Artificial competition shows the replicative superiority of KP elements over complete P elements in Drosophila...

Transposable elements (TEs) frequently generate incomplete derivative copies during transposition. The relative abundance of these variants is important in shaping the genomic landscape, but how these variants interact and compete within genomes remains poorly understood. To examine potential evolutionary conflicts among TE variants, we compared the replication behaviors of the full-length P element (FP) and one of its internally-deleted derivatives, the KP element, in Drosophila under three experimental conditions. KP elements were introduced into chromosomes at significantly higher frequencies than FP elements from a plasmid vector in both D. melanogaster and D. simulans. When both variants coexisted in D. simulans, KP elements also transposed between chromosomal sites more frequently than FP elements. Furthermore, the presence of KP elements reduced the long-term stability of FP elements in D. melanogaster. Together, these results demonstrate that KP elements possess an intrinsic replicative advantage over FP elements in competitive contexts, providing a mechanistic explanation for the global predominance of KP elements in D. melanogaster. This superiority is probably attributable to nucleotide sequence-specific properties of KP elements, rather than to differences in element size, genomic insertion position, or repression of transposition.