Will the use of genetic "barcodes" revolutionize the science and practical application of taxonomy?

Yes

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by Shawn Webster

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Will the Use of Genetic "Barcodes" Revolutionise the Science and Practical Application of Taxonomy?

Taxonomy, meaning the classification of living things, has existed for 250 years, ever since the Swedish botanist Carl Linnaeus developed the binomial classification system. This method is based on morphological identification, with the idea being that different species have contrasting physical features. However, this classification system has the major problem in that expertise in this field is diminishing. With recent calls to census all biological life, which doesn't seem possible through morphological classification it seems a new approach is needed. One means to address this is through a molecular based method called DNA barcoding. This method makes use of short, specific genes that can distinguish species from each other. So will this DNA barcoding approach improve taxonomy?

The Linnaean system of classification is based on the identification of morphological characteristics. As Linnaeus underestimated the number of animals and plants on Earth, subsequent workers became unaware of others work while naming more and more species. This led to great confusion and could have resulted in destroying the whole approach when it had just begun. This problem was solved, however, when an intricate set of rules were developed that determined how a species should be named and linked with a physical example. It also dealt with how generic and higher taxonomic categories should be handled, and how disagreements over the use of names should be resolved. All these rules revolved around information in scientific journals, which now form the present keys of biological classification. This approach to identification has served biology for centuries, with present taxonomy using this method to represent over 250 years of work. However there are believed to be major limitations to this approach, with some leading to serious implications.

The morphological approach to identify species has four main limitations. The first is that incorrect identifications can occur because of phenotypic plasticity (changes in physical characters due to environment changes). This approach also ignores morphologically cryptic taxa, which can be found in a lot of groups. Morphological keys can also pose a problem, as they're only effective for particular life stages or sexes and tend to require a high level of expertise in order to avoid misidentification. These limitations can, however, be quashed. Phenotypic plasticity is actually well recognized and understood, with repeated corrections of taxon definitions carried out when recognizing non-heritable variation. Morphologically cryptic taxa are only a problem in certain taxa, and could usually be resolved through further testing. There's also no evidence or data to suggest that morphological keys lead to misdiagnosis. There are, nether the less, still some major disadvantages to this traditional approach.

Physical features can suffer with age and environmental damage, increasing the difficulty in identification. Another main problem is that it depends heavily on specialists. When these specialists leave their field, their knowledge is lost. With these disadvantages to the classic approach, it seems that the science of taxonomy desperately needs an alternative, such as DNA barcoding.

DNA barcoding involves the identification of species by analysing a short standardized segment of a mitochondrial genome. Earlier studies have indicated the sequence diversity in a 650 base pair region near the 5' end of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene, can separate about 95% of species in tests on birds, fish and Lepidoptera. This can serve as the central point of a global bioidentification system for animals. Universal primers for CO1 are very strong and so this enables the recovery of the 5' end from representatives from most of the animal phyla. Evolution is also fast enough in this gene to allow separation of closely altered species, as well as phylogeographic groups within a species. The basic procedure of this method is simply to take a tissue sample from an individual, and extract the DNA from the tissue. This DNA then serves as a reference sample from which gene regions are highlighted by PCR and sequenced. The resulting sequences are then used for future reference, when other samples can be checked against them. So what are the advantages of this approach and why should we decide to use this method and not the morphological method, which has been around for over 250 years.

The greatest advantage of DNA based identification methods is the ease of which it is to diagnose species, with recently encountered species indicating their occurrence by their genetic differences from those of known species. A generation of CO1 profiles could also prove valuable as a solution to the depleting number of morphological taxonomists, by allowing storage of their knowledge before they leave the field. CO1 sequences can be taken from museum specimens, without damage, and so it is then possible to assign taxonomic groups for those that currently lack one. This method is digital and so it is not affected by age or environmental factors, which can have a major effect on the morphological approach. For this reason it is not influenced by subjective tests, so can be reproduced by any person, speaking any language, at any time. Therefore, it can be used as a universal communication tool for taxonomy, with questionable sequences being compared to others to either find an exact match or one that closely relates to it. This gives it great utility in conservation biology, where it can be used in biodiversity surveys. It can also allow the ability to identify egg and larval forms of species, and to determine food webs through analysis of stomach and faeces contents. DNA collection is fairly easy and because it is very stable, any sample can be split into many sub-samples, which then be delivered to other institutions, and so can aid in guarding against duplicate descriptions. But what evidence is there that DNA barcoding can correctly identify species? And what species would benefit from this approach?

Recent studies by Paul Hebert have established that CO1 amino acid sequence differences were enough to allow the assignment of an organism into its correct taxonomic group. The main goal for any taxonomic system is its ability to convey precise identifications. Hebert's study was 100% successful in identifying the taxonomically similar Lepidoptera species, using CO1 species profiles. Lepidoptera are one of the most diverse orders of animals, and so it would be expected that there would be similar results in other groups. DNA barcoding is extremely useful in identifying parasites, which are difficult to discriminate by physical features due to their small size. Barcoding has also been successful in identifying fish species, which are systematically very diverse. This enables the precise recognition of fish and fish products from all life stages, which enable the ability to make retail substitutions of species, aid in long-term sustainability of fisheries, and improve ecosystem conservation and research. Many unrecognised species of birds have also benefited from DNA barcoding, with barcoding able to split a species into two, with an example of this being Wilson's and Common snipes. Global application of CO1 barcodes could further increase the identification of hidden species, of not only birds, but also many other species. Despite the fact that barcoding would be an effective tool for identifying species, it does have some major problems, especially if we consider abandoning the traditional approach in favour of this.

Although DNA barcoding methods do identify species correctly, it can still be the case that non-identical sequences be unidentifiable or wrongly placed. This is because mitochondrial DNA is not consistent within and between species and so there is no standard level of divergence that can define the boundaries in which different species lie. So distinguishing intraspecific and interspecific will be difficult as ranges of variations differ between different groups of animals and plants. It's also the case that new species must match almost precisely to a previously sequenced species, which must have been identified by a morphological taxonomist. Other obstacles also remain: young species, like orangutans, may not be easily identified through barcodes. This is also the case for amphibians, where the CO1 gene varies so much between individuals that species can't be reliably distinguished. Field taxonomy is still likely to be based on the analysis of morphological traits despite the development of DNA barcoding, as most field researchers, like botanists, have neither the expertise nor the resources to attain and understand DNA sequences. So DNA methods might actually exclude the taxonomists who have restricted access to this technology. It's also hard to understand how taxonomy would be taught to students without first beginning with morphological features. So with both the morphological and molecular approaches having major flaws, what is the best way forward for taxonomy?

Traditional morphological classification still remains important; it provides a reference point to compare current work with earlier findings and is essential for organising the knowledge of organisms. Taxonomy can be advanced with appropriate DNA barcoding, as morphological studies have got limitations, but it can't solely rely on molecular methods. Modern Taxonomy must make room for both approaches with the best way forward to use traditional methods as a prerequisite for molecular studies, using barcoding to recognize those species that are difficult to identify through morphological methods.

The prospect of using DNA barcoding to conduct species identification, especially in those cases where previous taxonomic work is limited, is appealing. CO1 sequencing has shown sufficient diversity to discriminate species, but it's important that this method identifies the boundaries that identify different species. Traditional approaches to taxonomy still remain important, but the introduction of modern molecular methods, such as DNA barcoding, has the capability of improving taxonomy, with future identifications and classifications depending on both traditional morphology and modern molecular methods. Therefore, DNA barcoding will revolutionise and improve the application of taxonomy by making it easier to identify closely related species and allowing the crystallization of knowledge. It can't, however, realistically be the first and only method of classification, but more of a means to aid research.

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