USGS - science for a changing world

Upper Midwest Environmental Sciences Center

Developing Quantitative Environmental DNA Surveillance for Sea Lamprey (Petromyzon marinus)

Principal Investigators: Jon Amberg

Impact of UMESC Science

Results from this study will provide a framework to make surveillance for Sea Lamprey in the Great Lakes tributaries more efficient and informative for targeting bi-national control efforts.


Sea lamprey (SL, Petromyzon marinus) are an invasive species that were introduced to the Great Lakes after the formation of the Welland Canal in 1829.  Following their introduction, sea lamprey devastated the commercial and recreational fisheries of the Great Lakes. Sea lamprey populations are currently managed by various control techniques employed by the Great Lakes Fisheries Commission (GLFC). One significant method of control is using chemicals to target the ammocoetes (larval phase of the lamprey life cycle). Adult sea lamprey swim upstream to spawn where the female lamprey will lay eggs that are then fertilized externally by the male. The fertilized eggs will eventually hatch into ammocoetes. The ammocoetes will spend approximately 4-6 years burrowed in the sediment of the stream where they will filter feed on detritus and algae. This sedentary lifestyle has made the ammocoetes prime targets for chemical control. However, due to limitations in budget, personnel, and overcoming geographic logistics it is not feasible to treat every sea lamprey-infested stream of the Great Lakes. Therefore, the GLFC must prioritize streams according to estimated lamprey abundance, known treatment costs, and available budget.

Individual stream treatment needs are currently determined using a variety of assessments techniques which include semi-quantitative surveys of potential habitat as well as sea lamprey ammocoete abundance. These surveys are combined with expert judgment of streams gained by managers through years of sea lamprey control. This information is then used by managers to prioritize streams for treatment. These assessment techniques may not account for all lamprey present due to the inherent elusive lifestyle of the ammocoetes, and on some streams can be difficult due to stream conditions (MacKenzie et al. 2005; Darling and Mahon 2011).

One way to assist management with assessment and stream prioritization methods would be to easily provide a quantitative assessment of sea lamprey populations to supplement traditional assessment techniques.

Resource agencies have recently adopted molecular surveillance techniques to detect aquatic invasive species (Darling and Mahon, 2011; Lodge et al., 2012; Jerde et al., 2013) as an alternative to traditional sampling techniques. One example of a molecular surveillance technique has been the analysis of water samples for the presence of environmental deoxyribonucleic acids (eDNA) using polymerase chain reaction (PCR). Recently researchers used macrobiotic DNA to infer presence or abundance of multi-cellular organisms (Ogram et al. 1987; Valentini et al. 2009) in water samples. Some aquatic species such as Asian carp are easily detected using eDNA due to their life history, distribution, and DNA shedding characteristics (Kolar et al. 2007; Jerde et al. 2011; Jerde et al. 2013). Conventional polymerase chain reaction (cPCR) techniques target sections of the mitochondrial DNA of the species in question. Conventional PCR has been used to monitor for the presence of silver and bighead carp throughout the Chicago Area Waterway System (CAWS) and the Mississippi, Illinois, Wabash and Ohio rivers, and portions of Lake Erie. eDNA detection assays are now developed for numerous terrestrial and aquatic species of native or exotic origin (Ficetola et al. 2008; Goldberg et al. 2011; Dejean et al., 2012; Foote et al. 2012; Takahara et al., 2012; Thomsen et al., 2012a; Thomsen et al., 2012b; Egan et al. 2013; Goldberg et al., 2013; Pilliod et al., 2013; Takahara et al. 2013; Piaggio et al. 2014). eDNA is also useful in detecting rare, threatened, or endangered species in lotic aquatic environments (Dejean et al. 2011; Jerde et al. 2011; Minamoto et al. 2011; Minamoto et al., 2012; Thomsen et al. 2012a).

Docker et al. has produced eDNA primers and cPCR assays specific for sea lamprey. These assays have been optimized and validated to show they can detect the presence of eDNA from spawning and larval sea lamprey in streams. They also found positive correlations with larval densities in a laboratory study. The cPCR assays developed by Docker et al. are effective at determining presence or absence of the sea lamprey in a stream. However, due to the method of amplification, cPCR assays can be prone to amplifying DNA from non-target species and therefore require sequencing confirmation to ensure the target species is what was actually detected. This makes validating cPCR assays challenging due to the possibility of cross amplification of non-target DNA in aquatic environmental samples.

An alternative method to cPCR for eDNA detection is quantitative PCR (qPCR, or real-time PCR, probe-based PCR, fluorescence-based PCR). qPCR assays have primers that bind to the target DNA template and also use a probe that is highly specific to the DNA sequence of the species in question. There has been research to suggest that qPCR technologies allow correlation of eDNA quantity to species density and distribution (Takahara et al. 2011; Thomsen et al. 2012a). These types of assays have greater sensitivity as well as increased species specificity. qPCR assays carry another advantage over cPCR assays in that the fluorescence obtained during the reaction can provide quantitative estimates of DNA in a particular sample without the need for additional gel analysis and genetic sequencing.


  • Develop new probe-based qPCR assays specific to Sea Lamprey and test and validate their accuracy and specificity using previously collected samples archived at University of Manitoba.
  • Use newly developed and validated qPCR assays to determine if relative abundance of adult Sea Lamprey in laboratory and natural systems correlates with eDNA levels detected in tanks and streams.
  • Use newly developed and validated qPCR assays to determine if relative abundance of larval Sea Lamprey in laboratory and natural systems correlates with eDNA levels detected in tanks and streams.

Figure 3: Adult Sea Lamprey attached to Lake Trout

Figure 3: Adult Sea Lamprey attached to Lake Trout

Figure 1: Adult Sea Lamprey

Figure 1: Adult Sea Lamprey

Figure 2: UMESC Scientist preparing samples.

Figure 2: UMESC Scientist preparing samples.


Accessibility FOIA Privacy Policies and Notices

Take Pride in America logo logo U.S. Department of the Interior | U.S. Geological Survey

Page Contact Information: Contacting the Upper Midwest Environmental Sciences Center
Page Last Modified: March 15, 2016