| Summary: | With increasing pressures on marine ecosystems and little recovery being observed in commercially important fish, it is essential to understand ecosystem effects on species. Unfortunately, in many cases the habitat requirements of commercially important species are not well understood. Atlantic cod (Gadus morhua), haddock (Melanogrammus aeglefinus) and whiting (Merlangius merlangus) were of commercial importance within the Firth of Clyde, west coast of Scotland prior to the late 20th century. However, over fishing and other anthropogenic impacts led to declines in all three species. Despite the prohibition of targeted fishing for these gadoids in much of the Firth of Clyde, they have still not recovered and scientific bottom trawl surveys have shown that 90% of the biomass is made up of small M. merlangus. With increased concern regarding the state of the world's marine environment, efforts to implement ecosystem based fisheries management and restore ecosystems through spatially explicit management measures have developed. The array of ecosystem based research, management and monitoring initiatives has led to the use of a range of habitat-related terminology with different interpretations of the terms. Inconsistencies in terminology not only cause confusion between studies, but also make it difficult to understand the ecological requirements of fish. The second chapter of this PhD reviews the current terminology and sets the scene for the major habitat-related concepts used throughout the thesis. Photogrammetric techniques were used to collect data on gadoid distribution, abundance and size from June to September in 2013 and 2014. The study site was a recently designated Marine Protected Area (MPA) within the Firth of Clyde, west coast of Scotland. The two photogrammetric techniques used were stereo-video SCUBA transects and Stereo Baited Remote Underwater Video (SBRUV) deployments. 31 SCUBA transects were conducted in 2013 and a total of 258 SBRUV deployments were conducted over the two data collection periods. SBRUV deployments were chosen as the main technique to collect demersal fish and benthos related data due to the ability to collect an increased number of deployments at higher resolution, in addition to avoiding logistical constraints with SCUBA methods. From both SCUBA transects and SBRUV deployments, a higher abundance of G. morhua was observed in gravel-pebble substratum containing maerl and medium density algae, than boulder-cobble substratum with high algal cover or sandy areas with little or no macrophyte cover. A higher relative abundance of G. morhua was also observed in shallow and sheltered environments. Both M. aeglefinus and M. merlangus were observed in higher relative abundance in deeper sand and mud substratum types. All three species were observed in higher relative abundance in areas of increased benthic and demersal species diversity. On average G. morhua were smaller than M. aeglefinus and M. merlangus and exhibited the lowest growth rates. Seabed ground-truthed data from the stereo-video methods in combination with a range of observed environmental variables were used to predict substratum type, distribution and extent within the MPA. The predicted seabed map was used to understand landscape effects on gadoid distribution. G. morhua were observed in more heterogeneous landscapes than M. aeglefinus or M. merlangus. An increase in M. merlangus relative abundance was also observed with increasing substratum extent. The stereo-video photogrammetric methods in combination with the predicted substratum mapping have provided us with a better understanding of gadoid fish habitat requirements. This study has also provided fish and benthos baseline data within the MPA, trialled the use of non-damaging and extractive fisheries independent monitoring methods, and contributed evidence to support potential fisheries management options. The techniques used in this thesis could be rolled out on a larger scale across the UK to support sensitive seabed and fish monitoring and management measures.
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