A total of ve adult specimens per site sampled in 2016, and four larval specimens per site sampled in 2018 were randomly selected for DNA extraction. In addition, ve adult ies and four larval specimens were included from the International Centre of Insect Physiology and Ecology (icipe) fruit y laboratory colony. The sampled colony was derived from infested mango collected from different farms across Kenya and maintained for more than 40 generations with frequent wild infusions in the laboratory at 27 °C and 60% relative humidity. Adult ies were fed on a diet consisting of 3 parts sugar and 1-part enzymatic yeast hydrolysate ultrapure (USB Corporation, Cleveland, Ohio, USA), and water on pumice granules. For each generation, fresh mango domes were used as oviposition receptacles, from which embryos were washed in distilled water before inoculation on larval rearing diets [64] . Same age and generation of laboratory reared ies were used for this study.
DNA extraction and high throughput sequencing were carried out as previously described [63] . Larval DNA was sequenced at the Centre for Integrated Genomics, University of Lausanne, Switzerland and adult DNA at the Macrogen Europe Laboratory, the Netherlands. Adult and larval sequence sets were therefore analyzed separately.
DNA extraction and high throughput sequencing were carried out as previously described [63] . Larval DNA was sequenced at the Centre for Integrated Genomics, University of Lausanne, Switzerland and adult DNA at the Macrogen Europe Laboratory, the Netherlands. Adult and larval sequence sets were therefore analyzed separately.