Underwater Photogrammetry Captures the Initial Recovery of a Coral Reef at Lalo Atoll

Recovery of coral reefs after physical damage sustained from storm events can be affected by various factors. Here, we examined the initial recovery of a coral reef at the southern end of uninhabited Lalo Atoll of Papahānaumokuākea Marine National Monument after its complete destruction by Hurricane Walaka in 2018. While the site was still mostly (98%) covered by a mixture of rubble and sand, surveys utilizing underwater photogrammetry allowed for detailed quantitative assessments of benthic cover and confirmed colonization of coral (Pocillopora meandrina and Porites lobata), macroalgae and sponges. The proportion of sand in the rubble–sand mixture also decreased from the level observed in 2019. Visual fish surveys confirmed the presence of 35 reef fish species, a large increase from no reef fish in 2019, despite the low biotic benthic cover. Overall, the colonization of benthic organisms and the return of reef fish, which is potentially supported by the benthos and cryptofauna in the rubble bed, offer positive signs of reef recovery. The photogrammetric surveys in the present study captured the subtle changes in the benthic cover and provided us with a procedure to continue monitoring the succession of the site. Continuous monitoring of the site should reveal whether the reef returns to the original state of Acropora coral dominance or progresses towards a coral assemblage with a different composition.

Quantifying Mesophotic Fish Assemblages of Hawai‘i’s Au‘au Channel: Associations With Benthic Habitats and Depth

Mesophotic reefs (30–150 m) occur in the tropics and subtropics at depths beyond most scientific diving, thereby making conventional surveys challenging. Towed cameras, submersibles, and mixed-gas divers were used to survey the mesophotic reef fish assemblages and benthic substrates of the Au‘au Channel, between the Hawaiian Islands of Maui and Lāna‘i. Non-parametric multivariate analysis: Non-metric Multidimensional Scaling (NMDS), Hierarchical Cluster Analysis (HCA), Multi-Response Permutation Procedure (MRPP), and Indicator Species Analysis (ISA) were used to determine the association of mesophotic reef fish species with benthic substrates and depth. Between 53 and 115-m depths, 82 species and 10 genera of fish were observed together with 10 types of benthic substrate. Eight species of fish (Apolemichthys arcuatus, Centropyge potteri, Chaetodon kleinii, Chromis leucura, Chromis verater, Forcipiger sp., Naso hexacanthus, and Parupeneus multifasciatus) were positively associated with increasing depth, Leptoseris sp. coral cover, and hard-bottom cover, and one species (Oxycheilinus bimaculatus) of fish was positively associated with increasing Halimeda sp. algae cover. Fish assemblages associated with rubble were not significantly different from those associated with sand, Montipora coral beds and Leptoseris coral beds, but were distinct from fish assemblages associated with hard bottom. The patterns in the data suggested two depth assemblages, one “upper mesophotic” between 53 and 95 m and the other deeper, possibly part of a “lower mesophotic” assemblage between 96 and 115 m at the edge of the rariphotic and bottomfish complex.

Reproductive timing and investment decisions of a protogynous hermaphroditic coral reef fish species

<p>Life-history theory suggests that an organism must balance its available energy between two competing physiological processes to maximize fitness: reproduction and somatic growth. Energetic trade-offs are a fundamental concept of life history theory and form the basis of intra- and inter-specific variation in life-history strategies. In fishes, reproduction-growth trade-offs are an essential component of life-history optimization. This is particularly true for species with protogynous sex- change (the most common reproductive mode among coral reef fish species), where reproductive success rapidly and disproportionally increases with body size/ corresponding social status. In such systems, lifetime fitness is inherently linked to patterns of growth and energy allocation strategies determined by an individual’s size-specific rank within the dominance hierarchy. However, energy allocation strategies in a protogynous species may not only be a function of body size. Coral reef fish species are exposed to extremely variable environmental conditions and this can favour the evolution of strategies that utilize good times and avoid disadvantageous times for reproduction. Consequently, size- specific parental investment decisions may vary greatly in time and space according to environmental cues. My thesis focuses on the protogynous reef fish, Thalassoma hardwicke (the sixbar wrasse), which is extremely abundant on shallow coral reefs throughout the Indo-Pacific region. Specifically, I evaluate patterns of spawning and reproductive investment as a function of body size, social status, lunar phase and other environmental parameters. I address the question of whether females/males of differing size make different fitness-related decisions when away from spawning sites, and I evaluate context-dependency in these decisions. Finally, I will attempt to reconstruct the developmental histories (e.g., larval growth rates) of individuals from otoliths to evaluate potential relationships between developmental histories and fitness attributes.</p>

Reproductive timing and investment decisions of a protogynous hermaphroditic coral reef fish species

<p>Life-history theory suggests that an organism must balance its available energy between two competing physiological processes to maximize fitness: reproduction and somatic growth. Energetic trade-offs are a fundamental concept of life history theory and form the basis of intra- and inter-specific variation in life-history strategies. In fishes, reproduction-growth trade-offs are an essential component of life-history optimization. This is particularly true for species with protogynous sex- change (the most common reproductive mode among coral reef fish species), where reproductive success rapidly and disproportionally increases with body size/ corresponding social status. In such systems, lifetime fitness is inherently linked to patterns of growth and energy allocation strategies determined by an individual’s size-specific rank within the dominance hierarchy. However, energy allocation strategies in a protogynous species may not only be a function of body size. Coral reef fish species are exposed to extremely variable environmental conditions and this can favour the evolution of strategies that utilize good times and avoid disadvantageous times for reproduction. Consequently, size- specific parental investment decisions may vary greatly in time and space according to environmental cues. My thesis focuses on the protogynous reef fish, Thalassoma hardwicke (the sixbar wrasse), which is extremely abundant on shallow coral reefs throughout the Indo-Pacific region. Specifically, I evaluate patterns of spawning and reproductive investment as a function of body size, social status, lunar phase and other environmental parameters. I address the question of whether females/males of differing size make different fitness-related decisions when away from spawning sites, and I evaluate context-dependency in these decisions. Finally, I will attempt to reconstruct the developmental histories (e.g., larval growth rates) of individuals from otoliths to evaluate potential relationships between developmental histories and fitness attributes.</p>

Hidden Giants: The Story of Bolbometopon muricatum at Ningaloo Reef

Bolbometopon muricatum (bumphead parrotfish, Valenciennes, 1839) is a conspicuous, iconic and ecologically important coral reef fish species. B. muricatum plays an important role in the bioerosion of the reef framework and as a result has been described as both an ecosystem engineer and keystone species. Despite the complete absence of B. muricatum from 32 years of scientific surveys across the Ningaloo Reef World Heritage Area, we recorded a total of 155 individuals of B. muricatum across 63.2 ha of reef crest surveys, equating to mean density of 2.38 ind/ha. Our observations represent the first record of this iconic species in scientific surveys at Ningaloo and in combination with qualitative observations of B. muricatum by expert witnesses, indicate B. muricatum is likely to have been present in ecologically relevant densities since 2006. The densities of B. muricatum observed at northern Ningaloo in 2021 suggest this species is removing an estimated 13.42 tonnes/ha or 1.34 kg/m2 of calcium carbonate per year, which is broadly comparable with estimates of total parrotfish bioerosion across many reefs in the central Indian and Pacific Oceans. Although not currently afforded elevated conservation status within management plans, B. muricatum possess many life-history characteristics that make them vulnerable to overfishing and may justify consideration for increased protection within the world heritage listed Ningaloo Reef Marine Park.

Enhancing reef fish diversity using artificial reef-building: A case study of coral reef rehabilitation on Nyamuk Island, Anambas Islands

CCMRS-IPB conducted coral reef rehabilitation at damaged coral reefs around Nyamuk Island. Those artificial reef buildings for rehabilitation gave shelter spaces for reef fish. This research aims to calculate the effect of coral reef-building, which enhances rugosity to the reef fish diversity around the rehabilitation sites. The study was conducted on Nyamuk Island in the Anambas Islands. Reef fish were sampled annually from 2014 to 2019 using the underwater visual census. The Diversity index and non-Metric Multidimensional Scaling were built to discover reef fish diversity, and reef fish species were affected the most. Yearly data shows an escalation number of reef fish abundance and richness at the end of 2019. The major reef fish group is found to have constant diversity throughout the year compared to other functional groups. The target reef fish group came to this rehabilitation ecosystem primarily attracted by nourishment availability. There is a shift in the reef fish diversity from the early year to the project end. Generally, major reef fish groups will be refuged first around the rehabilitation sites, especially territorial types. Target fish groups from herbivorous and carnivorous types will mostly come along after their food availability and location to get around.

Effects of Macroalgal Habitats on the Community and Population Structure of Temperate Reef Fishes

<p>Two families of brown macroalgae that occur in sympatry dominate temperate subtidal rocky coasts: the Laminareales, and the Fucales. Both of these families are habitat-forming species for a wide variety of invertebrates and fishes. Variation in the presence, density, and composition of brown macroalgae can have large influences on the evolution and ecology of associated organisms. Here, using a series of observational and experimental studies, I evaluated the effects of heterogeneity in the composition of brown macroalgal stands at the population and community levels for reef fishes. A central ecological challenge is the description of patterns that occur at local scales, and how these are manifested at larger ones. I conducted further sampling across a set of sites nested within locations over three regions, Juan Fernandez Islands (Chile), Northern New Zealand, and Tasmania (Australia), to evaluate patterns of variation in the diversity and composition of fish assemblages. Specifically, I explored spatial variation in fish assemblages as a function of rocky reef habitats (dominated by brown-macroalgae) and other sources of variation (abiotic and biotic factors) that potentially mediate the relationship between fishes and reef habitats. Analyses suggest that spatial variation in diversity (e.g., species and trophic) may be explained by spatial variation in depth, temperature, and composition of macroalgal habitats. At each location, only 2-3 families dominated the composition of fish assemblages, but species identities varied among locations. In a subsequent study, I assessed the fish-habitat associations from sites within the Juan Fernandez Islands, an isolated eastern Pacific Island that lack large brown macroalgae. I found that, despite the close proximity of these Islands to the South American continent, fish assemblages were mostly composed of endemic representatives from families that dominate the fish assemblages in New Zealand and Australia. Spatial variation in depth and temperature did not contribute to the observed variation in fish abundance. Instead, I found that benthic habitat-forming species (particularly foliose brown macroalgae) appeared to limit the abundance of some reef fishes. These results suggest that a mixture of large-scale (e.g., stochastic recruitment) and small-scale processes (i.e., relating to habitat heterogeneity) influence the diversity, composition and abundance of fish assemblages. Subsequently, I evaluated relationships between reef fishes and macroalgae composition across multiple sites, surveyed repeatedly over four seasons. I found that fishes were associated with different components of heterogeneity in macroalgal habitats, potentially indicating interspecific partitioning of resources that may arise from differential feeding habits and sizesusceptibility to predation. Seasonal variation in the fish-habitat associations was detected, and site differences in macroalgal composition explained significant variation in the local diversity of fishes. Using a series of small-scale lab and field-based manipulative experiments, I determined the demographic and behavioural responses of reefassociated fishes to heterogeneity in the composition of brown macroalgal habitats. I found that (i) different fish species distinguished between monospecific macroalgae stands (macroalgal identity affected the abundance of 7 of 15 reef fish species); (ii) there is within-species variation in the response of fishes to macroalgal composition (suggesting ontogenetic habitat shifts); and (iii) the abundance of 5 of 7 reef fish species, and the overall structure of the local fish assemblage, varied with the composition of mixed-species macroalgal stands. Lastly, I evaluated the potential for fishes to provision demographic feedbacks to macroalgae. Specifically, I conducted a mesocosm experiment to evaluate the effects of fishes on grazing amphipods, and therefore, the potential indirect-effects of fishes on large-brown macroalgae. I found that only one of the two fish species studied reduced grazer abundance. Although the second fish species did not consume grazing amphipods, its presence altered amphipod behaviour to significantly reduce grazing efficiency on the macroalgal-host. This study illustrates how density and trait-mediated indirect interactions can have similar effects on primary producers. Overall, my observational and experimental components of this thesis emphasize the influence of heterogeneity in macroalgal structures on the breadth of habitat use for reef fishes at multiple locations. I found strong behaviourally mediated linkages between the abundance of reef fishes and composition of macroalgal stand. I also provide some evidence that mutualistic relationships may exist between kelp and associated fishes.</p>

Effects of Macroalgal Habitats on the Community and Population Structure of Temperate Reef Fishes

<p>Two families of brown macroalgae that occur in sympatry dominate temperate subtidal rocky coasts: the Laminareales, and the Fucales. Both of these families are habitat-forming species for a wide variety of invertebrates and fishes. Variation in the presence, density, and composition of brown macroalgae can have large influences on the evolution and ecology of associated organisms. Here, using a series of observational and experimental studies, I evaluated the effects of heterogeneity in the composition of brown macroalgal stands at the population and community levels for reef fishes. A central ecological challenge is the description of patterns that occur at local scales, and how these are manifested at larger ones. I conducted further sampling across a set of sites nested within locations over three regions, Juan Fernandez Islands (Chile), Northern New Zealand, and Tasmania (Australia), to evaluate patterns of variation in the diversity and composition of fish assemblages. Specifically, I explored spatial variation in fish assemblages as a function of rocky reef habitats (dominated by brown-macroalgae) and other sources of variation (abiotic and biotic factors) that potentially mediate the relationship between fishes and reef habitats. Analyses suggest that spatial variation in diversity (e.g., species and trophic) may be explained by spatial variation in depth, temperature, and composition of macroalgal habitats. At each location, only 2-3 families dominated the composition of fish assemblages, but species identities varied among locations. In a subsequent study, I assessed the fish-habitat associations from sites within the Juan Fernandez Islands, an isolated eastern Pacific Island that lack large brown macroalgae. I found that, despite the close proximity of these Islands to the South American continent, fish assemblages were mostly composed of endemic representatives from families that dominate the fish assemblages in New Zealand and Australia. Spatial variation in depth and temperature did not contribute to the observed variation in fish abundance. Instead, I found that benthic habitat-forming species (particularly foliose brown macroalgae) appeared to limit the abundance of some reef fishes. These results suggest that a mixture of large-scale (e.g., stochastic recruitment) and small-scale processes (i.e., relating to habitat heterogeneity) influence the diversity, composition and abundance of fish assemblages. Subsequently, I evaluated relationships between reef fishes and macroalgae composition across multiple sites, surveyed repeatedly over four seasons. I found that fishes were associated with different components of heterogeneity in macroalgal habitats, potentially indicating interspecific partitioning of resources that may arise from differential feeding habits and sizesusceptibility to predation. Seasonal variation in the fish-habitat associations was detected, and site differences in macroalgal composition explained significant variation in the local diversity of fishes. Using a series of small-scale lab and field-based manipulative experiments, I determined the demographic and behavioural responses of reefassociated fishes to heterogeneity in the composition of brown macroalgal habitats. I found that (i) different fish species distinguished between monospecific macroalgae stands (macroalgal identity affected the abundance of 7 of 15 reef fish species); (ii) there is within-species variation in the response of fishes to macroalgal composition (suggesting ontogenetic habitat shifts); and (iii) the abundance of 5 of 7 reef fish species, and the overall structure of the local fish assemblage, varied with the composition of mixed-species macroalgal stands. Lastly, I evaluated the potential for fishes to provision demographic feedbacks to macroalgae. Specifically, I conducted a mesocosm experiment to evaluate the effects of fishes on grazing amphipods, and therefore, the potential indirect-effects of fishes on large-brown macroalgae. I found that only one of the two fish species studied reduced grazer abundance. Although the second fish species did not consume grazing amphipods, its presence altered amphipod behaviour to significantly reduce grazing efficiency on the macroalgal-host. This study illustrates how density and trait-mediated indirect interactions can have similar effects on primary producers. Overall, my observational and experimental components of this thesis emphasize the influence of heterogeneity in macroalgal structures on the breadth of habitat use for reef fishes at multiple locations. I found strong behaviourally mediated linkages between the abundance of reef fishes and composition of macroalgal stand. I also provide some evidence that mutualistic relationships may exist between kelp and associated fishes.</p>

Species ecology explains the spatial components of genetic diversity in tropical reef fishes

Generating genomic data for 19 tropical reef fish species of the Western Indian Ocean, we investigate how species ecology influences genetic diversity patterns from local to regional scales. We distinguish between the α , β and γ components of genetic diversity, which we subsequently link to six ecological traits. We find that the α and γ components of genetic diversity are strongly correlated so that species with a high total regional genetic diversity display systematically high local diversity. The α and γ diversity components are negatively associated with species abundance recorded using underwater visual surveys and positively associated with body size. Pelagic larval duration is found to be negatively related to genetic β diversity supporting its role as a dispersal trait in marine fishes. Deviation from the neutral theory of molecular evolution motivates further effort to understand the processes shaping genetic diversity and ultimately the diversification of the exceptional diversity of tropical reef fishes.