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.Keywords : Aves, cryptic species, cytochrome c oxidase, DNA barcoding, intraspecific mitochondrial variation, selective sweeps Received 25 October 2006; revision accepted 20 November 2006Mitochondrial DNA (mtDNA) analysis has been employed in the evolutionary study of animal species for more than 30 years (Brown et al . 1979;Mindell et al . 1997;Avise & Walker 1999). Its higher mutation rate and lower effective population size than nuclear DNA make mtDNA a powerful tool to probe for evidence of reproductive isolation between lineages. This fact provoked a proposal to standardize DNA-based species identification by analysing a uniform segment of the mitochondrial genome. With this approach, a library of sequences from taxonomically verified voucher specimens serve as DNA identifiers for species, in short, DNA barcodes (Hebert et al . 2003). For animals, research has focused on a 648-bp segment of the mitochondrial gene cytochrome c oxidase I (COI), which can be readily recovered from diverse species with a limited set of primers. DNA barcoding translates expert taxonomic knowledge of diagnostic morphologic characters into a widely accessible format, DNA sequences, enabling more people to identify specimens. In addition to assigning specimens to known species, DNA barcoding can speed the discovery of new species, as large sequence differences in animal mtDNA generally signal species status.For this approach to be effective, it must be possible to distinguish between intraspecific and interspecific mtDNA variation. Pseudogenes, retention of ancestral polymorphisms, hybridization, and the idiosyncrasies of mtDNA Re-use (Benasson et al . 2001;Moritz & Cicero 2004;Thalman et al . 2004;. The simplest test is whether genetic distances within species are less than those between species. Surprisingly, 23% of 2319 animal species failed this test in...

Mitonuclear coevolution as the genesis of speciation and the mitochondrial DNA barcode gap

“…2007; Bucklin et al. 2011) and others arguing that reliance on a single gene to delimit species will frequently fail to identify closely related taxa (Will et al.…”

Bridging two scholarly islands enriches both: COI DNA barcodes for species identification versus human mitochondrial variation for the study of migrations and pathologies

“…The average pairwise difference among individuals of the same species (APD, equivalent to the term “ π ” which is often used in population genetics) is usually <1%, whereas the distance between even the most closely related animal species is typically 2% or more (Kerr et al. 2007; April et al. 2011; Hausmann et al.…”

Genetic Applications in the Conservation of Neotropical Freshwater Fish

“…The barcode sequence from each unknown specimen is then compared with a library of reference barcode sequences derived from individuals of known identity. Research has been carried out to evaluate the effectiveness of this technique in identifying cryptic species in insects [100], birds [101] and plants [102]. The diversity Neotropical freshwater ichthyofauna is the richest in the world and make up around 25% of the total freshwater fish fauna on Earth [5].…”