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In 2018, a new stock assessment was carried out for yellowfin in the IOTC area using Stock Synthesis III (SS3), a fully integrated model that is used for the three tropical tuna stocks in the IOTC (bigeye, yellowfin and skipjack). However, the lack of understanding of stock dynamics due to various uncertainties led the IOTC’s Scientific Committee (SC) to develop a workplan to address these uncertainties in 2019 before providing management advice. One of the items of this workplan is to characterize model uncertainty by using alternative stock assessment models. Here, we use a relatively simple biomass dynamic model that uses total catch and catch per unit of effort trends to estimate biomass and fishing mortality trajectories and to estimate fishery’s reference points. The 2018 SC acknowledged that the uncertainties on this fishery need to be explored and characterized and we do this by generating nine alternative scenarios for this stock assessment. We explore uncertainty in catch, abundance indices, population dynamics and the searching space for parameter estimation. Our preliminary results estimate a range of very different stock status and productivity and, corroborate that the existing uncertainty on this fishery can lead to opposite stock status estimates. However, we propose a series of diagnostics to help deciding on a reference case, a group of reference models or on a number of factors to be included in a potential grid of reference models. These diagnostics suggest that modelling choices such as the constraints on the searching space of parameters, initial values of parameters and the shape of the production function would be more influential on the result of the assessment than choices on the available datasets. The available catch and CPUE series seem to be insufficient to produce stable and robust estimates of stock status and reference points. Therefore, none of the results shown here should be taken as valid estimates of stock status trajectories or productivity.
