Genome-wide SNPs of vegetable leafminer, Liriomyza sativae: insights into the recent Australian invasion

Liriomyza sativae, the vegetable leafminer, is an important agricultural pest originally from the Americas which has now colonized all continents except Antarctica. In 2015, L. sativae arrived on the Australian mainland and established on the Cape York Peninsula in the north-east of the country near the Torres Strait, which provides a possible pathway for pests to enter Australia and evade quarantine. Here, we assessed genetic variation in L. sativae based on genome-wide single nucleotide polymorphisms (SNPs) generated by double-digest restriction-site associated DNA sequencing (ddRAD-seq), aiming to uncover the potential origin(s) of this pest in Australia and contribute to reconstructing its global invasion history. Our fineRADstructure results and Principal Components Analysis suggest Australian mainland populations are genetically close to populations from the Torres Strait, whereas populations from Asia, Africa, and Papua New Guinea (PNG) were more distantly related. Hawaii populations were genetically distinct from all other populations of L. sativae included in our study. Admixture analyses further revealed that L. sativae from the Torres Strait may have genetic variation originating from multiple sources including Indonesia and PNG, and which has now spread to the Australian mainland. The L. sativae lineages from Asia and Africa appear closely related. Isolation by distance (IBD) was found at a broad global scale, but not within small regions, suggesting human-mediated factors likely contribute to the local spread of this pest. Overall, our findings suggest that an exotic Liriomyza pest invaded Australia through the Indo-Papuan conduit, highlighting the importance of quarantine measures aimed at restricting invertebrate movement through this corridor.