Abstract
More than 2,500 species of copepods (Class Maxillopoda; Subclass Copepoda) occur in the marine planktonic environment. The exceptional morphological conservation of the group, with numerous sibling species groups, makes the identification of species challenging, even for expert taxonomists. Molecular approaches to species identification have allowed rapid detection, discrimination, and identification of species based on DNA sequencing of single specimens and environmental samples. Despite the recent development of diverse genetic and genomic markers, the barcode region of the mitochondrial cytochrome c oxidase subunit I (COI) gene remains a useful and – in some cases – unequaled diagnostic character for species-level identification of copepods. This study reports 800 new barcode sequences for 63 copepod species not included in any previous study and examines the reliability and resolution of diverse statistical approaches to species identification based upon a dataset of 1,381 barcode sequences for 195 copepod species. We explore the impact of missing data (i.e., species not represented in the barcode database) on the accuracy and reliability of species identifications. Among the tested approaches, the best close match analysis resulted in accurate identification of all individuals to species, with no errors (false positives), and out-performed automated tree-based or BLAST based analyses. This comparative analysis yields new understanding of the strengths and weaknesses of DNA barcoding and confirms the value of DNA barcodes for species identification of copepods, including both individual specimens and bulk samples. Continued integrative morphological-molecular taxonomic analysis is needed to produce a taxonomically-comprehensive database of barcode sequences for all species of marine copepods.
Highlights
Marine copepods represent a predominant component of the zooplankton throughout the world oceans in both abundance and biomass [1,2]
This study reports a total of 800 new DNA barcode sequences for identified specimens of 63 species not included in previous studies
This study presents results of comparative analysis of a large dataset of 1,381 barcode sequences for 195 copepod species, including 800 new barcode sequences for 63 copepod species not included in any previous study
Summary
Marine copepods represent a predominant component of the zooplankton throughout the world oceans in both abundance and biomass [1,2]. Copepods exhibit a wide variety of biogeographical patterns, from very limited distributions to cosmopolitan and global-ocean ones. Their high species diversity, together with their relatively small size and apparent similarity among 1 von 21 27.06.14 14:00. Use of a fragment of the cytochrome c oxidase subunit I (COI) gene for discrimination and identification of animal species, i.e., DNA barcoding [9,10], has moved rapidly from novelty to widespread use, it has not been free of controversy. Objections have focused on uses of barcodes beyond the original intent as a species assignment tool, including DNA taxonomy [11,12], ecological assessment 13, and species discovery 14. Recent improvements in methods for statistical analysis of barcode data [13,15,16,17] and growing focus on the appropriate use and limitations of barcode analysis 18 are advancing the field of DNA barcoding
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