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.

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...

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...

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The difficulty of censusing marine animal populations hampers effective ocean management. Analyzing water for DNA traces shed by organisms may aid assessment. Here we tested aquatic environmental DNA (eDNA) as an indicator of fish presence in the lower Hudson River estuary. A checklist of local marine fish and their relative abundance was prepared by compiling 12 traditional surveys conducted between 1988–2015. To improve eDNA identification success, 31 specimens representing 18 marine fish species were sequenced for two mitochondrial gene regions, boosting coverage of the 12S eDNA target sequence to 80% of local taxa. We collected 76 one-liter shoreline surface water samples at two contrasting estuary locations over six months beginning in January 2016. eDNA was amplified with vertebrate-specific 12S primers. Bioinformatic analysis of amplified DNA, using a reference library of GenBank and our newly generated 12S sequences, detected most (81%) locally abundant or common species and relatively few (23%) uncommon taxa, and corresponded to seasonal presence and habitat preference as determined by traditional surveys. Approximately 2% of fish reads were commonly consumed species that are rare or absent in local waters, consistent with wastewater input. Freshwater species were rarely detected despite Hudson River inflow. These results support further exploration and suggest eDNA will facilitate fine-scale geographic and temporal mapping of marine fish populations at relatively low cost.

Environmental DNA (eDNA) technology potentially improves the monitoring of marine fish populations. Realizing this promise awaits better understanding of how eDNA relates to fish presence and abundance. Here, we evaluate performance by comparing bottom trawl catches to eDNA from concurrent water samples. In conjunction with New Jersey Ocean Trawl Survey, 1-l water samples were collected at surface and depth prior to tows at about one-fourth of Survey sites in January, June, August, and November 2019. eDNA fish diversity from 1 l was same as or higher than trawl fish diversity from 66 M litres swept by one tow. Most (70–87%) species detected by trawl in a given month were also detected by eDNA, and vice versa, including nearly all (92–100%) abundant species. Trawl and eDNA peak seasonal abundance agreed for ∼70% of fish species. In log-scale comparisons by month, eDNA species reads correlated with species biomass, and more strongly with an allometric index calculated from biomass. In this 1-year study, eDNA reporting largely concorded with monthly trawl estimates of marine fish species richness, composition, seasonality, and relative abundance. Piggybacking eDNA onto an existing survey provided a relatively low-cost approach to better understand eDNA for marine fish stock assessment.

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Birds are a taxonomically well-described group of animals, yet DNA barcoding, i.e., the molecular characterization of species using a standardized genetic marker, has revealed unexpected patterns of genetic divergences among North American birds. We performed a comprehensive COI (cytochrome c oxidase subunit I) barcode survey of 296 species of Scandinavian birds, and compared genetic divergences among 78 trans-Atlantic species whose breeding ranges include both Scandinavia and North America. Ninety-four percent of the Scandinavian species showed unique barcode clusters; the remaining 6% had overlapping barcodes with one or more congeneric species, which may reflect incomplete lineage sorting or a single gene pool. Four species showed large intra-specific divergences within Scandinavia, despite no apparent morphological differentiation or indications of reproductive isolation. These cases may reflect admixture of previously isolated lineages, and may thus warrant more comprehensive phylogeographic analyses. Nineteen (24%) of 78 trans-Atlantic species exhibited divergent genetic clusters which correspond with regional subspecies. Three of these trans-Atlantic divergences were paraphyletic. Our study demonstrates the effectiveness of COI barcodes for identifying Scandinavian birds and highlights taxa for taxonomic review. The standardized DNA barcoding approach amplified the power of our regional studies by enabling independently obtained datasets to be merged with the established avian barcode library.