Correct species identification is fundamental to all areas of biology, but particularly the policy related areas of conservation and fisheries management. To enable guidelines to be developed for environmental management and conservation, such identifications need links to studies of the evolutionary history, biological factors and environmental influences driving species divergence and population dynamics for the target species. This study concerns two genera of gadiform fish, Muraenolepis and Macrourus, found in southern temperate and Antarctic waters, with a single species, Macrourus berglax, present in the North Atlantic. With similar distribution patterns to toothfish species, Dissostichus eleginoides and D. mawsoni, they are a major food source and by-catch of the toothfish fishery. Both are slow growing and long lived, with different evolutionary histories, life expectancies and strategies for reproduction. For both genera, the accuracy of morphological keys, number of described species and their distribution is under debate. This study has identified specimens to species level using both morphological and genetic techniques, redefining the range for morphological features and taxonomic keys. For Muraenolepis, this has clarified confusion over Mu. marmoratus and Mu. microps being a single species, confirmed some mis-identification from sexual dimorphism and provided genetic evidence for the recently described species Mu. evseenkoi. For Macrourus, this work has identified a new species, now named Ma. caml, and found that Ma. holotrachys and Ma. berglax are genetically identical, raising the question of bipolar distribution or recent divergence. The low level of genetic variation within both species suggests a recent evolution and expansion into Antarctic waters. Similar geographic species limits imply common processes influencing divergence, with the oceanographic fronts as potential barriers. Further investigation of niche overlap and fine scale population structure are required to fully understand the processes driving speciation and provide the underlying data required for fisheries management.

Marked shifts in the life history traits of fish have been reported in many exploited fish stocks, with a particular trend towards decreasing size and age at maturity. Though other environmental and behavioural factors have been implicated, the key driver of these changes links to fishing pressure, through both the direct selective effects of fishing itself, and indirectly through the manipulation of important biological and environmental factors. Although reproduction itself has been well described in teleosts, the mechanisms of environmental and endogenous entrainment of maturation remain unclear and it was the principal aim of this thesis to improve current understanding of these systems in gadoids. Photoperiod has been identified as the strongest environmental cue for entraining seasonal behaviours, including seasonal reproduction. Over the last decade, several of the key drivers involved in the photoneuroendocrine cascade have been elucidated in mammals and birds, with the Eya3 pathway merging as an important mechanism for entraining maturation. However, little is yet known of their influence on maturation in fish. In the first study, the photoperiodic regulation of the Eya3-Tshβ-Dio2 cascade was analysed in Atlantic cod exposed to either continuous light (reproductive inhibition) or simulated natural photoperiod (reproductive stimulation) from July to December. Monthly expression was measured through QPCR, demonstrating a strong activation of pituitary Eya3 under declining photoperiod. As this coincided with the onset of secondary gametogenesis, these results suggest that Eya3 may play a stimulatory role in the photoneuroendocrine cascade of Atlantic cod. Although photoperiod represents the most reliable and noise free proximate signal to entrain the reproductive process, it is clear that a minimum growth and energetic state must be reached for maturation to progress. This directed the second line of study – a series of diet restriction trials on haddock and cod designed to investigate the influence of naturally occurring lipid levels in the diet on growth and reproduction, define the “critical window” in which fish assess their energetic state and how this is analysed before commencing secondary gametogenesis, and to assess whether Eya3 is regulated by the growth axis in cod. The results of these experiments indicate that overall size around the autumn equinox is the most accurate indicator of maturation commitment in cod. Additionally, Eya3 expression was elevated in maturing fish indicating a role for this marker in linking the energetic signal with entrainment of the reproductive axis. Finally, an analysis of the physiological and genetic stock structure of cod from the North Sea IVa stock region and westward into VIa was performed. The results of this analysis support previous genetic studies, indicating further fine-scale structuring of these stocks, reflective of the structure indicate by the differences in maturation strategies of the component populations. The results identified both environmental and harvest related pressures which may be driving the current stock structure. The results of these studies greatly improves our understanding of the key drivers and mechanisms regulating maturation in cod, highlighting new avenues for future research.