Date of Award

Spring 5-10-2019

Level of Access Assigned by Author

Open-Access Thesis

Degree Name

Master of Science (MS)


Marine Biology


Damian Brady

Second Committee Member

Gayle Zydlewski

Third Committee Member

J. Michael Jech


Diadromous fish require both freshwater and marine habitat to complete their life cycle. Dams restrict the movement between these habitats and as a result, many populations are historically low across their range. The Penobscot River is the second largest river in Maine and once had large populations of diadromous fish and it has been the focus of mainstem dam removals, dam passage improvements, and stocking with the goal of restoring those populations. Since 2012, NOAA Fisheries has conducted surveys of the Penobscot Estuary using mobile, multi-frequency echosounders (SIMRAD EK60 split-beam 38 and 120 kHz) combined with mid-water trawl surveys to construct a time series of fish distribution to assess this large-scale restoration. Target strength (TS; dB re m2), the log10 of the backscattering cross section (σbs; m2), is an important variable in fisheries acoustics because it is used to compute biological metrics such as biomass and fish density. TS is difficult to characterize due to its stochastic properties from variability in fish physiology, orientation, behavior, depth, and size. When an assemblage consists of multiple species or multiple size classes, assigning TS to the component species or size classes is difficult due to the inability to distinguish individual components in the composite distributions. We addressed these challenges by a unique combination of techniques to characterize TS in the Penobscot River Estuary, Maine. From trawl data, we determined the estuarine species assemblage was dominated by Clupeids and Osmerids. We used single target detection and echo tracking algorithms to isolate TS values from individual fish. Next, we applied an expectation–maximization algorithm to identify components of the mixed normal TS distribution based on fish total length (TL; cm) data from trawl surveys. Finally, we used ordinary least squares regression to estimate the parameters of TS = α log10 (TL) + β. Our final parameters, α = 31.0 (SE 0.84) and β = -79.5 (SE 0.90), were similar to published studies from these species. However, our slope and intercept were higher than studies from freshwater and lower than from marine systems. These results suggest that acoustic surveys in estuarine systems with mixed species assemblages and large salinity ranges may need to develop site specific relationships between TS and fish length. The combination of these methods is an example of a novel technique to derive reproducible TS estimates in mixed pelagic fish assemblages. We used system-specific parameters to compute biomass from acoustic survey data. We assessed seasonal estimates of biomass from 2012 to 2017 a period spanning pre-restoration (2012-2014) and post-restoration (2015-2017). Biomass varied with season and year and was generally greater in summer and in post-restoration years. Biomass in pre-restoration years ranged from 9,000 to 114,000 kg per survey and 11 of 45 (23%) surveys had biomass greater than 50,000 kg. Compared to post-restoration years ranged from 23,000 to 316,000 kg per survey and 34 of 43 (76%) surveys had biomass greater than 50,000 kg. Changes in biomass were observed with changes in fish length and density where higher density resulted in higher biomass. This analysis demonstrates the utility of hydroacoustics in monitoring large-system restoration by describing multiple metrics in a complex ecosystem. The changes observed by increased density and biomass are indications that river restoration is changing the ecology of the estuary.