Data used to develop 3D models of coral reefs using structure-from-motion photogrammetry. The data used to generate photogrammetry models are pictures of the reef from ~1 m above the substratum and coordinates of ground control points for each of twelve distinct ~20 m x 10 m reef areas. The photogrammetry workflow to create the digital models included photo alignment, followed by geometry building, and lastly texture building using Agisoft Pro. Additionally included are the orthomosaics and digital elevation models derived from the 3D models and training data used to build a classification algorithm to classify reef vs sand benthic types using the site orthomosaics. Finally, the location and sizes of mixed shoals of Coryphopterus personatus and Coryphopterus hyalinus are included. All data were collected from Turneffe Atoll (17.3638° N, 87.8581° W), Belize in January 2017. These data are used in conjunction to develop a habitat usage model to understand what features of coral reefs are correlated with the distribution of C. personatus/hyalinus. All code associated with the analysis can be found here: https://github.com/jdselwyn/Habitat_Usage.

Introduced Indo-Pacific red lionfish (Pterois volitans/miles) have spread throughout the greater Caribbean and are associated with a number of negative impacts on reef ecosystems. Human interventions, in the form of culling activities, are becoming common to reduce their numbers and mitigate the negative effects associated with the invasion. However, marine managers must often decide how to best allocate limited resources. Previous work has identified the population size thresholds needed to limit the negative impacts of lionfish. Here we develop a framework that allows managers to predict the removal effort required to achieve specific targets (represented as the percent of lionfish remaining on the reef). We found an important trade-off between time spent removing and achieving an increasingly smaller lionfish density. The model used in our suggested framework requires relatively little data to parameterize, allowing its use with already existing data, permitting managers to tailor their culling strategy to maximize efficiency and rate of success.

In 2007, due to growing concerns of declines in nearshore fisheries in Hawai'i, a ban on gillnets was implemented in designated areas around the island of O'ahu in the main Hawaiian Islands. Utilizing a 17 year time-series of juvenile fish abundance beginning prior to the implementation of the gillnet ban, we examined the effects of the ban on the abundance of juveniles of soft-bottom associated fish species. Using a Before-After-Control-Impact (BACI) sampling design, we compared the abundance of targeted fishery species in a bay where gillnet fishing was banned (Kailua, O'ahu), and an adjacent bay where fishing is still permitted (Waimānalo, O'ahu). Our results show that when multiple juvenile fish species were combined, abundance declined over time in both locations, but the pattern varied for each of the four species groups examined. Bonefishes were the only species group with a significant BACI effect, with higher abundance in Kailua in the period after the gillnet ban. This study addressed a need for scientific assessment of a fisheries regulation that is rarely possible due to lack of quality data before enactment of such restrictions. Thus, we developed a baseline status of juveniles of an important fishery species, and found effects of a fishery management regulation in Hawai'i.

The regionally endemic Galapagos Grouper, locally known as bacalao, is one of the most highly prized finfish species within the Galapagos Marine Reserve (GMR). Concerns of overfishing, coupled with a lack of fishing regulations aimed at this species raises concerns about the current population health. We assessed changes in population health over a 30-year period using three simple indicators: (1) percentage of fish below reproductive size (Lm); (2) percentage of fish within the optimum length interval (Lopt); and (3) percentage of mega-spawners in the catch. Over the assessed period, none of the indicators reached values associated with healthy populations, with all indicators declining over time. Furthermore, the most recent landings data show that the vast majority of the bacalao caught (95.7%,) were below Lm, the number of fish within the Lopt interval was extremely low (4.7%), and there were virtually no mega-spawners (0.2%). Bacalao fully recruit to the fishery 15 cm below the size at which 50% of the population matures. The Spawning Potential Ratio is currently 5% of potential unfished fecundity, strongly suggesting severe overfishing. Our results suggest the need for bacalao-specific management regulations that should include minimum (65 cm TL) and maximum (78 cm TL) landing sizes, slot limits (64-78 cm TL), as well as a closed season during spawning from October to January. It is recognized that these regulations are harsh and will certainly have negative impacts on the livelihoods of fishers in the short term, however, continued inaction will likely result in a collapse of this economically and culturally valuable species. Alternative sources of income should be developed in parallel with the establishment of fishing regulations to limit the socio-economic disruption to the fishing community during the transition to a more sustainable management regime.

In this paper we report the result of an independent baseline fishery survey conducted in the islands of Old Providence and Santa Catalina, Colombia, in 2014, with the objective of characterising spatially explicit abundance and distribution of the sea cucumber communities. We included local artisanal fishers in the planning and data collection parts of this survey. Our results showed very limited diversity of sea cucumbers, with Holothuria mexicana being the most abundant. There were higher densities of H. mexicana in the sand and rubble habitat than in the seagrass and bioturbated areas. We found aggregation sites for sea cucumbers where density was an order of magnitude higher; this habitat was a narrow band between seagrass and sand and rubble. Total population size was considered too low to sustain a fishery, and mariculture experiments with sea cucumbers in the region should carefully consider the number of organisms taken when establishing breeding protocols.

The Galapagos Sailfin grouper,Mycteroperca olfax, locally known as bacalao and listed as vulnerable by the IUCN, is culturally, economically, and ecologically important to the Galapagos archipelago and its people. It is regionally endemic to the Eastern Tropical Pacific, and, while an important fishery resource that has shown substantial declines in recent years, to date no effective management regulations are in place to ensure the sustainability of the Galapagos fishery for this species. Previous estimates of longevity and size at maturity for bacalao are inconsistent with estimates for congeners, which brings into question the accuracy of prior estimates. We set out to assess the age, growth, and reproductive biology of bacalao in order to provide more accurate life history information to inform more effective fisheries management for this species. The oldest fish in our sample was 21 years old, which is 2–3 times greater than previously reported estimates of longevity. Parameter estimates for the von Bertalanffy growth function (k= 0.11,L∞= 110 cm TL, andto= − 1.7 years) show bacalao to grow much slower and attain substantially larger asymptotic maximum length than previous studies. Mean size at maturity (as female) was estimated at 65.3 cm TL, corresponding to a mean age of 6.5 years. We found that sex ratios were extremely female biased (0.009 M:1F), with a large majority of the individuals in our experimental catch being immature (79%). Our results show that bacalao grow slower, live longer, and mature at a much larger size and greater age than previously thought, with very few mature males in the population. These findings have important implications for the fishery of this valuable species and provide the impetus for a long-overdue species management plan to ensure its long-term sustainability.

Fisheries bycatch is a significant marine conservation issue as valuable fish are wasted and protected species harmed with potential negative ecological and socio-economic consequences. Even though there are indications that the small-scale handline fishery of the Galapagos Marine Reserve has a low selectivity, information on its bycatch has never been published. We used onboard monitoring and interview data to assess the bycatch of the Galapagos handline fishery by estimating the bycatch ratio, determining species compositions of landings and bycatch, identifying fishers' reasons for discarding certain individuals, and revealing historical trends in the bycatch ratio. The estimated bycatch ratio as a function of biomass of 0.40 and a diverse species composition of target catch and bycatch confirmed the low selectivity of this fishery. Most individuals were not landed for economic motivations, either because species (77.4%) or sizes (17.7%) are unmarketable or for regulatory reasons (5.9%). We found that bycatch contributes to growth overfishing of some target species because they are discarded or used as bait before reaching their first maturity. Moreover, over half of interviewees perceived a historical decrease in bycatch ratios that was explained by a diversification of the target catch due to the reduction in abundance of the traditionally most important target species. As some target species show signs of overfishing and to date there are no specific regulations for the finfish fishery species in place, we recommend the implementation of a series of management measures to protect critical life stages of overexploited species and to improve the selectivity of the Galapagos handline fishery.

The Galapagos Sailfin grouper, Mycteroperca olfax, locally known as bacalao and listed as vulnerable by IUCN, is culturally, economically, and ecologically important to the Galapagos archipelago and its people. It is regionally endemic to the Eastern Tropical Pacific, and, while an important fishery resource that has shown substantial declines in recent years, to date no effective management regulations are in place to ensure the sustainability of its Galapagos fishery. Previous estimates of longevity and size of maturity for bacalao are inconsistent with estimates for congeners, which questions the accuracy of prior estimates. We set out to rigorously assess the age, growth, and reproductive biology of bacalao in order to provide more accurate life history information to inform more effective fisheries management for this species. The oldest fish in our sample was 24 years old, which is 2-3 times greater than previously reported estimates of longevity. Parameter estimates for the von Bertalanffy growth function (k= 0.07, L∞= 119.1 cm TL, and to= -2.33 years) show bacalao to grow much slower and obtain substantially larger asymptotic maximum length than previous studies. Mean size at maturity (as female) was estimated at 61.1 cm TL, corresponding to an age of 7.8 years. As a protogynous hermaphrodite, size at sex change (from adult female to adult male) occurred at 83.7 cm TL, corresponding to 15.2 years of age. We found that sex ratios were extremely female biased (0.015 M:1F), with a large majority of the individuals in our experimental catch being immature (73%). Our results show that bacalao grow slower, live longer, and mature at a much larger size and greater age than previously thought, with very few mature males in the population. These findings have key implications for the fishery of this valuable species and urge for a long-due species management plan to ensure its long-term sustainability.

For coastal fishing communities, it is becoming increasingly clear that the key to success is community-based comanagement, which incorporates all users and stakeholders in the decision-making processes about fisheries management. Established regulations can easily fail due to lack of enforcement. However, many coastal communities do not have the economic resources for the necessary enforcement and therefore rely on compliance by fishers. There are about 400 local fishers in the Galapagos Marine Reserve (GMR), who depend on the exploitation of coastal resources for their living. Evidence shows that the GMR suffers from lack of compliance; coastal resources have been overexploited and illegal fishing has been observed. The results of interviewing 26 % of Galapagos' active fishers show no trust in scientific studies, lack of income alternatives provided, no dissemination of results, and lack of participation of fishers in the studies. We argue that the abovementioned problems can be tackled by using a collaborative approach, which includes fishing community members in each step of the research process. This would foster a sense of belonging among the Galapagos fishers, who are currently an underrepresented part of the already-established comanagement scheme, which has yet to achieve sustainable fisheries in the Galapagos Islands.

Ongoing greenhouse gas emissions can modify climate processes and induce shifts in ocean temperature, pH, oxygen concentration, and productivity, which in turn could alter biological and social systems. Here, we provide a synoptic global assessment of the simultaneous changes in future ocean biogeochemical variables over marine biota and their broader implications for people. We analyzed modern Earth System Models forced by greenhouse gas concentration pathways until 2100 and showed that the entire world's ocean surface will be simultaneously impacted by varying intensities of ocean warming, acidification, oxygen depletion, or shortfalls in productivity. In contrast, only a small fraction of the world's ocean surface, mostly in polar regions, will experience increased oxygenation and productivity, while almost nowhere will there be ocean cooling or pH elevation. We compiled the global distribution of 32 marine habitats and biodiversity hotspots and found that they would all experience simultaneous exposure to changes in multiple biogeochemical variables. This superposition highlights the high risk for synergistic ecosystem responses, the suite of physiological adaptations needed to cope with future climate change, and the potential for reorganization of global biodiversity patterns. If co-occurring biogeochemical changes influence the delivery of ocean goods and services, then they could also have a considerable effect on human welfare. Approximately 470 to 870 million of the poorest people in the world rely heavily on the ocean for food, jobs, and revenues and live in countries that will be most affected by simultaneous changes in ocean biogeochemistry. These results highlight the high risk of degradation of marine ecosystems and associated human hardship expected in a future following current trends in anthropogenic greenhouse gas emissions.

Breakwaters and related structures dominate near-shore environments in many Persian Gulf countries, but little is known of their ecology. To examine the influence of wave exposure on fish communities we surveyed exposed and sheltered breakwaters seasonally over 2 years and compared these with natural reef assemblages. Species richness and adult, juvenile, and total abundance were generally comparable among the three habitat types each season. However, differences in multivariate community structure indicated that each habitat contained a distinct assemblage, with strongest difference between sheltered breakwaters and the exposed natural reef. All communities were characterized by marked seasonality; abundance and richness were generally higher in the warmer seasons (summer, fall) than during cooler periods (winter, spring), and there were related seasonal changes in community structure, particularly on the natural reef. Results indicate that breakwaters are important fish habitats, but that breakwater communities vary with wave exposure and are distinct from natural reefs.

This study provides the first large-scale comparison of reef-associated fish communities in the northeastern Arabian Peninsula, with 24 sites spanning >3000 km of coastline in the southern Persian Gulf, the western Gulf of Oman, and the northwestern Arabian Sea, each with its own unique environmental conditions. Multivariate analyses revealed three distinct community types that were represented mainly by sites within each major water body, with >70% dissimilarity in community structure between each. Persian Gulf communities had low species richness, abundance, and biomass of reef fish compared with the other subregions, with communities dominated by herbivores and generalist predators that had little association with live coral. Reef fish biomass in the Gulf of Oman and Arabian Sea was comparable, and communities were dominated by fish with moderate coral association. However, there were relatively more herbivores and larger fish in the Arabian Sea than in the Gulf of Oman, where communities were dominated by planktivores. Species richness was highest in the Arabian Sea when differences in abundance among regions were accounted for. The influence of distinct environmental and oceanographic conditions on reef fish community structure in each of these areas is discussed.

Difficulties in scaling up theoretical and experimental results have raised controversy over the consequences of biodiversity loss for the functioning of natural ecosystems. Using a global survey of reef fish assemblages, we show that in contrast to previous theoretical and experimental studies, ecosystem functioning (as measured by standing biomass) scales in a non-saturating manner with biodiversity (as measured by species and functional richness) in this ecosystem. Our field study also shows a significant and negative interaction between human population density and biodiversity on ecosystem functioning (i.e., for the same human density there were larger reductions in standing biomass at more diverse reefs). Human effects were found to be related to fishing, coastal development, and land use stressors, and currently affect over 75% of the world's coral reefs. Our results indicate that the consequences of biodiversity loss in coral reefs have been considerably underestimated based on existing knowledge and that reef fish assemblages, particularly the most diverse, are greatly vulnerable to the expansion and intensity of anthropogenic stressors in coastal areas.

The Persian Gulf is a semi-enclosed marine system surrounded by eight countries, many of which are experiencing substantial development. It is also a major center for the oil industry. The increasing array of anthropogenic disturbances may have substantial negative impacts on marine ecosystems, but this has received little attention until recently. We review the available literature on the Gulf's marine environment and detail our recent experience in the United Arab Emirates (U.A.E.) to evaluate the role of anthropogenic disturbance in this marine ecosystem. Extensive coastal development may now be the single most important anthropogenic stressor. We offer suggestions for how to build awareness of environmental risks of current practices, enhance regional capacity for coastal management, and build cooperative management of this important, shared marine system. An excellent opportunity exists for one or more of the bordering countries to initiate a bold and effective, long-term, international collaboration in environmental management for the Gulf.

Palm Jumeirah is the most completely developed of several man-made coastal island megaconstructions in Dubai, United Arab Emirates. The palm-shaped island, surrounded by an elliptical breakwater, was developed 7 y ago, has an overall footprint of 23 km(2), of which the constructed island surface area is 7.9 km(2), and is connected to shore via a 5-km-long spine from the mainland to the crescent tip. Time-series observations of hydrographic variables and currents within the interior of the development (Palm Jumeirah Lagoon) during 30 d in April May 2008 were utilized to examine current flow, tide variability, water budget, vertical mixing, and turnover time within this megastructure. Currents within Palm Jumeirah Lagoon varied between stations; however, similar water temperatures and salinities were apparent throughout all the stations. Palm Jumeirah Lagoon tides were mixed and mainly semidiurnal, with spring and neap tidal ranges measuring 116 and 56 cm, respectively, and no difference in amplitude or phase throughout Palm Jumeirah Lagoon. There were substantial differences in water discharge between the east and west entrances, with high discharge on average exiting the eastern entrance and low discharge exiting the western entrance. These results indicate that the eastern and western halves of Palm Jumeirah Lagoon are flushed unequally and show differences in residence times (1.2 and 42 d, respectively), due to differences in tidal currents, wind influence, and variability of the bathymetric contour. Previous numerical modeling studies of water residence time within Palm Jumeirah Lagoon did not capture this difference, which could be associated with the exclusion of bathymetric variability in the previous modeling. Due to the strong shear and weak saline stratification, the water column throughout Palm Jumeirah Lagoon remained instable, with vertical mixing present during the spring-neap tidal cycle and well-mixed conditions predominating throughout the lagoon system.

To examine the role of climatic extremes in structuring reef fish communities in the Arabian region, reef fish communities were visually surveyed at four sites within the southern Persian Gulf (also known as the Arabian Gulf and The Gulf), where sea-surface temperatures are extreme (range: 12-35° C annually), and these were compared with communities at four latitudinally similar sites in the biogeographically connected Gulf of Oman, where conditions are more moderate (range: 22-31° C annually). Although sites were relatively similar in the cover and composition of coral communities, substantial differences in the structure and composition of associated fish assemblages were apparent. Fish assemblages in the southern Persian Gulf held significantly lower estimates of abundance, richness and biomass, with significantly higher abundances of smaller sized individuals than Gulf of Oman assemblages. Functionally, southern Persian Gulf sites held significantly lower abundances of nearly all the common fish trophic guilds found on Gulf of Oman sites, although higher abundances of herbivorous grazers were apparent. These results suggest the potential for substantial changes in the structure of reef-associated fish communities, independent of changes in habitat within an environment of increasing fluctuations in oceanic climate.

Tropical harmful algal blooms (HABs) are increasing in frequency and intensity and are substantially affecting marine communities. In October/November 2008 a large-scale HAB event (> 500 km(2), dinoflagellate Cochlodinium polykrikoides) in the Gulf of Oman caused the complete loss of the branching corals, Pocillopora and Acropora spp., and substantial reductions in the abundance, richness and trophic diversity of the associated coral reef fish communities. Although the causative agents of this C. polykrikoides bloom are unknown, increased coastal enrichment, natural oceanographic mechanisms, and the recent expansion of this species within ballast water discharge are expected to be the main agents. With rapid changes in oceanic climate, enhanced coastal eutrophication and increased global distribution of HAB species within ballast water, large-scale HAB events are predicted to increase dramatically in both intensity and distribution and can be expected to have increasingly negative effects on coral reef communities globally.