| Summary: | Large river systems can be challenging in relation to stock assessment and catchment management, especially those large rivers with numerous or important tributaries that may contain sub-populations or stocks. Initial testing of existing counter technology (resistivity, infra-red and split-beam hydroacoustics) in such a system - the River Moy, Co. Mayo - highlighted the difficulties in their use and operation. In this study, an alternative hydroacoustic system, DIDSON (Dual-frequency Identification Sonar), was deployed and assessed for the first time in Ireland. The DIDSON's near video quality imagery allowed for observations of fish migrations and it was easy to install and operate. Methodologies for the operation and data processing using DIDSON in Irish rivers for counting Atlantic salmon have been established, including software development of DIDSON SMC Software (SoundMetrics) (e.g. CSOT Analysis), allowing for the acquisition of real time data and quality fish length measurements. As an alternative to adult counts, mark-recapture estimates were successfully carried out on Atlantic salmon smolts on the River Deel (a tributary of the River Moy) using a screw trap. Both classic and Bayesian models were successfully applied. These stock assessment data were also used to determine the main environmental influences on Atlantic salmon migration in the River Deel. While air and water temperature were shown to be significant to adult migration, no direct correlations were determined with smolt migration. The combined use of DIDSON and Genetic Stock Identification was developed for salmon stock assessment. The genetically determined proportion of River Deel fish were used, along with the DIDSON count, to provide the first estimate of a large river system, the River Moy, using this unique methodology. This advance in stock assessment methodology allowed for a stock assessment of all discrete populations within a large river system.
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