Marine protected areas (MPAs) are designed to reduce threats to biodiversity and ecosystem functioning from anthropogenic activities. Assessment of MPAs effectiveness requires synchronous sampling of protected and non-protected areas at multiple spatial and temporal scales. We used an autonomous underwater vehicle to map benthic communities in replicate ‘no-take’ and ‘general-use’ (fishing allowed) zones within three MPAs along 7o of latitude. We recorded 92 taxa and 38 morpho-groups across three large MPAs. We found that important habitat-forming biota (e.g. massive sponges) were more prevalent and abundant in no-take zones, while short ephemeral algae were more abundant in general-use zones, suggesting potential short-term effects of zoning (5–10 years). Yet, short-term effects of zoning were not detected at the community level (community structure or composition), while community structure varied significantly among MPAs. We conclude that by allowing rapid, simultaneous assessments at multiple spatial scales, autonomous underwater vehicles are useful to document changes in marine communities and identify adequate scales to manage them. This study advanced knowledge of marine benthic communities and their conservation in three ways. First, we quantified benthic biodiversity and abundance, generating the first baseline of these benthic communities against which the effectiveness of three large MPAs can be assessed. Second, we identified the taxonomic resolution necessary to assess both short and long-term effects of MPAs, concluding that coarse taxonomic resolution is sufficient given that analyses of community structure at different taxonomic levels were generally consistent. Yet, observed differences were taxa-specific and may have not been evident using our broader taxonomic classifications, a classification of mid to high taxonomic resolution may be necessary to determine zoning effects on key taxa. Third, we provide an example of statistical analyses and sampling design that once temporal sampling is incorporated will be useful to detect changes of marine benthic communities across multiple spatial and temporal scales.


  • Most Marine Protected Areas (MPAs) encompass a range of management zones that restrict specific activities, including ‘no-take zones’ (NTZ) that exclude fishing, through to zones that allow various extractive activities

  • There were no differences in benthic community structure between NTZ and General Use Zones (GUZ) when considering all taxa (Fig 3, Table 1)

  • No differences in multivariate dispersion in community structure were found between zones or among MPAs (Table 2)

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Most Marine Protected Areas (MPAs) encompass a range of management zones that restrict specific activities, including ‘no-take zones’ (NTZ) that exclude fishing, through to zones that allow various extractive activities. MPAs are used to spatially reduce threats to species and ecological processes from anthropogenic activities, such as fishing or physical habitat disturbance [4,5,6] These activities can have direct negative effects on entire biotic communities, especially through reductions in the abundance and size of targeted predatory species [5]. Evaluating benthic species and community responses of individual MPAs is necessary to inform local adaptive management because (i) disturbances to benthic and habitat-forming species can reduce the amount of resources (food, shelter) available to other organisms in the system [5], and (ii) changes in higher trophic levels can have cascading effects on benthic communities [9]


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