Restaurant decision-maker perceptions of barriers and opportunities for invasive lionfish consumption

Lionfish (Pterois volitans, Pterois miles), invasive coral reef fishes in the western Atlantic, cause extensive negative impacts to marine ecosystems. Following their introduction in Florida in the 1980’s, lionfish colonized numerous coral reef ecosystems and have been documented at depths ranging from 1-300m. In addition to depleting native reef fish biomass and threatening macroalgae induced phase shifts on shallow reefs, the invasion of lionfish has caused severe economic damage in the form of reduced native fish yields for local fisher people and high costs of management. While few examples exist of successful management of marine invasive species, studies have shown that lionfish removal can decrease their density and increase prey species biomass. A critical component and challenge for any effective lionfish removal effort is to maintain consistently high levels of lionfish harvesting so as to reduce lionfish abundance to levels that mitigate their negative ecological impacts. One popular market-based option that may achieve this is increasing the demand for the consumption of lionfish. This management solution offers potential benefits to both human livelihoods and marine ecosystems. Our study focuses on Florida’s consumptive lionfish market and fills a gap in understanding the lionfish supply chain for Florida’s restaurant industry. Although lionfish are commercially available in Florida, they are not currently widely consumed with consistency. We conducted interviews with twenty restaurant decision-makers in FL to understand their perceptions of barriers and opportunities for increasing their use of invasive lionfish. The most commonly identified barriers were: price and consistency of supply, while the most prominent opportunities were: improved awareness and culinary potential to increase the demand for lionfish. Conservation managers and policymakers should leverage these findings to facilitate opportunities, address barriers, and promote public education about invasive lionfish and their impacts.

CRISPR/Cas9-mediated generation of biallelic F0 anemonefish (Amphiprion ocellaris) mutants

Genomic manipulation is a useful approach for elucidating the molecular pathways underlying aspects of development, physiology, and behaviour. However, a lack of gene-editing tools appropriated for use in reef fishes has meant the genetic underpinnings for many of their unique traits remain to be investigated. One iconic group of reef fishes ideal for applying this technique are anemonefishes (Amphiprioninae) as they are widely studied for their symbiosis with anemones, sequential hermaphroditism, complex social hierarchies, skin pattern development, and vision, and are raised relatively easily in aquaria. In this study, we developed a gene-editing protocol for applying the CRISPR/Cas9 system in the false clown anemonefish, Amphiprion ocellaris. Microinjection of zygotes was used to demonstrate the successful use of our CRISPR/Cas9 approach at two separate target sites: the rhodopsin-like 2B opsin encoding gene (RH2B) involved in vision, and Tyrosinase-producing gene (tyr) involved in the production of melanin. Analysis of the sequenced target gene regions in A. ocellaris embryos showed that uptake was as high as 73.3% of injected embryos. Further analysis of the subcloned mutant gene sequences combined with amplicon shotgun sequencing revealed that our approach had a 75% to 100% efficiency in producing biallelic mutations in F0 A. ocellaris embryos. Moreover, we clearly show a loss-of-function in tyr mutant embryos which exhibited typical hypomelanistic phenotypes. This protocol is intended as a useful starting point to further explore the potential application of CRISPR/Cas9 in A. ocellaris, as a platform for studying gene function in anemonefishes and other reef fishes.

Evaluating the Effects of a Deep-Water Marine Protected Area a Decade After Closure: A Multifaceted Approach Reveals Equivocal Benefits to Reef Fish Populations

Marine protected areas (MPAs) are increasingly used to rebuild fish populations. In 2009, eight MPAs were designated off the southeast United States with the goal of rebuilding populations of long-lived deep-water reef fishes. We tested whether reef fish within the largest of these MPAs, the Snowy Wreck Marine Protected Area (SWMPA), have increased in size and abundance relative to a nearby control area and compared to pre-closure. Hurdle models fitted through Bayesian inference on echosounder data collected in 2007–2009 and 2018–2020 yielded no evidence of an MPA effect. Comparisons of catch-per-unit-effort (CPUE) of all reef fishes yielded similar null results. However, CPUE of reef species with formal stock assessments increased 47% in the SWMPA and decreased 50% in the control area. We found significant increases in mean length of red porgy (Pagrus pagrus) inside the SWMPA but not in the control area. We also found community composition changes, including shifts away from groupers (Serranidae; Epinephelinae) and toward snappers (Lutjanidae) and tilefish (Malacanthidae) in both areas, though we did not detect an MPA effect with this analysis. Our equivocal results indicate that more time and stricter enforcement may be necessary before more biological effects of the SWMPA can be detected.

The alternative splicing landscape of a coral reef fish during a marine heatwave

Alternative splicing is a molecular mechanism that enables a single gene to encode multiple transcripts and proteins by post-transcriptional modification of pre-RNA molecules. Changes in the splicing scheme of genes can lead to modifications of the transcriptome and the proteome. This mechanism can enable organisms to respond to environmental fluctuations. In this study, we investigated patterns of alternative splicing in the liver of the coral reef fish Acanthochromis polyacanthus in response to the 2016 marine heatwave on the Great Barrier Reef. The differentially spliced (DS; n=40) genes during the onset of the heatwave (i.e. 29.49°C or +1°C from average) were related to essential cellular functions such as the MAPK signaling system, Ca(2+) binding and homeostasis. With the persistence of the heatwave for a period of one month (February to March), 21 DS genes were detected, suggesting that acute warming during the onset of the heatwave is more influential on alternative splicing than the continued exposure to elevated temperatures. After the heatwave, the water temperature cooled to ~24.96°C, and fish showed differential splicing of genes related to cyto-protection and post-damage recovery (n=26). Two-thirds of the DS genes detected across the heatwave were also differentially expressed, revealing that the two molecular mechanisms act together in A. polyacanthus to cope with the acute thermal change. This study exemplifies how splicing patterns of a coral reef fish can be modified by marine heatwaves. Alternative splicing could therefore be a potential mechanism to adjust cellular physiological states under thermal stress and aid coral reef fishes in their response to more frequent acute thermal fluctuations in upcoming decades.

An Evaluation of Prior Residency and Habitat Effects on the Persistence of Settling Reef Fishes

<p>Both habitat complexity and competitive interactions can shape patterns of distribution and abundance of species. I evaluated the separate and joint effects of competitive interactions and habitat complexity on the survival of young fishes (Family Labridae) on coral reefs. First, I developed (in Chapter 2) a quantitative approach to evaluate potential resource (i.e., niche) overlap among groups of co-occurring species. Using appropriate transformations and probability models, I show that different types of data (e.g., categorical, continuous, count or binary data, as well as electivity scores) give rise to a standard measure of niche overlap, with the overlap statistic between two species defined as the overlapping area between the distributions for each species. Measurements derived from different types of data can be combined into a single multivariate analysis of niche overlap by averaging over multiple axes. I then describe null model permutation tests that differentiate between species occupying similar and different niches within my unified indices. I then implemented this approach (in Chapter 3) to evaluate potential habitat overlap among eight species of wrasse (Gomphosus varius, Halichoeres hortulanus, H. trimaculatus, Pseudocheilinus hexataenia, Scarus sordidus, Stethojulis bandanensis, Thalassoma hardwicke and T. quinquevittatum), and used these results to inform my subsequent field experiments. In a field assay, I identified the presence of T. quinquevittatum as having the greatest negative effect on survival of transplanted T. hardwicke from a suite of three candidate species which were most similar in habitat use to T. hardwicke (the other two candidate species were G. varius and P. hexataenia). In a subsequent field experiment, I tested how competition with T. quinquevittatum and structural refuge interact to influence the postsettlement survival of T. hardwicke. Competition with T. quinquevittatum and structural refuge both altered the survival of T. hardwicke, although their effects were not interactive, indicating that structural complexity did not mitigate the negative effects of competition. Survival of T. hardwicke was 2.3 times greater in treatments without T. quinquevittatum relative to those with T. quinquevittatum, and 2.8 times greater in treatments with structural refuge relative to treatments without structural refuge. Thalassoma hardwicke and T. quinquevittatum often enter reef communities asynchronously, resulting in competitive pressures faced by earlyarriving individuals that potentially differ from those experienced by late-arriving individuals. In a series of field experiments, I investigated whether the strength of intra-cohort competitive interactions between recent T. hardwicke and T. quinquevittatum settlers were dependent upon the sequence and temporal separation of their arrival into communities. Survival rates for both species were greatest in the absence of competitors, but when competitors were present, survival rates were maximized when competitors arrived simultaneously. Survival rates declined as each species entered the community progressively later than its competitor. Further, reversals in the sequence of arrival reversed competitive outcomes. Results provide empirical evidence for competitive lotteries in the maintenance of species diversity in demographically open marine systems, while also highlighting the importance of temporal variation in the direction and magnitude of interaction strengths. To further our understanding of how timing of arrival influences interaction strengths, I tested whether increasing the availability of complex habitat attenuates or enhances timing-of-arrival effects. Results from this field experiment indicated that aggression by early-arriving individuals towards late-arriving individuals increased as arrival times diverged. When aggression was weak, subordinate individuals were not displaced from complex habitat. Experimental increases in the availability of complex habitat resulted in increased survival of subordinates, presumably by disrupting predation pressure. However, when aggression was intense, competitive subordinates were displaced from complex habitat (regardless of the amount of complex habitat available), and this likely increased their exposure to predators. Overall, the experimental and observational components of this thesis emphasise heterogeneity in competitive environments experienced by recently settled reef fishes. These results highlight the important role that priority effects and habitat complexity play in determining the persistence of reef fish settlers, and illustrate how ecological contexts can add considerable variation to realised interaction strengths.</p>

An Evaluation of Prior Residency and Habitat Effects on the Persistence of Settling Reef Fishes

<p>Both habitat complexity and competitive interactions can shape patterns of distribution and abundance of species. I evaluated the separate and joint effects of competitive interactions and habitat complexity on the survival of young fishes (Family Labridae) on coral reefs. First, I developed (in Chapter 2) a quantitative approach to evaluate potential resource (i.e., niche) overlap among groups of co-occurring species. Using appropriate transformations and probability models, I show that different types of data (e.g., categorical, continuous, count or binary data, as well as electivity scores) give rise to a standard measure of niche overlap, with the overlap statistic between two species defined as the overlapping area between the distributions for each species. Measurements derived from different types of data can be combined into a single multivariate analysis of niche overlap by averaging over multiple axes. I then describe null model permutation tests that differentiate between species occupying similar and different niches within my unified indices. I then implemented this approach (in Chapter 3) to evaluate potential habitat overlap among eight species of wrasse (Gomphosus varius, Halichoeres hortulanus, H. trimaculatus, Pseudocheilinus hexataenia, Scarus sordidus, Stethojulis bandanensis, Thalassoma hardwicke and T. quinquevittatum), and used these results to inform my subsequent field experiments. In a field assay, I identified the presence of T. quinquevittatum as having the greatest negative effect on survival of transplanted T. hardwicke from a suite of three candidate species which were most similar in habitat use to T. hardwicke (the other two candidate species were G. varius and P. hexataenia). In a subsequent field experiment, I tested how competition with T. quinquevittatum and structural refuge interact to influence the postsettlement survival of T. hardwicke. Competition with T. quinquevittatum and structural refuge both altered the survival of T. hardwicke, although their effects were not interactive, indicating that structural complexity did not mitigate the negative effects of competition. Survival of T. hardwicke was 2.3 times greater in treatments without T. quinquevittatum relative to those with T. quinquevittatum, and 2.8 times greater in treatments with structural refuge relative to treatments without structural refuge. Thalassoma hardwicke and T. quinquevittatum often enter reef communities asynchronously, resulting in competitive pressures faced by earlyarriving individuals that potentially differ from those experienced by late-arriving individuals. In a series of field experiments, I investigated whether the strength of intra-cohort competitive interactions between recent T. hardwicke and T. quinquevittatum settlers were dependent upon the sequence and temporal separation of their arrival into communities. Survival rates for both species were greatest in the absence of competitors, but when competitors were present, survival rates were maximized when competitors arrived simultaneously. Survival rates declined as each species entered the community progressively later than its competitor. Further, reversals in the sequence of arrival reversed competitive outcomes. Results provide empirical evidence for competitive lotteries in the maintenance of species diversity in demographically open marine systems, while also highlighting the importance of temporal variation in the direction and magnitude of interaction strengths. To further our understanding of how timing of arrival influences interaction strengths, I tested whether increasing the availability of complex habitat attenuates or enhances timing-of-arrival effects. Results from this field experiment indicated that aggression by early-arriving individuals towards late-arriving individuals increased as arrival times diverged. When aggression was weak, subordinate individuals were not displaced from complex habitat. Experimental increases in the availability of complex habitat resulted in increased survival of subordinates, presumably by disrupting predation pressure. However, when aggression was intense, competitive subordinates were displaced from complex habitat (regardless of the amount of complex habitat available), and this likely increased their exposure to predators. Overall, the experimental and observational components of this thesis emphasise heterogeneity in competitive environments experienced by recently settled reef fishes. These results highlight the important role that priority effects and habitat complexity play in determining the persistence of reef fish settlers, and illustrate how ecological contexts can add considerable variation to realised interaction strengths.</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>

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>

The U.S. South Atlantic Region

This chapter describes the South Atlantic region and the major issues facing this marine fisheries ecosystem, and presents some summary statistics related to the 90 indicators of ecosystem-based fisheries management (EBFM) criteria. The South Atlantic contains the third-highest number of managed taxa of the eight regional U.S. marine ecosystems, including commercially and recreationally important reef fishes (snappers and groupers), penaeid shrimps, coastal migratory pelagic fishes (cobia, mackerels, dolphin/wahoo), and coral reef resources. The South Atlantic is a species-rich environment subject to several major stressors that include habitat loss, sea-level rise, ocean acidification, and intermittent high category hurricanes with increasing frequency over the past decades, along with the consequences of overfishing that continue to affect LMRs in this region. Overall, EBFM progress has been made in terms of implementing ecosystem-level planning, advancing knowledge of ecosystem principles, and in assessing risks and vulnerabilities to ecosystems through ongoing investigations into climate vulnerability and species prioritizations for stock and habitat assessments. Although the South Atlantic is progressing toward EBFM, little overall progress has been observed toward applying ecosystem-level emergent properties into management frameworks. While the South Atlantic is advancing in terms of its LMR management priorities and ecosystem efforts, some challenges remain to effectively implement formalized EBFM planning. Limited information regarding the status and biomass of fishery stocks and protected species in this region, and data gaps for many environmental factors have constrained EBFM implementation and prevented the application of ecosystem-level properties into management actions.

Molecular Investigation of Recurrent Streptococcus iniae Epizootics Affecting Coral Reef Fish on an Oceanic Island Suggests at Least Two Distinct Emergence Events

Streptococcus iniae is an emerging zoonotic pathogen of increasing concern for aquaculture and has caused several epizootics in reef fishes from the Caribbean, the Red Sea and the Indian Ocean. To study the population structure, introduction pathways and evolution of S. iniae over recurring epizootics on Reunion Island, we developed and validated a Multi Locus Sequence Typing (MLST) panel using genomic data obtained from 89 isolates sampled during epizootics occurring over the past 40years in Australia, Asia, the United States, Israel and Reunion Island. We selected eight housekeeping loci, which resulted in the greatest variation across the main S. iniae phylogenetic clades highlighted by the whole genomic dataset. We then applied the developed MLST to investigate the origin of S. iniae responsible for four epizootics on Reunion Island, first in inland aquaculture and then on the reefs from 1996 to 2014. Results suggest at least two independent S. iniae emergence events occurred on the island. Molecular data support that the first epizootic resulted from an introduction, with inland freshwater aquaculture facilities acting as a stepping-stone. Such an event may have been facilitated by the ecological flexibility of S. iniae, able to survive in both fresh and marine waters and the ability of the pathogen to infect multiple host species. By contrast, the second epizootic was associated with a distinct ST of cosmopolitan distribution that may have emerged as a result of environment disturbance. This novel tool will be effective at investigating recurrent epizootics occurring within a given environment or country that is despite the fact that S. iniae appears to have low genetic diversity within its lineage.