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

Authors: DUPUIS, JULIAN - University Of Hawaii; Sim, Sheina; SAN JOSE, MICHAEL - University Of Hawaii; LEBLANC, LUC - Idaho State University; HOASSAIN, AFTAB - Bangladesh Atomic Energy Commission; RUBINOFF, DANIEL - University Of Hawaii; Geib, Scott

Submitted to: Biological Invasions
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/7/2017
Publication Date: 11/11/2017
Citation: Dupuis, J., Sim, S.B., San Jose, M., Leblanc, L., Hoassain, A., Rubinoff, D., Geib, S.M. 2017. Population genomics and comparisons of selective signatures in two invasions of melon fly, Bactrocera cucurbitae (Diptera: Tephritidae). Biological Invasions. 20(5):1211-1228. https://doi.org/10.1007/s10530-017-1621-z.
DOI: https://doi.org/10.1007/s10530-017-1621-z

Interpretive Summary: Population genetic methods are useful tools for understanding the invasion history and evolutionary biology of invasive pest species. Although genomics is greatly increasing the resolution of population genetic analyses, few studies have implemented genome-wide population genetic analyses for invasive pests. Here, we use a large dataset of single nucleotide polymorphisms to assess genome-wide population structure across the range of the melon fly, a serious pest of cucurbits and commercial fruit. We also assess whether there are similar signs of selection across the genome when comparing two independent invasive ranges of the melon fly. We find strong support for six genetic clusters across the range of melon fly, but find very similar selective signatures in invasive regions. These results suggest that despite genetic differentiation across the range of this species, management strategies are likely to work equally well across the range.

Technical Abstract: Population genetics is a powerful tool for invasion biology and pest management, 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 across the range of melon fly, Zeugodacus cucurbitae, 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 its range and when comparing 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 southeast and mainland Asia is confounded by variable sampling between studies. We find few signals of selection across the genome, and virtually no unique signatures when comparing the two independent introductions, which may suggest that similar management strategies are evolutionarily appropriate across melon fly’s range. This is the first use of genome-wide data to characterize range-wide 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 of this pest.