Data for: Harnessing environmental DNA (eDNA) to explore frugivorous interactions: A case study in Papaya (<em>Carica papaya</em>) and pineapple (<em>Ananas comosus</em>)

Plant-animal interactions (PAIs) are critical in ecosystem function, mediating energy flow and species interactions. Traditional methods of tracking PAIs, such as morphological identification and camera trapping, are limited in speed and scalability, posing challenges for comprehensive biodiversity monitoring. Recently, environmental DNA (eDNA) metabarcoding has emerged as a promising technique for detecting species interactions non-destructively. This pilot study explores the application of eDNA metabarcoding to investigate interactions involving partially consumed and intact fruits of Carica papaya and Ananas comosus. eDNA metabarcoding was performed from 36 partially consumed and 6 intact fruit samples. Metabarcoding of mitochondrial COI gene fragments revealed a diverse range of taxa, with Arthropoda, particularly insects, being the most abundant. Results indicated significant differences in taxonomic composition between pineapple and papaya samples, where both the fruits hold some unique as well as shared taxa. Furthermore, the diversity also differed between consumed and intact fruits, suggesting that partially consumed fruits serve as rich eDNA sources, capturing interactions with various frugivores and decomposers. Signals from various organisms detected through eDNA metabarcoding from consumed and damaged fruits allowed us to capture a wide array of taxa, revealing insights into species composition and ecological relationships. The unique ASVs associated with each fruit type suggest that certain taxa may be showing preferences based on fruit characteristics such as sugar content, texture, or chemical profile. The present work highlighted the importance of eDNA-based methods in unraveling the taxonomic composition of fruit-associated plant-animal interactions. This method needs limited taxonomic expertise, less labor, fast and effective, which can be implemented in monitoring ecological and economic species interactions. Methods Environmental DNA samples were sequenced through the Illumina MiSeq sequencing platform.