Early Detection and Monitoring for New Aquatic Invasive Species in Lake Michigan: 2016 Report Number: 2017-008 1 Harris, B.S., J. T. Richter, M. Shaffer, B.J. Smith and C-A. Hayer. 2016. Early detection and monitoring for new aquatic invasive species in Lake Michigan. U.S. Fish and Wildlife Service, Green Bay Fish and Wildlife Conservation Office, Green Bay, WI. Report Number 2017-008. i Table of Contents List of Figures ......................................................................................................................v List of Tables .................................................................................................................... vii Executive Summary ......................................................................................................... viii Introduction ..........................................................................................................................1 Objectives ............................................................................................................................4 Methods................................................................................................................................4 Study area........................................................................................................................4 Sampling gears ................................................................................................................5 Fish community sampling ...............................................................................................5 Benthic macroinvertebrate sampling ..............................................................................6 Ichthyoplankton sampling ...............................................................................................7 Analysis and Interpretation .............................................................................................8 Results ..................................................................................................................................9 Environmental DNA .......................................................................................................9 Fish community sampling ...............................................................................................9 Benthic macroinvertebrate sampling ............................................................................10 Ichthyoplankton sampling .............................................................................................11 Discussion ..........................................................................................................................11 Conclusions ........................................................................................................................14 Future Work .......................................................................................................................14 Acknowledgements ............................................................................................................14 References ..........................................................................................................................15 Figures................................................................................................................................21 Tables .................................................................................................................................36 vii List of Figures Figure 1. Lake Michigan study areas (hotspots) sampled by the Aquatic Invasive Species (AIS) program during 2016. All hotspot study sites are outlined in red while study rivers for eDNA sampling are drawn in black and labeled. Figure 2. Study area of rivers flowing into Lake Michigan for eDNA analysis. Figure 3. Lower Green Bay, WI traditional gear study area with sample locations for each gear type. Sampling was performed during May-October 2016. Five additional electrofishing runs were performed upstream in the Fox River near the De Pere Dam but are not depicted. Figure 4. Map of the Milwaukee, WI traditional gear study area with sample locations for each gear type. Sampling was performed during September 2016. Figure 5. Map of the Chicago, IL traditional gear study area with sample locations for each gear type. Sampling was performed during August 2016. Figure 6. Map of the Calumet Harbor, IL traditional gear study area with sample locations for each gear type. Sampling was performed during August 2016. Figure 7. Map of the Burns Harbor, IN traditional gear study area with sample locations for each gear type. Sampling was performed during August 2016. Figure 8. Map of light trap sampling locations in the Milwaukee River and Milwaukee Harbor, WI during 2016 ichthyoplankton surveys. Figure 9. Map of light trap sampling locations in the Lower Fox River, Green Bay, WI during 2016 ichthyoplankton surveys. Figure 10. Length-frequency histograms for nine species collected across all gear types and sites during 2016 Lake Michigan sampling. Note that the X and Y axes differ in scale across species. Figure 11. Dendrogram of fish communities at hotspot sampling sites calculated using average- linkage hierarchical cluster analysis in 2016. Figure 12. Sample size based rarefaction (solid lines) and extrapolation (dashed lines, up to double the reference sample size) of species richness for all gears used in 2016 with the five hotspots combined. The reference samples are denoted by the solid dots. The 95% confidence intervals (shaded regions) were obtained using a bootstrap method based on 200 replications. The rarefaction/extrapolation curves along with the asymptotic species richness for each gear were calculated by the Chao et al. 2014 estimator functions within the iNEXT package using the software program R. viii Figure 13. Sample size based rarefaction (solid lines) and extrapolation (dashed lines) of species richness for all traditional gears used in 2016 at the five hotspot locations. The reference samples are denoted by the solid dots. The 95% confidence intervals (shaded regions) were obtained using a bootstrap method based on 200 replications. The rarefaction/extrapolation curves along with the asymptotic species richness for each location were calculated using the Chao et al. 2014 estimator functions within the iNEXT package run in the software program R. Within the figure; y-axis levels vary, n = units of effort, S = # of species caught, and E = Sampling efficiency. ix List of Tables Table 1. River name, state, number of reaches, number of water samples taken, and dates sampled for environmental DNA analysis in nine hotspot rivers for Bighead and Silver Carp presence during 2016. Table 2. Total catch from all gears combined at five hotspot sampling locations in Lake Michigan during 2016 including catches from an early season (May) paired fyke net gear comparison in Green Bay. Names of invasive species are bolded. Table 3. Gear and units of effort allocations expended during 2016 at the five hotspot locations in Lake Michigan using three traditional fish sampling gears. Table 4. Environmental conditions and sampling site characteristics at light trap locations in the Milwaukee River and Milwaukee Harbor during 2016 ichthyoplankton surveys. Table 5. Environmental conditions and sampling site characteristics at light trap locations in the Lower Fox River – Green Bay during 2016 ichthyoplankton surveys. x Executive Summary For nearly two centuries, continual introductions of non-native species in the Laurentian Great Lakes have altered the ecosystem and cost millions of dollars in damage to fisheries and infrastructure. In recent decades, there has been increasing emphasis on prevention and early detection of new invasive species in the Laurentian Great Lakes. The aquatic invasive species (AIS) program at the Green Bay Fish and Wildlife Conservation Office performed early detection and monitoring throughout Lake Michigan in 2016. Water samples were collected to detect the presence of Bighead and Silver Carp DNA from the Fox and Milwaukee rivers in Wisconsin and the St. Joseph, Kalamazoo, Macatawa, Galien, Black, Grand and Muskegon rivers in Michigan. Fish and macroinvertebrates communities were sampled from the bay of Green Bay, Calumet Harbor, Burns Harbor, and nearshore waters of near Milwaukee and Chicago, five locations identified as hotspots for invasion of new invasive species. Sampling focused on detection of bigheaded carps (i.e., Bighead and Silver Carp) in rivers, monitoring fish and macroinvertebrate communities in five hotspot locations associated with densely populated port cities on Lake Michigan, and developing a monitoring protocol for ichthyoplankton. We found no evidence of Bighead or Silver Carp presence using environmental DNA sampling techniques on nine river systems in Michigan and Wisconsin. No new invasive or non-native species were detected in 2016 at the five hotspot locations in Lake Michigan. A total of 51,864 individual fish representing 73 species were collected with 411 units of sampling effort. Species accumulation curves indicated that fish communities were effectively sampled using nighttime boat electrofishing, experimental gill nets, and paired modified fyke nets that when combined, provided a representative sample of the fish community at each location (90-95% of species collected). Gears and methods for sampling fish were improved during 2016, allowing for reduced effort with similar, or better, efficiency