Post-invasion selection acts on standing genetic variation despite a severe founding bottleneck

Invasive populations often have lower genetic diversity relative to the native-range populations from which they derive.^1,2 Despite this, many biological invaders succeed in their new environments, in part due to rapid adaptation.^3,4,5,6 Therefore, the role of genetic bottlenecks in constraining the adaptation of invaders is debated.^7,8,9,10 Here, we use whole-genome resequencing of samples from a 10-year time-series dataset, representing the natural invasion of the Asian honey bee (Apis cerana) in Australia, to investigate natural selection occurring in the aftermath of a founding event. We find that Australia's A. cerana population was founded by as few as one colony, whose arrival was followed by a period of rapid population expansion associated with an increase of rare variants.¹¹ The bottleneck resulted in a steep loss of overall genetic diversity, yet we nevertheless detected loci with signatures of positive selection during the first years post-invasion. When we investigated the origin of alleles under selection, we found that selection acted primarily on the variation introduced by founders and not on the variants that arose post-invasion by mutation. In all, our data highlight that selection on standing genetic variation can occur in the early years post-invasion, even where founding bottlenecks are severe.