*Result*: Harnessing transposable elements: A new frontier in insect systematics.

*Insect genomes are largely composed of non-coding repetitive sequences, often exceeding 50 % of the total genomic content; these are also known as transposable elements (TEs). The increasing availability of extensive insect genomes, facilitated by advancements in sequencing technology, has made it feasible to explore the potential of TEs in insect systematics. Exhibiting varying degrees of differentiation across taxonomic levels, insect TEs may serve as informative characters for species-level analyses. This study focused on the Drosophiloidea as a case to evaluate the potential of TEs as phylogenetic markers and for insect phylogeny. We identified 2,390 species-specific TE families using genomes from 128 species and quantified their copy numbers in each species. Subsequently, we constructed phylogenetic trees based on the presence/absence (0/1 coding) of these TEs using Maximum Parsimony, Maximum Likelihood, and Bayesian Inference methods. Comparison with the recognized phylogeny showed incongruences in overall topology, especially at higher levels (suprageneric), where TE-based trees recovered about 51-55.8 % of nodes consistent with the phylogeny. At lower levels (infrageneric), TEs recovered monophyly in 54.5-68.2 % of nodes. Given the limitations of tree-based methods in resolving the relationships of species, we performed clustering analysis on normalized and dimensionally reduced TE copy numbers, which revealed that TEs can effectively distinguish closely related species. Furthermore, by considering the phylogenetic signal strength of TEs, we found that phylogenetic trees constructed using TEs with higher RI values (>0.5) exhibited the smallest normalized Robinson-Foulds distances to known phylogenies (0.379-0.408), indicating that accounting for phylogenetic signal may improve inference accuracy. Notably, we observed no significant difference (p-values = 0.7425) in the performance of TEs between genomes generated by next-generation and third-generation sequencing platforms. Clustering analysis of different TE types (including LTR, SINE, LINE, RC, DNA, and Unknown) indicated that all types provide comparable resolution for species delimitation. Overall, TEs show greater utility at lower taxonomic levels, particularly for species delimitation. This study provides insights into the use of genome-wide TE features for insect systematics, contributing to a better understanding of their application in phylogenetic and taxonomic studies.
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*Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.*