Abstract Most male individuals of all species of the genus Scarus which were reversed from females, are called ¡§secondary males¡¨. However, a few individuals of ¡§primary males¡¨ would have male¡¦s reproductive ability, but never process sex reversal in their lifespan, and keeping female¡¦s outlook (initial phase). Because parrotfishes have these two kinds of males existing in the same species, they belong to ¡§diandry¡¨ protogynous hermaphroditisms. Previous studies suggested that the mechanisms that cause primary male might be due to social effect or genetic control. In our experiments, Blue barred parrotfish (Scarus ghobban) and rivulated parrotfish (Scarus rivulatus) were used to study the sex reversal model of parrotfish and the possible reasons that cause the juveniles develop to be primary males. This study including three major parts: (1) the relationship between body size and sexual types of two species. (2) the comparison of the tissue structures of the testes in both male types by histological observation. (3) the possible karyotypes difference, i.e. the genetic differences between primary and secondary male. This study shown that the body size of blue barred parrotfish (initial phase: 100-475 mm; terminal phase: 275-525 mm) were larger than rivulated parrotfish (initial phase: 126-270 mm; terminal phase: 246-350 mm), and there was a wider overlap zone between both color phases in Blue Barred parrotfish (S. ghobban: 47.2%, then S. rivulatus: 10.7%). Histological results showed that no matter primary or secondary males, they all had classical lobular testes. But, by contrast of the pure testis tissue of primary male, there were many mature or atric oocytes that remained in the testis of secondary male. Additionally, a few secondary males of the blue barred parrotfish were discovered whose process of sex reversal occurred earlier or faster than that for normal secondary males. Histological evidence further suggested that these individuals had never had a female reproductive function. Furthermore, these males which had no difference with other secondary males was found on the chromosome level. In our study, a heteromorphic chromosome was observed between primary males and secondary males of the rivulated parrotfish (Scarus rivulatus), which could prove that being a primary male is predetermined by a genetic factor. Based on the ecological interactive diversity of the two species, a preliminary hypothesis was put forth to explain those phenomena. Due to the spawning tactics used, the proportion of primary males in rivulated parrotfish populations is much higher than that in blue-barred parrotfish populations. On the other hand, the appearance of premature males was suggested to be a way of supplying sperm which was lacking in the population of the blue-barred parrotfish.

Knowledge in the spatial patterns of fish larval dispersal is crucial for the establishment of a sustainable management of fisheries and species conservation. Direct quantification of larval dispersal is a challenging task due to the difficulty associated with larval tracking in the vast ocean. However, genetic approaches can be used to estimate it. Here, I employed genetic markers (microsatellites) as a proxy to determine dispersal patterns and self-recruitment levels using parentage analysis in the bumphead parrotfish (Bolbometapon muricatum) in the Solomon Islands. Tissue samples of 3924 fish (1692 juveniles, 1121 males and 1111 females) were collected from a spear-fishery at the Kia District in Santa Isabel Island. The samples come from three distinct zones with different fishing pressure histories (lightly fished, recently fished, and heavily fished). The mean dispersal distance estimated for the bumphead parrotfish was 36.5 Km (range 4 – 78 Km) and the genetic diversity for the population studied was low in comparison with other reef fishes. The parentage analysis identified 68 parent–offspring relationships, which represents a self-recruitment level of almost 50 %. Most of the recruits were produced in the zone that recently started to be fished and most of these recruits dispersed to the heavily fished zone. Comparisons of genetic diversity and relatedness among adults and juveniles suggested the potential occurrence of sweepstakes reproductive success. These results suggest that management measures must be taken straightaway to assure the sustainability of the spear-fishery. These measures may imply the ban on juveniles fishing in the heavily fished zone and the larger adults in the recently fished zone. Overall, the population dynamics of the studied system seem to be strongly shaped by self-recruitment and sweepstakes reproduction events.

Parrotfishes (Scarinae) are dominant Caribbean herbivores that play an important role in reducing coral-algae competition by grazing algae; yet some species are also occasional coral predators (corallivores) and thereby can have direct negative impacts on coral growth and survivorship. There is concern that parrotfish corallivory may contribute to substantial long-term declines in targeted coral species, particularly in areas with a high biomass of parrotfishes and low cover of corals. However, the capacity of target coral species to heal from parrotfish predation and the ecological drivers of corallivory are poorly understood. In Chapter 1, we examined the patterns of coral healing from parrotfish predation scars on Orbicella annularis – an ecologically important framework building coral that is one of the most intensely grazed Caribbean coral species and an endangered species. While some researchers have suggested that parrotfishes may have significant long-term impacts on heavily targeted species such as O. annularis, the patterns of coral recovery from parrotfish predation scars remain poorly understood. To address this knowledge gap, we tracked the fate of parrotfish bite scars on O. annularis colonies across two Caribbean islands for up to two months. We evaluated differences in coral healing between islands in response to a number of variables including the initial scar surface area, scar abundance per coral colony, colony surface area, and water depth. We used these data to develop a predictive model of O. annularis tissue loss from recent parrotfish bite scars. We then applied this model to surveys of the distribution of bite scars at a point in time to estimate long-term tissue loss of O. annularis colonies from a standing stock of bite scars. Our findings suggest that the initial scar surface area is one of the most important predictors of coral tissue loss. The data also indicate that there are thresholds in patterns of coral tissue regeneration: we observed that small scars (≤1.25 cm2) often fully heal, while larger scars (≥8.2 cm2) had minimal tissue regeneration. The vast majority of observed scars (~87%) were 1.25 cm2 or less and our model predicted that O. annularis colonies would regenerate nearly all the corresponding scar area. In contrast, while scars greater than or equal to than 8.2 cm2 were infrequent (~6% of all observed scars), our model predicted that these larger scars would account for over 96% of the total tissue loss for grazed colonies. Overall, our results suggest that the immediate negative impacts of parrotfish predation on coral tissue loss appear to be driven primarily by a few exceptionally large bite scars. While further work is needed to understand the long-term impacts of corallivory and quantify the net impacts of parrotfish herbivory and corallivory on Caribbean coral reefs, this study is an important step in addressing factors that impact the recovery of a heavily targeted and ecologically important Caribbean coral from parrotfish predation. In Chapter 2, we examined the ecological drivers of corallivory across all coral taxa and across three regions of the Greater Caribbean – the Florida Keys, St. Croix, and Bonaire. To do so, we observed how parrotfish grazing intensity varied using both size and abundance-based metrics across multiple spatial scales. At the reef community and regional scale, we found no effect of the biomass of corallivorous parrotfishes or the percent cover of target coral species on the intensity of parrotfish corallivory. However, at the scale of individual coral colonies, we found that coral taxa and colony size were important predictors of corallivory intensity, and that predation intensity increased as colony size increased. Our findings suggest that previous assertions that conservation of corallivorous parrotfishes may have net negative impacts on coral communities, particularly as live coral cover declines, are not supported at the reef-scale. Instead, our research suggests that colony-level traits such as coral taxa and colony size may be stronger drivers of predation intensity. Additionally, our research suggests that parrotfishes do not heavily graze upon the majority of coral species, but have a higher level of grazing intensity on three taxa, Orbicella annularis, Porites astreoides and other Porites spp. across multiple regions of the Caribbean. Therefore, the direct consequences of parrotfish corallivory for coral tissue loss are likely low for the majority of coral species, but further research is needed to better understand the ultimate causes of selective predation and the long-term consequences of corallivory for heavily targeted coral taxa.

Parrotfish are a diverse and ubiquitous group found on coral reefs worldwide. They are categorised into three main feeding modes; the browsers, scrapers and excavators, which together perform a number of important functional roles on coral reefs. Scraper and excavator parrotfish are common on most Indo-Pacific coral reefs where their roles in bioerosion, sediment production, grazing pressure and sediment reworking have been shown to influence benthic community composition, reef growth potential and sediment supply to reef habitats and reef associated sedimentary landforms. However, despite the widely known importance of parrotfish on coral reefs, our understanding of how their roles in carbonate cycling vary among species and among whole parrotfish communities in different reef habitats remains limited. This thesis produces original contributions to knowledge in the areas of species specific bioerosion estimates for the central Indian Ocean, bottom-up controls of habitat type on parrotfish assemblages and how variations in parrotfish assemblages translate to contributions to carbonate cycling processes among different reef habitats. The study was carried out across eight habitats on an atoll-edge reef platform in the central Maldives, where it was found that parrotfish community composition was driven by reef structural complexity and substrate type. Parrotfish occurred in six of the eight habitats, comprising ~44% of the platform area. Among these habitats, overall grazing pressure, bioerosion rates, sediment reworking and sediment production varied markedly. These processes were also found to have different spatial patterns over the reef platform, showing that they are not necessarily tightly coupled. In addition, reef habitats can vary in their importance for both sediment supply, and the relative importance of reworked sediment. Parrotfish produced a wide range of sediment size fractions, from < 32 to 2000 μm and produced predominantly coral sands (>80%) between 125 and 1000 μm in diameter. This is comparable to the grain types found on local reef islands, and it is likely that the most significant supply of this material is from habitats on the atoll-edge side of the platform (which make up ~20% of the total platform area). Quantifying parrotfish functional roles and understanding the drivers behind these processes is important for informing future empirical and modelling studies, particularly as coral reefs undergo a time of dramatic environmental change.

With increasing coastal development along southeastern Florida, nearshore coral reef communities are at an increased risk from anthropogenic impacts. Impact minimization and mitigation efforts associated with permitted coastal construction activities generally exclude nearshore small (< 10 cm diameter) Siderastrea siderea colonies from required coral transplantation due to an assumed high colony mortality associated with transplanting small stony corals. This study evaluated the efficacy of transplanting these small colonies by monitoring survival, growth, and zooxanthellae density post transplantation to an offshore reef area. Unexpected observations of parrotfish predation on the newly transplanted corals were made within the first 24 hours. Within 2 weeks, 94% of the transplants were affected and exhibited recent parrotfish grazing scars. A duplicate transplantation attempt was made at an alternate offshore reef area; however similar results were produced. Due to the high extent of colony tissue loss caused by parrotfish, the initial transplantation effort was repeated with the addition of partial cages to exclude large parrotfish. Zooxanthellae density analysis of the caged colonies revealed an adaptive capability of S. siderea to transplantation as one year post-transplantation, algal densities of the transplanted colonies reflected those of surrounding in situ colonies. A second component of this study investigated if transplantation alone was a direct cause for high predation by examining predation intensity and long-term survival for both transplanted and undisturbed small S. siderea colonies, as well as transplanted Dichocoenia stokesii and Porites porites colonies. Siderastrea siderea colonies were collected from areas surrounding the offshore transplant site and given various stress levels prior to being attached into the transplant grid inter-mixed with colonies transplanted from the shallow nearshore site. All colonies in the transplant grid were placed randomly to eliminate spatial bias. Some nearshore S. siderea transplants were partially caged for 80 days to provide a moderate acclimation period. Many non-caged transplanted colonies suffered some degree of parrotfish predation within 1 week post-transplantation, suggesting that transplantation alone did increase corals susceptibility to predation. However, predation intensity was significantly higher on S. siderea transplanted from nearshore than all in-site transplanted and undisturbed S. siderea colonies from the offshore transplant area. Despite minor parrotfish predation on the offshore in-site transplanted colonies, many displayed long term growth and survival. Partial cages were successful in excluding large parrotfish; however once removed, predation intensity was similar to the non-caged nearshore transplants. Predation on the transplants was selective across both species and place of origin. These results suggest that parrotfish differentiated between transplanted colonies and preferred nearshore S. siderea and P. porites transplants. Findings in this study may aid southeastern Florida resource managers as transplantation activities are frequently utilized due to coastal construction and vessel groundings. The impact of parrotfish corallivory on coral growth and survival should be of higher regard in the light of increasing threats to coral reefs.

The rainbow parrotfish Scarus guacamaia is a prominent herbivore in the coastal waters of southeastern Florida whose life history is strongly linked to a dependence on both mangrove and coral reef habitats. Rainbow parrotfish in turn serve in maintaining the health of coral reefs by keeping algal populations in check. This study used NOAA Fisheries data from the Mangrove Visual Census and the Reef Visual Census in Biscayne Bay and Upper Florida Bay. Observations of abiotic factors at individual sites were used to correlate and predict presence and absence of this species. This was done to visualize habitat presence and ontogenetic shifts present in this species between juvenile and adult stages through ArcGIS mapping. Logistic regression analysis was used to predict presence or absence using the environmental variables of temperature, dissolved oxygen, salinity, average depth, distance from channel openings, mangrove presence, temperature Δ, and salinity Δ. Average depth, distance from channel openings, temperature Δ and salinity Δ were significant in predicting the presence of this species, while salinity, temperature, dissolved oxygen, and mangrove presence were not. Conservation efforts for this species, listed as vulnerable under the IUCN, need to be given greater consideration. The health of this and other parrotfish may have a greater impact on coral reef ecosystems across the Caribbean Sea than currently acknowledged and management breadth and priorities should be adjusted to reflect this role.

Les poissons-perroquets, séparés en deux tribus les Scarini et les Sparisomatini, se sont diversifiés au sein des Labridae à partir d’ancêtres carnivores. L’un des facteurs essentiels pour expliquer cette diversification est leur exploitation d’une nouvelle niche trophique : les microorganismes. La plupart des Sparisomatini paissent des macroalgues pour y extraire les micro-organismes épiphytiques tandis que les poissons-perroquets brouteurs (tous les Scarini, certains Sparisoma) raclent ou creusent le substrat rocheux pour y récolter les microorganismes épilithiques et endolithiques. Ces changements de comportement alimentaire se sont accompagnés de nombreuses évolutions dentaires avec notamment la présence de plaques dentaires chez les brouteurs mais aussi certains paisseurs. Les phylogénies moléculaires ont contredit le précédent scénario évolutif sur la denture des poissons-perroquets qui stipulait l’apparition progressive de plaques dentaires à partir de dentures à dents non recouvertes d’os (dents libre s). Cette thèse se propose de réexaminer l’évolution de la denture chez les poissons -perroquets en se basant sur les progrès phylogénétiques mais aussi techniques (microtomographie 3D), tout en faisant le lien avec leur régime et leur fonction écologique. / Parrotfishes, divided into the tribes Scarini and Sparisomatini , are labrid fishes that arouse from carnivorous ancestors. One of the main factors that explain this radiation is the exploitation of microorganisms as a food source. While most Sparisomatini browse macroalgae to get epiphytic microorganisms, grazing parrotfishes (all Scarini and some Sparisoma) scrap or excavate hard substrate to obtain epilithic and endolithic microorganisms. Changes in feeding behaviour are associated with dentition specialization with notably dental plates in grazing but also some browsing parrotfishes. Gene-based phylogenies contradicted the previous evolutionary scenario about parrotfish dentition evolution, which states the progressive emergence of dental plates from non-coalesced dentitions. This thesis manuscript aims to re-examine the evolution of parrotfish dentitions in the light of the new phylogenies by using X-ray 3D microtomography, and to link this evolution with diet and ecology.

Ultraviolet light is damaging but fish have evolved protective mechanisms, which allows them to live in shallow water reefs, high in UV radiation. This thesis details my investigation into the physiological ecology of solar ultraviolet (UV) absorbing compounds, known as mycosporine-like amino acids found in the external epithelial mucus, and examines the supporting role potentially played by a UV-induced DNA repair mechanism in coral reef fish of the Indo-Pacific. Using reverse phase chromatography and UV spectrophotometry, I examined whether the distribution of MAA compounds across different areas of the body is correlated with differential UV exposure. Comparisons were made between the MAA content and the absorbance spectra of mucus from the dorsal, ventral, caudal and head body surface areas in five species of Scaridae (Chlorurus sordidus, Scarus schlegeli, S. niger, S. psittacus and S. globiceps) from Ningaloo Reef, Coral Bay, Western Australia. All fish analysed had at least five MAAs present, and results showed that fish had increased UV absorbance in mucus over the dorsal area, which receives the brunt of UV radiation. Little UV protection was found in mucus from the ventral area, which receives the lower level of UV radiation mostly via reflection of the sand and reef surfaces. Furthermore, UV absorbance per mg dry mucus versus standard fish length showed that there is a positive relationship in C. sordidus with increasing size. I examined whether there is a difference in the quantity of UV screening compounds found in the mucus of fish along a longitudinal geographical gradient from inshore reefs (Lizard Island, Great Barrier Reef) to the outer edge reefs to oceanic reefs (Osprey Reef). MAA absorbance increased with longitudinal distance from the mainland landmass of Australia to more oligotrophic outer reefs, where UV attenuation is reduced and the ocean is more transparent to UV wavelength. I determined that fish living on inshore, more turbid reefs where UV attenuation in shallow waters is high have lower levels of MAA protection than fish from clear oceanic reefs. Furthermore, there seems to be a direct relationship between light attenuation and exposure with the quantity of protective sunscreening found in the mucus of reef fish. It is know that UV irradiation decreases with water depth and that mucus from fish with deep habitats absorbs less UV than that of fish from shallow habitats. It is unknown however, whether this UV protection is variable within the same individuals and if so, how fast changes 11 occur. To test this, I relocated 9 ambon damselfish from a deep reef (18 m) to a shallow reef (1.5 m) to expose fish to increased levels of UV and relocated another 7 fish from a shallow to a deep reef to expose fish to decreased levels of UV. One week after relocation, all fish were returned to their original reef site to determine whether MAA levels would return to their initial levels. Fish relocated to a shallower depth were recovered and had a 60% (SD+/-2%) increase in mucus UV absorbance. Conversely, the fish relocated to a deeper depth were recovered and had a 41% (SD+/-1%) decrease mucus UV absorbance. No difference was found between UV absorbance of relocated and original fish at both depth. Six days after fish were returned to their original reef, mucus UV absorbance levels had returned to 67% +/- 4% of the original level. These results show that mucus UV absorbance is variable in individual ambon damselfish and that the sunscreen protection typical for a certain depth is reached in relocated fish within just a few days of relocation. The rate of MAA loss is higher than the accumulation of MAAs suggesting that diet is not the sole determining factor involved in the sequestration of MAAs to mucus. The cleaner fish Labroides dimidiatus performs a mutualistic service by removing ectoparasites such as gnathiid isopods as well other dead infected tissue from its clients. Cleaner fish however are also known to feed on client mucus. The benefits of eating mucus until recently were unclear. In this study, we analysed the mucus of several cleaner fish clients to determine whether mucus feeding has a nutritional advantage over gnathiids and whether cleaner fish obtain their own MAA protection through this dietary mucus ingestion. Results show that host fish that are infected with gnathiids of poor nutritional value, in contrast to those that harbour gnathiids with higher nutritional value, continuously exude mucus that has both high nutritional value and high MAA content. These findings support the conclusion that in a competitive market for cleaners some host fish are forced to offer more than parasites to cleaners. Ultraviolet light that is not filtered by UV absorbing compounds such as MAA may still lead to DNA damage such as the formation of cyclobutane pyrimidine dimers (CPDs) or 6-4 photoproducts (6-4 PPs). However, coral reef fish have alternative mechanisms to overcome UV induced damage via the photolyase DNA repair mechanisms. We experimentally demonstrated for the first time that a coral reef fish species, the moon wrasse Thalassoma lunare has the ability to repair DNA damage via photoreactivation. Fish both with and without MAA protection were irradiated with UVB wavelength to induce DNA lesions. Half of the experimental fish were then exposed to photoreactivating wavelength to induce DNA repair 12 while the other fish were blocked from the repair mechanisms. Fish which had undergone DNA repair had the lowest number of lesions regardless of mucus MAA protection. When fish were blocked from photoreactivation wavelengths MAA sunscreens clearly served a photoprotective role. The amount of damage was greatest in fish which both lacked MAAs and which were also blocked from photoreactivating wavelengths. Thus for the overall UV protection of fish both the MAA sunscreens as well as the DNA repair system play a significant role in counteracting UV damage. Ultraviolet protection by MAA sunscreens is ubiquitous in marine fish. To date the same 5 MAA compounds (palythine (λmax 320 nm), asterina (λmax 330 nm), palythinol (λmax 332 nm), usujirene (λmax 357 nm) and palythene (λmax 360nm) have been identified in the mucus of several different species of reef fish from Australia. Here we report the first evidence of the presence of additional UV absorbing compounds found in the mucus of fish from Indonesia. Using UV spectroscopy the mucus of four species of fish was compared between both geographical regions. The presence of an additional peak between 294-296 nm wavelengths suggests the presence of gadusol and/or deoxygadusol, which are photoprotective compounds, thought to be the precursors of MAAs. Thus, UV protecting compounds in the mucus of fish may not be as conserved between different regions as previously assumed. Our knowledge concerning the effect of UV radiation has advanced considerably in the past decade and my research findings contribute to the better understanding of protective mechanisms of marine fish. The correlations I have found between UV attenuation/exposure, depth, and longitude of sampled individuals lead me to believe that mucus UV absorbing MAA compounds are a highly efficient adaptive defence.