DNA Barcoding

The limitations inherent in morphology-based identification systems and the dwindling pool of taxonomists signal the need for a new approach to taxon recognition. Microgenomic identification systems, which permit life’s discrimination through the analysis of a small segment of the genome, represent one extremely promising approach to the diagnosis of biological diversity. By this, a small fraction of an organism’s total genome is used as an identifying tag, a barcode, for the organism.

DNA barcoding has the potential to be a practical method for identification of the estimated 10 million species of eukaryotic life on earth. As a uniform method for species identification, DNA barcoding will have broad scientific applications. It will be of great utility in conservation biology, including biodiversity surveys. It could also be applied where traditional methods are unrevealing, for instance identification of eggs and immature forms, and analysis of stomach contents or excreta to determine food webs. In addition to enabling species identification, DNA barcoding will aid phylogenetic analysis and help reveal the evolutionary history of life on earth.

An appropriate target gene for DNA barcoding is conserved enough to be amplified with broad-range primers and divergent enough to allow species discrimination. The initial target for DNA barcoding is mitochondrial cytochrome c oxidase subunit I (COI). Selection of an appropriate gene is a critical strategic and practical decision, with significant consequences for the overall success of this project. A number of genes may be likely to meet one or more of our goals (discrimination and identification of species, discovery of new and cryptic species, reconstruction of evolutionary relationships among species and higher taxa). The selection of COI as a target gene is supported by published and ongoing work, which demonstrates that barcoding via COI will meet the project goals for a wide diversity of animal taxa. DNA characterization has given us new means to understand the morphological disparity and the lack thereof among organisms. It has also provided new methods for grasping the evolutionary context and phylogenetic history of diversity. These new technologies have already made a large impact in most fields of biology, not least in systematics, and many recent taxonomic revisions are based on insights from DNA studies. The implementation of DNA barcoding will certainly provide new discoveries that must be pursued by research that requires a multitude of data about organisms and also wise taxonomic judgment. DNA barcoding may also be particularly useful for assessing diversity of small animals and microbes in the ocean, for which diagnostic morphological characters may be subtle or lacking.

The challenge
It is widely recognized that not only is the biotic diversity on planet Earth currently undergoing a mass extinction, but that the true extent of the extinction is unknown. Marine habitats are no exception to this. Although prominent marker taxa such as endangered vertebrates are well studied, most taxa remain to be discovered. It is estimated that there are ca. 1.5 million described species. we have described most of these relatively large organisms. The overall ratio of expected taxa to named taxa is thus approximately six fold. However this deficit, like all phylogenetic things, is not immune to systematic bias. For vertebrates, the current described species total is likely to be relatively close to the ‘true’ total: we have described most of these relatively large organisms. The same is true of most groups whose members have body sizes greater than 10 mm. However, the vast majority of organisms on the Earth have body sizes less than 1 mm, and for these groups the taxonomic deficit is likely to be several fold worse than for land plants and vertebrates. These meio- and micro-fauna and flora are, however, representing the majority of ocean life and they are the productive and saprophytic base upon which the macro-organisms rely. Their size precludes facile visual identification, and indeed much of their important morphology may be at scales that are beyond the resolution of light microscopy.

As visualized in Figure 1, in many major groups of marine animals the number of described taxa is a small proportion of the estimated diversity. For example the true species-level diversity of nematodes, with ca. 26 000 described species, is estimated to be in the low millions, whereas only ca. 25% of arthropods have been described, despite a ‘known’ species count of over one million.. It is obvious that different organism groups are not equally well determined. Molluscs, annelids, echinoderms and crustaceans are examples of groups that are common in the samples and are identified to a large part because they are well studied and documented with descriptions and identification keys. Nematodes, flatworms and nemerteans are examples of organism groups that are mostly undetermined, and they are also good examples of groups with more difficult anatomy from the identification viewpoint.