Scott L. Hamilton

Biophysical processes associated with large‐scale nearshore oceanographic upwelling can influence coral reef communities by increasing the delivery of nutrient subsidies and food resources to reefs. However, these processes occur alongside anthropogenic activities that may alter ecological patterns across coral reef ecosystems. We examined relationships among nearshore oceanic primary production, human habitation, and the abundance, biomass, body condition and life‐history traits of eight common coral reef fish species across six islands in the Northern Line Islands, central Pacific Ocean. Variation in oceanic primary production and habitation status was associated with differences in abundance, biomass, body condition and life‐history traits (i.e., growth rates, maximum size and longevity) of key coral reef fishes. These relationships varied among species and islands, with some taxa exhibiting more pronounced relationships with productivity and human habitation than others. Among uninhabited islands, several grazer‐detritivore species exhibited life‐history patterns that were consistent with variation in oceanic primary production, whereas these relationships between productivity and life‐history traits were less apparent among inhabited islands. In contrast, piscivore‐invertivore species generally exhibited stronger differences associated with human habitation status. These findings suggest that local human impacts may influence life‐history traits of reef fishes even when strong gradients in oceanic primary production are present. Although the mechanisms underlying these patterns were not evaluated directly, our results highlight the role of biophysical processes in shaping coral reef fish assemblages and suggest that human activities may alter ecological relationships linking environmental conditions and life‐history traits across tropical reef ecosystems.

Accurate estimates of age, growth and maturation are fundamental to fisheries assessment, conservation and the development of emerging aquaculture species. However, life‐history parameters can vary within species and may be influenced by factors such as sexual dimorphism, which is often poorly quantified in non‐commercial or understudied species. The monkeyface prickleback ( Cebidichthys violaceus ), one of the largest herbivorous fish along the west coast of North America and a potential aquaculture candidate, remains relatively understudied with respect to life‐history variation and sexual dimorphism. This study updates and expands previously reported life‐history parameters of C. violaceus by incorporating a wider size range of individuals, including juveniles, and evaluates sexual dimorphism in cranial morphology using geometric morphometric methods. Von Bertalanffy growth functions based on otolith sectioning and updated length‐weight relationships were developed for adult males, females and all fish combined. Length and age at maturation were estimated to be earlier than previously reported, with most individuals maturing before 28.2 cm in length and 5 years of age. Females were generally heavier than males of the same length, whereas males were longer than females of the same age and attained greater maximum lengths. Condition factor only differed between adult males and juveniles. Sexual dimorphism was assessed using body metrics and quantified through geometric morphometric analyses of head and supraorbital crest shape. Head shape, supraorbital crest shape and eye size differed significantly between sexes, with morphological differences becoming more pronounced with increasing body size, providing clear evidence of sexual dimorphism in adult C. violaceus . These findings will aid in the sustainable management of wild populations and optimise broodstock selection and aquaculture development for the species.

Hypoxia (low oxygen availability) is a common environmental stressor in estuarine ecosystems that negatively affects fish survival as well as physiological and behavioral responses. However, the effects of hypoxia on the brain remains poorly understood, particularly in non-model species. Here, we investigated how prolonged hypoxia influences neural, vascular, and molecular responses in the brain of the speckled sanddab (Citharichthys stigmaeus), an ecologically relevant estuarine flatfish. Fish were exposed to normoxic or hypoxic conditions for seven days, and responses were assessed using histological analyses of neural proliferation and vascular structure, alongside transcriptomic and proteomic profiling. Hypoxia increased neural cell proliferation and progenitor activation in the hypothalamic nucleus recessus lateralis (NRL) and optic tectum, while reducing survival of newly generated cells. At the tissue level, hypoxia induced region-specific vascular remodeling, characterized by increased vessel area and vessel number without evidence of widespread endothelial proliferation. At the molecular level, transcriptomic and proteomic analyses revealed consistent enrichment of biological processes related to stress responses, development, metabolism, and cellular homeostasis, despite limited overlap between individual genes and proteins. Gene- and protein-level analyses further indicated activation of hypoxia-responsive pathways, including HIF signaling and oxidative stress protection, alongside selective metabolic reprogramming. Together, these findings demonstrate that hypoxia induces multi-level changes in the brain, linking neural plasticity, vascular remodeling, and molecular responses. This integrated response likely supports brain function under reduced oxygen availability in dynamic estuarine environments and highlights the role of the brain in regulating responses to environmental stress.

Understanding the sequence of embryonic and larval development and the factors necessary to induce reproduction in captivity are critical for developing new species for commercial or conservation aquaculture. In this study, we describe the adult reproductive behaviours and development of eggs, embryos and early larvae of captive monkeyface pricklebacks, Cebidicthys violaceus , compared to previously documented wild observations. Eggs were laid in cohesive clutches and guarded by the male parent until hatching began 23 days post fertilization at 13°C. Fertilized eggs were spherical, approximately 1.5 mm in diameter, covered in an opaque chorion, and contained six adhesive pads around the outside. We characterized the rate of depletion of yolk and the oil globule and growth of the embryo from fertilization until hatching. Notable embryonic stages were documented, including the timing of the first heartbeat, and the development of otoliths, intestinal tract, eye pigmentation, mouth, fins and the circulatory system. Larval length at hatching was about 7.4 mm, and larvae were immediately mobile and feeding on live food. Larvae were cultured and observed up to 18 days post hatch.

Antifreeze proteins (AFPs) have enabled teleost fishes to repeatedly colonize polar seas. Four AFP types have convergently evolved in several fish lineages. AFPs inhibit ice crystal growth and lower tissue freezing point. In lineages with AFPs, species inhabiting colder environments may possess more AFP copies. Elucidating how differences in AFP copy number evolve is challenging due to the genes’ tandem array structure and consequently poor resolution of these repetitive regions. Here, we explore the evolution of type III AFPs (AFP III) in the globally distributed suborder Zoarcoidei, leveraging six new long-read genome assemblies. Zoarcoidei has fewer genomic resources relative to other polar fish clades while it is one of the few groups of fishes adapted to both the Arctic and Southern Oceans. Combining these new assemblies with additional long-read genomes available for Zoarcoidei, we conducted a comprehensive phylogenetic test of AFP III evolution and modeled the effects of thermal habitat and depth on AFP III gene family evolution. We confirm a single origin of AFP III via neofunctionalization of the enzyme sialic acid synthase B. We also show that AFP copy number increased under low temperature but decreased with depth, potentially because pressure lowers freezing point. Associations between the environment and AFP III copy number were driven by duplications of paralogs that were translocated out of the ancestral locus at which AFP III arose. Our results reveal novel environmental effects on AFP evolution and demonstrate the value of high-quality genomic resources for studying how structural genomic variation shapes convergent adaptation.

Marine protected areas (MPAs) are widely implemented tools for long‐term ocean conservation and resource management. Assessments of MPA performance have largely focused on specific ecosystems individually and have rarely evaluated performance across multiple ecosystems either in an individual MPA or across an MPA network. We evaluated the conservation performance of 59 MPAs in California's large MPA network, which encompasses 4 primary ecosystems (surf zone, kelp forest, shallow reef, deep reef) and 4 bioregions, and identified MPA attributes that best explain performance. Using a meta‐analytic framework, we evaluated the ability of MPAs to conserve fish biomass, richness, and diversity. At the scale of the network and for 3 of 4 regions, the biomass of species targeted by fishing was positively associated with the level of regulatory protection and was greater inside no‐take MPAs, whereas species not targeted by fishing had similar biomass in MPAs and areas open to fishing. In contrast, species richness and diversity were not as strongly enhanced by MPA protection. The key features of conservation effectiveness included MPA age, preimplementation fisheries pressure, and habitat diversity. Important drivers of MPA effectiveness for single MPAs were consistent across MPAs in the network, spanning regions and ecosystems. With international targets aimed at protecting 30% of the world's oceans by 2030, MPA design and assessment frameworks should consider conservation performance at multiple ecologically relevant scales, from individual MPAs to MPA networks.

Animal consumers excrete dissolved inorganic nitrogen, an essential nutrient for regulating primary production and macroalgal growth in the ocean. Often overlooked in attempts to explain kelp forest productivity, relatively little is known about the role of consumers in nutrient cycling in temperate systems, such as the magnitude of nutrients excreted and the factors that influence spatial and temporal variability in consumer‐derived nutrients. To investigate the supply of ammonium (NH₄⁺) excreted by the dominant members of the nearshore rocky reef fish community, we combined empirically‐measured relationships between excretion rate and body mass with data on fish density and size structure from visual SCUBA surveys conducted from 2005 to 2018 in the northern Channel Islands, California, USA. The fish community excreted a substantial amount of ammonium to the kelp forest (mean: 95.5–131.3 μmol·m⁻²·h⁻¹), however excretion varied substantially among sites and over time (range: 23.1–247.9 μmol·m⁻²·h⁻¹). The ammonium supply was influenced by the establishment of marine protected areas (MPAs) that restricted fishing activities and environmental characteristics that influenced geographic and temporal shifts in the overarching fish community structure. Fish‐derived ammonium excretion rates were 50%–80% greater inside MPAs compared to areas open to fishing, while environmental and habitat characteristics (e.g. habitat vertical relief, kelp biomass, wave exposure, chlorophyll a) explained 85% of the spatial variation in community excretion rates. In contrast, large‐scale oceanographic phenomena (e.g. North Pacific Gyre Oscillation index) and past patterns of fish recruitment explained 57% of the temporal variation in nutrient excretion over the 14‐year time series. Results suggest that fish‐derived ammonium may provide an important and underappreciated nutrient source to kelp beds, particularly during low‐nutrient periods (e.g. seasonal reductions in upwelling or El Niño‐Southern Oscillation events), and that fishing disrupts these nutrient cycling pathways. Fishes likely play a critical role in supporting the resiliency of kelp forest ecosystems by supplying a relatively constant source of reduced nitrogen that can be utilized by giant kelp and other macroalgae to fuel primary production of biogenic habitat. Read the free Plain Language Summary for this article on the Journal blog.

Antifreeze proteins (AFPs) have enabled teleost fishes to repeatedly colonize polar seas. Four AFP types have convergently evolved in several fish lineages. AFPs inhibit ice crystal growth and lower cellular freezing point. In lineages with AFPs, species inhabiting colder environments may possess more AFP copies. Elucidating how differences in AFP copy number evolve is challenging due to the genes′ tandem array structure and consequently poor resolution of these repetitive regions. Here we explore the evolution of type III AFPs (AFP III) in the globally distributed suborder Zoarcoidei, leveraging six new long-read genome assemblies. Zoarcoidei has fewer genomic resources relative to other polar fish clades while it is one of the few groups of fishes adapted to both the Arctic and Southern Oceans. Combining these new assemblies with additional long-read genomes available for Zoarcoidei, we conducted a comprehensive phylogenetic test of AFP III evolution and modeled the effects of thermal habitat and depth on AFP III gene family evolution. We confirm a single origin of AFP III via neofunctionalization of the enzyme sialic acid synthase B and show that AFP copies expanded under low temperature, but also decreased with depth, which reduces freezing point via pressure. Associations between the environment and AFP III copy number were driven by duplications of paralogs that were translocated out of the ancestral locus at which Zoarcoidei AFP arose. Our results reveal novel environmental effects on AFP evolution and demonstrate the value of high-quality genomic resources for studying how structural genomic variation shapes convergent adaptation.

Marine protected areas (MPAs) globally serve conservation and fisheries management goals, generating positive effects in some marine ecosystems. Surf zones and sandy beaches, critical ecotones bridging land and sea, play a pivotal role in the life cycles of numerous fish species and serve as prime areas for subsistence and recreational fishing. Despite their significance, these areas remain understudied when evaluating the effects of MPAs. We compared surf zone fish assemblages inside and outside MPAs across 3 bioregions in California (USA). Using seines and baited remote underwater videos (BRUVs), we found differences in surf zone fish inside and outside MPAs in one region. Inside south region MPAs, we observed higher abundance (Tukey's honest significant difference [HSD] = 0.83, p = 0.0001) and richness (HSD = 0.22, p = 0.0001) in BRUVs and greater biomass (HSD = 0.32, p = 0.0002) in seine surveys compared with reference sites. Selected live‐bearing, fished taxa were positively affected by MPAs. Elasmobranchs displayed greater abundance in BRUV surveys and higher biomass in seine surveys inside south region MPAs (HSD = 0.35, p = 0.0003 and HSD = 0.23, p = 0.008, respectively). Although we observed no overall MPA signal for Embiotocidae, abundances of juvenile and large adult barred surfperch ( Amphistichus argenteus ), the most abundant fished species, were higher inside MPAs (K–S test D = 0.19, p < 0.0001). Influence of habitat characteristics on MPA performance indicated surf zone width was positively associated with fish abundance and biomass but negatively associated with richness. The south region had the largest positive effect size on all MPA performance metrics. Our findings underscored the variability in species richness and composition across regions and survey methods that significantly affected differences observed inside and outside MPAs. A comprehensive assessment of MPA performance should consider specific taxa, their distribution, and the effects of habitat factors and geography.