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The cost-efficiency analysis of genetic HTS methodologies is aimed for understanding the potential of these methodologies for reducing the financial burden of aquatic and marine life assessments without increasing the uncertainty of the biological parameters relevant for such assessments which can be obtained through these methods. Even though several pieces of research have claimed that these methodologies are cost-efficient, most of them refer to uses different to the stock assessment of commercial fish species. The cost-efficiency analysis estimates the ratio of ‘program’ costs to outputs created, allowing to compare cost-per-output for programs producing equivalent outputs. In our case, outputs are the necessary data for performing an accurate stock assessment. The cost-efficiency analysis of the HTS methods compared to the currently used ones in the research surveys requires identifying the cost components in each case, to measure the relative efficiency and to understand the origin of the differences. Fisheries research surveys are not performed in a single way, they differ significantly one to another. A variety of stock assessment evaluation methods are regularly used. They also differ on the requirements on a priori information about the stock, in biological data and fishing parameters, in the time range of this data needed to run it with confidence, etc. A survey design conditions the efficiency of the surveys and the eventual optimization of the cost components. This study presents a contextualised approach for the cost comparison needed and identifies some potential pathways for efficiency both on the surveys at sea and on the lab, where the sampling processing takes place until the output data is made available for the stocks assessment.

Global marine fisheries are underperforming economically because of overfishing, pollution and habitat degradation. This fact has serious implications over marine habitats such as latitudinal and in-deep migrations and modifications of the stock – recruitment relationship. It generates a reduction in the number of individuals on fisheries and, subsequently, an increasing number of overexploited stocks. Nowadays the majority (85 percent) of Mediterranean and Black Sea stocks for which a validated stock assessment exists are fished outside biologically sustainable limits (GFCM, 2016). It is necessary to mitigate the negative impacts over marine fish stocks and improve the state of fish stocks reverting the negative ecological, economic and sociologic effects. Decreasing recruitment trend has also serious negative implications on stock dynamics and, subsequently, affects the accuracy of stock estimates. Stock estimates are the basis for fisheries managers to determine quotas and management regulations. On one side, the aim of the investigation is to replicate using Assessment for All (a4a) stock assessment tool the last 2016 Working Group on Demersal Species (WGSAD) Extended Survival Analysis (XSA) validated stock assessment for European hake in the Strait of Sicily (GSA’s 12-16). Main benefit of using a4a is the capability to introduce an uncertainty parameter in the stock assessment process. It allows to describe better the stock dynamics and, thus, increase the quality of the scientific advice. Also, an assessment of management scenarios was carried on finding possible alternatives in the management of the resource in the Strait of Sicily fishery. Those management scenarios were compared to identify dissimilarities related with the use of different models to assess the stock. On the other side the aim of the investigation is to investigate the implications of decreasing recruitment trends or consider constant recruitment values along the timeseries assessing the consequences along the management process and the calculation of reference points. Chapter one focuses as an example on the stock of Merluccius merluccius (Linnaeus, 1758) in the Strait of Sicily. This fishery was selected due the existence of a subregional multiannual management plan as well as for its economic importance and the fact that hake is considered an emblematic species within the Mediterranean, however subject to the highest overexploitation index (current fishing mortality / target fishing mortality) in the Mediterranean Sea. Chapter two takes as an example Sardina pilchardus (Walbaum, 1792) in ICES VIIIc and IXa subareas was use as target stock. We show that ignore recruitment trends ignores part of the risk of managers management strategy. We also show that biomass based harvest control rule decreases the volatility of the stock. No taking care about recruitment trends makes the manager to ignore a slight decreasing of the yield per recruit value. Finally, was noticed that biomass based harvest control rule reduces the risk (measured in probability of biomass bellow 0.5*Bmax) of surpass management boundaries.