The phylogeny of Eumalacostraca (Crustacea) has remained elusive, despite over a century of morphological and more recently molecular studies. Prior to this, no large scale combined evidence analyses of all eumalacostracan orders has been carried out. Evidence from four nuclear ribosomal and mitochondrial loci (18S rRNA, 28S rRNA, 16S rRNA, and cytochrome c oxidase subunit I) were combined with a newly synthesized morphological dataset to examine the utility of available data. With an aim to resolve conflict in the morphological dataset, fossils were added to the morphological dataset and their effects examined. The stratigraphic congruence of crustaceans was examined to determine the quality of existing trees. A modified protocol was developed to generate new molecular markers for the investigation of eumalacostracan phylogeny. Finally the effects of the new data on existing datasets were examined in a combined evidence approach. Significant conflict was detected between data partitions, especially between morphology and molecules. The addition of fossil data revealed the morphological dataset to be very sensitive to taxon sampling. Stratigraphic congruence was found to be poor for the five crustacean groups examined. Histone 3 and alanyl-tRNA synthetase were shown to be capable of successfully recovering relationships at the level of genus and above. Glutamyl-prolyl-tRNA synthetase failed to recover monophyletic groupings when analysed alone. Combining all molecular data produced well-supported phylogenies, but significant conflict between data partitions was identified and trees were very sensitive to taxon sampling. Rate heterogeneity and conflict between data partitions mean that the total sum of molecular and morphological evidence as presented here is currently unable to resolve a wellsupported eumalacostracan phylogeny. We recommend additional taxon sampling and further sampling of novel markers using the modified protocol developed here as well as the addition of fossil data and the exploitation of next generation sequencing technologies.

Molecular ecology is one of the most important branches of evolutionary biology, and it uses the advantages of molecular techniques such as PCR-RFLP, sequencing, microsatellite analysis, and most recently the introduction of next generation sequencing, to address outstanding issues in the fields of population genetics and phylogeny. The genomic approach has been influential in providing new information relevant to traditional questions in ecology, such as genetic differentiation, speciation, species adaptation and others. The rationale of the present thesis was to incorporate the advantages of both the PCR-RFLP and sequencing techniques to gain information on the genetic variability of two commercially-important crustacean species, namely the Norway lobster Nephrops norvegicus and the giant freshwater prawn Macrobrachium rosenbergii. Nephrops norvegicus exhibits large morphological variability even between adjacent populations. The first objective of this thesis was to investigate the genetic variability of N. norvegicus from three localities, the Clyde Sea area and North Minch (North Sea) as well as Icelandic waters. The phylogeographic study found no significant differentiation between populations from the studied areas (FST: 0.01819). This finding is consistent with outcomes from previous studies that N. norvegicus populations were not geographically structured. Outcomes from the present study strongly suggest that environmental factors, rather than genetic factors, are more likely to play a more significant role in the high morphological differentiation observed in this species. A study of the most important freshwater crustacean species, Macrobrachium rosenbergii was then undertaken as a contribution to understanding the most complex biogeography in the world, the Indo Australian Archipelago (IAA). The IAA has incredible species richness and endemism and is the location of 4 out of 25 world’s biodiversity hotspots, namely the Sundaland, the Philippines, Indonesia and Wallacea. Within the IAA is the location of Wallace’s line and Huxley’s line, the most abrupt faunal transition in the world that lies between the Sunda and Sahul shelves. The studied species used in the present thesis, M. rosenbergii is an ideal model species as it has a wide geographical distribution across the IAA. The present phylogeographic study screened the COI segment using the sequencing technique to study M. rosenbergii populations collected from eight locations in Malaysia in the peninsular and east of Malaysia. These populations exhibited high genetic differentiation (FST: 0.62503) mainly due to the sample from Sabah. However, the adjacent population (Sarawak) was similar to that in Peninsular Malaysia, even though Northern Sarawak showed sub-population differentiation from the main cluster (cluster I) indicating that the genetic diversity of Northern Sarawak was more restricted. Beside, cluster II observed in the study indicated and confirmed the recent aquaculture activities of restocking the Kedah, Perak and Sarawak populations. Knowledge of the levels of genetic differentiation in N. norvegicus and M. rosenbergii could assist in the management of the species. N. norvegicus could be managed as one stock and conservation and recovery programme could be carried out based on the knowledge that all studied populations exhibited lack genetic differentiation within and between populations. In contrast, M. rosenbergii that possessed high level of genetic differentiation have to be managed separately, especially for a unique population such as the one in Sabah. The outcomes of this study could also be useful for future research in the conservation of wild population, as well as aquaculture management and product improvement purposes. The finding of Sabah as a unique population could potentially be useful for aquaculture improvement programmes. One of the most important aspects is to see whether Sabah population possessed high resistant to the disease infection. A preliminary study was conducted to investigate the susceptibility of a Malaysian wild population of M. rosenbergii to infection by the human food-poisoning bacterium V. parahaemolyticus. Nonetheless, the virulence stage of the bacterial strain, the status of the immune system of the host, the size and age of the experimental animals as well as the dose of injected bacteria might all have contributed to the inconclusiveness of the results. However, the principle of screening wild populations for disease resistance is sound, and may lead to improvements in the quality of the broodstock used in the Malaysian aquaculture industry.

The studies presented in this thesis were designed to investigate the effects of reduced sea water pH on the behaviour of intertidal decapod crustaceans, both within the context of the variations occurring naturally in the pH of rock pool habitats, and in relation to predicted changes to ocean pH resulting from ocean acidification and potential carbon dioxide (CO2) leaks from carbon capture storage (CCS) sites. Recent studies on marine fish have shown behavioural disruptions as a result of increased CO2 concentrations in sea water and reduced pH, but the effects on crustaceans are as yet unknown. The first two studies investigated the effects of reduced pH upon the olfactory behaviour of the prawn Palaemon elegans and the hermit crab Pagurus bernhardus, focussing on their responses to food odours. Short-term (five day) exposures to highly reduced pH (pHNBS = 6.60, 6.80) revealed disruptions to the chemo-sensory behaviour of both species with a reduction in their ‘sniffing’ response, and the inability of P. bernhardus to locate the chemical cue. This was also accompanied by elevated haemolymph chloride ions. in In a further study P. bernhardus was subjected to a longer exposure (60 days) and to a range of pH levels (pHNBS = 8.00, 7.90, 7.70, 7.35 and 6.80) in order to detect a threshold for the behavioural disruptions observed, and to determine if there would be any sign of acclimation over a longer period. A clear gradient in the disruptions to the chemo-sensory responses and survival rates of the hermit crabs, and disruption to a physiological marker (elevated haemolymph calcium ions), was found. Possible thresholds for disruption were also identified at levels that match predictions for ocean acidification and leaks from proposed CO2 CCS sites. Some of the crabs in the lower pH treatments exhibited a recovery in their responses by day 60, possibly indicating an acclimation effect. The presence of disruption to haemolymph ion concentrations in both the short and longer term hermit crab studies suggest a mechanism for behavioural disruption. In a final study the effects of reduced sea water pH on a more complex behaviour, involving decision making, was investigated. Reduced sea water pH was shown to disrupt the shell assessment and selection behaviour of P. bernhardus affecting its decision making processes, although not all crabs were affected in the same way. The work presented here therefore demonstrates that reduced sea water pH could have disruptive effects upon both information gathering, via chemo-sensory processes, and decision making in intertidal crustaceans. The mechanism responsible is unlikely to be due to changes in the odour molecule, or physical damage to receptor organs. Rather the observed disruptions could be due (a) to ionic changes, causing metabolic depression or interference with neurotransmitter function, or (b) to disruption to chemoreception per se. Such disturbances to key behavioural processes have implications for inter and intraspecific species interactions and population dynamics in the marine environment. Changes in pH are already experienced by intertidal animals for short periods when rock pools are emersed, but future anthropogencially-induced reductions in sea water pH are likely to cause more sustained and widespread disruptions with, as yet, unpredictable consequences. The differential responses observed between individuals in these studies may warrant further investigation as such differences may provide the basis for selection and adaptation to projected changes in ocean pH.