DNA barcoding demystified

Abstract

Only 10% of the earth's biota has been described despite 250 years of taxonomic research (Wilson 2000). This is in large part a reflection of the extent and complexity of biological diversity, but it is also true that traditional taxonomic techniques are labourious and highly specialised, and taxonomic expertise is very thinly spread across the myriad groups of life (Scotland et al. 2003). As a result, obtaining species identifications, even for a modest sample of commonly encountered insects in a biologically diverse country, such as Australia, is at best time-consuming and costly and all too often impossible. This is a result of the difficulty that morphological taxonomic techniques encounter in dealing with phenotypic differences between immature and mature stages of a species, and among individuals of variable species, the lack of phenotypic differences among cryptic species, shifts in geographical distribution as a result of invasions or range expansions and the overwhelming diversity of life. Our reliance on morphological approaches, thus, places serious limitations on the diagnosis of biological diversity at a time when we are facing a biodiversity crisis of unprecedented magnitude. It has long been clear that new approaches to biodiversity assessment, description and diagnosis are needed, and indeed, the 1990s saw the emergence of many novel taxonomic initiatives, leading E.O. Wilson to conclude that ‘the 19th century culture of taxonomy has begun to be replaced’ (Wilson 2003). The emerging discipline of DNA barcoding (Floyd et al. 2002; Hebert et al. 2003) represents another advance and part of the solution to these problems. This paper provides a brief overview of DNA barcoding, and considers what barcoding offers researchers and industry alike. DNA barcodes are short DNA sequences (≥500 base pairs) that can be used to identify species. The ‘barcode’ analogy refers, of course to the universal product codes (UPC) affixed to merchandise in retail stores. The analogy suggests that DNA barcodes similarly provide a universal system of readily scannable, unique tags for products (species), speeding and automating transactions (identifications) and facilitating novel applications, such as automated stock management (biodiversity assessment) and so on. Unfortunately, the barcode analogy also has been used by the microbial diagnostics community to refer to the banding pattern of rep-polymerase chain reaction (PCR) products (a technique similar in principle to Random Amplification of Polymorphic DNA (RAPD)-PCR) visualised on a gel, which bears some resemblance to UPCs (Sutton & Cundell 2004). Love it or hate it, the term ‘DNA barcoding’ has caught the public imagination, and is likely here to stay. DNA sequence data from the mitochondrial genome have long been used to resolve difficult taxonomic questions and diagnose species in cases where morphology alone has proved inadequate (e.g. Brown et al. 1999; Mitchell & Samways 2005), so is DNA barcoding just molecular systematics and molecular diagnostics repackaged or is it a truly novel enterprise? The novelty in DNA barcoding is its combination of four main factors: standardisation on a particular gene region, the large scale of operation, compulsory vouchering of specimens and active curation of the resulting databases. First, standardisation on a particular gene region for all species in a particular branch of life leads to universality of the system. For animals the standard is the upstream half of the mitochondrial gene cytochrome c oxidase subunit I (COI or cox1). Without standardisation, molecular systematic data sets lack interoperability, building ‘Towers of Babel’ (Caterino et al. 2000). The same is true of molecular diagnostics – the literature contains a plethora of highly specialised methods for identifying particular organisms, and this leads to some circularity in that one has to have a well-developed idea of an organism's identity (e.g. which genus) to even know w