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opencc-zeroDec 2015View details →

Data from: Geographic extent of introgression in Sebastes mentella and its effect on genetic population structure

Genetic population structure is often used to identify management units in exploited species, but the extent of genetic differentiation may be inflated by geographic variation in the level of hybridization between species. We identify the genetic population structure of Sebastes mentella and investigate possible introgression within the genus by analyzing 13 microsatellites in 2,562 redfish specimens sampled throughout the North Atlantic. The data support an historical divergence between the "shallow" and "deep" groups, beyond the Irminger Sea where they were described previously. A third group, "slope," has an extended distribution on the East Greenland Shelf, in addition to earlier findings on the Icelandic slope. Furthermore, S. mentella from the Northeast Arctic and Northwest Atlantic waters are genetically different populations. In both areas, interspecific introgression may influence allele frequency differences among populations. Evidence of introgression was found for almost all the identified Sebastes gene pools, but to a much lower extent than suggested earlier. Greenland waters appear to be a sympatric zone for many of the genetically independent Sebastes groups. This study illustrates that the identified groups maintain their genetic integrity in this region despite introgression.

opencc-zeroDec 2011View details →

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).

opencc-zeroDec 2011View details →

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.

FIGURE 7 in Taxonomic review of the Sebastes pachycephalus complex (Scorpaeniformes: Scorpaenidae)

FIGURE 7. Plots of scores of principal components 2 and 3 based on 24 body measurements of the Sebastes pachycephalus complex: S. pachycephalus (open circles), S. nudus (crossed bars), hybrids (closed squares).

FIGURE 4 in Taxonomic review of the Sebastes pachycephalus complex (Scorpaeniformes: Scorpaenidae)

FIGURE 4. Type specimens of nominal species related to Sebastes pachycephalus. (A) Holotype of S. pachycephalus, RMNH- D 566, 261.8 mm SL; (B) holotype of S. nigricans, ZIN 22686, 150.0 mm SL; (C) holotype of S. latus, FAKU 133309, 138.1 mm SL.

FIGURE 1 in Taxonomic review of the Sebastes pachycephalus complex (Scorpaeniformes: Scorpaenidae)

FIGURE 1. Sebastes pachycephalus in life (A) and when fresh (B–F). (A) FAKU 130127, 129.6 mm SL, Maizuru, Kyoto, Japan; (B) FAKU 73673, 124.0 mm SL, Ushimado, Okayama, Japan; (C) FAKU 133431, 169.8 mm SL, Miyako, Iwate, Japan; (D) FAKU 133432, 166.8 mm SL, Miyako, Iwate, Japan; (E) FAKU 84110, 141.9 mm SL, Noto, Ishikawa, Japan; (F) OMNH- P 9214, 37.3 mm SL, Muroto, Kochi, Japan. A–E photograph by Y. Kai, F photograph by K. Hatooka (OMNH).

FIGURE 3 in Taxonomic review of the Sebastes pachycephalus complex (Scorpaeniformes: Scorpaenidae)

FIGURE 3. Distribution of Sebastes pachycephalus (A) and S. nudus (B). Closed circles based on specimens examined in this study; open circles based on literature records.

FIGURE 6 in Taxonomic review of the Sebastes pachycephalus complex (Scorpaeniformes: Scorpaenidae)

FIGURE 6. Type specimens of nominal species included under Sebastes nudus. (A) Holotype of S. nudus, FAKU 352, 198.5 mm SL; (B) holotype of S. chalcogrammus, FAKU 6317, 163.0 mm SL.

FIGURE 5 in Taxonomic review of the Sebastes pachycephalus complex (Scorpaeniformes: Scorpaenidae)

FIGURE 5. Sebastes nudus when fresh. (A) FAKU 13486, 92.0 mm SL, Hakodate, Hokkaido, Japan; (B) FAKU 133429, 162.5 mm SL, Miyako, Iwate, Japan; (C) FAKU 84037, 181.7 mm SL, Otaru, Hokkaido, Japan; (D) FAKU 133434, 166.3 mm SL, Miyako, Iwate, Japan; (E) FAKU 133430, 170.0 mm SL, Miyako, Iwate, Japan; (F) FAKU 84106, 97.1 mm SL, Noto, Ishikawa, Japan. All photographs by Y. Kai.

FIGURE 2 in Taxonomic review of the Sebastes pachycephalus complex (Scorpaeniformes: Scorpaenidae)

FIGURE 2. Schematic illustrations of Sebastes pachycephalus (A) and S. nudus (B), indicating the squamation pattern below the dorsal-fin spines. (A) FAKU 65097, 154.8 mm SL, Susaki, Shimoda, Shizuoka, Japan; (B) FAKU 84093, 158.3 mm SL, Miyako, Iwate, Japan.

opennotspecifiedMar 2013View details →

Figure 3. A in Hybridization of beaked redfish (Sebastes mentella) with small redfish (Sebastes viviparus) and diversification of redfish (Actinopterygii: Scorpaeniformes) in the Irminger Sea

Figure 3. A median joining network of Sebastes mitochondrial DNA haplotypes, calculated and drawn on the basis of nucleotide variations in the control region with lengths from 365 to 368 base pairs for different redfish species. V1–V3, haplotypes of Sebastes viviparus (black circles); F1, F2, haplotypes of Sebastes fasciatus (grey circles); MR1–MR6, haplotypes of Sebastes marinus (white circles). Haplotypes of Sebastes mentella are shown as hatched circles: haplotypes M-A1–M-A6, horizontally hatched circles; haplotypes M-B1–M-B4, vertically hatched circles; haplotype M-AB, cross-hatched circles. Abbreviations M-Hb1 and M-Hb2 denote haplotypes of fish heterozygous for MDH-2∗67/100. The area of circles is proportional to the number of carriers of relevant haplotypes. Length of connecting lines is proportional to the number of nucleotide polymorphisms (insertion-deletions and/or replacements) separating the haplotypes. Numbers next to the lines show nucleotide positions for the longest D-loop sequences of Sebastes (509-base-pair length; M-B haplotype group), which contain the relevant polymorphic sites that separate the haplotypes. Ovals denote groups of haplotypes belonging to fish of the same species. The position of M-Hb1 and M-Hb2 haplotypes in the group of haplotypes that belong to S. mentella suggests that it is the maternal species for hybrids.

opennotspecifiedMar 2013View details →

Figure 2 in Hybridization of beaked redfish (Sebastes mentella) with small redfish (Sebastes viviparus) and diversification of redfish (Actinopterygii: Scorpaeniformes) in the Irminger Sea

Figure 2. Gel electropherogram of liver malate dehydrogenase. Mr, Sebastes marinus; Mn, Sebastes mentella; V, Sebastes viviparus; F, Sebastes fasciatus; H, hybrid.

opencc-zeroSep 2021View details →

Nematode parasites of rockfish (Sebastes spp.) and cod (Gadus spp.) from waters near Kodiak Island Alaska, USA

Distribution and abundance of common parasitic nematodes in marine fishes is not well documented in many geographic regions. Understanding the influence of large-scale environmental changes on infection rates of fish by nematodes requires quantitative assessments of parasite abundance for multiple host species. We collected samples of two species of cod and eight species of rockfish (total of 232 specimens) from waters near Kodiak Island, Alaska, USA during Spring and Summer of 2015, and dissected and recorded all internal nematode parasites. We quantified the prevalence and intensity of nematode parasites in the ten host species, and tested for differences in prevalence among host species. We found three species of nematode: Anisakis simplex, sensu lato (Van Thiel), Pseudoterranova decipiens, sensu lato (Krabbe), and Hysterothylacium sp. (Ward and Magath). Eighty-two percent of the examined fish were infected with at least one parasitic nematode. The overall prevalence of P. decipiens, A. simplex, and Hysterothylacium sp. was 56%, 62%, and 2%, respectively. Anisakis simplex and P. decipiens were abundant and present in all ten species of host fish examined, whereas Hysterothylacium sp. was rare and found in only five of the host fish species. Prevalence and mean intensity of P. decipiens and A. simplex varied across the ten host species, and the number of parasites varied substantially among individual hosts within host species. The mean intensity of P. terranova and A. simplex in our study was substantially higher than the mean intensity for these same species from multiple other locations in a recent meta-analysis. This study provides a baseline of nematode parasite abundance in long-lived fish in waters near Kodiak Island, AK, and fills an important gap in our quantitative understanding of patterns of occurrence and abundance of these common and widespread parasites of marine fish.