Pritam, S. | Search bioRxiv

bioRxiv2025

Recent horizontal transfer of transposable elements in Drosophila

Transposable elements are small pieces of DNA which selfishly increase in copy number within genomes. Transposable elements can also move between species through unknown intermediaries in a process known as horizontal transfer, infecting novel genomes and increasing in copy number. In this manuscript we used almost 400 dipteran genomes to uncover 648 recent transposon invasions, mostly in Drosophila. We limited our results to transposons with 99% similarity to capture recent transfers. When our results overlapped with previous studies they were largely replicated. The majority of transfers occurred between closely related species, with the cosmopolitan melanogaster group showing the highest recent transfer activity. However, we documented 60 HT events spanning more than 30 million years of evolution. Gypsy and Mariner elements were involved in the most HT events. While the majority of elements were implicated in fewer than five transfers, we documented a single transposon with as many as with 16 recent transfers, many between different Drosophila groups. In addition, we found that while LTR elements engage in HT more frequently, DNA elements travel longer phylogenetic distances when engaging in HT. 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.

evolutionary biology↗

bioRxiv2024

The impact of insertion bias into piRNA clusters on the invasion of transposable elements

In our current understanding of transposable element (TE) invasions TEs move freely until they accidentally insert into a piRNA cluster. They are then silenced by the production of piRNA cognate to the TE. Under this model, one would expect that TEs might evolve to avoid piRNA clusters. Yet empirical observations show that some TEs, such as the P -element, insert into piRNA clusters preferentially. We were thus wondering if such a bias could be beneficial for the TE, for example by minimizing harm to the host while still being able to selfishly spread in populations. We decided to model insertion bias to determine if there was ever a situation in which insertion bias was beneficial to the TE. We performed extensive forward simulations of TE invasions with differing insertion biases into piRNA clusters. We found that insertion bias significantly altered the invasion dynamics of TEs, primarily by changing the copy number of the TE in individuals prior to silencing. Insertion into a piRNA cluster reduced the deleterious effects of TEs to the host population, but we found that TEs avoiding piRNA clusters out-compete TEs with a bias towards cluster insertions. Insertion bias was only beneficial to the TE when there was negative selection against TEs and a lack of recombination. Different TEs show different insertion biases into piRNA clusters suggesting they are an attribute of the TE not the host, yet scenarios in which this is beneficial to the TE are quite limited. This opens up an interesting area of future research into the dynamics of insertion bias during TE invasions. Significance StatementThis study challenges the pre-existing understanding of the TE dynamics by investigating the potential adaptive role of insertion bias into piRNA clusters. Using extensive forward simulations, we demonstrate that while insertion bias significantly alters TE invasion dynamics, it is generally not beneficial for the TEs spread in populations. Our results also show that transposable elements (TEs) that avoid piRNA clusters tend to do better than those that are more likely to preferencially insert into these clusters. This work provides novel insights into the complex dynamics between TEs and host genomes, showing the limited scenarios where the insertion bias could be advantageous to TEs. These results open new area for research into TE invasion dynamics and the evolution of host-TE interactions, further contributing to our understanding of genome evolution and stability.

evolutionary biology↗