Mark-Recapture Estimates of Atlantic Salmon Smolts in Maine Rivers: Habitat and Trapping- Location, Location, Location

NOAA Fisheries Service’s Northeast Fisheries Science Center has monitored Atlantic salmon smolt emigration from select Maine rivers since 1996.  Our most intensive studies were conducted on the Narraguagus and Sheepscot Rivers.  Both systems are coastal streams entering the Gulf of Maine but they differ with respect to flow regime, production habitat distribution, topography, and river access.  In both, we used rotary screw traps as platforms to estimate abundance, biosample smolts, insert tags for telemetry studies, and study emigration ecology.  The key to our abundance estimates was the design and implementation of efficient mark-recapture studies.  However, differences between rivers necessitated different approaches to study design and trap location.  We used a two-site method on the Narraguagus River, where there was a distance of four kilometers between suitable sites and both were accessible by boat.  We used a one-site method on the Sheepscot River, where fish were trapped and trucked upstream approximately five kilometers because river access was limited by a narrow, well-defined river valley.  Data was analyzed using Bjorkstedt’s program DARR (Darroch Analysis with Rank-Reduction) for R, which accommodated both of these methods.  In this paper we review challenges and lessons learned in our index river studies, including our analysis of the frequency of trap outages across systems.  We also present both our methods for categorizing these gaps in fishing, and our rationale/decision structure for deciding when to cease fishing.  Finally, we discuss the study design process and productive capacity of our two primary study rivers, and how these estimates inform estimates of recruitment, marine survival and life-history models.