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51 results for “rockfish”
Data from: Effects of multiple climate change stressors on gene expression in blue rockfish (Sebastes mystinus)
<p>Global climate change is predicted to increase the co-occurrence of high pCO2 and hypoxia in upwelling zones worldwide. Yet, few studies have examined the effects of these stressors on economically and ecologically important fishes. Here, we investigated short-term responses of juvenile blue rockfish (Sebastes mystinus) to independent and combined high pCO2 and hypoxia at the molecular level, using changes in gene expression and metabolic enzymatic activity to investigate potential shifts in energy metabolism. Fish were experimentally exposed to conditions associated with intensified upwelling under climate change: high pCO2 (1200 μatm, pH~7.6), hypoxia (4.0 mg O2/L), and a combined high pCO2/hypoxia treatment for 12 h, 24 h or two weeks. Muscle transcriptome profiles varied significantly among the three treatments, with limited overlap among genes responsive to both the single and combined stressors. Under elevated pCO2, blue rockfish increased expression of genes encoding proteins involved in the electron transport chain and muscle contraction. Under hypoxia, blue rockfish up regulated genes involved in oxygen and ion transport and down regulated transcriptional machinery. Under combined high pCO2 and hypoxia, blue rockfish induced a unique set of ionoregulatory and hypoxia responsive genes not expressed under the single stressors. Thus, high pCO2 and hypoxia exposure appears to induce a non-additive transcriptomic response that cannot be predicted from single stressor exposures alone, further highlighting the need for multiple stressor studies at the molecular level. Overall, lack of a major shift in cellular energetics indicates that blue rockfish may be relatively resistant to intensified upwelling conditions in the short term.</p>
Fig. 4 in First Record of the Rockfish Sebastes melanops from the Western North Pacific, with Comments on its Synonymy (Osteichthyes: Scorpaenoidei: Sebastidae)
Fig. 4. Unrooted neighbor-joining tree based on sequence variations of the mitochondrial control region. Sequences used here are referred to by catalog numbers of the specimens (determined here) or DDBJ registration numbers (indicated by asterisks, determined in previous studies). Numbers at branches indicate bootstrap probabilities in 1,000 bootstrap replications. The scale bar equals 0.01 of Kimura's (1980) distance.
Data from: Divergent population structure in five common rockfish species of puget sound, WA suggests the need for species-specific management
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Data from: Contrasting effect of hybridization on genetic differentiation in three rockfish species with similar life history
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Data from: Effects of multiple climate change stressors on gene expression in blue rockfish (Sebastes mystinus)
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Black rockfish otolith and early life history data
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Resolving the phylogenetic relationship among recently diverged members of the rockfish subgenus Sebastosomus
<p>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 <em>Sebastes</em>, which experienced an adaptive radiation between 3 to 5 mya. Here, we reconstructed the phylogenetic relationships among six species of rockfish within the subgenus <em>Sebastosomus</em> using over 11,600 SNPs. This reconstruction includes the two recently diverged species, <em>Sebastes</em> mystinus and <em>S. diaconus</em>, 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 <em>S. melanops</em> and <em>S. flavidus</em> 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 <em>Sebastosomus</em> are further supported by morphological, biological, and ecological justifications.</p>
Data from: Genetic architectures of postmating isolation and morphology of two highly diverged rockfishes (genus Sebastes)
<p>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 to other isolating mechanisms that drive the early stages of speciation, especially in non-model organisms. We characterized the genetic architecture of postmating isolation between two rockfishes, <em>Sebastes schlegelii</em> and <em>S. trivittatus</em>, whose reproductive isolation is complete. We examined transmission ratio distortion (TRD) patterns of genetic markers in two reciprocal backcross populations. Markers showing either of the two 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 two backcross families and two 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, 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 <em>agouti-signaling protein 1</em> (<em>asip1</em>) and <em>melanocortin 1 receptor</em> (<em>mc1r</em>), might underlie the horizontal and vertical color patterns on the body, respectively. These findings constitute an essential step towards a comprehensive understanding of speciation and morphological diversification of rockfishes.</p>
Convergent genomics of longevity in rockfishes highlights the genetics of human lifespan variation
<p>Longevity is a defining, heritable trait that varies dramatically between species. To resolve the genetic regulation of this trait, we have mined genomic variation in rockfishes, which range in longevity from 11 to over 205 years, along with the sea robin as an outgroup. We used the phylomapping methodology to target sequencing and assembly to conserved, functional loci, defined using available genomic resources from well-characterized species. These annotations are in the gtf. For analysis of coding elements, assembled contigs were trimmed to just the exons. Exons were concatenated and analyzed to generate gene trees with IQTree, fixed to match the species tree. Additional details of these assembly methods are available at DOI: <a href="https://doi.org/10.1038/s41559-019-0914-2">10.1038/s41559-019-0914-2</a> and <a href="https://doi.org/10.1126/sciadv.add2743">DOI: 10.1126/sciadv.add2743</a></p>
Using acoustic telemetry to quantify potential contaminant exposure of Vermilion Rockfish (Sebastes miniatus), Hornyhead Turbot (Pleuronichthys verticalis), and White Croaker (Genyonemus lineatus) at wastewater outfalls in southern California
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Data from: Genetic architectures of postmating isolation and morphology of two highly diverged rockfishes (genus Sebastes)
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Resolving the phylogenetic relationship among recently diverged members of the rockfish subgenus Sebastosomus
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Trophic level influences larval shortbelly rockfish (Sebastes jordani) development
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Data from: A comparison of the life history and distribution of vermilion rockfish (<em>Sebastes miniatus</em>) and its cryptic pair, sunset rockfish (<em>S. crocotulus</em>) along the Pacific Coast
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Momma's larvae: Maternal oceanographic experience and larval size influence early survival of rockfishes
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Data from: Sex matters: Otolith shape and genomic variation in deacon rockfish (Sebastes diaconus)
<p>Little is known about intraspecific <span class="il">variation</span> within the deacon rockfish (Sebastes diaconus), a recently described species found in the northeast Pacific Ocean. We investigated population structure among fish sampled from two nearshore reefs (Siletz Reef and Seal Rock) and one offshore site (Stonewall Bank) within a <50 km2 area off the Oregon coast. Fish from the three sample sites exhibited small but statistically significant differences based on genetic <span class="il">variation</span> at >15,000 neutral loci, whether analyzed independently or classified into nearshore and offshore groups. Male and females were readily distinguished using genetic data and 92 outlier loci were associated with <span class="il">sex</span>, potentially indicating differential selection between males and females. Morphometric results indicated that there was significant secondary sexual dimorphism in <span class="il">otolith</span> <span class="il">shape</span>, but further sampling is required to disentangle potential confounding influence of age. This study is the first step towards understanding intraspecific <span class="il">variation</span> within the deacon rockfish and the potential management implications. Since differentiation among the three sample sites was small, we consider the results to be suggestive of a single stock. However, future studies should evaluate how the stock is affected by differences in <span class="il">sex</span>, age, and gene flow between the nearshore and offshore environments.</p>
Data from: Replicate divergence between and within sounds in a marine fish: the copper rockfish (Sebastes caurinus)
The evolution of population structure in marine organisms and its relevance to conservation has recently received increasing attention. We tested the degree of genetic subdivision among ten populations of copper rockfish (Sebastes caurinus) representing paired samples of outer coast and the heads of five replicate sounds on the west coast of Vancouver Island, British Columbia using 17 microsatellite DNA loci. Overall, subdivision (FST) was low (FST = 0.031), but consistently higher between paired coast and head of inlet sites (mean FST = 0.047) compared to among five coast sites (mean FST = -0.001) or among the five head of inlet sites (mean FST = 0.026). Heterozygosity, allelic richness, and estimates of effective population size were also consistently lower in head of inlet sites than in coast sites. Bayesian analysis of population structure identified two genetic groups across all samples, a single genetic group amongst only coast samples, two genetic groups amongst head of inlet samples, and two genetic groups within each sound analysed separately. Head of inlet copper rockfish were also consistently shorter with lower condition factors, and grew more slowly than fish collected from coast sites. Our results implicate coast- head of inlet habitat transitions in driving the evolution of population structure, likely resulting from reduced physical connectivity and selection against immigrants in contrasting environments. Coast sites appear to be well served by existing marine protected areas. By contrast, head of inlet sites may require more specific local conservation measures as they appear to be less well connected to adjacent coast sites as well as to each other.
Data from: Shortspine thornyhead and rockfish (Scorpaenidae) distribution in response to substratum, biogenic structures and trawling
Learmonth Bank in northern British Columbia sustains an active trawl fishery that returns large bycatches of deep-sea sponges and corals. To examine effects of biogenic structures on the distribution of fish, we examined nearly 30 km of high-definition imagery from a remotely operated vehicle and documented locations of 2770 scorpaenid fish. The 2 local genera have similar abundances, averaging about 1.2 individuals 100 m–2, but have different spatial abundance patterns: shortspine thornyhead Sebastolobus alascanus are randomly distributed on featureless substrata and their abundance increases with depth. Rockfish Sebastes spp. associate with higher seafloor relief nonrandomly and select for sponges and corals over the inert substrata alone; 95% of the rockfish occurred on 27% of the seafloor surveyed. Sponges (Demospongia and Hexactinellida) were abundant on the bedrock and boulders of the bank and adjacent moraine and covered 30 to 55% of the seafloor compared with 1% of the sediment and aggregates of the surrounding basin. The majority of rockfish (80%) occurred with sponges ≥50 cm in height, and even beds of short sponges attracted 4 times as many rockfish than did substrata with no large epifauna. While over half of primnoid corals over 30 cm tall had associated rockfish, less than 2% of the seafloor had large coral, and small coral had no associated rockfish. On the adjacent seafloor with past trawling activity, Primnoa pacifica was 13 times less abundant, and large corals and sponges were rare. Thornyhead abundance doubled but rockfish had a 3-fold reduction in numbers. Our study indicates that degradation of biogenic structures is a long-term detriment to rockfish species and, although the mechanism remains unclear, our data suggest it occurs through the destruction of a habitat that is more effective for shelter than rough inert seafloor.
Data from: Estimation of genotyping error rate from repeat genotyping, unintentional recaptures and known parent-offspring comparisons in 16 microsatellite loci for brown rockfish (Sebastes auriculatus)
Genotyping errors are present in almost all genetic data and can affect biological conclusions of a study, particularly for studies based on individual identification and parentage. Many statistical approaches can incorporate genotyping errors, but usually need accurate estimates of error rates. Here, we used a new microsatellite data set developed for brown rockfish (Sebastes auriculatus) to estimate genotyping error using three approaches: (i) repeat genotyping 5% of samples, (ii) comparing unintentionally recaptured individuals and (iii) Mendelian inheritance error checking for known parent–offspring pairs. In each data set, we quantified genotyping error rate per allele due to allele drop-out and false alleles. Genotyping error rate per locus revealed an average overall genotyping error rate by direct count of 0.3%, 1.5% and 1.7% (0.002, 0.007 and 0.008 per allele error rate) from replicate genotypes, known parent–offspring pairs and unintentionally recaptured individuals, respectively. By direct-count error estimates, the recapture and known parent–offspring data sets revealed an error rate four times greater than estimated using repeat genotypes. There was no evidence of correlation between error rates and locus variability for all three data sets, and errors appeared to occur randomly over loci in the repeat genotypes, but not in recaptures and parent–offspring comparisons. Furthermore, there was no correlation in locus-specific error rates between any two of the three data sets. Our data suggest that repeat genotyping may underestimate true error rates and may not estimate locus-specific error rates accurately. We therefore suggest using methods for error estimation that correspond to the overall aim of the study (e.g. known parent–offspring comparisons in parentage studies).
Data from: Comparative population genetic analysis of bocaccio rockfish Sebastes paucispinis using anonymous and gene-associated simple sequence repeat loci
Comparative population genetic analyses of traditional and emergent molecular markers aid in determining appropriate use of new technologies. The bocaccio rockfish Sebastes paucispinis is a high-gene-flow marine species off the west coast of North America that experienced strong population decline over the past three decades. We used 18 anonymous and 13 gene associated simple sequence repeat loci (EST-SSRs) to characterize range-wide population structure with temporal replicates. No FST-outliers were detected using the LOSITAN program, suggesting that neither balancing nor divergent selection affected the loci surveyed. Consistent hierarchical structuring of populations by geography or year class was not detected regardless of marker class. The EST-SSRs were less variable than the anonymous SSRs, but no correlation between FST and variation or marker class was observed. General Linear Model analysis showed that low EST-SSR variation was attributable to low mean repeat number. Comparative genomic analysis with Gasterosteus aculeatus, Takifugu rubripes, and Oryzias latipes showed consistently lower repeat number in EST-SSRs than SSR loci that were not in ESTs. Purifying selection likely imposed functional constraints on EST-SSRs resulting in low repeat numbers that affected diversity estimates, but did not affect the observed pattern of population structure.
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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