Genetic divergences and hybridization within the Sebastes inermis complex

The Sebastes inermis complex includes three sympatric species (Sebastes cheni, viz Sebastes inermis, and Sebastes ventricosus) with clear ecomorphological differences, albeit incomplete reproductive isolation. The presence of putative morphological hybrids (PMH) with plausibly higher fitness than the parent species indicates the need to confirm whether hybridization occurs within the complex. In this sense, we assessed the dynamics of genetic divergence and hybridization within the species complex using a panel of 10 microsatellite loci, and sequences of the mitochondrial control region (D-loop) and the intron-free rhodopsin (RH1) gene. The analyses revealed the presence of three distinct genetic clusters, large genetic distances using D-loop sequences, and distinctive mutations within the RH1 gene. These results are consistent with the descriptions of the three species. Two microsatellite loci had signatures of divergent selection, indicating that they are linked to genomic regions that are crucial for speciation. Furthermore, nonsynonymous mutations within the RH1 gene detected in S. cheni and "Kumano" (a PMH) suggest dissimilar adaptations related to visual perception in dim-light environments. The presence of individuals with admixed ancestry between two species confirmed hybridization. The presence of nonsynonymous mutations within the RH1 gene and the admixed ancestry of the "Kumano" morphotype highlight the potential role of hybridization in generating novelties within the species complex. We discuss possible outcomes of hybridization within the species complex, considering hybrid fitness and assortative mating. Overall, our findings indicate that the genetic divergence of each species is maintained in the presence of hybridization, as expected in a scenario of speciation-with-gene-flow.

Distribution of nephrons in the head kidney of three species of Sebastes (Teleostei: Scorpaenidae)

Nephrons are generally not distributed in the head kidney of teleost. Nonetheless, in this study, the nephron structure was identified in the head kidney of three species of Sebastes (Sebastes inermis, Sebastes schlegelii and Sebastes thompsoni). The kidney is Y shaped, with the development in the head kidney. The nephron structure was confirmed in the head kidney and body kidney. In addition, the nephron consisted of renal corpuscles and tubules, and the renal corpuscle consisted of the Bowman's capsule and glomerulus. Histologically, previous studies reported that the nephron structure is similar to that of other marine teleost. The renal tubule is a simple columnar epithelial layer with microvilli and cilia on the free surface, which is observed as a brush border. The Rrk (relative area ratio of kidney to body surface) was 5.14%, 7.58% and 5.17% in S. inermis, S. schlegelii and S. thompsoni, respectively. The Gar (glomerular area ratio of the head kidney) was higher in the central area than in the peripheral area, and species, which showed significant difference (P < 0.05), were in the following order: S. thompsoni (1.60%) > S. schlegelii (0.90%) > S. inermis (0.66%).

Multiple-brooding rockfishes (Sebastes spp.) can utilize stored sperm from individual sires to fertilize consecutive broods

Viviparous rockfishes (Sebastes spp., family Scorpaenidae) mate and store sperm in the ovaries for several months prior to fertilization, as oocytes develop for the parturition season. Although multiple paternity has been documented in single-brooding rockfishes, paternity in consecutive broods of multiple-brooding species has not been studied. Analyses of multilocus microsatellite genotypes in both residual larvae left in the ovary from a previous parturition and upcoming fertilized broods in the same ovary demonstrated evidence of the same sires in consecutive broods in chilipepper (Sebastes goodei) and speckled (Sebastes ovalis) rockfishes. One S. goodei mother showed evidence of multiple paternity from the same two sires in both consecutive broods. The ability to retain sperm, even after a parturition event, for use in subsequent broods, confers an advantage to ensure fertilization and allows for extension of the parturition season. This life-history strategy provides a bet-hedging advantage in the California Current system, an environmentally dynamic ecosystem where larval survivorship and subsequent recruitment to adult populations can vary temporally by orders of magnitude.

Phylogenetic relationships of three rockfish: Sebastesmelanops, Sebastesciliatus and Sebastesvariabilis (Scorpaeniformes, Scorpaenidae) based on complete mitochondrial genome sequences

We characterise the complete mitochondrial genomes (mitogenomes) of Black rockfish (Sebastesmelanops Girard, 1856; n = 1), Dark rockfish (Sebastesciliatus Tilesius, 1813; n = 2) and Dusky rockfish (Sebastesvariabilis Pallas, 1814; n = 2). The lengths of the mitogenomes are 16,405 bp for S.melanops, 16,400 bp for both S.ciliatus and 16,400 and 16,401 bp for S.variabilis. We examine these species' phylogenetic relationships using 35 previously published rockfish mitogenomes, representing 27 species. We find that S.melanops is sister to a clade consisting of S.rubrivinctus, S.nigrocinctus, S.umbrosus and S.oculatus, whereas S.ciliatus and S.variabilis are sister to a clade consisting of S.norvegicus, S.viviparus, S.mentella and S.fasciatus. We were unable to separate S.ciliatus and S.variabilis using their complete mitogenomes.

Fish allergy tolerance 16 months after diagnosis

Fish allergy is generally thought to be persistent, and approximately 80% of patients with fish allergies do not develop tolerance even 10 years after diagnosis. There have been no reports of rapid tolerance development in patients with severe fish allergies. We report the development of tolerance 16 months after the diagnosis of fish allergies. A 13-month-old boy was diagnosed with rosefish allergy (Sebastes matsubarae) and Japanese jack mackerel allergy (Trachurus japonicus). To find out which species of fish he could consume safely, he underwent several oral food challenge (OFC) tests. It was determined that he could consume tuna, salmon, cod, sardine, chub mackerel (Scomber japonicus), and Japanese amberjack (Seriola quinqueradiata) without eliciting signs of allergy. He continued to eat the fish that did not produce allergic reactions three to four times a week. The titer of serum allergen-specific immunoglobulin E (IgE) to fish had decreased in a subsequent ImmunoCAP^®-specific IgE blood test performed 16 months after the diagnosis of the rosefish allergy. Following this test result, he underwent OFCs with rosefish and Japanese jack mackerel, both of which turned out to be negative, and it was determined that he had developed tolerance to fish. In this case, the repeated OFCs were useful in identifying fish species that were safe for consumption. In addition, the decrease in allergen-specific IgE was useful in predicting the development of tolerance. We hypothesize that proactive consumption of available fish species may lead to this rapid induction of tolerance to fish allergens.

Regions of genetic divergence in depth-separated Sebastes rockfish species pairs: Depth as a potential driver of speciation

Depth separation is a proposed driver of speciation in marine fishes, with marine rockfish (genus Sebastes) providing a potentially informative study system. Sebastes rockfishes are commercially and ecologically important. This genus encompasses more than one hundred species and the ecological and morphological variance between these species provides opportunity for identifying speciation-driving adaptations, particularly along a depth gradient. A reduced-representation sequencing method (ddRADseq) was used to compare 95 individuals encompassing six Sebastes species. In this study, we sought to identify regions of divergence between species that were indicative of divergent adaptation and reproductive barriers leading to speciation. A pairwise comparison of S. chrysomelas (black-and-yellow rockfish) and S. carnatus (gopher rockfish) F_ST values revealed three major regions of elevated genomic divergence, two of which were also present in the S. miniatus (vermilion rockfish) and S. crocotulus (sunset rockfish) comparison. These corresponded with regions of both elevated D_XY values and reduced nucleotide diversity in two cases, suggesting a speciation-with-gene-flow evolutionary model followed by post-speciation selective sweeps within each species. Limited whole-genome resequencing was also performed to identify mutations with predicted effects between S. chrysomelas and S. carnatus. Within these islands, we identified important SNPs in genes involved in immune function and vision. This supports their potential role in speciation, as these are adaptive vectors noted in other organisms. Additionally, changes to genes involved in pigment expression and mate recognition shed light on how S. chrysomelas and S. carnatus may have become reproductively isolated.

The sources and prevalence of anthropogenic noise in Rockfish Conservation Areas with implications for marine reserve planning

Underwater noise pollution is a recognized threat to marine life. In British Columbia, Canada, Pacific rockfish (Sebastes spp.) were historically overfished, prompting the establishment of Rockfish Conservation Areas (RCAs). However, there are no restrictions prohibiting vessel transits in RCAs. We hypothesized that RCAs do not protect rockfish from sub-lethal harm from noise. We compared noise levels at three RCAs with adjacent unprotected reference sites from August 2018-June 2019. While RCAs had lower levels of noise overall than reference sites, this trend was inconsistent; some RCA sites had higher levels of noise during certain time periods than non-RCA sites. A vessel noise detector was the best predictor of noise level over three frequency bands (20-100 Hz, 100-1000 Hz, 1-10 kHz), and predicted sound levels which could mask rockfish communication. We conclude that RCAs do not reliably protect rockfish from noise pollution, and recommend further study into potential impacts on stock recovery.

Population genomics and history of speciation reveal fishery management gaps in two related redfish species (Sebastes mentella and Sebastes fasciatus)

Understanding the processes shaping population structure and reproductive isolation of marine organisms can improve their management and conservation. Using genomic markers combined with estimation of individual ancestries, assignment tests, spatial ecology, and demographic modeling, we (i) characterized the contemporary population structure, (ii) assessed the influence of space, fishing depth, and sampling years on contemporary distribution, and (iii) reconstructed the speciation history of two cryptic redfish species, Sebastes mentella and S. fasciatus. We genotyped 860 individuals in the Northwest Atlantic Ocean using 24,603 filtered single nucleotide polymorphisms (SNPs). Our results confirmed the clear genetic distinctiveness of the two species and identified three ecotypes within S. mentella and five populations in S. fasciatus. Multivariate analyses highlighted the influence of spatial distribution and depth on the overall genomic variation, while demographic modeling revealed that secondary contact models best explained inter- and intragenomic divergence. These species, ecotypes, and populations can be considered as a rare and wide continuum of genomic divergence in the marine environment. This acquired knowledge pertaining to the evolutionary processes driving population divergence and reproductive isolation will help optimizing the assessment of demographic units and possibly to refine fishery management units.

Growth parameter k and location affect body size responses to spatial protection by exploited rockfishes

For many fish taxa, trophic position and relative fecundity increase with body size, yet fisheries remove the largest individuals, altering food webs and reducing population productivity. Marine reserves and other forms of spatial protection can help mitigate this problem, but the effectiveness of these management tools may vary interspecifically and spatially. Using visual survey data collected on the Central Coast of British Columbia, for 12 species of exploited rockfish we found that body size responses to spatial fishery closures depended on interspecific variation in growth parameter k (the rate at which the asymptotic body size is approached) and on location. For two closures, relative body sizes were larger at protected than at adjacent fished sites, and these differences were greater for species with lower k values. Reduced fishery mortality likely drove these results, as an unfished species did not respond to spatial protection. For three closures, however, body sizes did not differ between protected and adjacent fished sites, and for another closure species with higher k values were larger at fished than at protected sites while species with lower k values had similar sizes in both treatments. Variation in the age of closures is unlikely to have influenced results, as most data were collected when closures were 13 to 15-years-old. Rather, the lack of larger fish inside four of six spatial fishery closures potentially reflects a combination of smaller size of the area protected, poor fisher compliance, and lower oceanographic productivity. Interspecific differences in movement behavior did not affect body size responses to spatial protection. To improve understanding, additional research should be conducted at deeper depths encompassing the distribution of older, larger fish. Our study—which was conceptualized and executed by an alliance of Indigenous peoples seeking to restore rockfishes—illustrates how life history and behavioral theory provide a useful lens for framing and interpreting species differences in responses to spatial protection.

Juvenile rockfish show resilience to CO2-acidification and hypoxia across multiple biological scales

California's coastal ecosystems are forecasted to undergo shifting ocean conditions due to climate change, some of which may negatively impact recreational and commercial fish populations. To understand if fish populations have the capacity to respond to multiple stressors, it is critical to examine interactive effects across multiple biological scales, from cellular metabolism to species interactions. This study examined the effects of CO₂-acidification and hypoxia on two naturally co-occurring species, juvenile rockfish (genus Sebastes) and a known predator, cabezon (Scorpaenichthys marmoratus). Fishes were exposed to two PCO₂ levels at two dissolved oxygen (DO) levels: ~600 (ambient) and ~1600 (high) μatm PCO₂ and 8.0 (normoxic) and 4.5 mg l^-1 DO (hypoxic) and assessments of cellular metabolism, prey behavior and predation mortality rates were quantified after 1 and 3 weeks. Physiologically, rockfish showed acute alterations in cellular metabolic enzyme activity after 1 week of acclimation to elevated PCO₂ and hypoxia that were not evident in cabezon. Alterations in rockfish energy metabolism were driven by increases in anaerobic LDH activity, and adjustments in enzyme activity ratios of cytochrome c oxidase and citrate synthase and LDH:CS. Correlated changes in rockfish behavior were also apparent after 1 week of acclimation to elevated PCO₂ and hypoxia. Exploration behavior increased in rockfish exposed to elevated PCO₂ and spatial analysis of activity indicated short-term interference with anti-predator responses. Predation rate after 1 week increased with elevated PCO₂; however, no mortality was observed under the multiple-stressor treatment suggesting negative effects on cabezon predators. Most noteworthy, metabolic and behavioral changes were moderately compensated after 3 weeks of acclimation, and predation mortality rates also decreased suggesting that these rockfish may be resilient to changes in environmental stressors predicted by climate models. Linking physiological and behavioral responses to multiple stressors is vital to understand impacts on populations and community dynamics.

Harnessing mtDNA variation to resolve ambiguity in 'Redfish' sold in Europe

Morphology-based identification of North Atlantic Sebastes has long been controversial and misidentification may produce misleading data, with cascading consequences that negatively affect fisheries management and seafood labelling. North Atlantic Sebastes comprises of four species, commonly known as ‘redfish’, but little is known about the number, identity and labelling accuracy of redfish species sold across Europe. We used a molecular approach to identify redfish species from ‘blind’ specimens to evaluate the performance of the Barcode of Life (BOLD) and Genbank databases, as well as carrying out a market product accuracy survey from retailers across Europe. The conventional BOLD approach proved ambiguous, and phylogenetic analysis based on mtDNA control region sequences provided a higher resolution for species identification. By sampling market products from four countries, we found the presence of two species of redfish (S. norvegicus and S. mentella) and one unidentified Pacific rockfish marketed in Europe. Furthermore, public databases revealed the existence of inaccurate reference sequences, likely stemming from species misidentification from previous studies, which currently hinders the efficacy of DNA methods for the identification of Sebastes market samples.

Population assessment using multivariate time-series analysis: A case study of rockfishes in Puget Sound

Estimating a population's growth rate and year-to-year variance is a key component of population viability analysis (PVA). However, standard PVA methods require time series of counts obtained using consistent survey methods over many years. In addition, it can be difficult to separate observation and process variance, which is critical for PVA. Time-series analysis performed with multivariate autoregressive state-space (MARSS) models is a flexible statistical framework that allows one to address many of these limitations. MARSS models allow one to combine surveys with different gears and across different sites for estimation of PVA parameters, and to implement replication, which reduces the variance-separation problem and maximizes informational input for mean trend estimation. Even data that are fragmented with unknown error levels can be accommodated. We present a practical case study that illustrates MARSS analysis steps: data choice, model set-up, model selection, and parameter estimation. Our case study is an analysis of the long-term trends of rockfish in Puget Sound, Washington, based on citizen science scuba surveys, a fishery-independent trawl survey, and recreational fishery surveys affected by bag-limit reductions. The best-supported models indicated that the recreational and trawl surveys tracked different, temporally independent assemblages that declined at similar rates (an average of -3.8% to -3.9% per year). The scuba survey tracked a separate increasing and temporally independent assemblage (an average of 4.1% per year). Three rockfishes (bocaccio, canary, and yelloweye) are listed in Puget Sound under the US Endangered Species Act (ESA). These species are associated with deep water, which the recreational and trawl surveys sample better than the scuba survey. All three ESA-listed rockfishes declined as a proportion of recreational catch between the 1970s and 2010s, suggesting that they experienced similar or more severe reductions in abundance than the 3.8-3.9% per year declines that were estimated for rockfish populations sampled by the recreational and trawl surveys.

Marine reserves can enhance ecological resilience

The goals of ecosystem-based management (EBM) include protecting ecological resilience, the magnitude of a perturbation that a community can withstand and remain in a given state. As a tool to achieve this goal, no-take marine reserves may enhance resilience by protecting source populations or reduce it by concentrating fishing in harvested areas. Here, we test whether spatial management with marine reserves can increase ecological resilience compared to non-spatial (conventional) management using a dynamic model of a simplified fish community with structured predation and competition that causes alternative stable states. Relative to non-spatial management, reserves increase the resilience of the desired (predator-dominated) equilibrium state in both stochastic and deterministic environments, especially under intensive fishing. As a result, spatial management also increases the feasibility of restoring degraded (competitor-dominated) systems, particularly if combined with culling of competitors or stock enhancement of adult predators.

Three-dimensional post-glacial expansion and diversification of an exploited oceanic fish

Vertical divergence in marine organisms is being increasingly documented, yet much remains to be carried out to understand the role of depth in the context of phylogeographic reconstruction and the identification of management units. An ideal study system to address this issue is the beaked redfish, Sebastes mentella – one of four species of ‘redfish’ occurring in the North Atlantic – which is known for a widely distributed ‘shallow‐pelagic’ oceanic type inhabiting waters between 250 and 550 m, and a more localized ‘deep‐pelagic’ population dwelling between 550 and 800 m, in the oceanic habitat of the Irminger Sea. Here, we investigate the extent of population structure in relation to both depth and geographic spread of oceanic beaked redfish throughout most of its distribution range. By sequencing the mitochondrial control region of 261 redfish collected over a decadal interval, and combining 160 rhodopsin coding nuclear sequences and previously genotyped microsatellite data, we map the existence of two strongly divergent evolutionary lineages with significantly different distribution patterns and historical demography, and whose genetic variance is mostly explained by depth. Combined genetic data, analysed via independent approaches, are consistent with a Late Pleistocene lineage split, where segregation by depth probably resulted from the interplay of climatic and oceanographic processes with life history and behavioural traits. The ongoing process of diversification in North Atlantic S. mentella may serve as an ‘hourglass’ to understand speciation and adaptive radiation in Sebastes and in other marine taxa distributed across a depth gradient.

Oil platforms off California are among the most productive marine fish habitats globally

Secondary (i.e., heterotrophic or animal) production is a main pathway of energy flow through an ecosystem as it makes energy available to consumers, including humans. Its estimation can play a valuable role in the examination of linkages between ecosystem functions and services. We found that oil and gas platforms off the coast of California have the highest secondary fish production per unit area of seafloor of any marine habitat that has been studied, about an order of magnitude higher than fish communities from other marine ecosystems. Most previous estimates have come from estuarine environments, generally regarded as one of the most productive ecosystems globally. High rates of fish production on these platforms ultimately result from high levels of recruitment and the subsequent growth of primarily rockfish (genus Sebastes) larvae and pelagic juveniles to the substantial amount of complex hardscape habitat created by the platform structure distributed throughout the water column. The platforms have a high ratio of structural surface area to seafloor surface area, resulting in large amounts of habitat for juvenile and adult demersal fishes over a relatively small footprint of seafloor. Understanding the biological implications of these structures will inform policy related to the decommissioning of existing (e.g., oil and gas platforms) and implementation of emerging (e.g., wind, marine hydrokinetic) energy technologies.

Divergence by depth in an oceanic fish

Despite the striking physical and environmental gradients associated with depth variation in the oceans, relatively little is known about their impact on population diversification, adaptation and speciation. Changes in light associated with increasing depth are likely to alter the visual environment of organisms, and adaptive changes in visual systems may be expected. The pelagic beaked redfish, Sebastes mentella, exhibits depth-associated patterns of substructure in the central North Atlantic, with a widely distributed shallow-pelagic population inhabiting waters between 250 and 550 m depth and a deep-pelagic population dwelling between 550 and 800 m. Here we performed a molecular genetic investigation of samples from fish collected from ‘shallow’ and ‘deep’ populations, using the mitochondrial control region and the gene coding for the visual-pigment rhodopsin. We identify patterns suggestive of potential adaptation to different depths, by detecting a specific amino acid replacement at the rhodopsin gene. Mitochondrial DNA results reflect a scenario of long-term demographic independence between the two S. mentella groups, and raise the possibility that these ‘stocks’ may in fact be two incipient species.

CO2-induced ocean acidification increases anxiety in rockfish via alteration of GABAA receptor functioning

The average surface pH of the ocean is dropping at a rapid rate due to the dissolution of anthropogenic CO2, raising concerns for marine life. Additionally, some coastal areas periodically experience upwelling of CO2-enriched water with reduced pH. Previous research has demonstrated ocean acidification (OA)-induced changes in behavioural and sensory systems including olfaction, which is due to altered function of neural gamma-aminobutyric acid type A (GABAA) receptors. Here, we used a camera-based tracking software system to examine whether OA-dependent changes in GABAA receptors affect anxiety in juvenile Californian rockfish (Sebastes diploproa). Anxiety was estimated using behavioural tests that measure light/dark preference (scototaxis) and proximity to an object. After one week in OA conditions projected for the next century in the California shore (1125 ± 100 µatm, pH 7.75), anxiety was significantly increased relative to controls (483 ± 40 µatm CO2, pH 8.1). The GABAA-receptor agonist muscimol, but not the antagonist gabazine, caused a significant increase in anxiety consistent with altered Cl(-) flux in OA-exposed fish. OA-exposed fish remained more anxious even after 7 days back in control seawater; however, they resumed their normal behaviour by day 12. These results show that OA could severely alter rockfish behaviour; however, this effect is reversible.