Comprehensive DNA barcode coverage of North American birds

Abstract

DNA barcoding seeks to assemble a standardized reference library for DNA-based identification of eukaryotic species. The utility and limitations of this approach need to be tested on well-characterized taxonomic assemblages. Here we provide a comprehensive DNA barcode analysis for North American birds including 643 species representing 93% of the breeding and pelagic avifauna of the USA and Canada. Most (94%) species possess distinct barcode clusters, with average neighbour-joining bootstrap support of 98%. In the remaining 6%, barcode clusters correspond to small sets of closely related species, most of which hybridize regularly. Fifteen (2%) currently recognized species are comprised of two distinct barcode clusters, many of which may represent cryptic species. Intraspecific variation is weakly related to census population size and species age. This study confirms that DNA barcoding can be effectively applied across the geographical and taxonomic expanse of North American birds. The consistent finding of constrained intraspecific mitochondrial variation in this large assemblage of species supports the emerging view that selective sweeps limit mitochondrial diversity.

Fig. 1

Comparing barcode sequence clusters with species-level taxonomy. Categories A–C are described in the figure; by definition, all potential splits recognized by barcoding have distinct barcodes, so D is blank.

Fig. 4

Intraspecific and nearest-neighbour distances in North American birds. Applying these measures to the data set in the preliminary study (2) gave mean values of 0.24, 0.27, 8.02, and 5.86 for A–D, respectively.

Fig. 3

Intraspecific distance, population size, and apparent species age. (A) Linear regression of mean intraspecific distance and log₁₀ census population size. For illustration purposes, a box plot was generated as described in legend to Fig. 2. (B) Linear regression of mean intraspecific COI distance compared with apparent species age, as indicated by minimum interspecific Kimura 2-parameter (K2P) distance to nearest congeneric relative.

Fig. 2

Mean intraspecific variation according to number of individuals analysed. Boxes indicate mean, 25th and 75th percentile; bars, 10th and 90th percentile; and dots, values above or below 90th or 10th percentile, respectively.