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Parrotfishes contribute to more than 80% of the biomass of herbivorous fishes in the Caribbean and they have been the dominant grazers on reefs since 1983. Maintaining healthy parrotfish populations is essential to help conserve benthic habitat cover which is suitable for the settlement and growth of reef building corals. However, the key environmental factors that currently affect local parrotfish abundance and population structure are scarcely known. Many reef studies are constrained to a limited geographical scale which may not be applicable at larger spatial scales. Parrotfish data across the wider Caribbean will help to overcome such issues. This study investigates three relationships including parrotfish density and benthic habitat variables (Chapter 2); parrotfish density and fishing pressure (fisher density, human population, MPA protection) (Chapter 3); and parrotfish size at sex change and fishing pressure (Chapter 4). Fish and benthic habitat surveys at 7 to 15 sites were conducted in each of eight Caribbean countries including Antigua, Bonaire, Barbados, Curaçao, Dominican Republic, Jamaica, St. Lucia, and St. Vincent and the Grenadines. Parrotfish abundance was positively correlated with coral cover and negatively correlated with macroalgal cover. Parrotfish abundance had a significant correlation with reef complexity (Chapter 2). Different sizes of parrotfish were associated with different habitats (Chapter 2). Fishing is likely to have reduced fish numerical abundance and biomass even at Caribbean scale (Chapter 3). While parrotfish biomass was significantly higher within MPAs, parrotfish numerical density was not significantly different (Chapter 3). The density of terminal parrotfish was significantly different (Chapter 4). Furthermore, fishing pressure was significantly correlated with the size at which phase change between initial and terminal phases occurs (Chapter 4). This research demonstrates the major drivers of Caribbean parrotfish abundance and biomass which may help inform management of parrotfish and promote further coral reef ecosystem recovery.

Members of the annual killifish genus Austrolebias live in temporary ponds across South America and possess a remarkable life cycle. These fish live in small ponds that dry out completely; killing the adults but not before they have laid eggs in the substrate of their pond. The desiccation-resistant eggs develop during the dry season, going through multiple stages of diapause until the next wet season rains trigger hatching and the cycle is repeated. There is considerable variation in size in Austrolebias, the largest species can reach up to 150mm in length while the typical size is just 40mm. Phylogenetic trees and species distribution models were built and used together to identify the factors that influence patterns of co-occurrence within this genus. Differences in growth and morphology among Austrolebias species were examined to quantify how differences in growth pattern can lead to the large variation in size and shape seen within the genus. Genomic data was generated for hybrid offspring of two species of Austrolebias using double-digest RAD sequencing. These data were then used to build linkage maps that were in turn used to identify any regions associated with sex determination and potential chromosomal rearrangements. At a broader scale, a generic-level tree for the order Cyprinodontiformes was constructed. Austrolebias is a member of this order, as well as many model fish genera such as Fundulus, Nothobranchius and Poecilia. Two extraordinary reproductive life-history adaptations have evolved in this order; viviparity and annualism. The new tree was used to determine whether the evolution of viviparity or annualism lead to increased rates of diversification. Finally this generic-level tree was used to examine patterns of positive selection in the low-light vision gene, rhodopsin and whether sites under selection were linked to functional changes.

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No description available.

Organ morphogenesis depends on the precise orchestration of cell migration, cell fate specification and cell shape chages. Results in this thesis demonstrate that Notch signaling is an integral part of the feedback loop between Wnt and Fgf signaling that underlies the self‐organization of rosette‐shaped sensory organs in the zebrafish lateral line system. Notch cell autonomously induces apical constriction and cell adhesion downstream of Fgf signaling and organizes lateral line organs into rosettes independent of patterning cues normally provided by a Wnt/Fgf signaling system. We also show that the ectopic Notch signaling induces larger organs independently of proliferation and the Hippo pathway. Transplantation and RNASeq analyses revealed that Notch signaling induces cell adhesion and tight junction proteins that interact with cytoskeleton causing cells to self‐organize into fewer larger organs rather than several smaller ones. Thus, Notch plays an essential role in coordinating actomyosin induced cell shape changes and their transmission throughout the tissue via adhesion molecules.

In this study, the impact of anthropogenic in-stream structures on migration and dispersal of a variety of fish species was investigated. The effectiveness of attempted restoration of longitudinal connectivity in fragmented stream and river systems, through implementation of various fish pass designs, both technical and nature oriented, was evaluated for fish of varying age classes. The outcomes of this research are of importance for river management schemes that aim to restore degraded freshwater systems bound by legislation from the EU Water Framework Directive, which requires good connectivity and habitat quality within freshwater systems. Fish community composition in relation to effects of in-stream structures and habitat conditions was investigated on three degraded stream networks, so that future opportunities for longitudinal connectivity restoration could be identified. Differences in fish community composition above and below common types of structures were determined, whereby species richness and density per species showed greatest differences for flow manipulating culvert structures, especially pipe culverts. Obstacle effects on fish dispersal and migration, and the effectiveness of connectivity restoration - obstacle removal and design of various types of fish passes - on those same obstacles were evaluated using a variety of approaches. These included capture-mark-recapture of different life stages of a weak swimmer (European bullhead Cottus perifretum) and of a strong swimmer (brown trout Salmo trutta) tagged with passive integrated transponder (PIT) and/or visible implant elastomer (VIE), displacement studies of juvenile trout and radio telemetry of adult freshwater-resident and sea-going morphotypes of brown trout. Longitudinal connectivity for fish was shown to have improved post-restoration, exemplified by improved fish passage over the multiple structures in both directions, while permeability of unrestored structures remained low. The efficacy of a technical Larinier super active baffle fish pass, a widespread design in Europe, was assessed for upstream-migrating adult river lamprey. Situated next to a common Crump weir, the pass was designed to facilitate passage for a wide range of fish species. Over two migration seasons, with a variety of flow levels occurring in both, the pass was tested for efficacy before and after modification with studded tiles mounted on the inside wall. By using fixed PIT arrays, poor passage through the fish pass by river lamprey was shown before modification, and improved marginally post-modification. Acoustic telemetry identified direct passage over the weir to be two-fold higher than through the modified fish pass. In the context of the Water Framework Directive, there is a strong need to develop well-grounded fish passage criteria, not only for fish species with strong swimming capacity, but for a wide range of fish species and life stages. Ideally, all types of fishways should be critically assessed, in situ, to allow river managers to make more informed decisions on restoring fragmented stream systems.

Firstly I investigated the use of asocial and social information use; the potential for inexpensively acquiring information about prey resources is one advantage of social foraging. Threespine sticklebacks (Gasterosteus aculeatus) assimilated and used private information about prey distribution between different social information cues, and when these conflicted with their private information, they based their foraging decisions upon the former, suggesting that there are costs associated with non-conformist foraging behaviour. Secondly, I investigated prey competition, a major cost associated with social foraging. I found that increasing group stability, and by inference familiarity, led to a decrease in the rate of kleptoparasitic prey competition within shoals when they were foraging for dispersed prey. When prey were concentrated however there was no effect of group stability upon prey competition level. Prey competition was less intense between familiar individuals that were embedded in unfamiliar shoals than it was between these and their unfamiliar shoal mates. Finally I investigated the role of individual behavioural variation in relation to social information use and prey competition. Boldness across a number of contexts was seen to correlate with individual competitive ability, predicting the outcomes of both inter- and intra-specific prey competition interactions. Interestingly, the use of public information, a risk-averse strategy consistent with the shy behavioural phenotype, was not seen to be related to individual boldness. The broader significance of the findings of this thesis is considered in the context of previous research, and directions for future work are identified and discussed.

In Britain two species of stickleback, the threespine and the ninespine are often found living side-by-side in freshwater streams. The two stickleback species share a close life-history and in particular similar dietary habits. The situation of two such ecologically similar species being able to co-exist without high levels of competition removing one or the other from the habitat begs us to question exactly what ecological process is allowing this situation to occur. Three separate populations of stickleback were observed in the study; a population of allopatric threespine sticklebacks, a ninespine population and a population of threespines that live sympatrically with ninespine fish. Morphological analysis of the three populations of sticklebacks revealed divergence amongst the sympatric threespine fish. The sympatric threespine fish were shown to have a deep mid-body depth and deeper caudal peduncle, which possibly serve to increase the fish's body acceleratory skills. In addition the sympatric threespines have a small conical shaped mouth and meristic analysis indicates an increase in the number of the fish's gill rakers. Combination of these adaptations indicates that the sympatric threespine fish are effective zooplanktivores. It was questioned whether character displacement initiated by competition from the ninespine fish in the sympatric threespines environment is the process responsible for driving the observed divergence. In turn each of the criteria of the character displacement hypothesis was tested. Investigation of the allopatric and sympatric environment indicated little difference between the sites other than the presence of the ninespine fish in the sympatric sites. Stomach contents analysis showed that the sympatric fish have increased their consumption of zooplankton. Behavioural analysis showed how the morphological adaptations have improved the sympatric fish's foraging performance in the limnetic habitat.

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