Genetic tools for species-level identification
For species identification, DNA microarrays ("DNA-Chips") can here be of great value. Microarrays consist of a surface with thousands of covalently attached DNA oligonucleotides. This allows monitoring of thousands of different (i.e. species identifying) DNA sequences simultaneously with one array (size about 1x1cm). Theoretically, just one chip would enable the screening for all major economic fish species simultaneously (Kochzius et al., 2008). While the development of DNA-microarrays is laborious, the running costs are moderate. Other high-throughput and parallel processing methodologies for fish species identification have also been developed (Dooley et al., 2005). Such technologies might ultimately lead to the development of handheld analytical devices, enabling field use, which is critical with respect to the response time (the period between starting an investigation and the receipt of analytical results). For example, inspectors in the fisheries sector carry huge responsibility: if they decide to put landings "on hold" because of suspect content, there can be severe consequences for fishermen and stakeholders. Engineering of such machines is carried out in support of forensic genetic analysis at crime scenes (Liu et al., 2008). However, while recent publications show that progress has been made in this area (Arnaud, 2008), currently no cost-effective handheld analytical device supporting fisheries control and enforcement or traceability is available.
One of the most commonly employed species-level genetic identification systems is DNA barcoding. Although the approach utilises technologies that have been available for some time within the general field of "molecular systematics", initially based primarily on protein variation or allozyme electrophoresis, there are attributes of the approach of DNA barcoding that are highly distinctive and that enhance its utility within fisheries applications. Hebert et al (2003) proposed a new approach to species identification, which offered great promise. The new approach is based on the premise that the sequence analysis of a short fragment of a single gene (cytochrome c oxidase subunit 1), enables unequivocal identification of all animal species. Hence, analogously to the barcodes used in commercial products, the DNA barcode would provide a standardised tool for fast, simple, robust and precise species identification. Such a ‘barcode region' would also have to evolve at a rate that would distinguish species from each other while remaining more or less identical for all members of the same species. Finally it would have to be flanked by conserved DNA regions so as to make the polymerase chain reaction (PCR), a method of targeted gene replication. With the exception of certain groups of Cnidaria and sponges, studies have now confirmed that the target segment of COI ordinarily provides clear-cut discrimination of most animal species. An international consortium (Consortium for the Barcode of Life, CBOL) was established in 2004 to build support for global implementation of DNA barcoding. The critical mass of institutional and community participation required to progress the DNA barcoding effort for species identification now exists: the International Barcode of Life (iBOL) project. With the central goal of building a library of DNA barcodes for 5 million specimens and 500 K eukaryotic species by 2015, iBOL promises rapid progress toward aglobal identification system accessible to all. DNA barcoding differs in many ways from conventional taxonomic identification tools and approaches, over which it offers several advantages. It permits the identification of species from fragments, and from any life-history stage, as well as the standardisation of a universal master key in a format that reduces ambiguity and enables direct comparison of specimens to a global reference database.
DNA barcoding provides a standardised tool for describing and monitoring fish species diversity, not only in the wild, but also throughout the food supply chain in relation to legal enforcement and consumer protection. Moreover, a globally-accessible, standardised DNA barcoding data base means that non-experts may utilise the information to examine species identity, but importantly also allows a coordinated and extensive effort to document biodiversity from throughout species distributions.