Optimizing bioinformatic pipeline for profiling blow fly diets

Blow flies (Diptera: Calliphoridae) are widespread across the world and are observed feeding on decomposing remains, wildlife scat, and open wounds. Due to their rapid colonization of remains, these species have strong applications in the disciplines of forensic entomology and conservational biology. This work is especially interested in their application to conservational biology, where flies can be used as bio-monitors, providing insights into an ecosystem and its wildlife. Traditional conservation screening methods are costly, time-consuming, and require trained experts to accurately identify species. For these reasons, conservation efforts tend to be biased towards mammals and locations that are easily accessible. In response to these limitations, this work is investigating the diet of forensically relevant blow flies to determine their effectiveness as bio-monitors using project developed bioinformatic pipelines. This project gathers fly samples consisting of regurgitate or extracted gut content. These samples undergo PCR amplification to attach uniquely tagged primer sequences onto the 313-bp COI minibarcode of metazoans, and the 244-bp COI minibarcode of vertebrates. The resulting PCR products are then barcoded using ONT’s Native Barcoding Kit and sequenced using ONT’s MinION sequencer. Sequencing data is analyzed using an optimized bioinformatic pipeline to phylogenetically compare sample sequences to published mitochondrial genomes in NCBI’s databases, resulting in a taxonomic profile of collected environmental DNA. This work will further develop tools for forensic entomology and expand conservation efforts by lowering the time, cost, and effort required to survey a region and gain insight into wildlife diversity.