Potential for DNA-based identification of Great Lakes fauna: match and mismatch between taxa inventories and DNA barcode libraries

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.

18S rRNA metabarcoding diet analysis of a predatory fish community across seasonal changes in prey availability

“…Additionally, cannibalism and consumption of other Perciformes are a component in the diets of rock bass and smallmouth bass (Clady, ; Frey, Bozek, Edwards, & Newman, ) but could not be detected due to the low taxonomic resolution of the 18S V9 region of rRNA. Using markers for a more variable region in fishes (e.g., mitochondrial cytochrome oxidase I) would improve the ability to detect fishes in the diets of close relatives (Trebitz, Hoffman, Grant, Billehus, & Pilgrim, ). However, use of multiple primers that optimize classification potential of different groups would preclude our ability to estimate relative sequence abundance (and thus inferentially relative biomass) across all prey taxa.…”

“…Additionally, cannibalism and consumption of other Perciformes are a component in the diets of rock bass and smallmouth bass (Clady, 1974;Frey, Bozek, Edwards, & Newman, 2003) (Trebitz, Hoffman, Grant, Billehus, & Pilgrim, 2015). However, use of multiple primers that optimize classification potential of different groups would preclude our ability to estimate relative sequence abundance (and thus inferentially relative biomass) across all prey taxa.…”

Are genetic databases sufficiently populated to detect non-indigenous species?

“…Sus scrofa), and NIS having severe impact on environment and economy [e.g. Rattus rattus, Dreissena polymorpha, and Eichhornia crassipes; see also Briski et al (2011) and Trebitz et al (2015)] is exceptionally high compared to studies of other NIS . In this study, taxa such as aquatic Malacostraca (many species with environmental or economic impact), Maxillopoda, Bivalvia, and Ulvolaceae (many species of economic value and/ or causing impact) and terrestrial Insecta (many species causing environmental or economic impact) demonstrate an exceptionally high trend of sequence deposition.…”

Extensive cryptic diversity in the cosmopolitan sludge worm Limnodrilus hoffmeisteri (Clitellata, Naididae)

“…Single locus data are widely and conveniently used to estimate species boundaries in large samples of specimens of morphology-based taxa (Nicolas et al 2012;Lv et al 2014;Trebitz et al 2015). We tried to disentangle the mitochondrial diversity of the highly variable L. hoffmeisteri, by examining specimens from all continents of the northern hemisphere with ABGD and bGMYC.…”