Evaluation of the Bioinformatic tool RAM and Diversification of Carollia perspicillata and C. brevicauda (Chiroptera: Phyllostomidae)

Carollia species are commonly found in the Neotropic region. Their ancestral origins have been subject to debate. To shed light on their evolutionary history in the context of the Andean orogeny, this study employed a dual-pronged approach. It combined the use of RepeatAfterMe (RAM), a newly developed bioinformatics tool for enhanced Transposable Element (TE) family identification, with phylogenetic, divergence, and biogeographical analyses. RAM was used to identify 513 TE consensus sequences, with 349 classified as "complete." This tool accelerated the analysis compared to manual curation methods and demonstrated exceptional accuracy, requiring minimal manual intervention. Interestingly, RAM uncovered previously uncharacterized TE diversity, as distinct species-specific Ves SINE subfamilies were identified in C. perspicillata, despite reduced recent TE accumulation. Phylogenetic analyses supported the distinct clades within both C. brevicauda and C. perspicillata. The study estimated that the most recent common ancestor (MRCA) of both species lived in the Brazilian Amazon rainforest approximately 3.13 million years ago (Ma), with a minimal probability of 0.0314, supporting a shared South American ancestry. The divergence times of C. brevicauda (2.05 Ma) and C. perspicillata (2.04 Ma) closely align with the uplift of the northern Andes (5 Ma to present), potentially illuminating the dispersal events experienced by these species.

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