Summary 1.Severe events such as floods or cyclones can have large ecological effects on the structure and functioning of ecosystems. The capacity of an ecosystem to adapt to, or absorb, the effects of a severe event depends on the severity and longevity of the event and the tolerance of the species present.2. Seagrasses exhibit phenotypic plasticity at the plant to meadow scale through a variety of physiological and morphological acclimations to light stress to enhance photosynthetic capacity. These acclimations provide early warning of the possible risk of larger scale seagrass loss and can therefore be used in predicting how ecosystems might respond to severe events. 3.The physiological and morphological responses of 12 seagrass (Zostera muelleri) meadows to a severe flood were examined to test two main hypotheses: (i) that the physiological and morphological characteristics of seagrass would differ between meadows along the established chronic water quality gradient, in a pattern consistent with prior acclimations which have been shown to enhance photosynthetic capacity and (ii) that physiological and morphological responses to the flood would differ between meadows in a manner consistent with their position along the water quality gradient. 4.Meadows had different physiological and morphological characteristics across the water quality gradient, with meadows subject to chronically poorer water quality exhibiting characteristics consistent with those that maximize photosynthetic capacity. Despite a large discrepancy in impact among meadows, all meadows sampled responded consistently to the flood, exhibiting only physiological changes with no significant reduction in biomass. This suggests that photoacclimation to chronically poor conditions can enable seagrasses to withstand the effects of severe events, such as floods. 5.Synthesis. Phenotypic plasticity in habitat-forming species can result in a large variation in their responses to severe events, such as floods or cyclones. Acclimation to prior poor environmental conditions can promote persistence in habitat-forming species, such as seagrasses, following severe events. The measurement of phenotypic characteristics along an impact gradient can therefore provide an indication of the response of habitat-forming species to severe events.

Human activities are altering the processes that connect organisms within and among habitats and populations in marine and freshwater (aquatic) ecosystems. Connectivity can be quantified using graph theory, where habitats or populations are represented by ‘nodes’ and dispersal is represented by ‘links’. This approach spans discipline and systemic divides, facilitating identification of generalities in human impacts. We conducted a review of studies that have used graph theory to quantify spatial functional connectivity in aquatic ecosystems. The search identified 42 studies published in 2000–14. We assessed whether each study quantified the impacts of (1) habitat alteration (loss, alteration to links, and gain), (2) human movements causing species introductions, (3) overharvesting and (4) climate change (warming temperatures, altered circulation or hydrology, sea-level rise) and ocean acidification. In freshwater systems habitat alteration was the most commonly studied stressor, whereas in marine systems overharvesting, in terms of larval dispersal among protected areas, was most commonly addressed. Few studies have directly assessed effects of climate change, suggesting an important area of future research. Graph representations of connectivity revealed similarities across different impacts and systems, suggesting common strategies for conservation management. We suggest future research directions for studies of aquatic connectivity to inform conservation management of aquatic ecosystems.

Conservation of biodiversity is a major aim of marine reserves; however their effect on non-native invasive species, a major threat to biodiversity globally, is not widely known. Marine reserves could resist invasive species due to enhanced native diversity and biomass that heightens biotic resistance. Or invasive species could be enhanced by reserves by at least three mechanisms, including protection from harvesting, increased fishing pressure outside reserves facilitating invasions at a regional scale and increasing the exposure of reserves to more potential invaders, and increased propagule pressure from human visitation. We exhaustively searched the literature and found 13 cases that contained quantitative data on invasive species inside and outside marine reserves. In no cases did reserves resist invasive species. Of the seven cases where reserves were established prior to the arrival of the invasive species, five had no effect on the invasive species and two enhanced invasive species. Of the six cases where reserves were established in areas that had pre-existing invasive species, two had no effect on the invasive species and four enhanced the invasive species. These results suggest that while invasive species do equally well or better within marine reserves, too few data are currently available to draw broad, general conclusions regarding the effects of marine reserves on invasive species. Management plans for marine reserves rarely include guidelines for preventing or managing invasive species. If the trends we have detected here are supported by future studies, invasive species should be a priority for management of marine reserves.

Recent assessments of marine reserves have emphasized the importance of socio-economic factors in reserve performance. Debates continue, however, about whether we should avoid or promote the placement of reserves near potentially detrimental forces, including coastal cities or rivers. We performed a global meta-analysis to test whether proximity to major coastal influences affected the ability of marine reserves to enhance the abundance of organisms relative to surrounding areas. A strong effect of reserve performance was evident for a range of trophic groups. Positive effects of reserves were undiminished by proximity to coastal cities or river discharges for the majority of taxonomic groups under conservation. We conclude that reserves placed in coastal areas are likely to protect marine populations to a similar extent as reserves in remote or less-developed locations. Marine reserves in coastal settings can be an important tool to protect species and ecosystems in places threatened by human activities.