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The North Celtic and Irish seas are extensively fished and, due to their shallow coastal nature, are particularly vulnerable to climate change stressors. Fish species assemblages in the region are characterised by high levels of diversity and include species of commercial and recreational importance, however poor larval recruitment and high fishing mortality have led to declines in abundance for some species. Monitoring of larval recruits and heavily exploited fish populations is essential for future sustainable fisheries management in a changing climate. This work aimed to develop and optimize molecular techniques for assessing fish communities in spawning grounds and fine scale population structure using adaptive molecular markers. Firstly, metabarcoding of bulk fish larvae homogenates was optimised by standardizing input material and using conserved priming sites, resulting in quantitative relative abundance estimates. This demonstrated that bulk larvae metabarcoding is a feasible alternative to traditional morphological assessment for assessing community diversity and composition. Secondly, species detections in spawning grounds from water sample and bulk larval sample metabarcoding were compared resulting in a 75% average agreement in detections across sample sites. Thirdly, a class I major histocompatibility complex (MHC) marker was developed and tested to assess sea bass population structure, allelic diversity and positive selection. Private alleles within the Celtic Shelf and Portuguese populations were identified. Finally, signals of positive selection and trans-species functional supertype structure in the MHC class II alpha and beta domains of the clade (series) Eupercaria were compared. Contrary to findings in other vertebrates, both domains exhibited similar levels of selection and should therefore be considered candidate regions for population structure studies in this clade. This thesis demonstrates that the molecular techniques demonstrated supplement, and in some cases improve on, existing monitoring and population assessment techniques and contribute to the sustainable management of fishes in the North Celtic and Irish seas.

Optimisation of molecular tools for monitoring and population assessment of fish species in the North Celtic and Irish seas