Emigration dynamics of natural and hatchery Atlantic Salmon smolts in an impounded river system

ABSTRACT Objective The Gulf of Maine Distinct Population Segment of Atlantic Salmon Salmo salar is federally listed as endangered and is the last remaining population of Atlantic Salmon in the United States. The Penobscot River recovery program remains heavily reliant on hatchery-reared smolts to prevent extinction. The objectives of this study were to determine the proportion of emigrating natural and hatchery smolts, compare smolt size and run timing by origin, and assess whether location and timing of stocking affected recapture rates and emigration timing of hatchery smolts. Methods We analyzed a smolt sampling data set that was collected using rotary screw traps in the Penobscot River from 2001 to 2005. We identified smolts to origin (natural, hatchery, or unknown) based on scale pattern analysis and the presence of marks (adipose fin clip and/or visual implant elastomer). We calculated the proportion of emigrating natural and hatchery smolts, compared smolt size among origins, and compared capture timing with predicted emigration timing for natural smolts. We also calculated recapture rate and days at large for each group of marked smolts to assess the effects of timing and location of stocking on emigration. Results Over the 5 years of sampling, 57% of the captured smolts were hatchery origin, 40% were unknown origin, and 3% were natural smolts. Natural smolts were older and smaller than hatchery smolts. The measured 25% capture day of year was similar to the predicted 25% capture day of year for natural smolts. Hatchery smolt stocking and emigration timing was out of sync with the predicted out-migration timing for natural smolts. Recapture rates of hatchery smolts varied with stocking location and year, but days at large were not influenced by stocking location. Smolts that were stocked before April 30 took longer to reach rotary screw traps than did smolts that were stocked later. Conclusions Our finding that the timing of stocking influenced emigration of hatchery smolts provides useful information to guide management of the smolt stocking program. Aligning timing of hatchery stocking efforts with natural migration timing may improve marine survival rates of hatchery smolts and confer survival advantages to smolts of both origins.