Population genomics and comparisons of selective signatures in two invasions of melon fly, Bactrocera cucurbitae (Diptera: Tephritidae)

Abstract

Population genetics is a powerful tool for invasion biology and pest management, and useful for a range of questions from tracing invasion pathways to informing management decisions with inference of population demographics. Genomics greatly increases the resolution of population-scale analyses, yet outside of model species with extensive genomic resources, few studies have used population genomics in invasion biology. We use genome-wide single nucleotide polymorphisms (SNPs) to investigate population genomic structure with samples from across the range of melon fly, Bactrocera cucurbitae (Coquillett, 1849), a highly polyphagous pest of commercial produce. We then make use of a chromosome-scale genome assembly and gene set to compare signatures of selection across the melon fly’s genome, both across our sampling as a whole and in the context of two independent, established introductions. Using multiple approaches, we find support for six genetic clusters across melon fly’s distribution. Some of these agree with previously identified genetic clusters using microsatellites, but consensus of clusters in mainland and oceanic southeast Asia is confounded by variable sampling between studies. We find few adaptive signatures across the genome, and virtually no unique signatures when comparing the two independent introductions, which suggests that similar management strategies are appropriate across melon fly’s range. This is the first use of genome-wide data to characterize population structure in tephritid fruit fly pests, and our SNP dataset provides a foundation for objective and cost-effective genotyping of previously collected melon fly specimens. Future research needs to focus on truly comprehensive sampling across melon fly’s range to overcome the historic variability of range-wide estimates of population structure for this pest.