“…The present study investigates the population history and microbiome of the Mediterranean fruit fly C. capitata on a global scale, using a reduced representation of the genome in combination with a microbial characterisation, of samples from key geographical locations. We find strong evidence for the existence of two genetic clusters corresponding to the South African individuals and the other localities in the introduced range respectively, in agreement with virtually all previous studies using allozymes (Gasperi et al, 1991, 2002; Kourti, 2004; Malacrida et al, 1992), mitochondrial DNA markers (Arias et al, 2018; Elfekih et al, 2010, 2013; Karsten et al, 2013; Ruiz‐Arce et al, 2020), and microsatellites (Bonizzoni et al, 2004; Bonizzoni et al, 2001; Deschepper et al, 2021; Karsten et al, 2015; Nikolouli et al, 2020). In addition, when we analysed the five sampling sites from the introduced range only (i.e., we removed the South African samples), populations from Brazil represented a unique genetic cluster that had not been recognized in previous studies.…”