Review
DNA barcoding for ecologists

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DNA barcoding – taxon identification using a standardized DNA region – has received much attention recently, and is being further developed through an international initiative. We anticipate that DNA barcoding techniques will be increasingly used by ecologists. They will be able to not only identify a single species from a specimen or an organism's remains but also determine the species composition of environmental samples. Short DNA fragments persist in the environment and might allow an assessment of local biodiversity from soil or water. Even DNA-based diet composition can be estimated using fecal samples. Here we review the new avenues offered to ecologists by DNA barcoding, particularly in the context of new sequencing technologies.

Section snippets

A new name for an old concept

The term ‘DNA barcoding’ is of recent use in the literature 1, 2. It relies on the use of a standardized DNA region as a tag for rapid and accurate species identification [3]. Nevertheless, DNA barcoding is not a new concept. The term ‘DNA barcodes’ was first used in 1993 [4], in a paper that did not receive very much attention from the scientific community. The concept of species identification using molecular tools is older still [5]. However, the golden age of DNA barcoding began in 2003 [2]

New tools for new prospects

In the past 20 years the technology of DNA sequencing has greatly improved, from manual sequencing to automated sequencers. A single automated 96-capillary sequencer can provide more than 1000 sequences of 1000 base pairs (bp) per day. Even non-geneticists now have easy access to sequencing via companies that offer this service at a competitive price. Clearly, the development of DNA barcoding is linked to these improvements.

When using the classical sequencing approach via capillary

Single-species identification

The classical use of morphological traits for species identification has several limitations. They include, for example, the misidentification of a taxon due to the phenotypic plasticity of the trait studied or the existence of cryptic taxa [13]. Moreover, morphological keys are sometimes only effective for a particular life stage or gender, as for example in Diptera, where species identification is mainly based on male genitalia [14]. Thus, a high level of expertise is often required to

Biodiversity assessment

DNA barcoding might also play an important role in biodiversity assessment, both for present and for past animal and plant communities.

Diet analysis

The study of food webs and their dynamics is fundamental to understand how the feeding habits of different species can affect the community. Thus, diet analysis of the animal species present in a given environment can improve our understanding of the functioning of the ecosystem as a whole (e.g. Ref. [56]). Furthermore, the study of feeding ecology becomes crucial when it concerns endangered species. A precise knowledge of the diet of these species can identify key environmental resources for

Limitations and perspectives

The main limitation of the barcoding approach comes from its single-locus identification system. Even if several regions from these organelle DNAs are sequenced, this is still a single-locus approach because the different genes of mitochondrial or chloroplast DNA are linked. It is well known that identical mitochondrial or chloroplast DNA sequences can be present in different related species due to introgression, or due to incomplete lineage sorting since the time of speciation [71].

Acknowledgements

We thank four anonymous reviewers for constructive comments on the manuscript. We also thank Claude Miaud and Usman Ghani for kindly providing the photographs of environmental sampling (Figure 1) and of golden marmot and brown bear (Figure 2), respectively.

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