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Population Genomics Reveals Genetic Divergence and Adaptive Differentiation of Chinese Sea Bass (Lateolabrax maculatus)

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Abstract

The marine species usually show high dispersal capabilities accompanied by high levels of gene flow. On the other hand, many physical barriers distribute along the continental marginal seas and may prevent dispersals and increase population divergence. These complexities along the continental margin generate serious challenges to population genetic studies of marine species. Chinese sea bass Lateolabrax maculatus distributes broad latitudinal gradient spanning from the tropical to the mid-temperate zones in the continental margin seas of the Northwest Pacific Ocean. Using the double digest restriction-site-associated DNA tag sequencing (ddRAD) approach, we genotyped 10,297 SNPs for 219 Chinese seabass individuals of 12 populations along the Chinese coast in the Northwest Pacific region. Genetic divergence among these populations was evaluated, and population structure was established. The results suggested that geographically distant populations in the Bohai Gulf and the Beibu Gulf retain significant genetic divergence, which are connected by a series of intermediate populations in between. The results also suggested that Leizhou Peninsula, Hainan Island, and Shandong Peninsula are major physical barriers and substantially block gene flow and genetic admixture of L. maculatus. We also investigated the potential genetic basis of local adaptation correlating with population differentiation of L. maculatus. The sea surface temperature is a significantly differentiated environmental factor for the distribution of L. maculatus. The correlation of water temperature and genetic variations in extensively distributed populations was investigated with Bayesian-based approaches. The candidate genes underlying the local selection in geographically divergent populations were identified and annotated, providing clues to understand the potential mechanisms of adaptive evolution. Overall, our genome scale population genetic analysis provided insight into population divergence and local adaptation of Chinese sea bass in the continental marginal seas along Chinese coast.

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Data Accessibility

Sequence reads were submitted to the Sequence Read Archive (BioProject Number PRJNA356786).

Funding

This work was supported by the Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences (no. 2015C006), Fundamental Research Funds for the Central Universities, Xiamen University (no. 20720160110), the National Natural Science Foundation of China (no. 31422057), and the Local Science and Technology Development Project Guide by The Central Government of China (2017L3019).

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Author notes

  1. Yunfeng Zhao, Wenzhu Peng and Huayang Guo contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing, Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China

    Yunfeng Zhao & Jian Xu

  2. Fujian Collaborative Innovation Centre for Exploitation and Utilization of Marine Biological Resources, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China

    Wenzhu Peng, Baohua Chen, Zhixiong Zhou & Peng Xu

  3. South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, 510300, China

    Huayang Guo & Dianchang Zhang

  4. Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China

    Peng Xu

  5. State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, Fujian, 352103, China

    Peng Xu

Authors
  1. Yunfeng Zhao
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  4. Baohua Chen
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  5. Zhixiong Zhou
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  6. Jian Xu
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  8. Peng Xu
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Contributions

PX and DZ conceived the study. DZ and HG collected samples. YZ performed ddRAD genotyping and some bioinformatics analysis. WP performed bioinformatics and population genetic analysis. BC, ZZ, and JX worked on bioinformatics analysis. PX and WP wrote the manuscript. All authors read and approved the final manuscript.

Corresponding authors

Correspondence to Yunfeng Zhao, Dianchang Zhang or Peng Xu.

Electronic supplementary material

Supplementary Fig. S1

The principle component analysis of 12 populations of Chinese sea bass based on genotypes of all 221 samples. (PNG 72 kb)

Supplementary Fig. S2

Graph of BIC values for speculation of the potential number of genetic clusters based on all SNPs. The optimal K value was 2. (PNG 10 kb)

Supplementary Fig. S3

Gene flow models that were compared in MIGRATE-N. Arrows indicate the direction of suspected gene flow. (JPEG 262 kb)

Supplementary Fig. S4

Venn diagram of pairwise Fst comparisons among three groups. (GIF 437 kb)

High resolution image (TIFF 2152 kb)

Supplementary Fig. S5

Admixture analysis among all populations derived from neutral SNPs. (GIF 159 kb)

High resolution image (TIFF 806 kb)

Supplementary Fig. S6

Graph of ΔK as a function for speculation of the potential number of genetic clusters. In this case, the optimal value of K was 2. (PNG 7 kb)

Supplementary Fig. S7

Graph of BIC values for speculation of the potential number of genetic clusters based on neutral SNPs. The optimal K value was 1. (PNG 10 kb)

Supplementary Fig. S8

PCA and phylogenetic analysis based on selected SNPs and neutral SNPs, respectively. (a) Principle component analysis (PCA) for 12 populations of L. maculatus based on selected SNPs. (b) PCA analysis for 12 populations of L. maculatus based on neutral SNPs. (c) Neighbor-joining tree of all populations based on genetic distance matrix of selected SNPs. (d) Neighbor-joining tree of all populations based on neutral SNPs. (GIF 439 kb)

High resolution image (TIFF 4327 kb)

Supplementary Fig. S9

Venn diagram of outliers associated with temperature of three years. (PNG 146 kb)

Supplementary Fig. S10

Distribution of length of matched reads while alignment to European sea bass. (PNG 24 kb)

ESM 1

Supplementary Tables (XLSX 97 kb)

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Zhao, Y., Peng, W., Guo, H. et al. Population Genomics Reveals Genetic Divergence and Adaptive Differentiation of Chinese Sea Bass (Lateolabrax maculatus). Mar Biotechnol 20, 45–59 (2018). https://doi.org/10.1007/s10126-017-9786-0

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