Inference of potential genetic risks associated with large-scale releases of red sea bream in Kanagawa prefecture, Japan based on nuclear and mitochondrial DNA analysis

Since 1978, millions of hatchery-reared red sea bream (Pagrus major) juveniles have been released in Sagami Bay and Tokyo Bay in Kanagawa Prefecture, Japan. The stock enhancement program has contributed to total catch; however, no information regarding the genetic interactions with wild counterparts is available. Here, we combined 15 microsatellite loci and mitochondrial D-loop sequencing to characterize the genetic resources of red sea bream in Sagami Bay and Tokyo Bay and to elucidate the potential harmful genetic effects associated with fish releases. Both types of markers evidenced higher levels of genetic diversity in wild samples (SB and TB) compared with offspring before stocking (H07 and H08) as well as a hatchery-released sample recaptured in Sagami Bay (HR). Microsatellite F (ST) estimates and Bayesian clustering analysis found significant genetic differences among samples (F (ST) = 0.013-0.054), except for the two wild samples (F (ST) = 0.002) and HR vs. H07 (F (ST) = 0.007). On the other hand, mitochondrial-based Dcurrency sign (ST) suggested haplotypic similarity between SB, H07, and HR. The low effective number of females contributing to the offspring over multiple generations may be responsible for the lack of haplotypic differentiation. Moreover, the putative hatchery origin to three fish (8 %) without deformity in the inter-nostril epidermis was inferred for the first time. Our results showed the usefulness of combining nuclear and mitochondrial markers to elucidate genetic interactions between hatchery-released and wild red sea bream and warned about potential harmful genetic effects should interbreeding takes place

Data from: Effects of large-scale releases on the genetic structure of red sea bream (Pagrus major, Temminck et Schlegel) populations in Japan

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Effects of large-scale releases on the genetic integrity of red sea bream (Pagrus major, Temminck et Schlegel)

Large-scale hatchery releases are carried out for many marine fish species worldwide; nevertheless, the long-term effects of this practice on the genetic structure of natural populations remains unclear. The lack of knowledge is especially evident when independent stock enhancement programs are conducted simultaneously on the same species at different geographical locations, as occurs with red sea bream (Pagrus major, Temminck et Schlegel) in Japan. In this study, we examined the putative effects of intensive offspring releases on the genetic structure of red sea bream populations along the Japanese archipelago by genotyping 848 fish at fifteen microsatellite loci. Our results suggests weak but consistent patterns of genetic divergence (FST = 0.002, p < 0.001). Red sea bream in Japan appeared spatially structured with several patches of distinct allelic composition, which corresponded to areas receiving an important influx of fish of hatchery origin, either released intentionally or from unintentional escapees from aquaculture operations. In addition to impacts upon local populations inhabiting semi-enclosed embayments, large-scale releases (either intentionally or from unintentional escapes) appeared also to have perturbed genetic structure in open areas. Hence, results of the present study suggest that independent large-scale marine stock enhancement programs conducted simultaneously on one species at different geographical locations may compromise native genetic structure and lead to patchy patterns in population genetic structure

Genotype data

Genotype dat

Release data

Release dat

Sampling locations (solid circles, for details see Table 1) and main circulation features associated with major water masses around the Japanese archipelago.

<p>Broken red lines indicate the location of the three major barriers to gene flow inferred based on the microsatellite data. Broken grey lines delimit the eight coastal regions dividing the country: 1. Hokkaido, 2. Northern Japan Sea, 3. Western Japan Sea, 4. East China Sea, 5. Seto Inland Sea, 6. Southern Pacific, 7. Central Pacific, 8. Northern Pacific.</p

Annual variation in number of red sea bream juveniles releases (x1000) by prefectures (colored areas) and regions (dashed grey lines).

<p>For each region, colors of the prefectures in the map correspond to those used to represent the annual variation in number of releases. Note that no releases have been performed in Hokkaido and the Northern Pacific region.</p

Sample location, abbreviation (ID), latitude, longitude, sample size (<i>n</i>), number of alleles (<i>A</i>), allelic richness (<i>A</i>_r, n = 26), heterozygosity (<i>H</i>_S), <i>F</i>_IS and <i>p</i>-value.

<p>Loci deviating from Hardy-Weinberg proportions (either direction) are given in parenthesis (without adjustment for multiple tests). Bold values of <i>F</i>_IS denote significant values in either direction.</p><p>Sample location, abbreviation (ID), latitude, longitude, sample size (<i>n</i>), number of alleles (<i>A</i>), allelic richness (<i>A</i>_r, n = 26), heterozygosity (<i>H</i>_S), <i>F</i>_IS and <i>p</i>-value.</p

Genetic diversity among red sea bream samples at 15 loci.

<p>Allele counts (<i>A</i>), total gene diversity (<i>H</i>_T), level of genetic differentiation among samples (<i>F</i>_ST) and exact test <i>p</i>-values for allele frequency homogeneity (Fisher’s procedure, bold font indicates significant <i>p</i>-values).</p><p>Genetic diversity among red sea bream samples at 15 loci.</p