Estimation of annual mortality rates caused by early mortality syndromes (EMS) and their impact on salmonid stock-recruit relationships

In this paper, we demonstrate how information from broodstocks can be combined with lab information on sing a probabilistic alevins to obtain annual stock-specific mortality estimates from early mortality syndromes (EMS) using approach, how a hierarchical model structure can be used to predict these mortality rates for related, partly sampled, or unsampled stocks, and why these estimates should be used to remove the effect of this mortality on stock-recruit estimates. The approach has been illustrated for Atlantic salmon (Sahno salar) stocks in the Baltic Sea affected by the M74 syndrome. Results indicate that data on the proportion of M74-affected females, commonly used to approximate M74 mortality, overestimate actual M74-related mortality because of a declining trend in mortality among offspring of these females. The stock-specific M74 mortality estimates are used to account for nonstationarity in the stock-recruitment relationship caused by this fluctuating mortality. Because hierarchical meta-analyses assume exchangeability, the effect of M74 mortality is removed before including these stocks within hierarchical stock-recruit analyses of Atlantic salmon stocks, which are commonly unaffected by M74 mortality. Failure to remove the effect of M74 mortality on the stock-recruit data results in underestimation of the stock's productivity and resilience to exploitation, especially in the case of stocks with steep stock-recruit curves.