Identification of Birds through DNA Barcodes

By Paul D. N. Hebert, Marc Stoeckle, Tyler S. Zemlak, Charles M. Francis. PLoS Biology, 2004

2,726 citations recorded by the source corpus.

Short DNA sequences from a standardized region of the genome provide a DNA barcode for identifying species. Compiling a public library of DNA barcodes linked to named specimens could provide a new master key for identifying species, one whose power will rise with increased taxon coverage and with faster, cheaper sequencing. Recent work suggests that sequence diversity in a 648-bp region of the mitochondrial gene, cytochrome c oxidase I (COI), might serve as a DNA barcode for the identification of animal species. This study tested the effectiveness of a COI barcode in discriminating bird species, one of the largest and best-studied vertebrate groups. We determined COI barcodes for 260 species of North American birds and found that distinguishing species was generally straightforward. All species had a different COI barcode(s), and the differences between closely related species were, on average, 18 times higher than the differences within species. Our results identified four probable new species of North American birds, suggesting that a global survey will lead to the recognition of many additional bird species. The finding of large COI sequence differences between, as compared to small differences within, species confirms the effectiveness of COI barcodes for the identification of bird species. This result plus those from other groups of animals imply that a standard screening threshold of sequence difference (10× average intraspecific difference) could speed the discovery of new animal species. The growing evidence for the effectiveness of DNA barcodes as a basis for species identification supports an international exercise that has recently begun to assemble a comprehensive library of COI sequences linked to named specimens.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2422604446b80cca098ae237e4eaa679cf4586bb

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

In Molecular Biology

Citations in the corpus

Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo (2016, background): “%) correspond well to the species boundaries of several taxonomic groups (Hebert et al. , 2003, Hebert et al. , 2004; ; Smith et al. , 2005); however, these values are often far from optimal (Lin et al. , 2015).”
Plant DNA barcodes: Applications today and in the future (2017, background): “DNA barcodes as universally recoverable segments of DNA for the identification of species was initially designed and applied for animals in the early years of the present century (Hebert et al., 2004b).”
DNA barcoding: a tool for improved taxon identification and detection of species diversity (2011, background): “It was shown that animal species can be identified through the use of the mitochondrial cytochrome c oxidase 1 (CoI) sequence (Hebert et al. 2004a, b).”
Molecular markers and their applications in fisheries and aquaculture (2010, neutral): “lineages and may be helpful [70].”
DNA barcoding detects market substitution in North American seafood (2008, methodology): “Divergence thresholds for species identification were introduced in previous studies ( Hebert, Stoeckle, Zemlak, & Francis, 2004; Lefebure, Douady, Gouy, & Gibiert, 2006), however, the 3% used here can be considered a relatively loose criterion.”
The phylogeny of the living and fossil Sphenisciformes (penguins) (2006, neutral): “COI: Baker et al. (2006): DQ137167–72, DQ137174–86; Hebert et al. (2004): AY666477, AY666284; Slack et al. (2006): NC_007172.”
DNA barcoding of Scandinavian birds reveals divergent lineages in trans-Atlantic species (2010, neutral): “(2009) found that a high percentage (42%) of 36 Holarctic allopatric sister species pairs could not be distinguished based on the suggested threshold genetic distance for bird species at 10 times the average intraspecific distance (Hebert et al. 2004).”
On the utility of DNA barcoding for species differentiation among brown macroalgae (Phaeophyceae) including a novel extraction protocol (2009, positive): “This marker has been successfully used across diverse animal taxa (Herbert et al. 2004a,b), as well as red (Saunders 2005; Robba et al. 2006) and brown (Kucera & Saunders 2008) macroalgae.”
Cryptic polychaete diversity: a review (2014, methodology): “…mitochondrial and nuclear data to back up the number of inferred species, a barcode approach using the suggested 109 difference as a rule of thumb (Hebert et al. 2004; Carr et al. 2011), would identify the correct number of cryptic species in several (e.g. Pleijel et al. 2009; Nygren & Pleijel…”
A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region (2007, background): “…previously [7–8, 28 ] , but has The balance of within-and between-species sequence variation is an important aspect of barcode identification [1–2 , 29 ] and In conclusion a two-locus barcode that combines a subunit of the coding locus rbcL ( rbcL -a) with the non-coding trnH-psbA spacer .…”
Barcoding diatoms: evaluation of the V4 subregion on the 18S rRNA gene, including new primers and protocols (2011, background): “…in their genetic variation, so that different studies now use very different ratios and thresholds depending on the respective organism group and marker (e.g. Cywinska et al. 2006; Hajibabaei et al. 2006a; b; Hebert et al. 2004; Hickerson et al. 2006; Meyer and Paulay 2005; Ward et al. 2005).”