Abstract
DNA-based identification of mixed-organism samples offers the potential to greatly reduce the need for resource-intensive morphological identification, which would be of value both to bioassessment and non-native species monitoring. The ability to assign species identities to DNA sequences found depends on the availability of comprehensive DNA reference libraries. Here, we compile inventories for aquatic metazoans extant in or threatening to invade the Laurentian Great Lakes and examine the availability of reference mitochondrial COI DNA sequences (barcodes) in the Barcode of Life Data System for them. We found barcode libraries largely complete for extant and threatening-to-invade vertebrates (100% of reptile, 99% of fish, and 92% of amphibian species had barcodes). In contrast, barcode libraries remain poorly developed for precisely those organisms where morphological identification is most challenging; 46% of extant invertebrates lacked reference barcodes with rates especially high among rotifers, oligochaetes, and mites. Lack of species-level identification for many aquatic invertebrates also is a barrier to matching DNA sequences with physical specimens. Attaining the potential for DNA-based identification of mixed-organism samples covering the breadth of aquatic fauna requires a concerted effort to build supporting barcode libraries and voucher collections.
Highlights
Current efforts for developing DNA-based identification technology of aquatic samples fall into two general approaches
Hereafter referred to as metabarcoding ( “metagenomics” and “environmental barcoding” in the literature), the sequences obtained are clustered into operational taxonomic units (OTUs) based on genetic distance; taxonomic labels are assigned to those OTUs by matching the sequences to DNA barcodes for known specimens
The Consortium for the Barcode of Life exists for the express purpose of fostering the development of the necessary barcode reference libraries, and an on-line database and informatics workbench known as the Barcode of Life Data System (BOLD; < www. barcodinglife.com> ) has emerged as a central resource via which DNA barcode information is assembled, documented, and disseminated[9,10]
Summary
Current efforts for developing DNA-based identification technology of aquatic samples fall into two general approaches. We focus on metazoan taxa (reptiles, amphibians, fishes, zooplankton, and benthic macroinvertebrates) as these are the groups of most interest in Great Lakes bioassessment and non-native species monitoring and best documented in the BOLD database (as opposed to fungi, diatoms, protozoans). These metazoan groups exhibit diversity taxonomically but in traits such as body size, life history, and habitat occupied that make comprehensive assessments nontrivial. We recognize that the COI barcode does not successfully resolve all animal taxa and that there are other markers in use[2,7], but their discussion is outside the scope of this study
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