Genus Sebastes Research Articles

The Evolution of Redfishes of the Genus Sebastes (Perciformes: Sebastidae) of the Atlantic and Arctic Oceans: Budding Speciation in a Species Flock

The Evolution of Redfishes of the Genus Sebastes (Perciformes: Sebastidae) of the Atlantic and Arctic Oceans: Budding Speciation in a Species Flock

Momma's larvae: Maternal oceanographic experience and larval size influence early survival of rockfishes

AbstractIdentifying factors that affect larval mortality is critical for understanding the drivers of fish population dynamics. Although larval fish mortality is high, small changes in mortality rates can lead to large changes in recruitment. Recent studies suggest maternal provisioning can dramatically affect the susceptibility of larvae to starvation and predation, the major sources of early‐life mortality. We measured otolith core width‐at‐extrusion and validated that this is a proxy for larval size‐at‐extrusion for eight species of rockfishes (genus Sebastes) to examine the influence of initial larval size on larval growth and survival and to understand how oceanographic conditions experienced by gestating females affect larval size (i.e., quality). Otolith core width‐at‐extrusion was significantly positively related to larval rockfish recent growth rate (5/7 species with sufficient sample size) and survival (all eight species). This suggests that individuals that are larger at extrusion generally grow faster and are more likely to survive early life stages. Otolith core width‐at‐extrusion was positively related to higher presence of Pacific Subarctic Upper Water and was negatively related to warmer, saline waters at the depths gestating mothers inhabited during the months prior to larval collection. In addition, otolith core width was larger further from fishing ports, possibly because these locations were historically less fished, contained more older, larger females, and/or had inherently better habitat quality (higher Pacific Subarctic Upper Water) than sites closer to shore. These results indicate that the environmental conditions female rockfish experience during gestation drive the size of the larvae they produce and impact larval growth and survival.

First record of hyper melanosis in the Patagonian redfish Sebastes oculatus Valenciennes, 1833 (Scorpaenidae) in the southeastern Pacific Ocean

The coloration pattern alteration occurs at a low frequency in fish. The excesses of dark pigments in living organisms are known as melanism or melanosis, but a total blackening of the skin is known as hyper melanism or hyper melanosis. Little is known about why the extreme conditions of albinism and melanosis occur among fish. To date, there are no records of melanism for the genus Sebastes. Here, we report the first case of hyper melanosis in rockfish Sebastes oculatus (Patagonian redfish) in the southeastern Pacific Ocean. In 2005, small-scale fishers from Quintay Beach (Valparaiso, Chile) captured a single individual of Patagonian redfish covered with an excess of dark pigmentation. The specimen had a total length of 35.5 cm, and we followed the literature available to determine its morphometric and meristic features. The measurements led us to conclude that the specimen was a black S. oculatus with a rare melanosis condition. Our finding contributes to the knowledge of this species, and we infer that this melanosis case was caused by genetic heritage or some intergenetic hybridization. Still, genetic studies are necessary to confirm this hypothesis.

Occurrence and behavioral rhythms of the endangered Acadian redfish (Sebastes fasciatus) in the Sambro Bank (Scotian Shelf)

The genus Sebastes is a morphologically and ecologically diverse genus of rockfish characterized by high longevity, late-maturity and low natural mortality. On the northwest Atlantic continental shelf, the Acadian redfish (Sebastes fasciatus) is the most common rockfish species above 300 m depth. This species has been widely exploited resulting in the depletion or collapse of most of its stocks. Management of long-lived species with intricate life-history characteristics is challenging and requires highly integrated biological and oceanographic monitoring, which allow the identification of environmental drivers and demographic and behavioral trends. The present study uses high-temporal resolution imaging and environmental data, acquired with an autonomous lander deployed for 10-months at the Sambro Bank Sponge Conservation Area (Scotian Shelf) to elucidate S. fasciatus temporal dynamics and behavioral trends in response to near-bed environmental conditions. S. fasciatus, mostly displayed passive locomotion and static behaviors, in common with other shelf-dwelling Sebastes species. Structural complexity provided by sponges positively influenced S. fasciatus presence. Fish used sponges to avoid being dragged by bottom currents. Hydrodynamics appear to act as a synchronizing factor conditioning its swimming behavior. S. fasciatus total counts exhibited a seasonal shift in rhythm’s phase likely reflecting changes in lifestyle requirements. This study provides new insights on S. fasciatus dynamics and behavior. Nonintrusive monitoring approaches, such as the one used in this study, will be key to monitor this threatened species populations. Especially, since it is expected that S. fasciatus will experience distribution shifts to higher latitudes due to future climate stressors.

Comparative phylogeography of a bathymetrically segregated pair of sister taxa of rockfishes (genus Sebastes): black rockfish, Sebastes melanops, and yellowtail rockfish, Sebastes flavidus

Comparative phylogeography of a bathymetrically segregated pair of sister taxa of rockfishes (genus Sebastes): black rockfish, Sebastes melanops, and yellowtail rockfish, Sebastes flavidus

Genetic architectures of postmating isolation and morphology of two highly diverged rockfishes (genus Sebastes).

Postmating isolation is thought to be an important driver of the late stages of speciation. However, relatively little is empirically known about the process compared with other isolating mechanisms that drive the early stages of speciation, especially in non-model organisms. We characterized the genetic architecture of postmating isolation between 2 rockfishes, Sebastes schlegelii and S. trivittatus, whose reproductive isolation is complete. We examined transmission ratio distortion (TRD) patterns of genetic markers in 2 reciprocal backcross populations. Markers showing either of the 2 types of TRD was widespread across the genome, with some of the distorted markers forming extensive clusters around the recombination coldspots. These suggest that the postmating isolation effectively prevents gene flow across the genome and the recombination landscape contributes to the genetic architecture. Comparisons between 2 backcross families and 2 developmental stages showed little similarity in the distorted markers, suggesting asymmetry and stage specificity of the isolation. This may be due to hybrid incompatibility involving maternal factors or extrinsic selection. The lack of sex-ratio distortion in the mapping families suggested that Haldane's rule in terms of hybrid inviability does not hold. Additionally, quantitative trait loci (QTL) mapping detected significant QTLs for sex and the morphological traits relevant to speciation and convergence of rockfishes, including body coloration. Genes in the melanocortin system, including agouti-signaling protein 1 (asip1) and melanocortin 1 receptor (mc1r), might underlie the horizontal and vertical color patterns on the body, respectively. These findings constitute an essential step toward a comprehensive understanding of speciation and morphological diversification of rockfishes.

The fish assemblages associated with asphalt volcanoes in the Santa Barbara Channel, California, USA

Asphalt volcanoes and other extensive hard tar seafloor accumulations are known from the Gulf of Mexico, off Angola, and in the Santa Barbara Channel (SBC), Southern California. There are two major volcano features in the SBC: Il Duomo (about 20 m high, cresting at a bottom depth of 115 m) and Il Duomito (about 15 m high, cresting at 185 m). While the geology of these features has been well studied, their fish assemblages have not been well documented. Using an autonomous underwater vehicle, we surveyed the fishes that live on the volcanoes and on the surrounding mud. We observed 1836 fishes, which represented a minimum of 43 species. Of these species, at least 23 (53.5%) were of rockfishes (genus Sebastes). Most of the species were entirely or primarily associated with a specific habitat type, either asphalt or mud. The most abundant primarily asphalt-associated species were greenblotched, swordspine, greenspotted, and flag rockfishes, and bocaccio, cowcod, and bank rockfish. The most abundant mud-associated species included Pacific sanddab, slender, Dover, and English soles, and unidentified poachers. A few taxa (shortspine combfish, greenstriped rockfish, and spotted ratfish) were found both on the mud and over the edges of the asphalt. We observed relatively low densities of all fishes on the volcanoes compared to densities on many Southern California natural reefs within the same depth range. We suggest that this is due to (1) a lack of cobble fields around the volcanoes, creating limited habitat for either dwarf species or juvenile fishes, (2) a lack of complex habitat (volcanoes are relatively smooth) creating very limited habitat for adults that need to shelter, and (3) fishing pressure targeting economically important species. Given the unique nature of these tar volcanoes off California, we also suggest the state consider protecting this habitat and the organisms within it.

Evidence of the Genetic Mating System in Viviparity White-Edged Rockfish, <i>Sebastes taczanowskii</i> Steindachner, 1880

Internal fertilization and viviparity are characteristic of some species of the genus Sebastes. Polyandry has also been reported for some species of this genus. We used five microsatellite markers and three main statistical approaches to estimate the level of polyandry in a wild population of white-edged rockfish (Sebastes taczanowskii). In some clutches, we detected multiple paternity. This study is the first record of multiple paternity in white-edged rockfish from the Far East. Polyandry is probably quite a widespread strategy in this species inhabiting the Far Eastern seas, and also an important factor in the regulation of genetic diversity and productivity.

Identification and characterization of lipocalin-type prostaglandin D2 synthase homologs in the urine of male rockfish

Black rockfish (Sebastes schlegelii) and its relatives are viviparous marine fish. Males produce urinary proteins during the copulation season; however, the identity of these proteins was unknown. In this study, we focused on high-molecular-weight urinary proteins (HMWups) in male black rockfish. The HMWups were identified by liquid chromatography and tandem mass spectrometry (LC-MS/MS) of urine. In silico analyses of RNA-seq data predicted the tissue distribution of candidate HMWup transcripts and their gene structures. Candidate cDNAs were cloned and a recombinant protein of a major candidate was prepared. Western blotting of urine using an antiserum against the recombinant protein was performed to reconfirm the LC-MS/MS results. Quantitative real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry were employed to validate the prediction by RNA-seq and identify the cells producing HMWups, respectively. LC-MS/MS, in conjunction with Western blotting and cDNA cloning, identified the HMWups as lipocalin-type prostaglandin D2 synthase (l-PGDS) homologs. RNA-seq analyses and qRT-PCR revealed that the l-PGDS homolog transcripts were dominantly expressed in the testis and male kidney; Sertoli cells and epithelial cells in the renal tubules were immunoreactive. These results indicated that major protein components in the urine of male black rockfish are l-PGDS homologs, potentially produced by the renal tubules in the kidney. Male rockfish (genus Sebastes) are thought to release unknown pheromone substances during mating behavior. The knowledge and tools obtained in this study empower research into the role(s) of HMWups in pheromone systems underlying rockfish reproduction. No protein-type teleost pheromone has heretofore been discovered.

Speciation genomics and the role of depth in the divergence of rockfishes (Sebastes) revealed through Pool-seq analysis of enriched sequences.

Speciation in the marine environment is challenged by the wide geographic distribution of many taxa and potential for high rates of gene flow through larval dispersal mechanisms. Depth has recently been proposed as a potential driver of ecological divergence in fishes, and yet it is unclear how adaptation along these gradients' shapes genomic divergence. The genus Sebastes contains numerous species pairs that are depth‐segregated and can provide a better understanding of the mode and tempo of genomic diversification. Here, we present exome data on two species pairs of rockfishes that are depth‐segregated and have different degrees of divergence: S. chlorostictus–S. rosenblatti and S. crocotulus–S. miniatus. We were able to reliably identify “islands of divergence” in the species pair with more recent divergence (S. chlorostictus–S. rosenblatti) and discovered a number of genes associated with neurosensory function, suggesting a role for this pathway in the early speciation process. We also reconstructed demographic histories of divergence and found the best supported model was isolation followed by asymmetric secondary contact for both species pairs. These results suggest past ecological/geographic isolation followed by asymmetric secondary contact of deep to shallow species. Our results provide another example of using rockfish as a model for studying speciation and support the role of depth as an important mechanism for diversification in the marine environment.

Comparison of Trophic Niche Position, Size, and Overlap in an Assemblage of Pacific Rockfish (Genus Sebastes) for Testing Community Composition Models

Rockfish (genus Sebastes) assemblages can inform mechanisms of coexistence and maintenance of diversity in ecological communities. Coexistence theory characterizes ecological assemblages as following either a deterministic niche differentiation model, or a stochastic lottery model. We used natural abundances of carbon and nitrogen stable isotopes from the tissues of ten co-occurring species of rockfish to assess position, size, and overlap of trophic niches in this diverse assemblage. We created a stochastic null model and compared observed values against the null model to determine if patterns were consistent with a deterministic or a stochastic model. We classified rockfish species as either demersal or pelagic. Mean δ13C and δ15N values differed among pelagic and demersal rockfish species and mean position was more variable than what was predicted by our null model. All species had relatively small trophic niches compared to occupied trophic niche space for the entire assemblage and trophic niche size was smaller than what was predicted by our null model. Trophic niche overlaps varied from 32% to 189% but were substantially lower than predicted by our null mode. All observed trophic niche metrics were different than the stochastic null model. This rockfish assemblage follows a deterministic model of community composition.

A structured deepwater fish community in an isolated benthic feature off Southern California

Between September and November in 1995 and 1998–2011, we conducted surveys of demersal fishes and their associated benthic habitats using direct observations from human-occupied vehicles over the Footprint, an isolated submerged ridge located seawards of the Santa Cruz Island- Anacapa Island Passage, Southern California, extending over bottom depths of about 94–500 m. The observed fish fauna, consisting of 127,351 individuals of at least 79 species, was dominated by rockfishes (genus Sebastes; 94.5% of individuals, 47% of species). The Footprint is home to a complex of benthic habitats that are occupied by a number of fish assemblages. These were defined by bottom depth, habitat type, and the environmental tolerances and preferences of each species. While the habitat-limited benthic species that occupy the shallower parts of the Footprint are isolated from the Santa Cruz Island and Anacapa Island shelves, the fishes living on the Footprint are not reproductively isolated. Rather, through a web of connections, the fishes of the Footprint are likely well integrated into the Southern California Bight. This connectivity, flowing towards and away from the Footprint, means that events hundreds or thousands of kilometers away may have profound effects on the fish assemblages of this feature. For example, economically important species were relatively uncommon, possibly the result of past overfishing locally and a lack of immigration from other regions.

Resolving the phylogenetic relationship among recently diverged members of the rockfish subgenus Sebastosomus

Rapid speciation is an important aspect of adaptive radiations, but can obfuscate phylogenetic relationships among taxa. For recent radiations, there are challenges to reconstructing the relationships among the species due to often shorter branch lengths. Resolution of these relationships is further confounded when studies only use a few genetic markers. Double digest restriction-site associated DNA sequencing (ddRADseq) is a method of next generation sequencing that identifies many single nucleotide polymorphisms (SNPs) throughout the genome. This increases statistical power to resolve close phylogenetic relationships like those found within an adaptive radiation. We used this approach to understand the evolutionary history of the rockfishes of the genus Sebastes, which experienced an adaptive radiation between 3 and 5 mya. Here, we reconstructed the phylogenetic relationships among six species of rockfish within the subgenus Sebastosomus using over 11,600 SNPs. This reconstruction includes the two recently diverged species, Sebastes mystinus and S. diaconus, that were first described genetically in 2008 using mtDNA control region sequence data and six microsatellite loci. We confirmed the relationship of these cryptic species as sister-taxa and found evidence that S. melanops and S. flavidus were also sister-taxa. The latter contradicts prior studies but is supported by our reconstruction using nuclear DNA and measures of genetic differentiation tests and a discriminant analysis of principal components. The relationships between the species of Sebastosomus are further supported by morphological, biological, and ecological justifications.

Post-release survival and prolonged sublethal effects of capture and barotrauma on deep-dwelling rockfishes (genus Sebastes): implications for fish management and conservation

Abstract Barotrauma—injury induced by changes in pressure—is a widespread challenge for successfully releasing fishes following capture. We used acoustic telemetry to examine the long-term post-release survival and behaviour of four rockfish species (genus Sebastes) suffering from barotrauma following capture using recreational fishing techniques. We placed particular emphasis on examining Cowcod (Sebastes levis) and Bocaccio (Sebastes paucispinis), two historically overfished species along the United States West Coast that serve as good model species representing different ecological lifestyles. We show that fish survival was species specific and that 40% of observed mortality occurred more than 48 h post release—a typical time period used in many short-term survivorship studies. Cowcod survival was correlated with fish length, sea surface temperature, and dissolved oxygen concentration at the mean depth of capture. Generalized additive mixed models of Cowcod and Bocaccio behaviour showed that surviving individuals were negatively affected by capture and barotrauma for at least 30 d post-release. Our findings demonstrate the need for extended observations to accurately quantify the mortality of fishes suffering from barotrauma and show how such data can be successfully implemented into fisheries management through engagement between managers, scientists, and the fishing community.

Reproductive Biology, Size, and Age Structure of Harlequin Rockfish: Spatial Analysis of Life History Traits

AbstractMany rockfish (genus Sebastes) species within multispecies complexes have lacked basic biological data hindering their fisheries management. In this study, we provide essential information for stock assessment decision making for one of these species, Harlequin Rockfish Sebastes variegatus. We analyzed aspects of reproduction, size structure, and growth of Harlequin Rockfish in waters off Alaska using historical survey data and recent field collections. Results are reported primarily from the Gulf of Alaska (GOA) region, but important findings are noted from the Aleutian Islands (AI). Harlequin Rockfish reached an observed maximum age of 76 years in the AI, a new estimate for this species. Females exhibited group‐synchronous oocyte development; the parturition period occurred in the spring in both regions, ceasing as late as July in the GOA. Females from the GOA had an estimated length and age at 50% maturity of 187.6 mm (95% confidence limits [CL] = 152.0–215.6 mm; n = 318) and 4.7 years (95% CL = 1.6–6.2 years; n = 188), respectively, indicating that the Harlequin Rockfish is one of the earliest maturing rockfishes. We analyzed a 14‐year time series of bottom trawl survey data to examine the relationship between Harlequin Rockfish length and selected covariates. Spatial heterogeneity existed, with size showing a relationship with bottom temperature and ocean color (productivity index) across the GOA. The comparison of Harlequin Rockfish length at age indicated that larger fish were present in the western GOA but variable growth occurred across the region. Our findings contribute to understanding Harlequin Rockfish biology within multispecies management complexes, and our results demonstrate that key life history traits vary spatially, possibly influenced by regional environmental conditions. This study represents the most comprehensive biological examination for Harlequin Rockfish.

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) FST 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 DXY 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.

MiSebastes: An eDNA metabarcoding primer set for rockfishes (genus Sebastes)

Environmental DNA (eDNA) is a promising biomonitoring tool for marine ecosystems, but its effectiveness for North Pacific coastal fishes is limited by the inability of existing barcoding primers to differentiate among rockfishes in the genus Sebastes. Comprised of 110 commercially and ecologically important species, this recent radiation is exceptionally speciose, and exhibits high sequence similarity among species at standard barcoding loci. Here, we report new Sebastes-specific metabarcoding primers that target mitochondrial cytochrome B. Amongst the 110 Sebastes species, 85 unique barcodes (of which 62 are species-specific) were identified in our amplicon region based on available reference sequences. The majority of the remaining barcodes are shared by only two species. Importantly, MiSebastes yield unique barcodes for 28 of 44 commercially harvested species in California, a dramatic improvement compared to the widely employed MiFish-U 12 S primers which only recover one of 44. Tests of these primers in an aquarium mesocosm containing 16 rockfish species confirms the utility of these new primers for eDNA metabarcoding, providing an important biomonitoring tool for these key coastal marine fishes.

SITE FIDELITY AND RETURN TRIPS OF VISUALLY AND OLFACTORILY INHIBITED BLACK ROCKFISH (SEBASTES SCHLEGELII) INDIVIDUALS TRACKED BY ACOUSTIC TELEMETRY

For fish of the genus Sebastes, which have strong site fidelity, understanding the characteristics of their return trips and how their sensory cues influence behavior will be useful for conservation and resource management. Here, we conducted a behavioral tracking study for the black rockfish Sebastes schlegelii using acoustic telemetry and sensory inhibition. We compared aspects of the return process for individuals in a control group (CNT), and fish in blind (BLD) and olfactory inhibition (OLF) conditions. Nine individuals were released 850 m from the fishing site, and all of them returned. However, the time taken to complete the return varied, with BLD taking the longest, followed by OLF and then CNT. One CNT individual released at 2 km did not return. The return route of CNT individuals was through waters shallower than 10 m in west receiving area, Area 1, from north receiving area including release point, Area 2, while the BLD individuals swam in the opposite direction, at a depth of 40 m northeast of Area 2. OLF individuals took longer at Area 1, although they followed the same route as CNT individuals after release. Therefore, the visual cues were likely used to determine the direction of return, and the inhibition of vision probably affected return speed and activity patterns. Inhibition of olfaction likely affects the return process on small spatial scales. Though it may have less impact than visual inhibition, it may still prevent the perception of olfactory cues in specific environments and conspecifics.

The Role of Oil and Gas Conductors as Fish Habitat at Two Southern California Offshore Platforms

Worldwide, all oil and gas offshore platforms contain conductors, a series of closely spaced vertical pipes, that carry oil and gas from the wells. During decommissioning, these conductors are usually removed. However, worldwide, there has been no research on the relationship between conductor arrays and fish densities. During summer and fall of 2017 and 2018, at Platforms Holly and A, in the Santa Barbara Channel, California, we conducted visual scuba surveys of the fish densities associated with 1) conductors, 2) crossbeams, and 3) blue (open) water under these platforms. A minimum of 14 species were observed at Platform Holly and 14 species at Platform A. Substantially more fishes, and higher densities, were observed at Holly (17,533, 636 per 100 m–2, respectively) than at A (1,185, 171 per 100 m2). Although there were similarities, the dominant species at the two platforms were distinct. Rockfishes (genus Sebastes), particularly Sebastes hopkinsi, dominated the Holly assemblage, while the damselfish, Chromis punctipinnis, was the most abundant at A. Overall, at both platforms, there was no statistical difference between fish densities at conductors and at crossbeams and fish densities were higher at both conductors and crossbeams when compared to those in blue water. The species assemblage among three habitats were similar, although there were two survey occasions where no fish were observed in blue water. Our research strongly suggests that, to the extent possible, retaining conductors during partial removal will likely have a positive influence on both fish diversity and fish abundance, during at least some years.

Molecular identification of redfish (genus Sebastes) in the White Sea indicates patterns of introgressive hybridisation

The rare occurrence of redfish (genus Sebastes) in the White Sea encouraged Rolskii et al. (Polar Biol 43:385–389, 2020) to investigate the species identity of two animals captured near the Sredniy Island at 40 m depth. They reported that their morphological description proved unreliable and that genetic evidence “clearly demonstrated” these redfish belong to S. norvegicus. This was inferred using the S7 and the mitochondrial control region genes. However, while their S7 matched one S. norvegicus reference sequence, the S. norvegicus mitochondrial reference sequences used to infer species identity were previously shown to cluster with S. mentella. Therefore, both of their redfish samples belong to a S. norvegicus × S. mentella (deep-pelagic) hybrid which presents an interesting perspective into the complex species dynamics in this group.