Introduction {#s1}
============

Marine reserves (i.e. no-take areas) are widely used as a tool for marine conservation. Recent reviews demonstrate, on average, positive effects of reserve protection on biomass, numerical density, species richness and size of organisms within their boundaries e.g. [@pone.0061207-Halpern1], [@pone.0061207-Lester1]. However, these studies also show considerable variability in the responses to marine reserves. Two hypotheses have been suggested to explain this variability in Lester et al [@pone.0061207-Lester1]. The first is limitations in the experimental design of surveys, particularly the lack of temporal and spatial replication, and the small number of species sampled. The second is sensitivity of the response to conditions around the reserve (i.e. intensity of fishing outside the reserve and infringement into the reserve), and prior to the establishment of the reserve (i.e. historical fishing pressure). It is this last hypothesis that we test here using an end-to-end ecosystem model.

Until recently, modelling of MPA effects has mainly focussed on fisheries outcomes rather than conservation outcomes and primarily focussed on single species models (see review by Gerber et al [@pone.0061207-Gerber1] and White et al [@pone.0061207-White1]). However, non-spatial trophodynamic models (Ecopath with Ecosim or Ecotroph) are increasingly being used for exploring the effects of marine reserves on food webs [@pone.0061207-Collter1], [@pone.0061207-Valls1], [@pone.0061207-Libralato1], [@pone.0061207-Albouy1].

There are now a number of quantitative modelling approaches that explicitly represent spatial habitats, animal movements and high-level trophic interactions, all key processes in the response of ecosystems to the implementation of marine reserves (see recent reviews by Fulton [@pone.0061207-Fulton1] and Rose et al [@pone.0061207-Rose1], and [@pone.0061207-Maury1], [@pone.0061207-Travers1], [@pone.0061207-Oguz1]). To our knowledge, only ECOSPACE (the spatially resolved version of ECOPATH with ECOSIM or EwE [@pone.0061207-Pauly1]) has been used for marine reserves applications [@pone.0061207-Walters1], [@pone.0061207-Salomon1].This type of modelling enables us to explore the effects of marine reserves at a regional scale (as opposed to a comparison of inside/outside reserves) following recent recommendations from a review on marine protected area performances [@pone.0061207-Kemp1]. In the category of spatial trophodynamic models, Atlantis stands out due to its explicit representation of physical and biogeochemical processes, the use of a single biogeochemical framework allowing all trophic levels to be fully coupled without assumptions about bottom-up or top-down control, and its availability-based diet matrix that allows the trophic structure to evolve over time [@pone.0061207-Fulton1], [@pone.0061207-Fulton2], [@pone.0061207-Fulton3] and [@pone.0061207-Johnson1]. Atlantis has already been used to explore the impacts of marine reserves in a fisheries management context in the Gulf of California [@pone.0061207-Ainsworth1], as well as along the California coast [@pone.0061207-Kaplan1].

Protection of biodiversity is amongst the most frequently legislated driver behind the establishment of marine reserves (e.g. [@pone.0061207-Boersma1]). The metric of biodiversity most commonly used in their design and evaluation is taxonomic diversity or species richness [@pone.0061207-Micheli1], and overall, field data tend to suggest a positive effect of marine reserves (e.g. [@pone.0061207-Lester1] and [@pone.0061207-Worm1]). However, it has been argued recently that taxonomic diversity only provides an incomplete view of biodiversity as it does not distinguish between species (e.g. [@pone.0061207-Hillebrand1] and [@pone.0061207-Villeger1]). Functional biodiversity, defined as the functional multiplicity within a community [@pone.0061207-Tesfaye1], has been defined as a useful additional concept to taxonomic biodiversity, as it correlates with measures of ecosystem functioning [@pone.0061207-Clemente1], [@pone.0061207-Tilman1], resilience to disturbances [@pone.0061207-Bellwood1] and regulation in the flux of matter [@pone.0061207-Walbusser1]. Functional traits, i.e. the components of an organism\'s phenotype that influence ecosystem level processes, are generally considered the units defining functional diversity [@pone.0061207-Hillebrand1]. While taxonomic biodiversity is beyond the scope of end-to-end ecosystem models, functional biodiversity can be explored, as functional traits are generally - and certainly in our case - used to define the model functional groups (e.g. trophic group, size and mobility -- [@pone.0061207-Micheli1], [@pone.0061207-Stelzenmuller1]). The effect of marine reserves on functional biodiversity has been only recently investigated, and so far the effect seems to be positive [@pone.0061207-Micheli1], [@pone.0061207-Stelzenmuller1], [@pone.0061207-Mouillot1]. Whether functional biodiversity is correlated (e.g. [@pone.0061207-Micheli1] and [@pone.0061207-Stelzenmuller1]), or not correlated to species diversity (e.g. [@pone.0061207-Mouillot1]) is not relevant to our study and will not be discussed here.

Here we have used the Atlantis ecosystem model to explore long-term regional changes in response to reserves off the southeast coast of Australia. By considering a range of fisheries and reserve design scenarios we have been able to infer principles that can be applied more broadly to marine reserve design, management and performance assessment.

Methods {#s2}
=======

Model description {#s2a}
-----------------

Atlantis is a nutrient-based biogeochemical model that includes physical forcing, biogeochemical cycling, trophic interactions, and human influences on the ecosystem [@pone.0061207-Fulton1], [@pone.0061207-Fulton2] and [@pone.0061207-Fulton3]. The implementation used here has been described in detail in Savina et al [@pone.0061207-Savina1]. It covered the length of Australia\'s New South Wales (NSW) coastline and extended offshore to the upper continental slope ([Figure 1](#pone-0061207-g001){ref-type="fig"}). This area was divided into a total of 43 horizontally layered polygonal cells that resolved major bays and estuaries, coastal waters to 50 m, shelf waters to 200 m, and upper slope waters to 800 m. Alongshore divisions were based on land-use characteristics, coastal morphology [@pone.0061207-Roy1], and the broader pelagic bioregional structure [@pone.0061207-Condie1]. Vertically, the model resolved a single sediment layer and five water column layers selected on the basis of the general vertical zonation of water properties and pelagic organisms (interfaces at 20, 50, 100 and 200 m).

![Polygonal cell structure of the model and percentage of model cells open to fishing as a consequence of three marine reserves (left, scenarios 2 and 5) or five marine reserves (right, scenarios 3, and 6).\
More details in the text.](pone.0061207.g001){#pone-0061207-g001}

The model time-step was set at 0.5 days so as to resolve key physical processes (e.g. large-scale current and eddy transports) and key biological processes. Temperatures and salinities within each cell and three-dimensional physical exchanges between cells were estimated at every time-step utilising archived output from a data-assimilating global ocean circulation model referred to as the Bluelink Reanalysis or BRAN [@pone.0061207-Oke1]. Estuarine inputs were represented as point sources of freshwater and nutrients based on data from local monitoring programs (centralised in the PINEENA database [@pone.0061207-NSW1]). Offshore nutrient concentrations followed seasonal cycles based on CARS (CSIRO Atlas of Regional Seas) [@pone.0061207-Condie1]. Solar irradiance at the sea-surface was specified as a function of latitude and the time of year. At the seafloor, a sediment chemistry sub-model calculated nutrient remineralisation and oxygen exchange [@pone.0061207-Fulton4].

The model included 48 biological groups ranging from phytoplankton and bacteria through to sharks and whales ([Table 1](#pone-0061207-t001){ref-type="table"}). Selection of groups was largely determined by the need to capture key ecosystem functional characteristics with the level of aggregation guided by taxonomy, shared predators and preys, size, turnover rate, and habitat use [@pone.0061207-Gardner1], [@pone.0061207-Fulton5]. Experience with implementing and running Atlantis at larger scales in this region [@pone.0061207-Fulton6] assisted with these selections. A significant number of individual species were also represented in the food-web to address identified management issues related to conservation and fishing. For more details please refer to Savina et al [@pone.0061207-Savina1].

10.1371/journal.pone.0061207.t001

###### Functional groups included in the model.

![](pone.0061207.t001){#pone-0061207-t001-1}

  Categories       Sub-categories         Functional groups                                           Description
  --------------- ---------------- ------------------------------- ---------------------------------------------------------------------------------
  Nutrients                            Reduced nitrogen (NHx)                                Ammonia (NH3), ammonium (NH4)
                                       Oxidised nitrogen (NOx)                               Nitrate (NO3), nitrite (NO2)
                                          Dissolved silica         
  Detritus                                 Labile detritus                                   Rapidly decomposing detritus
                                         Refractory detritus                                  Slowly decomposing detritus
                                           Detrital silica                                          Biogenic silica
                                               Carrion             
  Bacteria                                Benthic bacteria         
                                          Pelagic bacteria         
  Plants           Phytoplankton         Large phytoplankton                                            Diatoms
                                         Small phytoplankton       
                    Phytobenthos             Macroalgae            
                                              Seagrass             
  Invertebrates     Zooplankton        Gelatinous zooplankton                                      Salps and medusa
                                          Large zooplankton                                       Krill, Chaetognaths
                                           Mesozooplankton                                             Copepods
                                          Small zooplankton                                    Heterotrophic flagellates
                       Nekton                Cephalopods                                     Squids, calamari, and octopus
                                               Prawns                                       Eastern king and school prawns
                     Zoobenthos              Meiobenthos           
                                         Benthic carnivores                                       Polychaetes mainly
                                       Benthic deposit feeders                            Echinoderms, holothurians, bivalves
                                         Deep filter-feeders                              Sponges, corals, crinoids, bivalves
                                       Shallow filter-feeders                             Sponges, corals, crinoids, bivalves
                                      Commercial filter-feeders                                  Scallops and oysters
                                           Benthic grazers                                 Abalone, gastropods, echinoderms
                                           Macrozoobenthos                                 Crustaceans, Asteroids, molluscs
                                     Commercial macrozoobenthos                              Octopus and commercial crabs
                                              Lobsters                                       Shovelnosed and rock lobsters
  VERTEBRATES        Bony Fish      Demersal shallow herbivorous                      Mullets, luderick, garfish, silver drummer
                                    Demersal shallow territorials                Pipefish, seahorses, gobies, damselfish, diamondfish
                                     Demersal shallow omnivores     Flounders, gurnards, wrasses, flathead, whiting, bream, snapper, emperors, eels
                                             Ocean perch                                          *Helicolenus spp*.
                                               Whiting                                              *Sillago spp*.
                                           Tiger flathead                                      Platycephalus richardsoni
                                             Trevallies                                    *Caranx spp., Pseudocaranx spp*.
                                         Demersal deep fish                             Dories, whiptails, cardinalfish, hapuku
                                              Morwongs                                   Cheilodactylus spp., Nemadactylus spp
                                           Blue Grenadier                                      Macruronus novaezelandiae
                                              Pink ling                                           Genypterus blacodes
                                        Warehou and trevalla                           Seriolella spp., Hyperoglyphe antarctica
                                               Redfish                                            Centroberyx affinis
                                               Gemfish                                              Rexea solandri
                                     Pelagic small planktivores                                Pilchards, anchovy, scad
                                     Pelagic large planktivores                                        Mackerels
                                     Pelagic shallow piscivores                      Bonito, Mulloway, Teraglin, Australian salmon
                                        Mesopelagic migratory                              Myctophids, frostfish, lancetfish
                                      Mesopelagic non-migratory                         Sternophychids, cyclothene (lightfish)
                                        Oceanic planktivores                                 Flying fish, sauries, redbait
                                         Oceanic piscivores                                   Tunas, swordfish, billfish
                       Sharks              Demersal sharks                                Gummy, school, wobbegong, sawsharks
                                      Reef sharks -- grey nurse                                    Carcharias taurus
                                           Skates and Rays         
                                           Pelagic sharks                            Whalers, blue, mako, white, tiger, hammerhead
                                              Dogsharks                                             *Squalus spp*.
                                           Spiky dogshark                                          Squalus megalops
                      Mammals               Baleen whales                                Humpback, southern right, minke, blue
                                              Dolphins                                                Bottlenose
                                           Toothed whales                                                Orca
                                              Pinnipeds                                  Australian and New Zealand fur seals
                       Birds                  Sea birds                                 Albatross, shearwaters, gulls, gannets

The biomass of each lower trophic level functional group was computed over time for each of the model cells in nutrient-based units (mg m^−3^ of nitrogen and silica, which are the limiting elements in the system). Higher trophic levels were followed using an age-structured formulation that allowed for changes in reproduction and mortality that may be critical in the response of populations to marine reserves (e.g. [@pone.0061207-Kaplan2]).

The functional groups were linked through local trophic interactions and influenced by environmental and habitat conditions in the water column and bottom sediments. Nutrients, planktonic groups and detritus were exchanged between cells on the basis of physical flows estimated from the aforementioned ocean circulation model. The movements of vertebrates were modelled so as to maintain particular distribution patterns, some of which were constant (e.g. demersal shallow herbivorous), while others varied through the year (in case of spawning or other migrations - e.g. Grey nurse shark *Carcharias taurus*). The demersal shallow territorial group was sedentary (i.e. could not move from one box to the others), and a limited set of groups (pelagic large planktivores and shallow piscivores, oceanic piscivores and planktivores, pelagic sharks) had a foraging behaviour that allowed them to move among boxes to optimise their potential growth (calculated on the basis of food resources, existing local fish density and their swimming speed). Other biological processes explicitly represented in the model included consumption and growth, waste production and decomposition, reproduction, habitat dependency, bioturbation and bioirrigation, and predation and other forms of natural mortality. Detailed mathematical formulations for these processes can be found in [@pone.0061207-Fulton4].

Fishing mortality was prescribed in terms of a realised catch based on historical distributions (i.e. extraction continued until the regulated catch quota was reached). The only exceptions were sharks and rays, for which fishing mortality rates were estimated from the literature.

Scenarios {#s2b}
---------

Between 3 and 5 reserves were considered in our scenarios ([Figure 1](#pone-0061207-g001){ref-type="fig"}). They covered 2.4% (1157 km^2^) or 6.2% (2979 km^2^) of the total modelled domain (48000 km^2^). Although they corresponded in location and total area to the real reserves declared off NSW over the past decade (<http://www.mpa.nsw.gov.au/>), no attempt was made to replicate the complex mosaic of zones with varying degrees of protection. Instead, reserves were idealised as either strictly no-take areas when the reserves covered whole model cells ([Figure 1](#pone-0061207-g001){ref-type="fig"} -- red cells with 0% open to fishing); or as areas where fishing mortality (all groups) was reduced in proportion to the ratio of the reserve size to the model cell size ([Figure 1](#pone-0061207-g001){ref-type="fig"} -- orange to light green cells). In the rest of the text, we use the term reserve to refer to both of these cases.

The scenarios used the calibrated model and outputs from the start of 1976, see [@pone.0061207-Savina1], as initial conditions to explore the potential regional impacts of a system of marine reserves over a 30-year period. To isolate the effects of the marine reserves, catches were held constant at either the historical 1976 levels (referred to here as low fishing scenarios) or double the 1976 levels (high fishing scenarios, in line with the levels of increased pressure seen in historical time series [@pone.0061207-Stelzenmuller1]). Individual scenarios varied in the number of reserves (3 or 5) and the level of fishing prior to the introduction of reserves ([Table 2](#pone-0061207-t002){ref-type="table"}).

10.1371/journal.pone.0061207.t002

###### Summary of model scenarios. Low historical fishing corresponded to 1976 levels off the NSW coast and high fishing to double this level.

![](pone.0061207.t002){#pone-0061207-t002-2}

  Scenario    No. of reserves   Historical fishing          
  ---------- ----------------- -------------------- --- --- ---
  1                  x                                   x  
  2                                     x                x  
  3                                                  x   x  
  4                  x                                       x
  5                                     x                    x
  6                                                  x       x

Metrics {#s2c}
-------

The results were analysed for the whole model domain using the following metrics related to changes in the higher functional groups (defined here as vertebrates, cephalopods and prawns) over the 30-year simulations. These metrics are different from the ones used in field studies, which usually compare one or several sites within and outside of the marine reserves, but with no indication of what is happening at the scale of the whole region.

i.  Change in the *biomass of functional groups* expressed as the ratio of the biomass at the end of a given scenario with reserves in place to the biomass at the end of the corresponding baseline scenario with no reserves (i.e. 1 or 4 in [Table 2](#pone-0061207-t002){ref-type="table"}).

ii. Change in the *fishery catch value* expressed as the ratio of the total catch value at the end of a given scenario to the total catch value at the end of the corresponding baseline scenario. The average prices for each group were calculated from the NSW Department of Primary Industries catch statistics database (1985--1996). While this metric ignores short-term volatility in prices due to factors such as market preferences, international influences and scarcity, it captures any broad trends in catch composition between high and low value species.

iii. Change in the *functional diversity index* (Q90 defined below) expressed as the ratio of the functional diversity index at the end of a given scenario to the functional diversity index at the end of the corresponding baseline scenario. Q90 is derived from Kempton\'s diversity index and adapted to measure functional biodiversity [@pone.0061207-Ainsworth2]. Refer to Savina et al [@pone.0061207-Savina1] for more details on the use of the index within the model.

Results {#s3}
=======

The introduction of reserves influenced the biomass of up to 15 of the 34 higher functional groups (i.e. vertebrates, cephalopods and prawns, see [Table 1](#pone-0061207-t001){ref-type="table"}). Under low fishing pressure, 7 of these groups increased in biomass and 5 decreased in biomass in the case of 3 reserves (scenario 2--[Figure 2a](#pone-0061207-g002){ref-type="fig"}). The addition of reserves (scenario3 -- [Figure 2c](#pone-0061207-g002){ref-type="fig"}) caused the total number of groups impacted to increase (15) while the proportion of negatively (7) to positively (8) impacted groups increased slightly. Under high fishing pressure, the proportion of impacted groups stayed roughly the same, but with a much higher proportion of positively impacted groups. In scenario 5, 13 groups increased in biomass and none decreased ([Figure 2b](#pone-0061207-g002){ref-type="fig"}). The addition of reserves (scenario 7 -- [Figure 2d](#pone-0061207-g002){ref-type="fig"}) again caused the total number of groups impacted to increase (15) while increasing slightly the proportion of negatively (2) to positively (13) impacted groups. The strongest responses were amongst groups that lived mostly in the coastal and inner-shelf habitat types protected by the marine reserves (shallow groups in [Figure 3a](#pone-0061207-g003){ref-type="fig"}). Under high fishing the presence of reserves prevented the collapse of demersal herbivores, although two other groups (demersal omnivores and redfish *Centroberyx affinis*) collapsed irrespective of their presence ([Figure 3b](#pone-0061207-g003){ref-type="fig"}).

![Fraction of all vertebrates, cephalopods and prawns (34 groups) that show an increase, decrease or no significant change in biomass under the four scenarios.](pone.0061207.g002){#pone-0061207-g002}

![Percentage final biomass changes over 30 years (a) for scenarios 2 and 3 relative to scenario 1 (i.e. low fishing scenarios) (b) for scenarios 5 and 6 relative to scenario 4 (i.e. high fishing scenarios). for the nine functional groups that showed a decrease/increase of more than 8% in at least one of the scenarios.\
Relative fishery catch value and the biodiversity index are also shown.](pone.0061207.g003){#pone-0061207-g003}

When fishing was removed from reserve areas, biomasses increased for pelagic sharks, demersal sharks, reef sharks, skates and rays, demersal omnivores, demersal herbivores, and cephalopods (the last only in the case of the heavy fishing scenarios). In most of these cases the relative changes increased roughly in proportion to the size of the area protected (compare scenarios 2 and 3, or 5 and 6 in [Figure 3](#pone-0061207-g003){ref-type="fig"}).

For migratory sharks, such as grey nurse (*Carcharias taurus*), the effects of reduced fishing in reserves necessarily pertained to the entire population. However, even in the case of more sedentary groups, such as demersal omnivores, there was sufficient dispersal in the model for positive effects to extend along most of the coast rather than being restricted to the reserve areas.

The increases in predatory sharks and omnivorous fish tended to have a negative impact on their prey groups. For groups normally being fished in the coastal zone (where the marine reserves are) such as demersal herbivores, increases in predation only partially offset the benefits of reduced fishing pressure. For groups not being fished in the coastal zone, such as demersal territorials (not fished at all) or redfish (*Centroberyx affinis* fished offshore), it resulted in a net decline in scenarios 2 and 3 ([Figure 3a](#pone-0061207-g003){ref-type="fig"}). These indirect impacts were evident along the entire NSW coastline, consistent with the widespread increase in predators. Even though redfish only spent their juvenile phase in bays and coastal areas, they were strongly impacted by the increased predation ([Figure 3a](#pone-0061207-g003){ref-type="fig"}). They totally collapsed in all the high fishing pressure scenarios ([Figure 3b](#pone-0061207-g003){ref-type="fig"}).

Introduction of reserves usually had a small negative impact on fishery catches (\<10%, not shown), much of which occurred in estuarine fisheries where the reserve coverage was highest. The associated decline in economic value of catches was smaller still as reductions in total catch were partially offset by increases in the proportion of high value fish groups, such as the shallow demersal omnivores in the scenarios 2 and 3, or the shallow demersal herbivores in the scenarios 5 and 6 ([Figure 3](#pone-0061207-g003){ref-type="fig"}). In the scenario 5, the reductions in total catch were indeed completely offset by increases in the proportion of demersal herbivores ([Figure 3b](#pone-0061207-g003){ref-type="fig"}).

Removing low fishing from reserves caused a very small increase in the functional diversity index ([Figure 3a](#pone-0061207-g003){ref-type="fig"}), while removing high fishing significantly increased the functional diversity index (\>10%, [Figure 3b](#pone-0061207-g003){ref-type="fig"}). Similar to the biomass results, functional biodiversity increased with the number (and area) of reserves.

Discussion {#s4}
==========

In this paper, we used an Atlantis ecosystem model of the NSW continental shelf and upper slope to test the effects of coastal no-take marine reserves at a large regional scale over a 30-year period. The results were analysed using metrics related to the higher functional groups (defined here as vertebrates, cephalopods and prawns) over the 30-year simulations, i.e.: changes in biomass for each functional group and in the functional biodiversity index (Q90), both of which were computed for the whole model domain. This modelling approach contrasts with experimental studies on the impact of marine reserves (which generally measure biomass and biodiversity at a small number of sampling sites inside and outside the marine reserves, and sometimes before and after reserve implementation [@pone.0061207-Lester1]) and addresses Kemp et al\'s [@pone.0061207-Kemp1] recommendation that MPA management objectives and monitoring programs should be set at a regional scale so the overall performance can be assessed.

The model results suggest that the ecosystem response to the establishment of marine reserves is dependent upon the pre-existing disturbance state of the system. Here, that disturbance state was expressed as either relatively low fishing pressure (i.e. the 1976 fishing level), or high fishing pressure (i.e. double the 1976 fishing level).

The high fishing scenarios (twice the 1976 fishing level) resulted in a strongly perturbed system, where the introduction of marine reserves had clear and mostly direct effects (i.e. directly through the removal of fishing pressure) on biomass and functional biodiversity. However, under lower 1976 fishing level scenarios, the introduction of marine reserves caused both direct positive effects, mainly on shark groups, and indirect negative effects through trophic cascades (e.g. increased predation on shallow demersal territorials and juvenile redfish *Centroberyx affinis*). Low fishing levels generated an intermediate level of disturbance in the model that sustained relatively high levels of functional biodiversity [@pone.0061207-Savina1]. In this context, the potential positive effect of reducing fishing pressure on functional biodiversity was offset by the effect of an increased large predator (i.e. sharks) biomass, leading to virtually unchanged Q90 index values. Increased predation has been proposed as an alternative mechanism to competitive exclusion to explain the decline of biodiversity at low levels of disturbance in the intermediate disturbance hypothesis model [@pone.0061207-Menge1]. Sandin et al [@pone.0061207-Sandin1] similarly observed on coral reefs that with decreasing human disturbance, diversity increased until top predators (including sharks) reached a threshold fraction of the total biomass in the system, leading to declines in their prey.

The ecosystem response also depended on the size of the protected areas, although to a lesser extent than the disturbance rate. All the groups impacted by the establishment of marine reserves show a biomass response proportional to the size/number of the area protected. This is consistent with the meta-analysis findings of Halpern et al [@pone.0061207-Halpern1] and Claudet et al [@pone.0061207-Claudet1], as our metrics measure the system-wide effect (i.e. absolute effect, *sensu* [@pone.0061207-Halpern1]) of marine reserves on the system.

The model results support previous empirical studies e.g. [@pone.0061207-Claudet2]; [@pone.0061207-Fanshawe1], [@pone.0061207-GarciaCharton1], [@pone.0061207-Guidetti1], [@pone.0061207-Lamb1] in finding clear benefits of reserves to top predators, such as sharks and rays, and those benefits extended well beyond the reserve boundaries. Given the identified critical role of top predators in maintaining the structure and function of ecosystems e.g. [@pone.0061207-Myers1], it can be argued that their conservation should be a major driver and a key performance indicator for the establishment and management of marine reserves.

Our study illustrates the need to carefully align the design and implementation of marine reserves with policy and management objectives. Trade-offs may exist not only between fisheries and conservation objectives, but also among conservation objectives. In a low fishing context, functional biodiversity might be negatively affected by the recovery of large predators, and therefore might not be the best indicator of marine reserve performance. This finding is particularly pertinent given that reserve areas are often selected to minimise conflicts with existing fisheries.

The implications of our model results for the effects of marine reserves on species diversity are uncertain, but interestingly, Hockey and Bosman [@pone.0061207-Hockey1] similarly questioned the use of species richness as an indicator for the management of exploited intertidal rocky shores. The higher species diversity they observed in harvested shores (where there was human collection of intertidal invertebrates) was associated with the dominance of inedible species and small individuals, while undisturbed shores with relatively lower species diversity had a species composition close to or at climax equilibria, which render these communities a far more valuable resource.

Our thanks to Karen Astles, Bob Creese, Robyn Forrest, Philip Gibbs, Steve Kennelly, Keith Sainsbury and James Scandol for their input into the study. Thank also to Russ Babcock, Cathy Bulman, Alan Jordan, David Smith, Kate Wilson, Eva Plaganyi and two anonymous reviewers for their insightful comments on the paper.

[^1]: **Competing Interests:**The authors have declared that no competing interests exist.

[^2]: Conceived and designed the experiments: MS EAF. Performed the experiments: MS. Analyzed the data: MS SAC EAF. Wrote the paper: MS SAC.
