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DEVELOPMENT OF DNA-BASED TOOLS FOR IDENTIFICATION AND MONITORING OF AQUATIC INTRODUCED SPECIES
Citation:
DARLING, J., C. TEPOLT, M. J. BLUM, AND M. BAGLEY. DEVELOPMENT OF DNA-BASED TOOLS FOR IDENTIFICATION AND MONITORING OF AQUATIC INTRODUCED SPECIES. Presented at International Conference on Aquatic Invasive Species, Key Biscayne, FL, May 14 - 19, 2006.
Impact/Purpose:
The goals of this research are to:
(1) determine how landscape characteristics relate to the spread of red shiner through southeastern river systems,
(2) identify behavioral and genetic mechanisms underlying interspecific hybridization, and
(3) develop models to assess the vulnerability of tributary streams to invasion by red shiner.
Description:
Claims for potential applications of DNA taxonomy range from identification of unknown specimens and the discovery of new species to the study of biodiversity through comprehensive characterizations of complex biotic communities drawn from environmental samples. Recently, these applications have been widely recommended for the identification and monitoring of introduced and invasive species. DNA-based approaches have the capacity to provide rapid, inexpensive, and technically accessible tools for managers tasked with recognizing and preventing the importation and/or spread of potential invasives. Some recent studies have demonstrated the feasibility of such tools, at least for the most straightforward applications. However, significant technological hurdles must be overcome before more ambitious applications are realized. Here we explore the promise of a number of DNA-based tools for various applications associated with the identification and monitoring of aquatic invasive species, and review potential limitations in their application and technical difficulties associated with their development. By categorizing these tools based on characteristics of target samples and the desired outcomes of each application, we provide a conceptual framework for assessing the appropriateness of particular tools for solving particular problems. We also summarize some recent empirical data illustrating the promise of DNA-based applications, along with the challenges involved in their development. Specifically, we review the design of targeted PCR approaches to screening for green crab (Carcinus maenas) and mitten crab (Eriocheir sinensis) larvae in ballast water, and describe attempts to characterize complex ballast water communities based on the determination of DNA "barcode" sequences (mitochondrial cytochrome C oxidase subunit I, COI). Green crab- and mitten crab-specific PCR primers have been developed based on comparison of COI sequence from these target species and other brachyurans, and by testing green and mitten crab microsatellite loci for cross-amplification with congeners and other closely related species. We explore the specificity and sensitivity of these primers by screening both control communities of known composition and ballast samples collected from a number of US west coast ports. We also present results of ballast community characterization based on shotgun cloning and sequencing of COI fragments generated by universal PCR of bulk-extracted DNA. These results clearly demonstrate that such approaches are seriously constrained by biases in PCR and/or DNA extraction efficiencies, and by the limitations of available sequence databases.