Ecological extinction caused by overfishing precedes all other pervasive human disturbance to coastal ecosystems, including pollution, degradation of water quality, and anthropogenic climate change. Historical abundances of large consumer species were fantastically large in comparison with recent observations. Paleoecological, archaeological, and historical data show that time lags of decades to centuries occurred between the onset of overfishing and consequent changes in ecological communities, because unfished species of similar trophic level assumed the ecological roles of overfished species until they too were overfished or died of epidemic diseases related to overcrowding. Retrospective data not only help to clarify underlying causes and rates of ecological change, but they also demonstrate achievable goals for restoration and management of coastal ecosystems that could not even be contemplated based on the limited perspective of recent observations alone.Few modern ecological studies take into account the former natural abundances of large marine vertebrates. There are dozens of places in the Caribbean named after large sea turtles whose adult populations now number in the tens of thousands rather than the tens of millions of a few centuries ago (1, 2).

Marine reserves are a spatial approach to marine management and conservation aimed at protecting and restoring multispecies assemblages and the structure and function of marine ecosystems. We used meta‐analyses of published data to address the questions of how and over what time frames marine assemblages change within no‐take marine reserves as they recover from fishing and other human uses. We used 20 studies of coastal fish assemblages from 31 temperate and tropical locations, reporting abundances, and in some cases biomass, of 10–134 species from reserve and reference conditions (i.e., conditions in nearby fished sites or before reserve establishment) spanning 1–25 years of protection. Synthesis of data from these diverse sets of assemblages showed that: (1) a species' level of exploitation, trophic level, and the duration of protection through the no‐take reserve explain small but significant amounts of variation in individual species responses to protection, with only species that are targeted by fishing or by aquarium trade showing overall enhanced abundances in protected areas, and increasing positive effects of protection on abundances at top trophic levels through time; (2) up to a third of species in different studies (19% on average) appeared to be negatively affected by protection, indicating that indirect effects of protection through competitive or predatory interactions may be common; and (3) variation and lags in species responses to protection resulted in protected assemblages diverging from reference conditions, with greater proportions of total fish biomass at top trophic levels in protected compared to fished assemblages. These results indicate that marine reserves are effective in enhancing local abundances of exploited species and restoring the structure of whole communities, though these changes occur through a series of transient states and, for some communities, over long time frames (decades). In contrast with the more predictable increases of aggregate community variables such as total abundance and biomass, individual species and community structure exhibited broad variation in their responses to protection. Marine protected areas represent multiple human‐exclusion “experiments,” replicated in a variety of ecosystem types and geographic locations, providing key insights on community‐wide impacts of the removal of human extraction. Long‐term monitoring of community trajectories in marine protected areas and modeling studies scaling up local effects to relevant spatial and temporal scales are needed to increase our ability to protect and restore whole marine systems and to set realistic targets for the conservation and restoration of specific assemblages.

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We synthesize results from existing models of marine reserves to identify key theoretical issues that appear to be well understood, as well as issues in need of further exploration. Models of marine reserves are relatively new in the scientific literature; 32 of the 34 theoretical papers we reviewed were published after 1990. These models have focused primarily on questions concerning fishery management at the expense of other objectives such as conservation, scientific understanding, recreation, education, and tourism. Roughly one‐third of the models analyze effects on cohorts while the remaining models have some form of complete population dynamics. Few models explicitly include larval dispersal. In a fisheries context, the primary conclusion drawn by many of the complete population models is that reserves increase yield when populations would otherwise be overfished. A second conclusion, resulting primarily from single‐cohort models, is that reserves will provide fewer benefits for species with greater adult rates of movement. Although some models are beginning to yield information on the spatial configurations of reserves required for populations with specific dispersal distances to persist, it remains an aspect of reserve design in need of further analysis. Other outstanding issues include the effects of (1) particular forms of density dependence, (2) multispecies interactions, (3) fisher behavior, and (4) effects of concentrated fishing on habitat. Model results indicate that marine reserves could play a beneficial role in the protection of marine systems against overfishing. Additional modeling and analysis will greatly improve prospects for a better understanding of the potential of marine reserves for conserving biodiversity.

There is a need for better description and heuristic understanding of the sustainability of populations connected over space by a dispersing stage, both for management purposes and to increase our basic knowledge of the dynamics of these populations. We show that persistence of such a population of connected subpopulations depends on whether the sum of the reproductive gains through all possible closed, between-patch reproductive paths through multiple generations, relative to the shortfall in selfpersistence in each path, exceeds unity plus extra terms, which only appear if there are four or more patches. These extra terms have the heuristic explanation that they avoid double counting of reproductive paths that arise with four or more patches because there can be nonoverlapping subnetworks. Thus only those patterns of reproduction and connectivity which eventually lead to descendants returning to the patch from which they originate contribute to persistence. This result provides the basis for evaluating connectivity and habitat heterogeneity to understand reserve design, the effects of human fragmentation, the collapse of marine fisheries, and other conservation issues.connectivity ͉ M-matrix ͉ population dynamics ͉ spatial dynamics ͉ marine reserves U nderstanding conditions for the persistence of populations that are distributed over space is a central issue in population biology that has received increasing attention in recent years from both a theoretical and empirical perspective (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20). This general question of persistence can be viewed in a variety of particular contexts. The large body of theory that has been developed to describe metapopulation dynamics poses this question as a balance between colonization and extinction. Yet, in many instances, especially where extinctions do not occur or management depends on limited information, a different question is more useful to ask, namely whether growth rates with spatial heterogeneity are positive, looking only at deterministic rather than stochastic aspects (12). This question, or variants of it, arises in the context of reserve design, both for marine and terrestrial populations, in understanding the consequences of habitat fragmentation and for understanding the dynamics of infectious agents. We address this question by using a particular simple, general system that will allow us to deduce principles of biological interest.Our goals are to understand how the interplay between connectivity (dispersal) and local population dynamics allows persistence in a network of heterogeneous patches, and to develop a simple general understanding of conditions for persistence. This question is the analogue of the similar question for persistence of a single species in a single patch. For a single species with age structure and no density dependence, dynamics are described by the Leslie matrix. Obviously, the population persists if the growth rate of the population, the largest eigenvalue of the Leslie matr...

The theory underlying the design of marine reserves, whether the goal is to preserve biodiversity or to manage fisheries, is still in its infancy. For both of these goals, there is a need for general principles on which to base marine reserve design, and because of the paucity of empirical experience, these principles must be based on models. However, most of the theoretical studies to date have been specific to a single situation, with few attempts to deduce general principles. Here we attempt to distill existing results into general principles useful to designers of marine reserves. To answer the question of how fishery management using reserves compares to conventional management, we provide two principles: (1) the effect of reserves on yield per recruit is similar to increasing the age of first capture, and (2) the effect of reserves on yield is similar to reducing effort. Another two principles answer the question of how to design reserve configurations so that species with movement in various stages will be sustainable: (3) higher juvenile and adult movement lowers sustainability of reserves for biodiversity, but an intermediate level of adult movement is required for reserves for fishery management, and (4) longer larval dispersal distance requires larger reserves for sustainability. These principles provide general guidelines for design, and attention to them will allow more rapid progress in future modeling studies. Whether populations or communities will persist under any specific reserve design is uncertain, and we suggest ways of dealing with that uncertainty.

Design and decision-making for marine protected areas (MPAs) on coral reefs require prediction of MPA effects with population models. Modeling of MPAs has shown how the persistence of metapopulations in systems of MPAs depends on the size and spacing of MPAs, and levels of fishing outside the MPAs. However, the pattern of demographic connectivity produced by larval dispersal is a key uncertainty in those modeling studies. The information required to assess population persistence is a dispersal matrix containing the fraction of larvae traveling to each location from each location, not just the current number of larvae exchanged among locations. Recent metapopulation modeling research with hypothetical dispersal matrices has shown how the spatial scale of dispersal, degree of advection versus diffusion, total larval output, and temporal and spatial variability in dispersal influence population persistence. Recent empirical studies using population genetics, parentage analysis, and geochemical and artificial marks in calcified structures have improved the understanding of dispersal. However, many such studies report current self-recruitment (locally produced settlement/settlement from elsewhere), which is not as directly useful as local retention (locally produced settlement/total locally released), which is a component of the dispersal matrix. Modeling of biophysical circulation with larval particle tracking can provide the required elements of dispersal matrices and assess their sensitivity to flows and larval behavior, but it requires more assumptions than direct empirical methods. To make rapid progress in understanding the scales and patterns of connectivity, greater communication between empiricists and population modelers will be needed. Empiricists need to focus more on identifying the characteristics of the dispersal matrix, while population modelers need to track and assimilate evolving empirical results.

Marine reserves have been proposed as a remedy for overfishing and declining marine biodiversity, but concern that reserves would inherently reduce yields has impeded their implementation. It was found that management of fisheries through reserves and management through effort control produce identical yields under a reasonable set of simplifying assumptions corresponding to a broad range of biological conditions. Indeed, for populations with sedentary adults (invertebrates and reef fishes), reserves have important advantages for sustainability, making marine reserves the preferred management approach.