## 2 Materials and Methods
### Fish Tracking  
The tagged fish were located using a REMUS 100 AUV (Hydroid Inc., Pocasset, Maine, a subsidiary of Kongsberg Maritime, Kongsberg, Norway). This torpedo-shaped, propeller-driven vehicle (Figure 2) was 2 m in length, 19 cm in diameter, weighed 31 kg, had a maximum operating depth of 100 m, and cruising speed of 2.4 ms\({}^{-1}\). Prior to launch, a pre-programmed mission, including operational parameters and instructions (e.g., vehicle speed, depth, and survey route), was uploaded to the AUV's on-board navigational computer. An integrated GPS receiver provided positioning information while on the surface. Since GPS fixes can't be obtained underwater, the vehicle's position while submerged was estimated using either trilateration based on acoustic beacons moored at known locations within the study area, or dead reckoning where the route was recorded in an analogous 2-s interval from dead reckoning computations. Position estimates were rectified during post-processing. The error between the initial position at depth and the new GPS position acquired after surfacing was smeared across the submerged point estimates of the route using the RENAV feature of the AUV's native software. The AUV was equipped with an integrated omnidirectional coaxial hydrophone and acoustic receiver (Model WHS 3050: Lotek Wireless) mounted on the nose of the vehicle (Figure 2) and running the proprietary data logging software MAPHost (Lotek Wireless). The equipment was capable of detecting, identifying and recording CDMA transmitters used to tag the fish. The vehicle was also equipped with a 600 kHz side-scan sonar and suite of environmental sensors for chemical, bathymetric, and biological oceanographic studies [43]. The vehicle was instrumented with a payload control hardware/software stack that operated using software called Synthetic Aperture OverRide (SAOVR) designed to map the location of acoustically tagged fish [22]. The software and a series of operational scripts were uploaded to an internal guest computer that communicated with the AUV's proprietary control system through the factory-installed RECON communications protocol (Hydroid Inc.). After detecting a transmitter and meeting certain operational criteria [22], the vehicle deviated from its pre-programmed route and performed a maneuver designed to (1) enhance the location estimate of the tagged fish and (2) move the AUV closer to the fish to obtain proximal information on the environmental conditions associated with the location. Based on simulation results, a base-forward equilateral triangle was selected as the preferred maneuver [23]. The vehicle would begin the maneuver by turning 30\({}^{\circ}\) to the right of the pre-programmed route, then 60\({}^{\circ}\) left (crossing the default pathway), and then 60\({}^{\circ}\) left to return to the original deviation point and resume the pre-programmed route (Figure 3). This maneuver ensured that the target (i.e., the tagged fish) was approached from several different angles to optimize the creation of a synthetic aperture [12]. Travel time for the maneuver was 60 s/segment, with the vehicle traveling approximately 120 m/segment based on an average cruising speed of 2.0 ms\({}^{-1}\). Figure 3: Payload control (PC) maneuver, consisting of a base-forward triangle, used by an autonomous underwater vehicle to estimate the location of acoustically tagged fish. SYNAPS software was used to calculate a series of location estimates using multiple signal detections, starting with the first 8 detections (Estimate 1) and increasing incrementally (Estimate 2 based on 9 detections, Estimate 3 based on 10 detections, etc.). Figure 2: Remus 100 autonomous underwater vehicle (**left panel**) used during field trials in marine waters of southeastern Alaska during 2016.