT P/L for the current B. jarvisi dataset, and the fragments (up to 90bp) were sequenced on an Illumina Hiseq2500 as single end reads.