Abstract
Transposable elements are genetic elements also known as "jumping genes" that increase their copy number within a host through various mechanisms of transposition. TEs can also move between species through unknown intermediaries in a process known as horizontal transfer, infecting novel genomes and increasing in copy number. While many individual invasions have been documented, a large dataset of recent horizontal transfer events that will allow us to understand larger more general HT patterns has not been assembled. In this manuscript we used almost 400 dipteran genomes to uncover 637 recent transposon invasions, mostly in Drosophila. The majority of transfers occurred between closely related species, with the cosmopolitan melanogaster group showing the highest recent transfer activity. We even documented a single transposon with 16 recent transfers, many between different Drosophila groups. Using species distance on a phylogenetic tree to measure the distance that transposons travel, we found that DNA transposons transfer between distantly related species much more frequently compared to retrotransposons. This potentially represents a different evolutionary strategy for exploiting naive genomes. Our phylogenetic framework advances the understanding of horizontal transfer dynamics at the species level within Drosophila.