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Interactions among selection, gene flow, and drift affect the trajectory of adaptive evolution. In natural populations, the direction and magnitude of these processes can be variable across different spatial, temporal, or ontogenetic scales. Consequently, variability in evolutionary processes affects the predictability or stochasticity of microevolutionary outcomes. We studied an intertidal fish, Bathygobius cocosensis (Bleeker, 1854), to understand how space, time, and life stage structure genetic and phenotypic variation in a species with potentially extensive dispersal and a complex life cycle (larval dispersal preceding benthic recruitment). We sampled juvenile and adult life stages, at three sites, over three years. Genome-wide SNPs uncovered a pattern of chaotic genetic patchiness, that is, weak-but-significant patchy spatial genetic structure that was variable through time and between life stages. Outlier locus analyses suggested that targets of spatially divergent selection were mostly temporally variable, though a significant number of spatial outlier loci were shared between life stages. Head shape, a putatively ecologically responsive (adaptive) phenotype in B. cocosensis also exhibited high temporal variability within sites. However, consistent spatial relationships between sites indicated that environmental similarities among sites may generate predictable phenotype distributions across space. Our study highlights the complex microevolutionary dynamics of marine systems, where consideration of multiple ecological dimensions can reveal both predictable and stochastic patterns in the distributions of genetic and phenotypic variation. Such considerations probably apply to species that possess short, complex life cycles, have large dispersal potential and fecundities, and that inhabit heterogeneous environments.

Small multidrug resistance (SMR) transporters efflux toxic substrates from bacterial cells. These transporters were recently divided into two subfamilies: the GdX-like and EmrE-like SMRs. The EmrE-like subfamily of SMRs is predicted to contain transporters that are highly promiscuous in both substrate specificity and mechanism based on extensive characterization of the founding member of this subfamily, EmrE. However, there is only limited functional analysis of other members of this family from pathogenic strains such as Staphylococcus aureus and Francisella tularensis. Here, we use a small compound screen to explore the substrate specificity and diversity of EmrE-subfamily SMRs from these two bacterial species and confirm that they are functionally more like EmrE than the GdX-like subfamily of toxic-metabolite transporters. The results of these experiments lay the foundation for understanding the complex substrate specificity profiles of SMR family transporters and assess the potential for targeting these transporters for future antibiotic development, either broadly or in a species-specific manner.

To meet consumer expectations, white wines must be clear and stable against haze formation. Temperature variations during transport and storage may induce protein aggregation, mainly caused by thaumatin like-proteins (TLPs) and chitinases (CHIs), which thus need to be fined before bottling of the wine. Currently, bentonite clay is employed to inhibit or minimize haze formation in wines. Alternatively, peptidases have emerged as an option for the removal of these thermolabile proteins, although their efficacy under winemaking conditions has not yet been fully demonstrated. The simultaneous understanding of the chemistry behind the cleavage of haze proteins and the haze formation may orchestrate alternative methods of technological and economic importance in winemaking. Therefore, we provide an overview of wine fining by peptidases, and new perspectives are developed to reopen discussions on the aforementioned challenges.

Climate change is altering the latitudinal distributions of species, with their capacity to keep pace with a shifting climate depending on the stochastic expression of population growth rates, and the influence of compensatory density feedback on age‐specific survival rates. We use population‐abundance time series at the leading edge of an expanding species’ range to quantify the contribution of stochastic environmental drivers and density feedbacks to the dynamics of life stage‐specific population growth. 2. Using a tropical, range‐shifting Indo‐Pacific damselfish (Abudefduf vaigiensis) as a model organism, we applied variants of the phenomenological Gompertz‐logistic model to a 14‐year dataset to quantify the relative importance of density feedback and stochastic environmental drivers on the separate and aggregated population growth rates of settler and juvenile life stages. 3. The top‐ranked models indicated that density feedback negatively affected the growth of tropical settlers and juveniles. Rates of settlement were negatively linked to temperatures experienced by parents at potential source populations in the tropics, but their subsequent survival and that of juveniles increased with the temperatures experienced at the temperate sink. Including these stochastic effects doubled the deviance explained by the models, corroborating an important role of temperature. By incorporating sea‐surface temperature projections for the remainder of this century into these models, we anticipate improved conditions for the population growth of juvenile coral‐reef fishes, but not for settlers in temperate ecosystems. 4. Previous research has highlighted the association between temperature and the redistribution of species. Our analyses reveal the contrasting roles of different life stages in the dynamics of range‐shifting species responding to climate change, as they transition from vagrancy to residency in their novel ranges.

Effective conservation planning requires biotic data across an entire region. In data-poor ecosystems conservation planning is informed by using environmental surrogates (e.g. temperature) predominantly in two ways: to develop habitat classification schemes (1) or develop species distribution models (2). We test the utility of both approaches for conservation planning of marine ecosystems, and rank environmental surrogates, such as depth and distance from shore, according to their power to predict the distribution and abundance of biotic species. Specifically, we compared a habitat classification scheme; based on coarse levels of habitat types derived from depth and distance from shore; against species distribution models, which predict fish abundance and prevalence as a function of environmental surrogates (depth, distance from shore, latitude, reef area, zoning, and several metrics of habitat structural complexity). We consistently set conservation target levels to 21% of each conservation feature, following global standards and a sensitivity analyses. Thus when running scenarios to protect fish species we aimed to protect at least 21% of each species, and when running scenarios of habitat classes, we aimed to protect at least 21% of each habitat class. We found that when aiming to protect 21% of the chosen conservation targets, distribution models protected 21% of the predicted abundance/occurrence of all modelled species and functional groups, but did not protect most habitats. Contrastingly, using a habitat classification scheme protected 21% of all habitat types and 34% of all species and functional groups, but required protecting three times more area. Thus, using only distribution models as targets in data-poor ecosystems could be a risky conservation planning strategy. Ultimately the best conservation outcomes were achieved by incorporating local knowledge to synthesize the conservation outcomes of both scenarios.

Increasingly, urbanised coastlines are being armoured by shoreline protection structures, such as seawalls. Seawalls typically lack the complex microhabitats and protective spaces of natural shorelines and consequently organisms that settle on them may be particularly susceptible to predation. We tested whether the addition of complex microhabitats to seawalls enhances the survivorship of oysters, key habitat-forming species on intertidal shores, by reducing the intensity of predation. At two sites in Sydney Harbour, we compared the magnitude and sources of mortality of juvenile oysters among (1) flat tiles, without crevices or ridges; (2) complex tiles, with 2.5 cm high ridges, separated by crevices; and (3) complex tiles, with 5 cm high ridges, separated by crevices. We also compared predatory fish visitation and feeding among sites and treatments using GoPro® cameras. The abundance and feeding of predatory fish was much greater at one of the study sites than the other, but at neither site differed among treatments. At the site with greater predatory fish abundances, survivorship of juvenile oysters was 50% greater on the 5 cm complex tiles than flat tiles, and on complex tiles approximately 300% greater in crevices than on ridges. Of the dead oysters, almost all were cracked, indicative of fish predation. In contrast, at the site with fewer predatory fish, there were no detectable differences in oyster survivorship between treatments. These results suggest that the addition of complex habitat to seawalls could be an effective strategy in reducing fish predation pressure on juvenile oysters at sites with abundant predatory fish. A greater understanding of the site-specific pressures is required to enhance the abundances of desirable species and functions on seawalls.

Adequately sampling benthic cover in marine ecosystems is a challenge with most methods encompassing only a small portion of the area for which cover is estimated. Recent advances in photogrammetric techniques are providing opportunity to map expansive areas of reef. This study aimed to evaluate the adequate level of sampling for traditional quadrat-based designs at ecologically relevant scales. We used large-area (~250 m2), high-resolution (0.911 ± 0.143 mm/pixel) mosaics to assess the precision and reproducibility of quadrat-based benthic sampling and identify the most efficient strategy (size and number of quadrats). There was a strong relationship between the percent cover of benthic classes and the level of sampling effort required to adequately sample them. As expected, larger quadrats were found to be more efficient when sampling effort was expressed in number of quadrats. This study aims to identify the optimal level of sampling (least effort that would result in a given target precision) to characterize coral reef benthic communities (whatever they are) within each site. As such, the sites selected were intentionally very different and together represented the broad scale of heterogeneity found in shallow coral reef communities. Abundance data can be used in combination with the relationships presented here to determine the optimal sampling protocols for management approaches to coral reef monitoring.

Complex life cycles may evolve to dissociate distinct developmental phases in an organism's lifetime. However, genetic or environmental factors may restrict trait independence across life stages, constraining ontogenetic trajectories. Quantifying covariance across life stages and their temporal variability is fundamental in understanding life-history phenotypes and potential distributions and consequences for selection. We studied developmental constraints in an intertidal fish (Bathygobius cocosensis: Gobiidae) with a discrete pelagic larval phase and benthic juvenile phase. We tested whether traits occurring earlier in life affected those expressed later, and whether larval traits were decoupled from postsettlement juvenile traits. Sampling distinct cohorts from three annual breeding seasons afforded tests of temporally variability in trait covariance. From otoliths (fish ear stones), we measured hatch size, larval duration, pelagic growth (larval traits) and early postsettlement growth (juvenile trait) in 124 juvenile B. cocoensis. We used path analyses to model trait relationships with respect to their chronological expression, comparing models among seasons. We also modelled the effect of season and hatch date on each individual trait to quantify their inherent variability. Our path analyses demonstrated a decoupling of larval traits on juvenile growth. Within the larval phase, longer larval durations resulted in greater pelagic growth, and larger size-at-settlement. There was also evidence that larger hatch size might reduce larval durations, but this effect was only marginally significant. Although pelagic and postsettlement growth were decoupled, pelagic growth had postsettlement consequences: individuals with high pelagic growth were among the largest fish at settlement, and remained among the largest early postsettlement. We observed no evidence that trait relationships varied among breeding seasons, but larval duration differed among breeding seasons, and was shorter for larvae hatching later within each season. Overall, we demonstrate mixed support for the expectation that traits in different life stages are independent. While postsettlement growth was decoupled from larval traits, pelagic development had consequences for the size of newly settled juveniles. Temporal consistency in trait covariances implies that genetic and/or environmental factors influencing them were stable over our three-year study. Our work highlights the importance of individual developmental experiences and temporal variability in understanding population distributions of life-history traits.

Marine Protected Areas (MPAs) are a key management tool for the conservation of biodiversity and restoration of marine communities. While large, well-designed and enforced MPAs have been found to be effective, results from small MPAs vary. The Hawkesbury Shelf, a coastal bioregion in New South Wales, Australia, has ten small, near-shore MPAs known as Aquatic Reserves with a variety of protection levels from full no-take to partial protection. This study assessed the effectiveness of these MPAs and analysed how MPA age, size, protection level, wave exposure, habitat complexity, and large canopy-forming algal cover affected fish, invertebrate and benthic communities. We found aspect, protection level, complexity and algal canopy to be important predictors of communities in these MPAs. Most MPAs, however, were not effective in meeting their goals. Only full no-take protection (three out of ten MPAs) had a significant impact on fish assemblages. One no-take MPA—Cabbage Tree Bay—which is naturally sheltered from wave action and benefits from an active local community providing informal enforcement, accounted for most of the increased richness of large fish and increased biomass of targeted fish species. Our findings suggest that small MPAs can enhance biodiversity and biomass on a local scale but only if they have full no-take protection, are in sheltered locations with complex habitat, and have positive community involvement to engender support and stewardship. These results provide a baseline for robust assessment of the effectiveness of small MPAs and inform future management decisions and small MPA design in other locations.

Habitat structural complexity influences biotic diversity and abundance, but its influence on marine ecosystems has not been widely addressed. Recent advances in computer vision and robotics allow quantification of structural complexity at higher-resolutions than previously achieved. This provides an important opportunity to determine the ecological role of habitat structural complexity in marine ecosystems. We used high-resolution three-dimensional (3D) maps to test multiple structural complexity metrics, depth and benthic biota as surrogates of fish assemblages across hundreds of meters on subtropical reefs. Non-parametric multivariate statistics were used to determine the relationship between these surrogates and the entire fish assemblage. Fish were divided into functional groups, which were used to further investigate the relationship between surrogates and fish abundance using generalized linear models. Fish community composition and abundance were strongly related to habitat complexity metrics, benthic biota and depth. Surface rugosity and its variance had a significant positive influence on the abundance of piscivores and sediment infauna predators, and a negative effect on the abundance of predators, herbivores, planktivores and cleaners. Final models for fish functional groups explained up to 68% of the variance. The best metrics to explain the variance in fish abundance were benthic biota (25 7.5% of variance explained, mean  SE) and complexity metrics (16 6.6%, mean  SE). Our results show that high-resolution 3D maps and derived metrics can predict a large percentage of variance in fish abundance and potentially serve as useful surrogates of fish abundance across all functional groups in spatially dynamic reefs.

The United States of America, as most other countries, emphasizes commercial fisheries when reporting statistics to the Food and Agriculture Organization of the United Nations (FAO), and excludes data from other sectors, such as recreational fisheries. Our study is a first attempt to account comprehensively for all sources of total U.S. marine catches from the Exclusive Economic Zone waters along the West Coast of the continental USA from 1950 to 2017 in one dataset, i.e., excluding the states of Alaska and Hawaii. Total reconstructed catches for 1950–2017 were 1.2 times higher than the data reported by the USA to the FAO. Commercial landings dominated catches, with 65% from large-scale, industrial fisheries and 31% from small-scale, commercial fisheries. Recreational fisheries accounted for 4% of the total catch, after accounting for post-release mortality. Total catches were highest in 1950 at around 750,000 t and declined to 570,000 t by 2017. Internationally unreported discards increased from 24,000 t in 1950 to 86,000 t in 1989, but declined after the introduction of bycatch reduction devices to around 10,000 t year−1 by the mid-2010s. Total catches by taxonomic category suggest a decline in the diversity in catches. Levels of reporting for total catches is excellent for recent decades, with around 95% of total catches accounted for by the mid-2010s, but around 40% of catches were missing from data reported to the FAO between the late 1960s and early 1990s. This discrepancy was largely driven by industrial catches of North Pacific hake (Merluccius productus) that were not in the officially reported data. Our results suggest that recreational fisheries and discards can make up a considerable component of total catches over time. We suggest that the USA include their recreational catch estimates in their annual data submission to the FAO, retroactively to 1950.

Natasha Hardy, Tina Berry, Brendan P. Kelaher, Simon D. Goldsworthy, Michael Bunce, Melinda A. Coleman, Bronwyn M. Gillanders, Sean D. Connell, Michelle Blewitt, Will Figueira