DNA bacoding is a popular DNA diagnostic technique especially for specific and generic level identification during various quarantine activities. BOLD Systems, an internet accessible DNA barcode data portal, currently includes over 12,000 DNA barcodes for the fruit fly family Tephritidae, of which 8,940 barcodes are open to public. These data represent 655 tephritid species, majority of which are pest species. These figures are rapidly increasing as the tephritid barcoding research is increasing every year. Therefore, BOLD has established as the most important DNA barcode source for tephritid identification. It is, therefore, also important to understand the limitations and problems of the DNA barcoding analysis. We here discussed the following potential problems and their possible solutions: (1) misidentification of species listed in BOLD; (2) sibling species with identical or near-identical barcodes; (3) NUMT (nuclear mitochondrial DNA) or pseudogene; and (4) introgression by hybridization between closely related species.

Bactrocera zonata (Peach fruit flies) is a polyphagous fruit pest native to South and South-East area and now foundin more than 20 countries. This species is not only a serious pest of peach but also is capable of infesting various speciesof 14 plant families. In Korea, they are potential pests of a number of economically important crops including peach,apricot, apple, and even Citrus spp. In northern India, B. zonata is currently considered to be more important fruit pestthan the notorious oriental fruit flies (B. dorsalis). Due to the high risk of potential introduction to southern part of Korea,we put together a national action plan against the peach fruit fly in order to quickly and completely suppress invadingpopulation of this pest species.

For building up the Tephritid Tree of Life, we have so far accumulated fresh samples of 570 species of 220 tephritid genera, covering 11% and 44% of World species and genera, respectively. Based on the molecular systematics approach, the followings are examples of our findings: (1) two monophyletic groups within the superfamily Tephritoidea were clearly recognized (compatible with Willi Hennig’s Pallopteroidea and Otitoidea that are not currently used); (2) expanded concept of the family Tephritidae including parasitic taxa (Tachiniscinae, Ctenostylidae and Pyrgotidae); (3) reconfirmation of monophyletic Trypetini, Carpomyini, Tephritinae, and Dacinae; and (4) the first Tephritoidea might have evolved around the middle of Paleocene Epoch (~59 mya) and the family Tephritidae around the late Eocene (~36 mya).

The superfamily Tephritoidea is a large group of acalyptrate flies including over 7,300 described species arranged in nine families. All the tephritoid families excluding Richardiidae are represented in Korea, but their taxonomy has not been well studied. For example, a total of 80 species of the family Tephritidae are currently known in Korea, but our personal data shows that there actually are at least 150 species. Presence of highly variable or cryptic species has been hampering taxonomic progress involving this group of flies. Some genera such as Trypeta, Campiglossa, Oxyna, and Tephritis are good examples of taxonomically difficult taxa. We find that DNA barcoding is extremely helpful to clarify such taxonomic problems. We are currently trying to bacode multiple samples for every single Korean tephritoid species. A total of 271 specimens representing 185 species have been barcoded so far. Neighbor-Joining analysis of our preliminary data shows many interesting findings that are potentially useful to resolve long standing taxonomic problems. The followings are some of our findings through the DNA barcoding analyses: 1) multiple samples for each included species were almost always clustered together showing utility for specific identification; 2) multiple species per each genus were mostly clustered together; 3) clarification of male and female association of two closely resembling new Acidiella species; 4) strongly support synonymy of Sinacidia and Chetostoma; 5) possible existence of two cryptic species within Campiglossa defasciata; 6) possible synonymy of Dioxyna and Campiglossa; 7) possible synonymy of Herina zojae and H. hennigi; and 8) discrimination of two closely resembling Chaetostomella species.