Hydroacoustic counting and a three-year mark–recapture study with passive integrated transponders (PIT tags) were used to estimate the size of a spawning population of nase Chondrostoma nasus, a threatened potamodromous cyprinid that undertakes annual spawning migrations into a tributary of the Danube River. In 2005, the estimates of the size of the spawning population from the hydroacoustic counts (N = 2234, 95% CL 1929–2538) and from the Jolly–Seber model (N = 1198, 95% CL 461–5842) corresponded well. Estimates from the jackknife-estimator based on the hydroacoustic counts yielded slightly higher values (N = 2783, 95% CL 2529–3037), but were still in the same order of magnitude as those from the hydroacoustic and mark–recapture approach. At low run-size, hydroacoustic counting was more time consuming and technically demanding than mark–recapture studies. At the same time, it was non-invasive, provided real-time data on a fine temporal scale, and estimates showed less variability than the Jolly–Seber model. Mark–recapture of fish in spawning streams involved substantial disturbance at a sensitive stage of the life cycle. Hence, hydroacoustics is highly suited for population estimates of threatened potamodromous fishes, where interference needs to be minimized.
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