title: Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring.
abstract: BACKGROUND
  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. Here, we compare these two platforms for identification of an important group, the mammals.
  
  
  RESULTS
  Our 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.
  
  
  CONCLUSIONS
  This 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.
authors.affiliation: Biodiversity Institute of Ontario, Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada. mhajibab@uoguelph.ca
authors.forename: Mehrdad
authors.initials: M
authors.lastname: Hajibabaei
authors.forename: Gregory A C
authors.initials: GA
authors.lastname: Singer
authors.forename: Elizabeth L
authors.initials: EL
authors.lastname: Clare
authors.forename: Paul D N
authors.initials: PD
authors.lastname: Hebert
mesh_terms: D000818:Animals; D044822:Biodiversity; D019295:Computational Biology; D045303:Cytochromes b / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D003576:Electron Transport Complex IV / Q000235:genetics; D008322:Mammals / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes / Q000235:genetics; D013045:Species Specificity
chemical_list: D004272:DNA, Mitochondrial; D015345:Oligonucleotide Probes; D045303:Cytochromes b; D003576:Electron Transport Complex IV