Comparative analysis of the population diversity of black rockfish (Sebastes schlegelii) in northern China

Peng, Lei; Hua, Wenyuan; Chen, Yan; Wang, Wei; Xue, Zhuang

doi:10.1007/s11033-023-08821-7

Cited by 3 publications

(2 citation statements)

References 38 publications

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“…In addition, all of the pairwise F ST values between the populations indicated low levels of genetic divergence (F ST < 0.05), consistent with the previously reported lack of population genetic differentiation of S. schlegelii based on mtDNA control region sequences [16,17]. This result was also in accordance with the results of Peng et al, who used comparative mtDNA loop analysis to study the population structure and genetic diversity of the S. schlegelii populations in the Bohai Sea (Qingdao, Jinzhou, and Dalian), where there was no significant population genetic structural differences and low population genetic differentiation (F ST = −0.0113-0.0061) within the geographical range of the S. schlegelii population [36]. In addition, the pairwise F ST values obtained were also similar to those obtained by Cao et al (wild populations: F ST < 0.05) with a similar sampling design and 2b-RAD sequencing method [37].…”

Section: Genetic Differentiation Analysissupporting

confidence: 90%

Population Genomics of Commercial Fish Sebastes schlegelii of the Bohai and Yellow Seas (China) Using a Large SNP Panel from GBS

Zhu,

Gao,

et al. 2024

Genes

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Sebastes schlegelii is one of the most commercially important marine fish in the northwestern Pacific. However, little information about the genome-wide genetic characteristics is available for S. schlegelii individuals from the Bohai and Yellow Seas. In this study, a total of 157,778, 174,480, and 188,756 single-nucleotide polymorphisms from Dalian (DL), Yantai (YT), and Qingdao (QD) coastal waters of China were, respectively, identified. Sixty samples (twenty samples per population) were clustered together, indicating shallow structures and close relationships with each other. The observed heterozygosity, expected heterozygosity, polymorphism information content, and nucleotide diversity ranged from 0.14316 to 0.17684, from 0.14035 to 0.17145, from 0.20672 to 0.24678, and from 7.63 × 10−6 to 8.77 × 10−6, respectively, indicating the slight difference in genetic diversity among S. schlegelii populations, and their general genetic diversity was lower compared to other marine fishes. The population divergence showed relatively low levels (from 0.01356 to 0.01678) between S. schlegelii populations. Dispersing along drifting seaweeds, as well as the ocean current that flows along the western and northern coasts of the Yellow Sea and southward along the eastern coast of China might be the major reasons for the weak genetic differentiation. These results form the basis of the population genetic characteristics of S. schlegelii based on GBS (Genotyping by Sequencing). In addition to basic population genetic information, our results provid a theoretical basis for further studies aimed at protecting and utilizing S. schlegelii resources.

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Section: Genetic Differentiation Analysissupporting

confidence: 90%

Population Genomics of Commercial Fish Sebastes schlegelii of the Bohai and Yellow Seas (China) Using a Large SNP Panel from GBS

Zhu,

Gao,

et al. 2024

Genes

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“…Recent studies have explored the genetic diversity of the black rockfish from a total of three populations in northern China using mtDNA loop analysis, and the results showed no significant genetic differentiation and low genetic differentiation. 33 These results indicate that the wild and cultured populations in this study may have been degraded to varying degrees, and effective protection of wild germplasm and supplementation of cultured populations are urgently needed. The Fis of five wild populations (0.004-0.024) were all positive, and the other two populations (-0.007, -0.069) were all minus, suggesting that the degree of inbreeding was low levels.…”

Section: Discussionmentioning

confidence: 89%

Population genetics analysis of the black rockfish Sebastes schlegelii in Northern China based on 2b-RAD simplified genome sequencing

Cao,

Zhang,

et al. 2023

Israeli Journal of Aquaculture - Bamidgeh

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The black rockfish Sebastes schlegelii is an important fishery species in Japan, South Korea, and China. Overfishing has severely depleted the natural resources of S. schlegelii in recent years, leading to the initiation of programs aimed at enhancing fish stock. However, the genetic structure of northern populations remains elusive, posing challenges in collecting and preserving germplasm resources. In this study, a total of 191 S. schlegelii individuals from seven populations, including one cultured population (Changdao: CDYZ) and six wild populations (Lianyungang: LYG; Qingdao: QD; Weihai: WH; Changdao: CDYS; Beidaihe: BDH) sequenced by 2b-RAD method and their population genetics was analyzed using 27,064 SNPs obtained. The results indicated low genetic diversity in both wild and cultured populations (PIC < 0.25, Ho: 0.174-0.273, He: 0.173-0.234), with the cultured population exhibiting higher diversity than the wild ones. Moderate genetic differentiation existed between the cultured population and six wild populations (0.05 < Fst < 0.25). However, the genetic differentiation was lower among the other wild populations (Fst < 0.05). The analyses of population genetic structure indicated that the wild populations clustered together first and finally with the cultured population CDYZ, which clustered separately except for one individual. Therefore, scientific breeding programs and germplasm conservation can be important in stabilizing genetic structure. In addition, gene flow among the seven populations was high (Nm > 1). This study provides a theoretical basis for conserving and rationalizing germplasm resources for S. schlegelii.

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Endemic demographics of the Jomon people estimated based on complete mitogenomes reveal their regional diversity

Yoshida,

Wakiyama,

Valverde

et al. 2024

Preprint

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The Jomon culture that spread across Japanese archipelago began about 16,000 years ago and lasted for over 10,000 years. The genetic diversity of the Jomon people, prehistoric hunter-gatherers bearing the Jomon culture, is of great interest in understanding prehistoric East Eurasians. Until now, their demographic history has been estimated using archaeological sites and present-day genomes, but detailed studies using Jomon genomes has not been sufficient. To investigate the Jomon demography, we determined complete mitochondrial genome (mitogenome) sequences from 13 Jomon individuals and conducted population genetic analysis on 40 Jomon genomes including previously published data. Our results revealed an effective population size increase during the Incipient - Initial phase of Jomon period, which was not observed in present-day Japanese populations. This endemic demographic pattern is pronounced in the eastern part of the archipelago, suggesting regional diversity in Jomon demographic history.

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Comparative analysis of the population diversity of black rockfish (Sebastes schlegelii) in northern China

Cited by 3 publications

References 38 publications

Population Genomics of Commercial Fish Sebastes schlegelii of the Bohai and Yellow Seas (China) Using a Large SNP Panel from GBS

Population Genomics of Commercial Fish Sebastes schlegelii of the Bohai and Yellow Seas (China) Using a Large SNP Panel from GBS

Population genetics analysis of the black rockfish Sebastes schlegelii in Northern China based on 2b-RAD simplified genome sequencing

Endemic demographics of the Jomon people estimated based on complete mitogenomes reveal their regional diversity

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