Megabarcoding dark taxa - Assessing the utility of mass DNA barcoding for phorid fly species discovery
Many hyperdiverse, small-bodied insect families contain numerous undescribed species, generally termed "dark taxa". Scuttle flies (Diptera: Phoridae), being among the most diverse insect groups globally, are a prime example. DNA barcoding can help delineating dark taxa, particularly when integrated with morphology, and/or additional molecular evidence. We sequenced COI-barcodes from 9,120 Finnish phorid specimens and initially identified them using BOLD database. Furthermore, species identifications of all 843 non-Megaselia specimens were confirmed morphologically. Initially, the BOLD-based identifications matched the morphological identifications only in 68% of the cases, which resulted from many misidentifications in BOLD. After adjusting the BOLD reference identifications based on morphological analyses of male features, we established a reliable framework for female identification. This is advantageous for future identification of females, as they are often excluded from traditional identification keys. Only two species was discovered as new to Finland, demonstrating that Finnish non-Megaselia fauna is well-known. Although DNA barcodes show great promise for identifying phorids, incorrectly identified reference sequences remain challenging, not the functionality of COI itself. The number of Megaselia BINs greatly exceeded the known Finnish species count, with many sequences lacking matches in BOLD. This further highlights Megaselia as a particularly dark group, for which genetic tools are essential for uncovering species identities and assessing diversity.