Species identification is essential for large-scale biodiversity monitoring and conservation . Several molecular methods have been employed for biodiversity studies, but traditional methods such as allozyme analysis are usually labor-intensive and irreproducible. 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 hybridization signal. Although array-based technologies have been widely used in gene expression studies, their use in biodiversity research has been less rigorous, mainly targeting pathogenic microorganisms  and arrays of environmental samples . Pfunder et al , however, have advocated an array-based method for the identification of voles and shrews for biodiversity monitoring. Although 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 .
Species identification by DNA barcoding is based on sequencing a short standardized genomic region of the target specimen and comparing this information to a sequence library from known species . The proposed standard barcode sequence for animal species is a 650-bp fragment of the mitochondrial gene cytochrome c oxidase I (COI, cox1). This DNA barcode has successfully been used for the identification of species in various vertebrate and invertebrate groups from birds to Lepidoptera [6–8], and in different geographical settings from the arctic to the tropics [6, 9]. Additionally, smaller fragments (i.e. 100 bases) of the standard COI barcode – 'mini-barcodes' – have been shown to be effective for species identification in specimens whose DNA is degraded or potentially in other situations where obtaining a full-length barcode is not feasible . Barcoding is now being extended to other groups such as fungi, plants and protists, and the Barcode of Life Initiative has gained international momentum by the establishment of the Consortium for the Barcode of Life (CBOL), which plans to assemble DNA barcode libraries for all fish and birds .
Here, we compare the design and applicability of both array-based and barcoding platforms for specimen identification in mammalian species. We have chosen mammals because they constitute an important target for biodiversity studies and include many endangered species. However, mammalian species have not been broadly targeted for developing array-based or barcoding identification systems previously. A rapid identification method will aid in the tracking of illegal trafficking of mammalian species and their tissues. We have selected two mitochondrial loci for our analysis: COI – the proposed standard animal DNA barcode – and cytochrome b (cytb), which is commonly used as a species-level marker and particularly so in mammalian biosystematics [4, 12]. We used both of these genes to test the possibility of designing a Mammalia Chip. We also used these sequences and various size fragments of them to test the feasibility of DNA barcoding analysis for mammalian species. We targeted three datasets of mammalian species for these analyses: 121 species across the taxonomy of mammals (mammalian dataset), a dense sampling of 87 species of neotropical bats (bat dataset), and a wide geographical sampling of a single genetically diverse bat species (Sturnira lilium dataset).