Use of Microsatellite Locus Flanking Regions for Phylogenetic Analysis? A Preliminary Study of Sebastes subgenera

The systematics of the species-rich genus of Sebastes rockfish has not been resolved, and is unlikely to be resolved using morphological criteria. Using an alternative approach based on DNA sequence variation, we sampled the genome for random, presumably neutral, nuclear DNA sequences, by sequencing microsatellite flanking regions of 15 Sebastes species (representing 15 of 22 extant subgenera) and Hozukius emblemarius. We aligned sequences of flanking regions of eight of the 13 loci that amplified, which presumably are homologous. In aggregate, the aligned sequences included 848 bp, 53 bp of which were polymorphic. The base changes among species included 27 transitions, 20 transversions, three multiple substitutions, and three deletions or insertions. The flanking regions at different loci had different base substitution rates. Nucleotide divergence among Sebastes species ranged from 0.0012 to 0.0216, whereas nucleotide divergence between Sebastes and Hozukius species ranged from 0.0095 to 0.0240. We used maximum parsimony, neighbor-joining, and maximum likelihood methods to examine relationships among the species. H. emblemariusformed a separate group, and five of the western Pacific Ocean species of rockfish clustered together, suggesting that they may have shared an evolutionary history distinct from many North American species. The flanking regions of some microsatellite loci contain DNA sequence variation that distinguishes rockfish species and may prove useful for clarifying relationships among rockfish, or other closely related species.     

Cloning and characterization of novel microsatellite DNA markers for the grass rockfish,Sebastes rastrelliger,and cross‐species amplification in 10 related Sebastes spp

Here we report development and characterization of seven polymorphic loci derived from grass rockfish (Sebastes rastrelliger) genomic DNA phagemid libraries enriched for microsatellite motifs. Within grass rockfish, average allelic diversity was 11.3 alleles per locus and average heterozygosity was 0.73. The seven loci also were surveyed in 10 related species of Sebastes, where allelic diversity ranged from highly polymorphic to monomorphic. Deviations from Hardy–Weinberg were nonsignificant in all but one species/locus combination suggesting low occurrence of null alleles. Significant linkage disequilibrium was detected among three loci, but these events were limited to a single species in each case.     

The utility and limitations of genetic data for stock identification and management of North Pacific rockfish (Sebastes spp.)

Rockfishes (Sebastes spp.) represent a speciose and ecologically important group of marine fishes found in both the Pacific and Atlantic oceans, with approximately 105 species found world-wide (Hyde and Vetter 2007). They also comprise the majority of species found in the Pacific groundfish fishery. Thorough species assessments in terms of harvest management have been done for only 11 species, and of the 11 species, seven have been declared overfished. Having accurate genetic information is critical to the continuing effort at stock assessments, but sampling is often difficult in marine fishes. Genetic techniques are a powerful tool in the effort to better characterize the ecology of these species. These techniques can be used to investigate multiple biological traits, including species identity, intra- and interspecific genetic variation, migration patterns, and effective population size. There are important caveats and limitations when applying specific genetic methods, especially in marine species that lack discrete spawning aggregates. Nevertheless, it is clear from a review of recent literature that genetic tools have already provided very specific insight regarding rockfish population dynamics. The results are diverse and difficult to synthesize; however, existing studies show five primary patterns to population groupings in rockfishes: no obvious pattern of structure, structure consistent with isolation by distance, structure evident but inconsistent with isolation by distance, structure that correlates to oceanographic features, and potential genetic introgression. Clearly the study of rockfish population genetics is poised for rapid expansion that will unquestionably aid management of the rockfish fisheries and general understanding of rockfish evolutionary systematics. A principle challenge at this point is to derive generalized inferences from such a diverse array of study results across the vast North Pacific range of Sebastes. This review summarizes existing genetic studies in Sebastes spp. in the North Pacific to assist in identifying knowledge gaps for this ecologically important and diverse group.     

Distribution, Habitat, and Behavior of Rockfishes, Sebastes spp., in Nearshore Waters of Southeastern Alaska: Observations From a Remotely Operated Vehicle

We examined distribution, habitat, and behavior of rockfishes, Sebastes spp., with a remotely operated vehicle (ROV) in coastal waters <90m deep of southeastern Alaska from 1998 to 2000. We identified black, S. melanops, canary, S. pinniger, China, S. nebulosus, copper, S. caurinus, dusky, S. ciliatus, harlequin, S. variegatus, Puget Sound, S. emphaeus, quillback, S. maliger, redstripe, S. proriger, rosethorn, S. helvomaculatus, silvergray, S. brevispinis, tiger, S. nigrocinctus, yelloweye, S. ruberrimus, and yellowtail, S. flavidus, rockfish. Quillback and dusky rockfish were the most widely distributed species, China and harlequin rockfish were the least widely distributed species. Species richness was greater at sites on or near the outer coast than at sites in more inside, sheltered waters. Most (>75%) observations of rockfish were over complex bottoms of boulder and rock or in vertical bedrock wall habitats. Few rockfish were observed over soft bottoms with no relief. Median depth of observation was 30m for black, copper, dusky, and yellowtail rockfish and >30m for all other species. Median temperature of observation ranged from 6.1°C for harlequin rockfish to 9.4°C for black rockfish. Size of fish was positively correlated (p 0.036) with depth for dusky, quillback, and yelloweye rockfish. Species often observed alone were China (67%), copper (46%), quillback (46%), and rosethorn (43%) rockfish. Most (70%) observations of harlequin, Puget Sound, silvergray, tiger, and yelloweye rockfish were in mixed species assemblages. When first observed, the behavior of most rockfish species was swimming or hovering. Notable exceptions were China, harlequin, rosethorn, and tiger rockfish; 33–57% were resting on bottom or in a hole or crevice.     

Temperature effects on low-light vision in juvenile rockfish (Genus <Emphasis Type="Italic">Sebastes</Emphasis>) and consequences for habitat utilization

The absolute low-light sensitivity of four congeneric species of rockfish (genus Sebastes) was studied from analysis of electroretinograms measured in living fish. The purpose was: (1) to determine if temperature sensitive noise in rod photoreceptors affects the absolute limit to low-light sensitivity at environmentally realistic temperatures and light levels, and (2) to examine whether interspecific variations in habitat utilization within rockfish communities correlate with differences in visual sensitivity. It was found that the low-light sensitivity of individual retinae is inversely dependent on temperature, decreasing tenfold with a 10°C increase in temperature. While in all four species, temperature had a similar effect on sensitivity, the absolute sensitivity levels were different. The four species could be divided into two groups based on measured sensitivity. Kelp and olive rockfish form a high-sensitivity group capable of responding to light levels approximately 50-fold lower than blue and black rockfish. The sensitivity groups correlated with reported diel activity patterns; the high-sensitivity group forages nocturnally, whereas members of the low-sensitivity group are quiescent during twilight and night and forage during the day.     

Genetic Evidence of Postglacial Population Expansion in Puget Sound Rockfish (Sebastes emphaeus)

Several rockfish species (genus Sebastes) along the northeastern Pacific Ocean have rapidly declined in abundance owing in part to overfishing. A striking exception is the dwarf-like Puget Sound rockfish Sebastes emphaeus, whose densities have increased by several orders of magnitude over the last several decades. To describe their genetic structure, we sequenced 395 bp from the mitochondrial control region of 128 S. emphaeus adults from 5 locations spanning approximately 120 km of the Northwest Straits of Washington state. We detected no significant genetic differentiation among these populations and substantial genetic variation within populations, a pattern that may indicate high levels of ongoing gene flow. Preliminary data from 2 microsatellite loci are also consistent with panmixia. The mtDNA sequences also suggest that Puget Sound rockfish populations have expanded substantially since the retreat of Pleistocene glaciers made habitat in Puget Sound region available approximately 12,000 years ago.     

Summer and fall microhabitat utilization of juvenile bull trout and cutthroat trout in a wilderness stream, Idaho

Microhabitat use and availability were evaluated and compared between different size classes of juvenile resident bull trout (Salvelinus confluentus) and cutthroat trout (Oncorhynchus clarki) in a small wilderness stream within the South Fork Clearwater River basin, Idaho. The objective was to determine if utilization of measured habitat characteristics changed from summer to late fall. Sampling of fish was conducted with night snorkeling. During the summer, smaller juvenile bull trout (<66 mm) total length (TL) were associated with shallow stream margins over coarse substrates. In the fall, they moved to significantly deeper, lower velocity water, and closer to cover (p<0.05), but maintained their association with coarse substrates. During the summer, larger juvenile bull trout and larger juvenile cutthroat trout (66–130 mm TL) occupied significantly deeper water than smaller juvenile bull trout (p<0.05). Generally, larger juvenile bull trout were found closer to the bottom and in lower velocity water than larger juvenile cutthroat trout (p<0.05). In the fall, larger juvenile bull trout and larger juvenile cutthroat trout were associated with significantly deeper, lower velocity water located closer to cover than in summer (p<0.05). However, cutthroat trout occupied slightly deeper water over finer substrates than bull trout. Deep water with low velocities evidently provide important rearing areas for large bull trout and large cutthroat trout in the fall. Land management practices that maintain such environments will benefit these species.     

Structural complexity in relation to the habitat preferences,territoriality, and hatchery rearing of juvenile China rockfish (<Emphasis Type="Italic">Sebastes nebulosus</Emphasis>)

Conservation efforts require an understanding of the basic behavior and ecology of target species. However, limited information exists for a wide range of taxa, including declining species of rockfish (genus Sebastes). First, we observed captive juvenile China rockfish (S. nebulosus) to determine how they interact with their environment and conspecifics. Juveniles exhibited site fidelity and territoriality. These aggressive interactions occurred within the context of size-biased dominance, centered on competition for structurally complex habitat. Given the apparent importance of structure and the absence of structure in typical hatchery environments, we then asked how the absence of structure affects future behavior. When barren-reared and structure-reared juveniles were combined into a structurally complex aquarium, barren-reared fish displayed less structure use and less site fidelity than structure-reared fish. However, after 1 to 2 weeks, barren-reared fish began to use structure and showed site fidelity that eventually equaled that of structure-reared juveniles, showing that those behavioral effects of the rearing environment were not permanent. Though these short-term effects may still impact survival after hatchery release, we were unable to detect significant effects on vulnerability to a predator (lingcod, Ophiodon elongatus) in laboratory trials.     

Sexual dimorphism inSebastes

Synopsis Sexual dimorphism and factors that may cause it were investigated in 34 species of the genusSebastes. Sexual dimorphism in standard length and morphometric characters are fairly common in rockfish. In many species males are shorter than females. However in males head length, width of orbit, interorbital width, length of upper jaw, longest pectoral fin ray and longest dorsal spine tend to be larger at a specified size than in females. Water-column species tend to be more dimorphic than demersal species. We suggest that the observed differences in dimorphism in standard length may be related to differences in mating and territorial behavior. Dimorphisms in morphometric measurements may be related to compensation in feeding ability for reduced standard length of males, mating and territorial behavior.     

Molecular phylogenetic perspective on speciation in the genus <Emphasis Type="Italic">Sebastes</Emphasis> (Scorpaenidae) from the Northwest Pacific and the position of <Emphasis Type="Italic">Sebastes</Emphasis> within the subfamily Sebastinae

In the Northeast and the Northwest Pacific, 26 and 68 species of Sebastes occur, respectively, the similar appearance of some pairs of shallow coastal water species in the two regions having been interpreted as evidence either for migration of ancestral species or of morphological convergence. To distinguish between these competing hypotheses, a portion of the mitochondrial DNA (mtDNA) cytochrome b gene was sequenced from 23 species of Sebastes from the Northwest Pacific and phylogenetic trees constructed so as to include the existing data from Northeastern species of Sebastes. The results clearly indicated separate origins for external morphology in Northeast and Northwest Pacific species. The shallow coastal water species in the Northwest Pacific are thought to have diverged from about 9.8MYA. Furthermore, the phylogenetic position of Sebastes was inferred among the subfamily Sebastinae, Helicolenus, Hozukius, Sebastes, and Sebastiscus, the results suggesting that Helicolenus and Hozukius are more closely related to Sebastes than Sebastiscus.     

Demersal fish assemblages in the Southern California Bight based on visual surveys in deep water

Between 1995 and 2006, manned submersible fish surveys were conducted on the sea floor throughout the Southern California Bight. A total of 401 dives (comprising 1,015 transects and 14,373 habitat patches) were made in waters between 19 and 365 m deep. All natural habitat types were included, although both soft sea floors and rocky reefs were surveyed more than any other type. A total of 717,526 fishes, representing a minimum of 137 species and 47 families, were observed. Rockfishes (genus Sebastes), with a minimum of 50 species and 647,495 individuals (90.2% of all fishes observed), dominated most of the habitats. The most abundant species, squarespot (Sebastes hopkinsi), halfbanded (Sebastes semicinctus), shortbelly (Sebastes jordani), and pygmy rockfishes (Sebastes wilsoni), are dwarf taxa that either school or aggregate. The most abundant non-rockfish species was the benthic and territorial blackeye goby (Rhinogobiops nicholsii). Both species richness and overall fish densities were highest in the shallowest sites. Most of the fishes in all habitats were small (≤20 cm TL long) and economically important species were generally uncommon. Forty-four species were found to be characteristic of the study area (occurring in at least 5% of the transects) and these species formed three faunal associations centered around depths of 62, 105, and 168 m. Based on size frequency distributions, at least 18 of the characteristic species exhibited ontogenetic movements, with young-of-the-year and older juveniles living in relatively shallow waters and larger individuals generally in deeper depths. In this study, the abundance of juvenile widow rockfish (Sebastes entomelas), and the virtual absence of adults, in southern California waters may demonstrate an ontogenetic northward movement of this species. This research implies that substantial harvesting of larger species by commercial and recreational fishers has helped alter some fish assemblages, allowing small and “weedy” species to thrive. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.

Habitat characteristics of juvenile cowcod, <Emphasis Type="Italic">Sebastes levis</Emphasis> (Scorpaenidae), in Southern California

We characterized habitat requirements of juvenile cowcod, Sebastes levis, using information from surveys conducted aboard the manned research submersible Delta. We conducted 303 dive surveys on rocky banks and outcrops in water depths between 28 and 365 m in southern and central California, covering 483 km (963,940 m²) of seafloor. We counted 549,263 fishes from at least 134 species; 216 individuals were juvenile cowcod, S. levis, of 45 cm or less in total length (TL). Juvenile cowcod occupied depths between 52 and 330 m and demonstrated ontogenetic shifts in their habitat associations. Small fish (5–20 cm TL) lived primarily among cobbles or cobbles and small boulders. As fish grew, they moved into high-relief rock habitats, including boulder fields and rock ridges. Small cowcods were found with pygmy, Sebastes wilsoni, and swordspine, Sebastes ensifer, rockfishes. Larger juveniles often associated with juvenile bocaccio, Sebastes paucispinis, juvenile widow rockfish, Sebastes entomelas, and squarespot rockfish, Sebastes hopkinsi. Our study resulted in a characterization of seafloor habitats on a small spatial scale that is relevant to juvenile cowcod nursery areas, which is important when considering effective management strategies for this overfished species.     

Diversification of body shape in Sebastes rockfishes of the north‐east Pacific

Body shape variation is integrally related to many aspects of fish ecology, including locomotion and foraging, and can indicate the functional diversity of fish assemblages. Few studies have thoroughly characterized body shape in a diverse marine fish clade, or investigated both temporal and spatial patterns of variation in body shape disparity. Here, I use digital photographs to measure geometric body shape in 66 species of north‐east Pacific rockfish (Sebastes spp.), including a correction for error introduced by arching of specimens. Different components of interspecific shape variation show associations with fish size, depth habitat, trophic niche and phylogenetic relationships. Overall, the accumulation of body shape disparity appears to have been near‐constant over time, and shows little variation across the latitudinal range of rockfish.     

Some data on the distribution,occurrence, and biology of rockfish of the genus <Emphasis Type="Italic">Sebastes</Emphasis> (Sebastidae) off the western coast of Sakhalin

Results of trawl surveys performed by SakhNIRO in Tatar Strait in the end of the 1970s and 1990s, as well as in the beginning of the current century, made it possible to clarify former concepts of rockfish species of the genus Sebastes dwelling off the western coast of Sakhalin, specific features of their distribution, and some aspects of biology. According to specified data, the number of rockfish species in the area of western Sakhalin attains ten.     

SMURFs: standard monitoring units for the recruitment of temperate reef fishes

I evaluated a standard monitoring unit for the recruitment of reef fishes (SMURF) as a tool for ascertaining spatial and temporal patterns of reef fish recruitment in central California, USA. SMURFs consisted of a 1.0×0.35 m dia. cylinder of fine mesh plastic grid that contained a folded section of larger mesh plastic grid. SMURFs collected new recruits of 20 species of fish with 92% of the individuals collected from 10 species, mostly rockfish (genus Sebastes). An experiment varying depth of SMURFs in the water column (surface, mid-depth, or bottom) showed that surface SMURFs collected the greatest diversity of species and significantly greater abundance for eight species, with two species having significantly greater abundance on mid-depth SMURFs and three species having significantly greater abundance on bottom SMURFs. A comparison of cumulated recruitment from SMURFs that varied in sampling frequency (removal of new recruits every 1-3, 7, or 28 days) suggested that increasing the time between sampling caused a significant decrease in recruitment estimates for some species but not for others. To determine how well temporal patterns of recruitment to SMURFs reflected patterns to nearby reefs, I compared within season temporal patterns of recruitment to SMURFs with that at nearby reefs, estimated by visual transect surveys conducted on scuba. Temporal patterns of recruitment to SMURFs were significantly and positively related to early recruitment on reefs for one group of benthic-algal associated rockfish species when diver surveys were lagged by 30 days (r=0.87) and for another group of canopy-algal associated rockfish species when lagged by 5 days (r=0.72). SMURFs appeared to be an effective and efficient method for indexing relative rates of delivery of competent juveniles for many temperate nearshore reef fishes.     

Depth and habitat distributions of three species of rockfish (Sebastes) in British Columbia: observations from the submersible PISCES IV

Synopsis I describe a technique to quantify spatial distribution patterns of deep reef-fishes, and apply this technique to inshore rockfish (Sebastes) communities in the Strait of Georgia, British Columbia, Canada. Observations were made along vertical transects between 21–140 m using the submersible PISCES IV. A total of 31 transects were completed at 14 sites during 16 submersible dives. S. elongatus, S. maliger and S. ruberrimus were the dominant rockfish species that were observed. S. elongatus and S. ruberrimus had similar depth distributions, but tended to segregate by habitat type. S. elongatus was most abundant on mud and cobble substrates that interspersed rocky areas. S. maliger and S. ruberrimus were both abundant in complex rock habitats, but tended to segregate by depth. For all three species there was an increase in size with depth. Hence, habitat type and depth were important influences on distribution patterns of this species group.     

Otolith shape lends support to the sensory drive hypothesis in rockfishes

The sensory drive hypothesis proposes that environmental factors affect both signalling dynamics and the evolution of signals and receivers. Sound detection and equilibrium in marine fishes are senses dependent on the sagittae otoliths, whose morphological variability appears intrinsically linked to the environment. The aim of this study was to understand if and which environmental factors could be conditioning the evolution of this sensory structure, therefore lending support to the sensory drive hypothesis. Thus, we analysed the otolith shape of 42 rockfish species (Sebastes spp.) to test the potential associations with the phylogeny, biological (age), ecological (feeding habit and depth distribution) and biogeographical factors. The results showed strong differences in the otolith shapes of some species, noticeably influenced by ecological and biogeographical factors. Moreover, otolith shape was clearly conditioned by phylogeny, but with a strong environmental effect, cautioning about the use of this structure for the systematics of rockfishes or other marine fishes. However, our most relevant finding is that the data supported the sensory drive hypothesis as a force promoting the radiation of the genus Sebastes. This hypothesis holds that adaptive divergence in communication has significant influence relative to other life history traits. It has already been established in Sebastes for visual characters and organs; our results showed that it applies to otolith transformations as well (despite the clear influence of feeding and depth), expanding the scope of the hypothesis to other sensory structures.     

Investigating the complexities of sustainable fishing at a prehistoric village on western Vancouver Island, British Columbia, Canada

Zooarchaeological data provide direct evidence of long-term human resource utilization relevant to the modern study of sustainability and conservation. On the northwest coast of North America, prehistoric aboriginal communities relied heavily on nearshore marine fish species, many of which have life history characteristics that make them vulnerable to overexploitation. This study examines temporal trends in the abundance and distribution of nearshore fish from skeletal remains recovered from three separate areas of a prehistoric coastal village on the west coast of Vancouver Island (ca. 1800–250 yr BP). Over the course of 1500 years, site inhabitants from these contemporaneously occupied areas regularly utilized Sebastes spp. (rockfish), with varying impacts on abundance and total length. Contrasting temporal trends in Sebastes spp. total length in separate village areas suggest different consequences to prehistoric harvesting practices, differences that can be linked to ethnographic and archaeological evidence of lineage-based territories. These long-term zooarchaeological data provide unique insights into the context and challenges of sustainable resource use in prehistory and can inform contemporary conservation efforts focused on similar species in this modern-day marine protected area.     

Immunochemical identification and partial characterization of female-specific serum proteins in white-edged rockfish,Sebastes taczanowskii

Synopsis Female-specific serum proteins (FSSPs) in white-edged rockfish,Sebastes taczanowskii, were identified and partially characterized by immunochemical procedures. Two FSSPs, which clearly reacted with antiserum against egg proteins, were confirmed in the serum of mature females, and estrogen treatment induced similar FSSPs in the serum of mature males. Hence, the FSSPs were considered to be vitellogenin. The vitellogenin concentration in female fish was high during the vitellogenic period and low during gestation, parturition and the recovery period, indicating that vitellogenin is used only for yolk formation in the oocytes and not as a direct nutritional source for developing embryos during gestation. On the other hand, an FSSP (FS3), which was considered not to be vitellogenin, was also identified in the sera of mature females and males after estradiol-17β administration by using an antiserum (a-FS3) that removed the components of the male serum and egg extracts from the anti-mature female serum antiserum. Moreover, immunohistochemical observation with a-FS3 illustrated that FS3 was a major constituent of the ovarian fluid but not of vitellogenic oocytes. The cross-reactivities of these FSSPs among seven viviparous rockfishes demonstrated that vitellogenin existed in the sera of all rockfishes studied belonging to the generaSebastes andSebastiscus, whereas FS3 was not present in several species ofSebastes.     

Effects of hypoxia on the behavior and physiology of kelp forest fishes

Forecasts from climate models and oceanographic observations indicate increasing deoxygenation in the global oceans and an elevated frequency and intensity of hypoxic events in the coastal zone, which have the potential to affect marine biodiversity and fisheries. Exposure to low dissolved oxygen (DO) conditions may have deleterious effects on early life stages in fishes. This study aims to identify thresholds to hypoxia while testing behavioral and physiological responses of two congeneric species of kelp forest fish to four DO levels, ranging from normoxic to hypoxic (8.7, 6.0, 4.1, and 2.2 mg O₂/L). Behavioral tests identified changes in exploratory behavior and turning bias (lateralization), whereas physiological tests focused on determining changes in hypoxia tolerance (pCrit), ventilation rates, and metabolic rates, with impacts on the resulting capacity for aerobic activity. Our findings indicated that copper rockfish (Sebastes caurinus) and blue rockfish (Sebastes mystinus) express sensitivity to hypoxia; however, the strength of the response differed between species. Copper rockfish exhibited reduced absolute lateralization and increased escape time at the lowest DO levels, whereas behavioral metrics for blue rockfish did not vary with oxygen level. Both species exhibited decreases in aerobic scope (as a function of reduced maximum metabolic rate) and increases in ventilation rates to compensate for decreasing oxygen levels. Blue rockfish had a lower pCrit and stronger acclimation response compared to copper rockfish. The differences expressed by each species suggest that acclimatization to changing ocean conditions may vary, even among related species that recruit to the same kelp forest habitat, leading to winners and losers under future ocean conditions. Exposure to hypoxia can decrease individual physiological fitness through metabolic and aerobic depression and changes to anti‐predator behavior, with implications for the outcome of ecological interactions and the management of fish stocks in the face of climate change.