## 2 Materials and Methods
### Fish Tracking
The vehicle was equipped with payload control hardware and software (internal), a receiver and hydrophone for detecting and recording acoustic transmitters, an acoustic Doppler current profiler (ADCP), environmental sensors, a side-scan sonar, and a GPS receiver for collecting positioning data. A boat equipped with an acoustic receiver and dual hydrophones was used to conduct concurrent surveys (**right panel**). The hydrophone struts were lowered into the water and vertically oriented during tracking, with the hydrophones submerged to a depth of 1 m.  
A series of missions with multiple legs were conducted in Big Port Walter using the SAOVR software to override the pre-programmed route and execute a maneuver when a tagged fish was detected. The AUV traveled along a route generally running southwest to northeast (legs 1, 3, and 5) and northeast to southwest (legs 2, 4, and 6) as shown in Figure 1. The surveys were conducted at depths of 20-25 m with a flat trajectory once the AUV reached its cruising depth. A single mission with multiple legs was conducted in Port Walter at a depth of 35 m, with the AUV traveling along a rectangular route with multiple repetitions. All missions ran at a cruising speed of approximately 2 ms\({}^{-1}\). The vehicle surfaced at the end of each leg to obtain a GPS fix for course correction. The survey data collected by the AUV included time-stamped records identifying the fish detected, signal strength of the transmitter, environmental sensor data, and the corresponding position of the AUV. These data were also collected for any other fish detected during the maneuver. Additional maneuvers were temporarily suspended to prevent the AUV from getting locked in a positive feedback loop [22]. Sequential transmitter detections recorded during the maneuver (Figure 3) were used to create a series of location estimates for each fish detected using synthetic apertures [12] with the stipulation that the set of detections not exceed 90 s from the first to the last detection. Multiple synchronous position solutions were calculated based on permutations of the different subsets of sequential detections (Figure 3) and filtered by several quality metrics. The proprietary software SYNAPS (Lotek Wireless) was used to calculate these estimates. The software applies a differencing engine to find the best intersection between the surfaces of the multiple detection spheres obtained, similar to the approach used by GPS [44; 45] after removing the cumulative transmission interval from the timestamps of the set of transmitter detections. SYNAPS also provided diagnostic variables that measured the overall quality of each location solution, including residual (_Resid_) and dilution of precision (_DOP_). _Resid_ is a stability metric based on the error estimate of the signal flight time (i.e., propagation delay associated with the signal) with smaller _Resid_ values indicating a better location estimate [23]. The _DOP_ metric is a measure of the intersection of the spheres delineating possible times of signal arrival to different hydrophone locations within the aperture, and thus is sensitive to the geometry of the aperture. Smaller _DOP_ values result from apertures with a good parabolic shape and are associated with more accurate location estimates [23]. _Resid_ was used as the primary screening metric, with _DOP_ used as a secondary assessment variable. Location estimates with _Resid_ values <30.0 were considered reasonable. Since multiple estimates were obtained using different combinations of signal detections (Figure 3), the estimate with the smallest _Resid_ was selected as the best location estimate for a given tag during a particular detection event. The multiple legs of the mission typically resulted in a series of temporally distinct detection events (and associated location estimates) for the individual fish.