Asian Carp Early Detection
Science Center Objects
Increased threat of Asian carp entering the Great Lakes and spreading to other basins such as the Upper Mississippi River and Ohio River basins, has led to increased prevention and control efforts since 2010. In collaboration with partners, USGS scientists are testing early detection methods and technologies to enhance the ability of agencies to manage Asian carp to minimize their influence and spread.
Early detection is a vital part of managing any invasive species. Asian carp are difficult to detect because they avoid nets and other capture gear, making them hard to catch when populations are small. The USGS is contributing to development and improvements of new genetic approaches to detect Asian carp at low populations and identify initial invasions. Early detection of Asian carp is critical to initiate rapid or early response efforts to block population establishment. An overview of USGS early detection research is described below. For more details on these USGS projects and other Asian carp activities check out the Asian Carp Action Plan at asiancarp.us.
Genetics and Early Detection - Molecular approaches that detect genetic fingerprints such as the DNA or RNA shed by fish or other organisms into the environment (eDNA) have great promise for natural resource managers for species detection, and have become a vital tool for early detection of invasive Asian carp. USGS scientists have tested and refined a number of molecular tools and approaches for Asian carp detection such as loop-mediated isothermal amplification [LAMP], digital PCR [dPCR], and quantitative PCR [qPCR]1 and high-throughput sequencing [HTS]. LAMP, dPCR, and qPCR are processes used to generate multiple copies (amplification) of a target DNA from a single molecule, rather than isolating a single copy from many cells. HTS is a rapid method of determining the sequence of bases in a DNA molecule.
To date, studies have indicated that other potential applications of eDNA beyond detecting presence may include detection of spawning events, fish movement, and habitat utilization. Refinements to eDNA methodology have improved detection sensitivity, minimized false negatives from PCR inhibition, increased cost-effectiveness, and decreased time between sampling and results. Much more work is needed to improve the interpretation of eDNA detections. One project will aim to identify differential degradation patterns of DNA and breakage ‘hotspots’ so that new markers can be designed that will indicate how recently the DNA was deposited. Using existing data, models will be developed that will identify the probability of a detection coming from a live fish or some other vector. These models will be used to help recognize data gaps and inform future studies.
Scientists are also evaluating the use of Next Generation Sequencing, a powerful technology that provides rapid and simultaneous sequencing of millions of individual strands of DNA or RNA within samples. USGS is collaborating with the U.S. Fish and Wildlife Service to evaluate its use for detecting invasive Asian carp and other aquatic invasive species in the Great Lakes and Mississippi and Ohio Rivers. This technology can be used to obtain information on species absence/presence, community composition, and species diversity in aquatic and terrestrial systems.
Hand-held eDNA Detection Kits - Early detection and rapid response is a critical component of invasive species prevention. There are some invasion pathways that cannot be monitored in reasonable time by traditional methods and others that just cover too much ground to effectively monitor with limited funding and personnel. In 2015, USGS developed a portable eDNA detection kit that can be used by minimally trained individuals to collect and analyze environmental DNA (eDNA) samples to detect Bighead Carp and Silver Carp on site in under one hour. In 2016, USGS provided training and deployed 10 of those kits to law enforcement in Illinois, Michigan, and Ohio to do preliminary screening of transported bait. So far, the kit has been used successfully to screen bait shops, and no transported Bighead Carp or Silver Carp have been detected. In 2017, USGS provided training and 6 portable eDNA detection kits to U.S. Fish and Wildlife biologists for use at Fish and Wildlife Conservation Offices. Methods have been refined to make it useful for testing open waters and checking boats or fishing gear. Along with additional sample types, new assays have been developed new assays to detect additional species as well. New assays can detect Bighead Carp, Silver Carp, Grass Carp, or Black Carp; Zebra Mussels or Quagga Mussels; and Round Goby with more on the way.