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The Galápagos Archipelago is home to a diverse range of marine bioregions due to the confluence of several cold and warm water currents, resulting in some of the most productive tropical marine ecosystems in the world. These ecosystems are strongly influenced by El Niño events which can reduce primary production by an order of magnitude, dramatically reducing energy available throughout the food web. Fisheries are an important component of the local economy, although artisanal and illegal overfishing have dramatically reduced the productivity of invertebrate and finfish resources in recent decades, resulting in reductions in catches for local fishers. The regionally-endemic sailfin grouper (Myctereoperca olfax), locally known as bacalao, was once the most important fished species in the Galápagos, but is now listed as vulnerable by the IUCN due to its limited range and dramatic declines in catch over time. It is unknown how reduction of this predatory species has affected ecosystem structure and function. In the absence of stock assessments, we used an estimate of unfished bacalao biomass from fishers’ ecological knowledge along with unfished biomass estimates of other heavily exploited stocks—lobster (Panulirus penicillatus and P. gracilis) and sea cucumber (Isostichopus fuscus)—to create historical, unfished versions of existing modern day ecosystem models. We used the unfished and modern versions of the ecosystem models to test the ecosystem effects of bacalao exploitation at the Bolivar Channel, located in the cold, west upwelling bioregion of the archipelago during both El Niño and non El Niño years, and at Floreana Island, in the warmer, central bioregion. Fishers’ ecological knowledge indicates that at present, the biomass of bacalao is at least seven times lower than when unfished. This reduced bacalao biomass is linked with a greatly reduced ecosystem role compared to when unfished, and ecosystem role is further reduced in El Niño years. Allowing bacalao populations to rebuild to at least half of unfished biomass would partially restore their role within these ecosystems, while also resulting in greater fisheries catches. Comparing ecosystem impacts caused by fishing and El Niño, fishing has had a greater negative impact on bacalao ecosystem role than regular El Niño events.

Coral reefs are important habitats that represent global marine biodiversity hotspots and provide important benefits to people in many tropical regions. However, coral reefs are becoming increasingly threatened by climate change, overfishing, habitat destruction, and pollution. Historical baselines of coral cover are important to understand how much coral cover has been lost, e.g., to avoid the ‘shifting baseline syndrome’. There are few quantitative observations of coral reef cover prior to the industrial revolution, and therefore baselines of coral reef cover are difficult to estimate. Here, we use expert and ocean-user opinion surveys to estimate baselines of global coral reef cover. The overall mean estimated baseline coral cover was 59% (±19% standard deviation), compared to an average of 58% (±18% standard deviation) estimated by professional scientists. We did not find evidence of the shifting baseline syndrome, whereby respondents who first observed coral reefs more recently report lower estimates of baseline coral cover. These estimates of historical coral reef baseline cover are important for scientists, policy makers, and managers to understand the extent to which coral reefs have become depleted and to set appropriate recovery targets.

Coastal ecosystems are among the most productive yet increasingly threatened marine ecosystems worldwide. Particularly vegetated habitats, such as eelgrass (Zostera marina) beds, play important roles in providing key spawning, nursery and foraging habitats for a wide range of fauna. To properly assess changes in coastal ecosystems and manage these critical habitats, it is essential to develop sound monitoring programs for foundation species and associated assemblages. Several survey methods exist, thus understanding how different methods perform is important for survey selection. We compared two common methods for surveying macrofaunal assemblages: beach seine netting and underwater visual census (UVC). We also tested whether assemblages in shallow nearshore habitats commonly sampled by beach seines are similar to those of nearby eelgrass beds often sampled by UVC. Among five estuaries along the Southern Gulf of St. Lawrence, Canada, our results suggest that the two survey methods yield comparable results for species richness, diversity and evenness, yet beach seines yield significantly higher abundance and different species composition. However, sampling nearshore assemblages does not represent those in eelgrass beds despite considerable overlap and close proximity. These results have important implications for how and where macrofaunal assemblages are monitored in coastal ecosystems. Ideally, multiple survey methods and locations should be combined to complement each other in assessing the entire assemblage and full range of changes in coastal ecosystems, thereby better informing coastal zone management.