Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring.

Mehrdad Hajibabaei,Gregory A C Singer,Paul D N Hebert,Elizabeth L Clare

doi:10.1186/1741-7007-5-24

Mehrdad Hajibabaei, Gregory A C Singer + Show 2 more

Open Access

https://doi.org/10.1186/1741-7007-5-24

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Abstract

BackgroundThe rapid and accurate identification of species is a critical component of large-scale biodiversity monitoring programs. DNA arrays (micro and macro) and DNA barcodes are two molecular approaches that have recently garnered much attention. Here, we compare these two platforms for identification of an important group, the mammals.ResultsOur analyses, based on the two commonly used mitochondrial genes cytochrome c oxidase I (the standard DNA barcode for animal species) and cytochrome b (a common species-level marker), suggest that both arrays and barcodes are capable of discriminating mammalian species with high accuracy. We used three different datasets of mammalian species, comprising different sampling strategies. For DNA arrays we designed three probes for each species to address intraspecific variation. As for DNA barcoding, our analyses show that both cytochrome c oxidase I and cytochrome b genes, and even smaller fragments of them (mini-barcodes) can successfully discriminate species in a wide variety of specimens.ConclusionThis study showed that DNA arrays and DNA barcodes are valuable molecular methods for biodiversity monitoring programs. Both approaches were capable of discriminating among mammalian species in our test assemblages. However, because designing DNA arrays require advance knowledge of target sequences, the use of this approach could be limited in large scale monitoring programs where unknown haplotypes might be encountered. DNA barcodes, by contrast, are sequencing-based and therefore could provide more flexibility in large-scale studies.

Highlights

The rapid and accurate identification of species is a critical component of large-scale biodiversity monitoring programs
This study focuses on a limited number of species, the authors have predicted that such an approach can be used for the development of a so called 'Mammalia Chip', in the case of mammalian species, or even a 'Biodiversity Chip' for monitoring key species of different taxa from bacteria to mammals [4]
Resolution in neighbor-joining analysis [13]; K2P, genetic distances based on Kimura two-parameter nucleotide substitution model [20]; var, variable sites

Summary

Introduction

The rapid and accurate identification of species is a critical component of large-scale biodiversity monitoring programs. DNA arrays (micro and macro) and DNA barcodes are two molecular approaches that have recently garnered much attention. We compare these two platforms for identification of an important group, the mammals. Because of advances in DNA-based technologies, approaches such as DNA arrays and DNA barcoding have recently gained attention. Both of these methods are based on comparative DNA sequence analysis, but they have significant differences. Micro- and macro-arrays rely on the hybridization of short (i.e. 25 base) specific nucleotide probes to DNA from the target organism and subsequent detection of the (page number not for citation purposes). This study focuses on a limited number of species, the authors have predicted that such an approach can be used for the development of a so called 'Mammalia Chip', in the case of mammalian species, or even a 'Biodiversity Chip' for monitoring key species of different taxa from bacteria to mammals [4]

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