Empirical validation of integrated stock assessment models to ensuring risk equivalence: A pathway to resilient fisheries management.

The Precautionary Approach to Fisheries Management requires an assessment of the impact of uncertainty on the risk of achieving management objectives. However, the main quantities, such as spawning stock biomass (SSB) and fish mortality (F), used in management metrics cannot be directly observed. This requires the use of models to provide guidance, for which there are three paradigms: the best assessment, model ensemble, and Management Strategy Evaluation (MSE). It is important to validate the models used to provide advice. In this study, we demonstrate how stock assessment models can be validated using a diagnostic toolbox, with a specific focus on prediction skill. Prediction skill measures the precision of a predicted value, which is unknown to the model, in relation to its observed value. By evaluating the accuracy of model predictions against observed data, prediction skill establishes an objective framework for accepting or rejecting model hypotheses, as well as for assigning weights to models within an ensemble. Our analysis uncovers the limitations of traditional stock assessment methods. Through the quantification of uncertainties and the integration of multiple models, our objective is to improve the reliability of management advice considering the complex interplay of factors that influence the dynamics of fish stocks.

Conservation successes and challenges for wide-ranging sharks and rays.

Overfishing is the most significant threat facing sharks and rays. Given the growth in consumption of seafood, combined with the compounding effects of habitat loss, climate change, and pollution, there is a need to identify recovery paths, particularly in poorly managed and poorly monitored fisheries. Here, we document conservation through fisheries management success for 11 coastal sharks in US waters by comparing population trends through a Bayesian state-space model before and after the implementation of the 1993 Fisheries Management Plan for Sharks. We took advantage of the spatial and temporal gradients in fishing exposure and fisheries management in the Western Atlantic to analyze the effect on the Red List status of all 26 wide-ranging coastal sharks and rays. We show that extinction risk was greater where fishing pressure was higher, but this was offset by the strength of management engagement (indicated by strength of National and Regional Plan of Action for sharks and rays). The regional Red List Index (which tracks changes in extinction risk through time) declined in all regions until the 1980s but then improved in the North and Central Atlantic such that the average extinction risk is currently half that in the Southwest. Many sharks and rays are wide ranging, and successful fisheries management in one country can be undone by poorly regulated or unregulated fishing elsewhere. Our study underscores that well-enforced, science-based management of carefully monitored fisheries can achieve conservation success, even for slow-growing species.

Shallow seamounts represent speciation islands for circumglobal yellowtail Seriola lalandi.

Phenotypic plasticity in life-history traits in response to heterogeneous environments has been observed in a number of fishes. Conversely, genetic structure has recently been detected in even the most wide ranging pelagic teleost fish and shark species with massive dispersal potential, putting into question previous expectations of panmixia. Shallow oceanic seamounts are known aggregation sites for pelagic species, but their role in genetic structuring of widely distributed species remains poorly understood. The yellowtail kingfish (Seriola lalandi), a commercially valuable, circumglobal, epipelagic fish species occurs in two genetically distinct Southern Hemisphere populations (South Pacific and southern Africa) with low levels of gene-flow between the regions. Two shallow oceanic seamounts exist in the ocean basins around southern Africa; Vema and Walters Shoal in the Atlantic and Indian oceans, respectively. We analysed rare samples from these remote locations and from the South African continental shelf to assess genetic structure and population connectivity in S. lalandi and investigated life-history traits by comparing diet, age, growth and maturation among the three sites. The results suggest that yellowtail from South Africa and the two seamounts are genetically and phenotypically distinct. Rather than mere feeding oases, we postulate that these seamounts represent islands of breeding populations with site-specific adaptations.

Half a century of global decline in oceanic sharks and rays.

Overfishing is the primary cause of marine defaunation, yet declines in and increasing extinction risks of individual species are difficult to measure, particularly for the largest predators found in the high seas1-3. Here we calculate two well-established indicators to track progress towards Aichi Biodiversity Targets and Sustainable Development Goals4,5: the Living Planet Index (a measure of changes in abundance aggregated from 57 abundance time-series datasets for 18 oceanic shark and ray species) and the Red List Index (a measure of change in extinction risk calculated for all 31 oceanic species of sharks and rays). We find that, since 1970, the global abundance of oceanic sharks and rays has declined by 71% owing to an 18-fold increase in relative fishing pressure. This depletion has increased the global extinction risk to the point at which three-quarters of the species comprising this functionally important assemblage are threatened with extinction. Strict prohibitions and precautionary science-based catch limits are urgently needed to avert population collapse6,7, avoid the disruption of ecological functions and promote species recovery8,9.

The conservation status and population decline of the African penguin deconstructed in space and time.

Understanding changes in abundance is crucial for conservation, but population growth rates often vary over space and time. We use 40 years of count data (1979-2019) and Bayesian state-space models to assess the African penguin Spheniscus demersus population under IUCN Red List Criterion A. We deconstruct the overall decline in time and space to identify where urgent conservation action is needed. The global African penguin population met the threshold for Endangered with a high probability (97%), having declined by almost 65% since 1989. An historical low of ~17,700 pairs bred in 2019. Annual changes were faster in the South African population (-4.2%, highest posterior density interval, HPDI: -7.8 to -0.6%) than the Namibian one (-0.3%, HPDI: -3.3 to +2.6%), and since 1999 were almost -10% at South African colonies north of Cape Town. Over the 40-year period, the Eastern Cape colonies went from holding ~25% of the total penguin population to ~40% as numbers decreased more rapidly elsewhere. These changes coincided with an altered abundance and availability of the main prey of African penguins. Our results underline the dynamic nature of population declines in space as well as time and highlight which penguin colonies require urgent conservation attention.

Bayesian inference reveals positive but subtle effects of experimental fishery closures on marine predator demographics.

Global forage-fish landings are increasing, with potentially grave consequences for marine ecosystems. Predators of forage fish may be influenced by this harvest, but the nature of these effects is contentious. Experimental fishery manipulations offer the best solution to quantify population-level impacts, but are rare. We used Bayesian inference to examine changes in chick survival, body condition and population growth rate of endangered African penguins Spheniscus demersus in response to 8 years of alternating time-area closures around two pairs of colonies. Our results demonstrate that fishing closures improved chick survival and condition, after controlling for changing prey availability. However, this effect was inconsistent across sites and years, highlighting the difficultly of assessing management interventions in marine ecosystems. Nevertheless, modelled increases in population growth rates exceeded 1% at one colony; i.e. the threshold considered biologically meaningful by fisheries management in South Africa. Fishing closures evidently can improve the population trend of a forage-fish-dependent predator-we therefore recommend they continue in South Africa and support their application elsewhere. However, detecting demographic gains for mobile marine predators from small no-take zones requires experimental time frames and scales that will often exceed those desired by decision makers.

Environmental correlates of geographic divergence in a phenotypic trait: A case study using bat echolocation.

Divergence in phenotypic traits may arise from the interaction of different evolutionary forces, including different kinds of selection (e.g., ecological), genetic drift, and phenotypic plasticity. Sensory systems play an important role in survival and reproduction, and divergent selection on such systems may result in lineage diversification. Such diversification could be largely influenced by selection in different environments as a result of isolation by environment (IbE). We investigated this process using geographic variation in the resting echolocation frequency of the horseshoe bat species, Rhinolophus damarensis, as a test case. Bats were sampled along a latitudinal gradient ranging from 16°S to 32°S in the arid western half of southern Africa. We measured body size and peak resting frequencies (RF) from handheld individual bats. Three hypotheses for the divergence in RF were tested: (1) James' Rule, (2) IbE, and (3) genetic drift through isolation by distance (IbD) to isolate the effects of body size, local climatic conditions, and geographic distance, respectively, on the resting frequency of R. damarensis. Our results did not support genetic drift because there was no correlation between RF variation and geographic distance. Our results also did not support James' Rule because there was no significant relationship between (1) geographic distances and RF, (2) body size and RF, or (3) body size and climatic variables. Instead, we found support for IbE in the form of a correlation between RF and both region and annual mean temperature, suggesting that RF variation may be the result of environmental discontinuities. The environmental discontinuities coincided with previously reported genetic divergence. Climatic gradients in conjunction with environmental discontinuities could lead to local adaptation in sensory signals and directed dispersal such that gene flow is restricted, allowing lineages to diverge. However, our study cannot exclude the role of processes like phenotypic plasticity in phenotypic variation.

The relative contribution of drift and selection to phenotypic divergence: A test case using the horseshoe bats Rhinolophus simulator and Rhinolophus swinnyi.

Natural selection and drift can act on populations individually, simultaneously or in tandem and our understanding of phenotypic divergence depends on our ability to recognize the contribution of each. According to the quantitative theory of evolution, if an organism has diversified through neutral evolutionary processes (mutation and drift), variation of phenotypic characteristics between different geographic localities (B) should be directly proportional to the variation within localities (W), that is, B âˆ W. Significant deviations from this null model imply that non-neutral forces such as natural selection are acting on a phenotype. We investigated the relative contributions of drift and selection to intraspecific diversity using southern African horseshoe bats as a test case. We characterized phenotypic diversity across the distributional range of Rhinolophus simulator (n = 101) and Rhinolophus swinnyi (n = 125) using several traits associated with flight and echolocation. Our results suggest that geographic variation in both species was predominantly caused by disruptive natural selection (B was not directly proportional to W). Evidence for correlated selection (co-selection) among traits further confirmed that our results were not compatible with drift. Selection rather than drift is likely the predominant evolutionary process shaping intraspecific variation in traits that strongly impact fitness.

Density-dependent changes in effective area occupied for sea-bottom-associated marine fishes.

The spatial distribution of marine fishes can change for many reasons, including density-dependent distributional shifts. Previous studies show mixed support for either the proportional-density model (PDM; no relationship between abundance and area occupied, supported by ideal-free distribution theory) or the basin model (BM; positive abundance-area relationship, supported by density-dependent habitat selection theory). The BM implies that fishes move towards preferred habitat as the population declines. We estimate the average relationship using bottom trawl data for 92 fish species from six marine regions, to determine whether the BM or PDM provides a better description for sea-bottom-associated fishes. We fit a spatio-temporal model and estimate changes in effective area occupied and abundance, and combine results to estimate the average abundance-area relationship as well as variability among taxa and regions. The average relationship is weak but significant (0.6% increase in area for a 10% increase in abundance), whereas only a small proportion of species-region combinations show a negative relationship (i.e. shrinking area when abundance increases). Approximately one-third of combinations (34.6%) are predicted to increase in area more than 1% for every 10% increase in abundance. We therefore infer that population density generally changes faster than effective area occupied during abundance changes. Gadiformes have the strongest estimated relationship (average 1.0% area increase for every 10% abundance increase) followed by Pleuronectiformes and Scorpaeniformes, and the Eastern Bering Sea shows a strong relationship between abundance and area occupied relative to other regions. We conclude that the BM explains a small but important portion of spatial dynamics for sea-bottom-associated fishes, and that many individual populations merit cautious management during population declines, because a compressed range may increase the efficiency of harvest.

Sensory Drive Mediated by Climatic Gradients Partially Explains Divergence in Acoustic Signals in Two Horseshoe Bat Species, Rhinolophus swinnyi and Rhinolophus simulator.

Geographic variation can be an indicator of still poorly understood evolutionary processes such as adaptation and drift. Sensory systems used in communication play a key role in mate choice and species recognition. Habitat-mediated (i.e. adaptive) differences in communication signals may therefore lead to diversification. We investigated geographic variation in echolocation calls of African horseshoe bats, Rhinolophus simulator and R. swinnyi in the context of two adaptive hypotheses: 1) James' Rule and 2) the Sensory Drive Hypothesis. According to James' Rule body-size should vary in response to relative humidity and temperature so that divergence in call frequency may therefore be the result of climate-mediated variation in body size because of the correlation between body size and call frequency. The Sensory Drive Hypothesis proposes that call frequency is a response to climate-induced differences in atmospheric attenuation and predicts that increases in atmospheric attenuation selects for calls of lower frequency. We measured the morphology and resting call frequency (RF) of 111 R. simulator and 126 R. swinnyi individuals across their distributional range to test the above hypotheses. Contrary to the prediction of James' Rule, divergence in body size could not explain the variation in RF. Instead, acoustic divergence in RF was best predicted by latitude, geography and climate-induced differences in atmospheric attenuation, as predicted by the Sensory Drive Hypothesis. Although variation in RF was strongly influenced by temperature and humidity, other climatic variables (associated with latitude and altitude) as well as drift (as suggested by a positive correlation between call variation and geographic distance, especially in R. simulator) may also play an important role.

Bottom-up effects of a no-take zone on endangered penguin demographics.

Marine no-take zones can have positive impacts for target species and are increasingly important management tools. However, whether they indirectly benefit higher order predators remains unclear. The endangered African penguin (Spheniscus demersus) depends on commercially exploited forage fish. We examined how chick survival responded to an experimental 3-year fishery closure around Robben Island, South Africa, controlling for variation in prey biomass and fishery catches. Chick survival increased by 18% when the closure was initiated, which alone led to a predicted 27% higher population compared with continued fishing. However, the modelled population continued to decline, probably because of high adult mortality linked to poor prey availability over larger spatial scales. Our results illustrate that small no-take zones can have bottom-up benefits for highly mobile marine predators, but are only one component of holistic, ecosystem-based management regimes.

Marine protected area improves yield without disadvantaging fishers.

Potential fishery benefits of Marine Protected Areas (MPAs) are widely acknowledged, yet seldom demonstrated, as fishery data series that straddle MPA establishment are seldom available. Here we postulate, based on a 15-year time series of nation-wide, spatially referenced catch and effort data, that the establishment of the Goukamma MPA (18 km alongshore; 40 km²) benefited the adjacent fishery for roman (Chrysoblephus laticeps), a South African endemic seabream. Roman-directed catch-per-unit-effort (CPUE) in the vicinity of the new MPA immediately increased, contradicting trends across this species' distribution. The increase continued after 5 years, the time lag expected for larval export, effectively doubling the pre-MPA CPUE after 10 years. We find no indication that establishing the MPA caused a systematic drop in total catch or increased travel distances for the fleet. Our results provide rare empirical evidence of rapidly increasing catch rates after MPA implementation without measurable disadvantages for fishers.

The influence of environmental variables on the presence of white sharks, Carcharodon carcharias at two popular Cape Town bathing beaches: a generalized additive mixed model.

Shark attacks on humans are high profile events which can significantly influence policies related to the coastal zone. A shark warning system in South Africa, Shark Spotters, recorded 378 white shark (Carcharodon carcharias) sightings at two popular beaches, Fish Hoek and Muizenberg, during 3690 six-hour long spotting shifts, during the months September to May 2006 to 2011. The probabilities of shark sightings were related to environmental variables using Binomial Generalized Additive Mixed Models (GAMMs). Sea surface temperature was significant, with the probability of shark sightings increasing rapidly as SST exceeded 14 °C and approached a maximum at 18 °C, whereafter it remains high. An 8 times (Muizenberg) and 5 times (Fish Hoek) greater likelihood of sighting a shark was predicted at 18 °C than at 14 °C. Lunar phase was also significant with a prediction of 1.5 times (Muizenberg) and 4 times (Fish Hoek) greater likelihood of a shark sighting at new moon than at full moon. At Fish Hoek, the probability of sighting a shark was 1.6 times higher during the afternoon shift compared to the morning shift, but no diel effect was found at Muizenberg. A significant increase in the number of shark sightings was identified over the last three years, highlighting the need for ongoing research into shark attack mitigation. These patterns will be incorporated into shark awareness and bather safety campaigns in Cape Town.