DNA barcoding and mini-barcoding as molecular tools for identification of fruit flies (Diptera: Tephritidae)

The objectives of this study were to assess the proportions of correct identifications (ID) in 
tested genera and to elucidate the efficacy of three fragments (min-barcode) of COI barcode region 
in providing comparable information. The DNA barcoding in three tephritid genera was tested by 
considering 493 DNA barcodes involving 86 species belonging to the genera Bactrocera (33 
species), Ceratitis (21 species) and Dacus (32 species). Barcoding simulations were performed by 
using a reference dataset of 15,948 insect DNA barcodes. It was performed under a “best case 
scenario” viz. by providing one or more potential con-specific matches in the reference dataset for 
each query. Results showed that the Best Match (BM) criterion (i.e. the criterion currently adopted 
by BOLD) yielded different proportions of correctly identified taxa in Bactrocera (BM=0.839), 
Ceratitis (BM=0.868) and Dacus (BM=0.962). The proportions of correctly identified queries by 
using three mini-barcode fragments (MB1, MB2, MB3) of 220bp (corresponding to the first, second 
and last third of the COI barcode region) ranged from 0.71 ± 0.17 in MB1 to 0.83 ± 0.10 in MB2. 
Currently, however, the application of DNA barcoding in tephritid species is limited by the low 
number of barcoded taxa in the reference databases. This situation increases the probability of 
making Type II errors (i.e. incorrect ID for queries without conspecifics in the reference database).  
On the other hand, the probability of making Type I errors (incorrect ID for queries with 
conspecifics in the database) is relatively limited (4-16% in our simulations). These considerations 
suggest that DNA barcoding may not be a fool proof method for the molecular ID of tephritid fruit 
flies. Still, DNA barcoding could be effective under well-defined conditions, where only a limited 
number of well-known tephritid taxa, with well characterized intraspecific variation, are to be 
distinguished.