Search

Hydrodynamic processes are important in all marine environments and on coral reefs drive patterns of habitat zonation, community structure, and biodiversity. Abrupt geomorphological features like pinnacles and seamounts often possess distinct localized currents and these habitats are also often characterized by high abundance and biomass of fishes. However, differences in fish community structure between pinnacles and emergent reefs, and their key drivers are poorly understood. In this study, we compared fish communities among emergent fringing and offshore coral reefs, and submerged pinnacle reefs in Papua New Guinea. Submerged pinnacles possessed higher fish biomass, abundance, and species richness than both fringing and offshore emergent reefs. We collected in‐situ current speed and temperature data over a full year at each reef and used random forest analysis to investigate the relative influence of hydrodynamics compared to other well‐established drivers of reef fish biodiversity, including habitat and biogeographic factors. Environmental variables explained 70%, 52%, and 5% of variability in models for species richness, abundance and biomass respectively. In all models, average current speed, current speed variability, and reef area were consistently among the most influential variables. Models examining relationships between fish biodiversity metrics and current speed did not yield conclusive results but did highlight the association of distinct hydrodynamic regimes on pinnacles with high fish richness, abundance, and biomass. Our study highlights the strong influence of reef‐scale hydrodynamics on fish biodiversity and demonstrates the ecological value of small, submerged coral reefs, which are globally numerous yet remain understudied in coral reef ecology. [ABSTRACT FROM AUTHOR]

Body size influences many life‐history traits, with small‐bodied animals tending to have short life spans, high mortality and greater reproductive effort early in life. In this study, the authors investigated the life‐history traits and reproductive strategies of three small‐bodied coral reef gobies of the genus Trimma: Trimma benjamini, Trimma capostriatum and Trimma yanoi. The authors found all Trimma species studied attained a small body size of <25 mm, had a short life span of <140 days and experienced high estimated daily mortality of 3.0%–6.7%. Furthermore, the pelagic larval phase accounted for 25.3%–28.5% of the maximum life span, and maturation occurred between 74.1 and 82.1 days at 15.2–15.8 mm, leaving only 35%–43% of the total life span as a reproductively viable adult. All mature individuals had gonad structures consistent with bidirectional sex change, with bisexual gonads including both ovarian and testicular portions separated by a thin wall of connective tissue. In the female and male phases, only ovaries or testes were mature, whereas gonadal tissue of the non‐active sex remained. One T. benjamini individual and one T. yanoi individual had ovarian and testicular tissue active simultaneously. The results of this study highlight the life‐history challenges small CRFs face on their path to reproduction and reproductive strategies that could be beneficial in fishes with high and unpredictable mortality and short reproductive life spans. [ABSTRACT FROM AUTHOR]

Plasticity, the capacity of individuals to respond to changing environments by modifying traits, may be critically important for population persistence by allowing for adaptive responses on shorter timescales than genetic change. Here, we use the clown anemonefish Amphiprion percula, whose access to resources is constrained by their anemones, to test the role of plasticity in generating variation in reproductive success among groups. We surveyed a wild clownfish population and found positive correlations between anemone area, fish size, reproduction and parental care. We used structural equation modeling to test the hypothesis that these correlations emanate from variation in anemone area and found support for a pathway linking anemone area to female investment, female investment to male investment and male investment to embryo survival. Next, we experimentally tested whether plasticity in response to resource availability can result in variation in parental traits using a feeding manipulation and found substantial plasticity in reproduction and parental care in response to changes in the availability of food resources. The results of this study reveal the role of plasticity in response to local resource availability in generating variation among individuals in reproductive strategies, linking studies of behavior and demography in this model species, and ultimately contributing to our ability to predict how populations might cope with environmental changes. [ABSTRACT FROM AUTHOR]

Hybridization and introgression are evolutionarily significant phenomena breaking down species boundaries. "Hybrid zones" (regions of species overlap and hybridization) enable quantification of hybridization frequency and examination of mechanisms driving and maintaining gene flow. The hybrid anemonefish Amphiprion leucokranos is found where parent species (A. chrysopterus; A. sandaracinos) distributions overlap. Here, we examine geographic variation in hybridization and introgression, and potential impacts on parent species integrity through assessing relative abundance, social group composition, and genetic structure (mtDNA cytochrome b, 21 microsatellite loci) of taxa at three hybrid zone locations: Kimbe Bay (KB) and Kavieng (KA), Papua New Guinea; the Solomon Islands (SO). Relative abundances of and size disparities between parent species apparently drive hybridization frequency, introgression patterns, and genetic composition of taxa. Conspecific groups are most common in KB (65%) where parent species are similarly abundant. Conversely, mixed species groups dominate SO (82%), where A. chrysopterus is more abundant. Hybrids most commonly cohabit with A. sandaracinos in KB (17%), but with A. chrysopterus in KA (22%) and SO (50%). Genetic differentiation (nDNA) analyses indicate that parent species remain distinct, despite ongoing hybridization and hybrids are genetically similar to A. sandaracinos—resulting from persistent backcrossing with this smallest species. This study shows that hybridization outcomes may depend on the social and ecological context in which taxa hybridize, where relative abundance and disparate size of parent species explain the frequency and patterns of hybridization and introgression in the A. leucokranos hybrid zone, reflecting size‐based dominance behaviors of anemonefish social groups. [ABSTRACT FROM AUTHOR]

Combining no‐take marine reserves with exclusive access by communities to unreserved waters could provide the required incentives for community management to achieve positive impacts. However, few protected areas have been critically evaluated for their impact, which involves applying counterfactual thinking to predict conditions within protected areas if management had never occurred. Here, we use statistical matching to conduct a rigorous impact evaluation of dual management systems on coral reef fishes in Tonga, with communities having both full no‐take areas and areas of exclusive fishing rights. No‐take areas generally had positive impacts on the species richness, biomass, density, and size of target reef fish, while exclusive access areas were similar to predicted counterfactual conditions. The latter is likely because overall fishing pressure in exclusive access areas might not actually change, although more fish could be exploited by communities with access rights. Our findings suggest that dual management is effective at incentivizing effective community‐based no‐take areas for biodiversity conservation and resource management. [ABSTRACT FROM AUTHOR]

The expansion of coastal marine protected areas can suffer from two key drawbacks: (a) the difficulty of incentivizing local communities to manage areas for conservation when their livelihoods also depend on resource use; and (b) that many protected areas get situated residually, or in locations with limited value for either biodiversity conservation or livelihoods. Here, we discuss and analyze key characteristics of Tonga's Special Management Area (SMA) program, including both the mechanisms that have motivated its successful national expansion and its ability to configure no‐take reserves in areas that are considered to have high value to resource users. Granting communities exclusive access zones in exchange for implementing no‐take reserves has encouraged conservation actions while fostering long‐term relationships with resources. Ensuring no‐take reserves occurred within the boundaries of exclusive access zones enabled communities to protect areas of greater extractive values than they would have otherwise. We conclude that the success of this program offers a way forward for achieving targets in the global expansion marine protected areas. [ABSTRACT FROM AUTHOR]

The relative contributions of environmental, maternal and additive genetic factors to the Lifetime reproductive success (LRS) determine whether species can adapt to rapid environmental change. Yet to date, studies quantifying LRS across multiple generations in marine species in the wild are non‐existent. Here we used 10‐year pedigrees resolved for a wild orange clownfish population from Kimbe Island (PNG) and a quantitative genetic linear mixed model approach to quantify the additive genetic, maternal and environmental contributions to variation in LRS for the self‐recruiting portion of the population. We found that the habitat of the breeder, including the anemone species and geographic location, made the greatest contribution to LRS. There were low to negligible contributions of genetic and maternal factors equating with low heritability and evolvability. Our findings imply that our population will be susceptible to short‐term, small‐scale changes in habitat structure and may have limited capacity to adapt to these changes. [ABSTRACT FROM AUTHOR]

Spatial refuges in peripheral habitats will become increasingly important for species persistence as climate change and other disturbances progressively impact habitat quality and assemblage compositions. However, the capacity for persistence will be determined in part by species‐specific abilities to absorb costs related to altered or decreased quantities and quality of resources at range peripheries.We compared variations in dietary strategies and energy acquisition trade‐offs along depth gradients in two obligate corallivores that differ in level of diet specialization. We also assessed depth‐related changes in energy pathways and energy content of their mixotrophic prey. We found no changes in feeding effort or total resource availability (total coral cover) towards deep range margins, but availability of the preferred resource (Acropora coral) decreased. While both species selectively targeted Acropora, the more specialized species (Chaetodon baronessa) exhibited limited feeding plasticity along the depth gradient. The degree of selectivity towards the preferred coral increased rather than decreased with depth, being 40 times greater than expected, given availability, at their range periphery. In contrast, the generalist's diet (Chaetodon octofasciatus) varied greatly in response to changes in resource availability with depth.Unexpectedly, the energy content of Acropora did not decline with depth, likely due to increased coral heterotrophy in deeper water, indicated by shifts in their molecular isotope geochemistry. This shift was accompanied by a 20% increase in plankton‐sourced carbon in the muscle tissue of deep‐resident fish, despite no observations of direct feeding on plankton food sources.Our results indicate that deep ranges in coral‐obligate reef fishes are supported by multiple mechanisms of trophic versatility in both the fish and corals. This nutritional plasticity likely serves a compensatory role in the resilience and eventual adaptation of organisms at their range peripheries.For species vulnerable to increasing anthropogenic impacts at range cores, variable and multi‐trophic functional responses can act to buffer against costs and increase the refuge potential of range peripheries. Specialist consumers may also be supported indirectly at range margins via trophic plasticity within their preferred prey. A free Plain Language Summary can be found within the Supporting Information of this article. [ABSTRACT FROM AUTHOR]

Many vertebrates form monogamous pairs to mate and care for their offspring. However, genetic tools have increasingly shown that offspring often arise from matings outside of the monogamous pair bond. Social monogamy is relatively common in coral reef fishes, but there have been few studies that have confirmed monogamy or extra‐pair reproduction, either for males or for females. Here, long‐term observations and genetic tools were applied to examine the parentage of embryos in a paternally mouth‐brooding cardinalfish, Sphaeramia nematoptera. Paternal care in fishes, such as mouth‐brooding, is thought to be associated with a high degree of confidence in paternity. Two years of observations confirmed that S. nematoptera form long‐term pair bonds within larger groups. However, genetic parentage revealed extra‐pair mating by both sexes. Of 105 broods analysed from 64 males, 30.1% were mothered by a female that was not the partner and 11.5% of broods included eggs from two females. Despite the high paternal investment associated with mouth‐brooding, 7.6% of broods were fertilized by two males. Extra‐pair matings appeared to be opportunistic encounters with individuals from outside the immediate group. We argue that while pair formation contributes to group cohesion, both males and females can maximize lifetime reproductive success by taking advantage of extra‐pair mating opportunities. [ABSTRACT FROM AUTHOR]

Abstract: Marine reserves are a commonly applied conservation tool, but their size is often chosen based on considerations of socioeconomic rather than ecological impact. Here, we use a simple individual‐based model together with the latest empirical information on home ranges, densities and schooling behaviour in 66 coral reef fishes to quantify the conservation effectiveness of various reserve sizes. We find that standard reserves with a diameter of 1–2 km can achieve partial protection (≥50% of the maximum number of individuals) of 56% of all simulated species. Partial protection of the most important fishery species, and of species with diverse functional roles, required 2–10 km wide reserves. Full protection of nearly all simulated species required 100 km wide reserves. Linear regressions based on the mean home range and density, and even just the maximum length, of fish species approximated these results reliably, and can therefore be used to support locally effective decision making. [ABSTRACT FROM AUTHOR]

Abstract: Dispersal kernels are the standard method in biology for describing and predicting the relationship between dispersal and distance. Statistically fitted dispersal kernels allow observations of a limited number of dispersal events to be extrapolated across a wider landscape, and form the basis of a wide range of theories and methods in ecology, evolution and conservation. Genetic parentage data are an increasingly common source of dispersal information, particularly for species where dispersal is difficult to observe directly. In particular, parentage analysis is now routinely applied to coral reef fish, whose larvae can potentially disperse over many kilometres, and are too small to track in situ. It is not straightforward to estimate dispersal kernels from parentage data, and existing methods all have substantial limitations. These include the omission of important population processes such as density‐dependent mortality, and data on unassigned juveniles. Here we develop and proof a new likelihood estimator for fitting dispersal kernels to parentage data, applying it to simulated parentage datasets for coral reef fish on the Great Barrier Reef (GBR). The method incorporates a series of factors not previously considered in other methods: the partial sampling of adults and juveniles on sampled sites; the existence of unassigned dispersers from unsampled habitat patches; and post‐settlement processes (e.g. density‐dependent mortality) that follow dispersal but precede parentage sampling. Including these additional factors requires an estimate of adult populations on unsampled habitat patches, but the result is a superior estimate of dispersal kernels and mean dispersal distances. Our power analyses suggest that the parentage datasets currently available for reef fishes are large enough to fit accurate dispersal kernels. Based on the analyses in one particular region of the GBR, parentage sampling should be distributed equally between adults and juveniles, and should sample more than 3% of the adult population. However, while the resulting dispersal kernels offer reasonable estimates of mean dispersal, they fail to capture important variation in realistic dispersal patterns. [ABSTRACT FROM AUTHOR]

Coral reefs are highly diverse ecosystems, where numerous closely related species often coexist. How new species arise and are maintained in these high geneflow environments have been long-standing conundrums. Hybridization and patterns of introgression between sympatric species provide a unique insight into the mechanisms of speciation and the maintenance of species boundaries. In this study, we investigate the extent of hybridization between two closely related species of coral reef fish: the common coral trout ( Plectropomus leopardus) and the bar-cheek coral trout ( Plectropomus maculatus). Using a complementary set of 25 microsatellite loci, we distinguish pure genotype classes from first- and later-generation hybrids, identifying 124 interspecific hybrids from a collection of 2,991 coral trout sampled in inshore and mid-shelf reefs of the southern Great Barrier Reef. Hybrids were ubiquitous among reefs, fertile and spanned multiple generations suggesting both ecological and evolutionary processes are acting to maintain species barriers. We elaborate on these finding to investigate the extent of genomic introgression and admixture from 2,271 SNP loci recovered from a dd RAD library of pure and hybrid individuals. An analysis of genomic clines on recovered loci indicates that 261 SNP loci deviate from a model of neutral introgression, of which 132 indicate a pattern of introgression consistent with selection favouring both hybrid and parental genotypes. Our findings indicate genome-wide, bidirectional introgression between two sympatric species of coral reef fishes and provide further support to a growing body of evidence for the role of hybridization in the evolution of coral reef fishes. [ABSTRACT FROM AUTHOR]

Abstract: Diet specificity is likely to be the key predictor of a predator's vulnerability to changing habitat and prey conditions. Understanding the degree to which predatory coral reef fishes adjust or maintain prey choice, in response to declines in coral cover and changes in prey availability, is critical for predicting how they may respond to reef habitat degradation. Here, we use stable isotope analyses to characterize the trophic structure of predator–prey interactions on coral reefs of the Keppel Island Group on the southern Great Barrier Reef, Australia. These reefs, previously typified by exceptionally high coral cover, have recently lost much of their coral cover due to coral bleaching and frequent inundation by sediment‐laden, freshwater flood plumes associated with increased rainfall patterns. Long‐term monitoring of these reefs demonstrates that, as coral cover declined, there has been a decrease in prey biomass, and a shift in dominant prey species from pelagic plankton‐feeding damselfishes to territorial benthic algal‐feeding damselfishes, resulting in differences in the principal carbon pathways in the food web. Using isotopes, we tested whether this changing prey availability could be detected in the diet of a mesopredator (coral grouper, Plectropomus maculatus). The δ13C signature in grouper tissue in the Keppel Islands shifted from a more pelagic to a more benthic signal, demonstrating a change in carbon sources aligning with the change in prey availability due to habitat degradation. Grouper with a more benthic carbon signature were also feeding at a lower trophic level, indicating a shortening in food chains. Further, we found a decline in the coral grouper population accompanying a decrease in total available prey biomass. Thus, while the ability to adapt diets could ameliorate the short‐term impacts of habitat degradation on mesopredators, long‐term effects may negatively impact mesopredator populations and alter the trophic structure of coral reef food webs. [ABSTRACT FROM AUTHOR]

Larval dispersal by ocean currents is a critical component of systematic marine protected area ( MPA) design. However, there is a lack of quantitative methods to incorporate larval dispersal in support of increasingly diverse management objectives, including local population persistence under multiple types of threats (primarily focused on larval retention within and dispersal between protected locations) and benefits to unprotected populations and fisheries (primarily focused on larval export from protected locations to fishing grounds). Here, we present a flexible MPA design approach that can reconcile multiple such potentially conflicting management objectives by balancing various associated treatments of larval dispersal information. We demonstrate our approach based on alternative dispersal patterns, combinations of threats to populations, management objectives, and two different optimization strategies (site vs. network-based). Our outcomes highlight a consistently high effectiveness in selecting priority locations that are self-replenishing, inter-connected, and/or important larval sources. We find that the opportunity to balance these three dispersal attributes flexibly can help not only to prevent meta-population collapse, but also to ensure effective fisheries recovery, with average increases in the number of recruits at fishing grounds at least two times higher than achieved by standard habitat-based or ad-hoc MPA designs. Future applications of our MPA design approach should therefore be encouraged, specifically where management tools other than MPAs are not feasible. [ABSTRACT FROM AUTHOR]

Larval dispersal is the key process by which populations of most marine fishes and invertebrates are connected and replenished. Advances in larval tagging and genetics have enhanced our capacity to track larval dispersal, assess scales of population connectivity, and quantify larval exchange among no-take marine reserves and fished areas. Recent studies have found that reserves can be a significant source of recruits for populations up to 40 km away, but the scale and direction of larval connectivity across larger seascapes remain unknown. Here, we apply genetic parentage analysis to investigate larval dispersal patterns for two exploited coral reef groupers ( Plectropomus maculatus and Plectropomus leopardus) within and among three clusters of reefs separated by 60-220 km within the Great Barrier Reef Marine Park, Australia. A total of 69 juvenile P. maculatus and 17 juvenile P. leopardus (representing 6% and 9% of the total juveniles sampled, respectively) were genetically assigned to parent individuals on reefs within the study area. We identified both short-distance larval dispersal within regions (200 m to 50 km) and long-distance, multidirectional dispersal of up to ~250 km among regions. Dispersal strength declined significantly with distance, with best-fit dispersal kernels estimating median dispersal distances of ~110 km for P. maculatus and ~190 km for P. leopardus. Larval exchange among reefs demonstrates that established reserves form a highly connected network and contribute larvae for the replenishment of fished reefs at multiple spatial scales. Our findings highlight the potential for long-distance dispersal in an important group of reef fishes, and provide further evidence that effectively protected reserves can yield recruitment and sustainability benefits for exploited fish populations. [ABSTRACT FROM AUTHOR]

Bleaching (whitening) of cnidarians such as corals and sea anemones has caused widespread degradation of coral reefs around the world and is therefore an urgent issue for coral reef science and conservation. Although cnidarians often bleach in aquaria, methods for experimental induction of bleaching in wild cnidarians are lacking, which impedes scientists' ability to understand the ultimate effects of bleaching on the broader ecosystem. In this study, we investigated the utility of an in situ method for experimental induction of bleaching in the tropical sea anemone Heteractis crispa. Healthy, wild anemones were covered with opaque black plastic sheets, mesh cages or left undisturbed (controls) and tentacle colour and body size were monitored with a colour reference card and flexible tape, respectively, every 1-3 days for 15 days. Caged and control anemones remained unchanged for the duration of the experiment, but covered anemones commenced whitening after 4-6 days and were completely white after 7-14 days (mean time to bleaching ± SE = 10.1 ± 0.7 days). Experimental bleaching occurred without reduction in anemone body size and was visibly similar to natural bleaching seen previously in H. crispa. We hypothesize that light-deprivation, reduced water flow, physical contact or some combination of these factors caused the bleaching. This study provides the basis for a simple and rapid method of inducing bleaching in situ, which releases scientists' dependence on sporadic natural bleaching events or artificial aquarium experiments, and provides a means to investigate the effects of bleaching on other ecosystem components such as fishes. [ABSTRACT FROM AUTHOR]

Marine reserves are often established in areas that support fisheries. Larval export from reserves is argued to help compensate for the loss of fishable habitat; however, previous modeling studies have focused on long-term equilibrium outcomes. We examined the transient consequences of reserve establishment for fished metapopulations, considering both a well-mixed larval pool and a spatially explicit model based on a coral trout ( Plectropomus spp.) metapopulation. When fishing pressure was reallocated relative to the area protected, yields decreased initially, then recovered, and ultimately exceeded pre-reserve levels. However, recovery time was on the order of several years to decades. If fishing pressure intensified to maintain pre-reserve yields, reserves were sometimes unable to support the increased mortality and the metapopulation collapsed. This was more likely when reserves were small, or located peripherally within the metapopulation. Overall, reserves can achieve positive conservation and fishery benefits, but fisheries management complementary to reserve implementation is essential. [ABSTRACT FROM AUTHOR]

The development of parentage analysis to track the dispersal of juvenile offspring has given us unprecedented insight into the population dynamics of coral reef fishes. These tools now have the potential to inform fisheries management and species conservation, particularly for small fragmented populations under threat from exploitation and disturbance. In this study, we resolve patterns of larval dispersal for a population of the anemonefish Amphiprion melanopus in the Keppel Islands (southern Great Barrier Reef). Habitat loss and fishing appear to have impacted this population and a network of no-take marine reserves currently protects 75% of the potential breeders. Using parentage analysis, we estimate that 21% of recruitment in the island group was generated locally and that breeding adults living in reserves were responsible for 79% (31 of 39) of these of locally produced juveniles. Overall, the network of reserves was fully connected via larval dispersal; however, one reserve was identified as a critical source of larvae for the island group. The population in the Keppel Islands also appears to be well-connected to other source populations at least 60 km away, given that 79% (145 of 184) of the juveniles sampled remained unassigned in the parentage analysis. We estimated the effective size of the A. melanopus metapopulation to be 745 (582-993 95% CI) and recommend continued monitoring of its genetic status. Maintaining connectivity with populations beyond the Keppel Islands and recovery of local recruitment habitat, potentially through active restoration of host anemone populations, will be important for its long-term persistence. [ABSTRACT FROM AUTHOR]

Recent theory suggests that a mix of lottery and niche processes can facilitate coexistence between competing species, but this has not yet been empirically tested. Previous research has suggested that a competitive lottery for space promotes coexistence between two ecologically similar species, Gobiodon histrio and Gobiodon erythrospilus. However, not all the assumptions of lottery competition have been tested, and patterns of habitat use by adults suggest niche partitioning. Here, we investigated the hypothesis that the mechanism of competition changes with ontogeny, with a lottery for space operating at settlement and niche partitioning occurring in adults. Patterns of resource use in the field were compared for juveniles and adults of the two species. Pelagic larval duration (PLD) and size-at-settlement was also estimated to determine if size differences at settlement could affect the outcome of competitive interactions among juveniles. Habitat preference and size-based competitive ability were then tested for juveniles and adults in laboratory experiments. Finally, a transplant experiment was performed to test the fitness-associated consequences of niche partitioning among adults and its implications for coexistence of the two species. G. histrio had a similar PLD (20.7 ± 2.0 days) to G. erythrospilus (18.5 ± 1.9 days), and there was no difference in size-at-settlement between the species. Juveniles of the two species had similar patterns of habitat use and similar competitive abilities, supporting the lottery mechanism at settlement. However, adults differ in their habitat use, supporting the prediction that resource partitioning increases with ontogeny. In laboratory experiments, adults of each species preferred colonies of Acropora nasuta. However, G. histrio was a superior competitor and prevented G. erythrospilus from using A. nasuta in >70% of the trials. In the field transplant experiment, G. erythrospilus (inferior competitor) suffered less of a fitness loss when occupying the non-preferred coral (A. spathulata) compared with G. histrio, which could explain its ability to persist when displaced by the superior competitor. These results suggest that the competitive mechanism operating between the two Gobiodon species shifts from a lottery for space to niche partitioning through ontogeny, and that these two mechanisms of competitive coexistence are not mutually exclusive. [ABSTRACT FROM AUTHOR]

Habitat degradation is predicted to exacerbate competition for critical resources; however, the relationship between habitat quality and competition is poorly understood. In this study, we used a manipulative experiment to test the effects of habitat degradation on competition between two planktivorous, coral-dwelling damselfishes, Chrysiptera parasema and Dascyllus melanurus. Experimental reefs were constructed with either healthy (100% live) or degraded (10% live) Acropora longicyathus coral, stocked with varying densities of these two fish species, and monitored for two months. On healthy habitat, the mortality of C. parasema was density dependent, and increased substantially in the presence of the dominant interspecific competitor D. melanurus. In contrast, on reefs where habitat was degraded, C. parasema mortality was highly variable, density independent, and was no longer influenced by the presence of dominant competitor D. melanurus. Behavioral observations revealed that agonistic interactions for both species increased with density on degraded habitat, but not on healthy habitat. In addition, on degraded reefs, both species displayed a reduced association with reef habitat and ventured further away from shelter with increasing densities of the dominant competitor D. melanurus. These results suggest that reduced habitat quality can have such a profound effect on reef fishes, that it eliminates density-dependent mortality and competitive dominance hierarchies, thereby substantially altering the mechanisms that structure reef fish communities. [ABSTRACT FROM AUTHOR]

Microsatellites are often considered ideal markers to investigate ecological processes in animal populations. They are regularly used as genetic barcodes to identify species, individuals, and infer familial relationships. However, such applications are highly sensitive the number and diversity of microsatellite markers, which are also prone to error. Here, we propose a novel framework to assess the suitability of microsatellite datasets for parentage analysis and species discrimination in two closely related species of coral reef fish, Plectropomus leopardus and P. maculatus ( Serranidae). Coral trout are important fisheries species throughout the Indo-Pacific region and have been shown to hybridize in parts of the Great Barrier Reef, Australia. We first describe the development of 25 microsatellite loci and their integration to three multiplex PCRs that co-amplify in both species. Using simulations, we demonstrate that the complete suite of markers provides appropriate power to discriminate between species, detect hybrid individuals, and resolve parent-offspring relationships in natural populations, with over 99.6% accuracy in parent-offspring assignments. The markers were also tested on seven additional species within the Plectropomus genus with polymorphism in 28-96% of loci. The multiplex PCRs developed here provide a reliable and cost-effective strategy to investigate evolutionary and ecological dynamics and will be broadly applicable in studies of wild populations and aquaculture brood stocks for these closely related fish species. [ABSTRACT FROM AUTHOR]

Genetic parentage analyses provide a practical means with which to identify parent-offspring relationships in the wild. In Harrison et al.'s study (2013a), we compare three methods of parentage analysis and showed that the number and diversity of microsatellite loci were the most important factors defining the accuracy of assignments. Our simulations revealed that an exclusion-Bayes theorem method was more susceptible to false-positive and false-negative assignments than other methods tested. Here, we analyse and discuss the trade-off between type I and type II errors in parentage analyses. We show that controlling for false-positive assignments, without reporting type II errors, can be misleading. Our findings illustrate the need to estimate and report both the rate of false-positive and false-negative assignments in parentage analyses. [ABSTRACT FROM AUTHOR]

Parentage studies and family reconstructions have become increasingly popular for investigating a range of evolutionary, ecological and behavioural processes in natural populations. However, a number of different assignment methods have emerged in common use and the accuracy of each may differ in relation to the number of loci examined, allelic diversity, incomplete sampling of all candidate parents and the presence of genotyping errors. Here, we examine how these factors affect the accuracy of three popular parentage inference methods ( colony, famoz and an exclusion- Bayes' theorem approach by Christie ( Molecular Ecology Resources, 2010a, 10, 115) to resolve true parent-offspring pairs using simulated data. Our findings demonstrate that accuracy increases with the number and diversity of loci. These were clearly the most important factors in obtaining accurate assignments explaining 75-90% of variance in overall accuracy across 60 simulated scenarios. Furthermore, the proportion of candidate parents sampled had a small but significant impact on the susceptibility of each method to either false-positive or false-negative assignments. Within the range of values simulated, colony outperformed Fa Moz, which outperformed the exclusion- Bayes' theorem method. However, with 20 or more highly polymorphic loci, all methods could be applied with confidence. Our results show that for parentage inference in natural populations, careful consideration of the number and quality of markers will increase the accuracy of assignments and mitigate the effects of incomplete sampling of parental populations. [ABSTRACT FROM AUTHOR]

Connectivity, the demographic linking of local populations through the dispersal of individuals, is one of the most poorly understood processes in population dynamics, yet has profound implications for conservation and harvest strategies. For marine species with pelagic larvae, direct estimation of connectivity remains logistically challenging and has mostly been limited to single snapshots in time. Here, we document seasonal and interannual patterns of larval dispersal in a metapopulation of the coral reef fish Amphiprion polymnus. A 3-year record of larval trajectories within and among nine discrete local populations from an area of approximately 35 km was established by determining the natal origin of settled juveniles through DNA parentage analysis. We found that spatial patterns of both self-recruitment and connectivity were remarkably consistent over time, with a low level of self-recruitment at the scale of individual sites. Connectivity among sites was common and multidirectional in all years and was not significantly influenced by seasonal variability of predominant surface current directions. However, approximately 75% of the sampled juveniles could not be assigned to parents within the study area, indicating high levels of immigrations from sources outside the study area. The data support predictions that the magnitude and temporal stability of larval connectivity decreases significantly with increasing distance between subpopulations, but increases with the size of subpopulations. Given the considerable effort needed to directly measure larval exchange, the consistent patterns suggest snapshot parentage analyses can provide useful dispersal estimates to inform spatial management decisions. [ABSTRACT FROM AUTHOR]

Aim To determine the applicability of biogeographical and ecological theory to marine species at two remote island locations. This study examines how biogeography, isolation and species geographic range size influence patterns of species richness, endemism, species composition and the abundance of coral reef fishes. Location Christmas Island and the Cocos (Keeling) Islands in the tropical eastern Indian Ocean. Methods Published species lists and underwater visual surveys were used to determine species richness, endemism, species composition and abundance of reef fishes at the islands. These data were statistically compared with patterns of species composition and abundance from the neighbouring 'mainland' Indonesian region. Results The two isolated reef fish communities were species-poor and contained a distinct taxonomic composition with an overrepresentation of species with high dispersal potential. Despite low species richness, we found no evidence of density compensation, with population densities on the islands similar to those of species-rich mainland assemblages. The mix of Indian and Pacific Ocean species and the proportional representations of the various regional faunas in the assemblages were not influenced by the relative proximity of the islands to different biogeographical provinces. Moreover, species at the edge of their range did not have a lower abundance than species at the centre of their range, and endemic species had substantially higher abundances than widespread species. At both locations, endemism was low (less than 1.2% of the community); this may be because the locations are not sufficiently isolated or old enough to promote the evolution of endemic species. Main conclusions The patterns observed generally conform to terrestrial biogeographical theory, suggesting that similar processes may be influencing species richness and community composition in reef fish communities at these remote islands. However, species abundances differed from typical terrestrial patterns, and this may be because of the life history of reef fishes and the processes maintaining isolated populations. [ABSTRACT FROM AUTHOR]

Increased habitat diversity is often predicted to promote the diversity of animal communities because a greater variety of habitats increases the opportunities for species to specialize on different resources and coexist. Although positive correlations between the diversities of habitat and associated animals are often observed, the underlying mechanisms are only now starting to emerge, and none have been tested specifically in the marine environment. Scieractinian corals constitute the primary habitat-forming organisms on coral reefs and, as such, play an important role in structuring associated reef fish communities. Using the same field experimental design in two geographic localities differing in regional fish species composition, we tested the effects of coral species richness and composition on the diversity, abundance, and structure of the local fish community. Richness of coral species overall had a positive effect on fish species richness but had no effect on total fish abundance or evenness. At both localities, certain individual coral species supported similar levels of fish diversity and abundance as the high coral richness treatments, suggesting that particular coral species are disproportionately important in promoting high local fish diversity. Furthermore, in both localities, different microhabitats (coral species) supported very different fish communities, indicating that most reef fish species distinguish habitat at the level of coral species. Fish communities colonizing treatments of higher coral species richness represented a combination of those inhabiting the constituent coral species. These findings suggest that mechanisms underlying habitat-animal interaction in the terrestrial environment also apply to marine systems and highlight the importance of coral diversity to local fish diversity. The loss of particular key cOral species is likely to have a disproportionate impact on the biodiversity of associated fish communities. [ABSTRACT FROM AUTHOR]

Disturbance can result in the fragmentation and/or loss of suitable habitat, both of which can have important consequences for survival, species interactions, and resulting patterns of local diversity. However, effects of habitat loss and fragmentation are typically confounded during disturbance events, and previous attempts to determine their relative significance have proved ineffective. Here we experimentally manipulated live coral habitats to examine the potential independent and interactive effects of habitat loss and fragmentation on survival, abundance, and species richness of recruitment-stage, coral-associated reef fishes. Loss of 75% of live coral from experimental reefs resulted in low survival of a coral-associated damselfish and low abundance and richness of other recruits 16 weeks after habitat manipulations. In contrast, fragmentation had positive effects on damselfish survival and resulted in greater abundance and species richness of other recruits. We hypothesize that spacing of habitat through fragmentation weakens competition within and among species. Comparison of effect sizes over the course of the study period revealed that, in the first six weeks following habitat manipulations, the positive effects of fragmentation were at least four times stronger than the effects of habitat loss. This initial positive effect of fragmentation attenuated considerably after 16 weeks, whereas the negative effects of habitat loss increased in strength over time. There was little indication that the amount of habitat influenced the magnitude of the habitat fragmentation effect. Numerous studies have reported dramatic declines in coral reef fish abundance and diversity in response to disturbances that cause the loss and fragmentation of coral habitats. Our results suggest that these declines occur as a result of habitat loss, not habitat fragmentation. Positive fragmentation effects may actually buffer against the negative effects of habitat loss and contribute to the resistance of reef fish populations to declines in coral cover. [ABSTRACT FROM AUTHOR]

While ocean acidification is predicted to threaten marine biodiversity, the processes that directly impact species persistence are not well understood. For marine species, early life history stages are inherently vulnerable to predators and an innate ability to detect predators can be critical for survival. However, whether or not acidification inhibits predator detection is unknown. Here, we show that newly hatched larvae of the marine fish Amphiprion percula innately detect predators using olfactory cues and this ability is retained through to settlement. Aquarium-reared larvae, not previously exposed to predators, were able to distinguish between the olfactory cues of predatory and non-predatory species. However, when eggs and larvae were exposed to seawater simulating ocean acidification (pH 7.8 and 1000 p.p.m. CO2) settlement-stage larvae became strongly attracted to the smell of predators and the ability to discriminate between predators and non-predators was lost. Newly hatched larvae were unaffected by CO2 exposure and were still able to distinguish between predatory and non-predatory fish. If this impairment of olfactory preferences in settlement-stage larvae translates to higher mortality as a result of increased predation risk, there could be direct consequences for the replenishment and the sustainability of marine populations. Ecology Letters (2010) 13: 68–75 [ABSTRACT FROM AUTHOR]

Climate change will impact coral-reef fishes through effects on individual performance, trophic linkages, recruitment dynamics, population connectivity and other ecosystem processes. The most immediate impacts will be a loss of diversity and changes to fish community composition as a result of coral bleaching. Coral-dependent fishes suffer the most rapid population declines as coral is lost; however, many other species will exhibit long-term declines due to loss of settlement habitat and erosion of habitat structural complexity. Increased ocean temperature will affect the physiological performance and behaviour of coral reef fishes, especially during their early life history. Small temperature increases might favour larval development, but this could be counteracted by negative effects on adult reproduction. Already variable recruitment will become even more unpredictable. This will make optimal harvest strategies for coral reef fisheries more difficult to determine and populations more susceptible to overfishing. A substantial number of species could exhibit range shifts, with implications for extinction risk of small-range species near the margins of reef development. There are critical gaps in our knowledge of how climate change will affect tropical marine fishes. Predictions are often based on temperate examples, which may be inappropriate for tropical species. Improved projections of how ocean currents and primary productivity will change are needed to better predict how reef fish population dynamics and connectivity patterns will change. Finally, the potential for adaptation to climate change needs more attention. Many coral reef fishes have geographical ranges spanning a wide temperature gradient and some have short generation times. These characteristics are conducive to acclimation or local adaptation to climate change and provide hope that the more resilient species will persist if immediate action is taken to stabilize Earth’s climate. [ABSTRACT FROM AUTHOR]

Fishes that feed from live corals (corallivores) are a conspicuous component of healthy coral reef environments. However, knowledge of the occurrence and ecological significance of this feeding mode is fragmentary. Historically, very few fish were considered capable of feeding from live coral, and those few that did were considered ecologically insignificant. More recently, the role of corallivores has been re-evaluated; published records document 128 corallivorous fish species from 11 different families, with 69 of these belonging to the family Chaetodontidae. Other families, including the Labridae, Tetraodontidae, Balistidae, Monacanthidae, Pomacentridae and Scaridae, all have between seven and ten coral-feeding species. One-third of coral-feeding fishes feed almost exclusively on corals, with more than 80% of their diet based on coral. Corallivorous fish show distinct prey preferences and consume only a small subset of available corals, usually the genera Acropora, Pocillopora and Porites. This selective predation by corallivores can limit abundance and distribution of preferred corals. Chronic predation by corallivores may also exacerbate effects of coral disturbance (e.g. climate-induced coral bleaching), impeding reef recovery and causing further coral loss. Conversely, the cover of preferred corals can be a primary determinant of corallivore abundance and physiological condition. Owing to this close association, obligate corallivores invariably decline in response to loss of coral cover. Increased knowledge of the number of corallivores and their diets suggest that this feeding mode is more important to coral reef food webs than traditionally thought. [ABSTRACT FROM AUTHOR]

The relative roles of competition and predation in demographic density dependence are poorly known. A tractable experimental design to determine such effects and their interactions for demersal (seafloor oriented) fishes and similar sedentary species is cross-factoring multiple densities of new recruits with the presence and absence of predators. This design allows one to distinguish between density-dependent mortality due to competition alone, predation alone, or an interaction between the two, especially when supplemental field observations are available. To date, 14 species of marine fish have been examined with some variant of this design, and for 12 species predation was demonstrated to be the sole or major cause of density dependence. However, as competition may be slow acting relative to predation, the importance of competition can be underestimated in short-term experiments. On the Great Barrier Reef, we conducted a long-term field experiment in which multiple densities of new recruits of a planktivorous damselfish were cross-factored with the presence or absence of resident piscivorous fish on patch reefs. During the first 10 months, no density-dependent mortality was detected, regardless of whether resident predators were present or absent. By the end of the experiment at 17 months, per capita mortality was strongly density dependent and highly compensatory in both predator treatments; all reefs ultimately. supported nearly the same adult density regardless of experimental treatment. Examination of treatment effect sizes suggested that competition was the main source of density-dependent mortality, with predation being merely a proximate agent of death. We hypothesize that predators were ineffective in this system compared, with similar studies elsewhere because prey density was low relative to ample prey refuges provided by highly complex corals. Combined with previous studies, these findings indicate that density-dependent mortality in demersal marine fishes is often caused by interplay of predation and competition, whose roles may be altered by variation in habitat complexity and larval supply. These conclusions are relevant to marine fisheries models, which typically assume that density dependence is due solely to intraspecific competition. [ABSTRACT FROM AUTHOR]

Focuses on a study that examined the separate effects if habitat availability, fragmentation and degradation on the species richness and abundances of commensal species occupying coral colonies at the Great Barrier Reef in Australia. Review of related literature; Methods used; Results and discussion.

Investigates the effects of interspecific competition for coral habitats on the abundance and coexistence of six gobies (Gobiodon) species at Lizard Island in the Great Barrier Reef, Queensland. Habitat use; Competitive ability; Competitor reduction; Habitat overlap; Recolonization.

Examines the effects of fish removal and habitat disturbance on the structure of fish assemblages occupying small coral patch reefs at Lizard Island, Australia. Importance of distrubance in the dynamics of a wide variety of ecological communities; Effect of disturbance-induced heterogeniety into patches; Central role of habitat as a mediator of interactions.

Compares the persistence and resilience of a temperate blennoid fish guild at three scales spanning an order of magnitude. Assessment of the stability of a community; Within-year changes in guild composition due to species-specific settlement timing and survivorship; Community structure; Direct disturbance; Edge effects; Fish removal.

An experiment on a coral reef fish is described that assesses the effects of recruitment success on adult abundance over a 3-yr period. The damselfish Pomacentrus amboinensis was examined on natural patch reefs of °8 m2 in the lagoon of One Tree Reef. Recruitment levels were adjusted to 0, 0.5, 1, and 2 recruits m-2°yr-1 by transplanting juveniles among reefs at the end of four successive recruitment seasons (with four replicates per treatment). Natural recruitment success was monitored on 16 undisturbed reefs, and adult numbers were monitored at irregular intervals on both experimental and undisturbed reefs. The adult population density at the end of the experiment increased significantly with recruitment within the 0-1 recruit/m2 range. However, doubling recruitment from 1 to 2 recruits/m2 did not lead to any further increase in adult density. The recruitment treatments did not affect adult density until a 2-yr period had elapsed (corresponding to average maturation time). At this time, treatments receiving 1 and 2 recruits/m2 showed a dramatic increase in adult numbers, whereas in the low-recruitment treatments, adult densities declined. The experiment indicated that a recruitment success of between 0.5 and 1 recruit/m2 was necessary to maintain adult numbers at pre-experimental levels. Natural recruitment success was highly variable among years, but adult densities remained relatively constant over time at °0.8 adult/m2. Differences in the final adult densities among reefs were correlated with average recruitment levels, but above 0.8-1.0 recruit/m2, adult densities did not increase with increasing recruitment success. The results from experimental and undisturbed reefs suggest that natural variation in recruitment success affects the importance of post-recruitment processes. In good recruitment years, adult densities on a substantial number of reefs may be limited by density-dependent processes, which may affect the majority of individuals in a region. Density-dependent juvenile growth may buffer adult populations on these reefs against the effects of poor recruitment years, since input may come from a number of immature age classes. Where recruitment success is always below a certain level, the dynamics of adult populations will reflect variation in recruitment success. [ABSTRACT FROM AUTHOR]

Marine reserve networks are increasingly implemented to conserve biodiversity and enhance the persistence and resilience of exploited species and ecosystems. However, the efficacy of marine reserve networks in frequently disturbed systems, such as coral reefs, has rarely been evaluated. Here we analyze a well‐mixed larval pool model and a spatially explicit model based on a well‐documented coral trout (Plectropomus spp.) metapopulation in the Great Barrier Reef Marine Park, Australia, to determine the effects of marine reserve coverage and placement (in relation to larval connectivity and disturbance heterogeneity) on the temporal stability of fisheries yields and population biomass in environmentally disturbed systems. We show that marine reserves can contribute to stabilizing fishery yield while increasing metapopulation persistence, irrespective of whether reserves enhance or diminish average fishery yields. However, reserve placement and the level of larval connectivity among subpopulations were important factors affecting the stability and sustainability of fisheries and fish metapopulations. Protecting a mix of disturbed and non‐disturbed reefs, rather than focusing on the least‐disturbed habitats, was the most consistently beneficial approach across a range of dispersal and reserve coverage scenarios. Placing reserves only in non‐disturbed areas was the most beneficial for biomass enhancement, but had variable results for fisheries and could potentially destabilize yields in systems with well‐mixed larval or those that are moderately fished. We also found that focusing protection on highly disturbed areas could actually increase variability in yields and biomass, especially when degraded reef reserves were distant and poorly connected to the meta‐population. Our findings have implications for the design and implementation of reserve networks in the presence of stochastic, patchy environmental disturbances. [ABSTRACT FROM AUTHOR]

During the planning phase the efficacy of different strategies to manage marine resources should ultimately be assessed by their potential impact, or ability to make a difference to ecological and social outcomes. While community‐based and systematic approaches to establishing marine protected areas have their strengths and weaknesses, comparisons of their effectiveness often fail to explicitly address potential impact. Here, we predict conservation impact to compare recently implemented community‐based marine reserves in Tonga to a systematic configuration specifically aimed at maximizing impact. Boosted regression tree outputs indicated that fishing pressure accounted for ∼24% of variation in target species biomass. We estimate that the community‐based approach provides 84% of the recovery potential of the configuration with the greatest potential impact. This high potential impact results from community‐based reserves being located close to villages, where fishing pressure is greatest. These results provide strong support for community‐based marine management, with short‐term benefits likely to accrue even where there is little scope for systematic reserve design. [ABSTRACT FROM AUTHOR]