Multilocus Phylogeography and Population Genetic Analyses of Opsariichthys hainanensis Reveal Pleistocene Isolation Followed by High Gene Flow around the Gulf of Tonkin
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection, Microsatellite Genotyping, and Mitochondrial Sequencing
2.2. Data Analysis
2.2.1. Mitochondrial DNA and Nuclear DNA Analysis
2.2.2. Microsatellite DNA Analysis
2.2.3. ABC Analyses Using DIYABC
3. Results
3.1. Mitochondrial DNA and Nuclear DNA Analysis
3.2. Historical Population Demography
3.3. Microsatellite DNA
3.4. Approximate Bayesian Computation
4. Discussion
4.1. Genetic Diversity
4.2. Population Structure
4.3. Phylogeography of O. hainanensis
4.4. Demographic History of O. hainanensis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene | Mitochondrial DNA (cyt b Gene and d-Loop Region) | Nuclear DNA (RAG1) | ||||||||
---|---|---|---|---|---|---|---|---|---|---|
Locations (Abbreviation) | Sample Size (N) | Haplotype Numbers (Nh) | Haplotype Diversity (h) | Nucleotide Diversity (π) | Nucleotide Diversity (θ) | Sample Size (N) | Haplotype Numbers (Nh) | Haplotype Diversity (h) | Nucleotide Diversity (π) | Nucleotide Diversity (θ) |
Hainan Island | 215 | 80 | 0.975 | 1.148 | 1.311 | 183 | 45 | 0.908 | 0.199 | 0.850 |
Changhua River (CH) | 27 | 19 | 0.960 | 0.742 | 0.728 | 24 | 6 | 0.725 | 0.250 | 0.445 |
Nandu River (ND) | 30 | 12 | 0.897 | 0.204 | 0.244 | 20 | 13 | 0.947 | 0.185 | 0.281 |
Wanqan River (WQ) | 30 | 14 | 0.924 | 1.062 | 0.635 | 24 | 11 | 0.902 | 0.157 | 0.249 |
Lingshui River (LS) | 30 | 5 | 0.703 | 0.311 | 0.220 | 20 | 10 | 0.905 | 0.151 | 0.206 |
Longgun River (LG) | 15 | 3 | 0.600 | 1.071 | 0.640 | 15 | 9 | 0.876 | 0.166 | 0.204 |
Longshou River (LOS) | 10 | 4 | 0.533 | 0.029 | 0.051 | 9 | 5 | 0.722 | 0.125 | 0.171 |
Longwei River (LW) | 10 | 3 | 0.378 | 0.019 | 0.034 | 10 | 2 | 0.200 | 0.013 | 0.023 |
Tengqiao River (TQ) | 4 | 3 | 0.833 | 0.169 | 0.185 | 4 | 4 | 1.000 | 0.243 | 0.254 |
Wanglou River (WL) | 9 | 2 | 0.500 | 0.024 | 0.018 | 8 | 5 | 0.893 | 0.175 | 0.154 |
Baisha River (BS) | 10 | 4 | 0.533 | 0.106 | 0.188 | 10 | 3 | 0.378 | 0.027 | 0.047 |
Zhubi River (ZB) | 10 | 6 | 0.867 | 0.110 | 0.137 | 10 | 3 | 0.378 | 0.134 | 0.164 |
Chunjiang River (CJ) | 10 | 9 | 0.978 | 0.314 | 0.342 | 9 | 5 | 0.861 | 0.148 | 0.147 |
Beimen River (BM) | 10 | 5 | 0.844 | 0.267 | 0.222 | 10 | 6 | 0.889 | 0.174 | 0.117 |
Wenchang River (WC) | 10 | 2 | 0.200 | 0.029 | 0.051 | 10 | 2 | 0.467 | 0.031 | 0.023 |
Mainland China | 90 | 37 | 0.960 | 0.737 | 0.754 | 74 | 19 | 0.817 | 0.172 | 0.463 |
Red River (HH) | 30 | 13 | 0.885 | 0.184 | 0.244 | 21 | 2 | 0.095 | 0.006 | 0.018 |
Beilun River (BL) | 10 | 5 | 0.822 | 0.090 | 0.086 | 10 | 5 | 0.822 | 0.099 | 0.094 |
Fangheng River (FC) | 10 | 3 | 0.600 | 0.158 | 0.188 | 10 | 3 | 0.378 | 0.053 | 0.094 |
Nanliu River (NL) | 10 | 6 | 0.867 | 0.125 | 0.154 | 10 | 7 | 0.911 | 0.274 | 0.399 |
Jian River (JR) | 10 | 5 | 0.756 | 0.075 | 0.120 | 5 | 3 | 0.700 | 0.186 | 0.223 |
Moyang River (MY) | 10 | 4 | 0.533 | 0.065 | 0.068 | 10 | 4 | 0.533 | 0.103 | 0.164 |
Tan River (TR) | 10 | 1 | 0.000 | 0.000 | 0.000 | 8 | 4 | 0.821 | 0.164 | 0.128 |
Total | 305 | 117 | 0.984 | 1.076 | 1.576 | 257 | 59 | 0.897 | 0.194 | 1.073 |
Mitochondrial cyt b + D-Loop Gene | nuDNA RAG1 Genes | Microsatellite DNA | |||||||
---|---|---|---|---|---|---|---|---|---|
Scenario Ⅰ: two independent groups divided by the Qiongzhou Strait | |||||||||
Among groups | 1.24 | FCT = 0.012 | 0.292 | −0.11 | FCT = −0.001 | 0.317 | 1.72 | FCT = 0.017 | 0.004 |
Among populations within groups | 68.09 | FSC = 0.690 | 0.000 | 30.53 | FSC = 0.305 | 0.000 | 18.24 | FSC = 0.186 | 0.000 |
Within populations | 30.66 | FST = 0.693 | 0.000 | 69.58 | FST = 0.304 | 0.000 | 80.03 | FST = 0.200 | 0.000 |
Scenario Ⅱ: three independent groups divided by the Qiongzhou Strait and Beibu Gulf; | |||||||||
Among groups | 17.14 | FCT = 0.171 | 0.242 | 3.46 | FCT = 0.035 | 0.389 | 3.09 | FCT = 0.031 | 0.370 |
Among populations within groups | 54.43 | FSC = 0.657 | 0.000 | 26.98 | FSC = 0.279 | 0.000 | 12.31 | FSC = 0.127 | 0.000 |
Within populations | 28.43 | FST = 0.716 | 0.000 | 69.56 | FST = 0.304 | 0.000 | 84.6 | FST =0.154 | 0.000 |
Scenario Ⅲ: four groups divided by the WY Range, the Qiongzhou Strait and Beibu Gulf. | |||||||||
Among groups | 0.35 | FCT = 0.004 | 0.317 | 0.93 | FCT = 0.009 | 0.266 | −1.95 | FCT = −0.019 | 0.635 |
Among populations within groups | 63.59 | FSC = 0.638 | 0.000 | 24.82 | FSC = 0.251 | 0.000 | 13.99 | FSC = 0.137 | 0.000 |
Within populations | 36.06 | FST = 0.639 | 0.000 | 74.25 | FST =0.258 | 0.000 | 87.96 | FST = 0.120 | 0.000 |
SAMOVA | |||||||||
Among groups | 63.12 | FCT = 0.631 | 0.000 | 31.2 | FCT = 0.312 | 0.000 | 14.93 | FCT = 0.149 | 0.000 |
Among populations within groups | 7.59 | FSC = 0.206 | 0.000 | 11.45 | FSC = 0.166 | 0.000 | 10.04 | FSC = 0.118 | 0.000 |
Within populations | 29.28 | FST = 0.707 | 0.000 | 57.35 | FST = 0.426 | 0.000 | 75.03 | FST = 0.250 | 0.000 |
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Wang, J.; Zhang, W.; Wu, J.; Li, C.; Ju, Y.-M.; Lin, H.-D.; Zhao, J. Multilocus Phylogeography and Population Genetic Analyses of Opsariichthys hainanensis Reveal Pleistocene Isolation Followed by High Gene Flow around the Gulf of Tonkin. Genes 2022, 13, 1908. https://doi.org/10.3390/genes13101908
Wang J, Zhang W, Wu J, Li C, Ju Y-M, Lin H-D, Zhao J. Multilocus Phylogeography and Population Genetic Analyses of Opsariichthys hainanensis Reveal Pleistocene Isolation Followed by High Gene Flow around the Gulf of Tonkin. Genes. 2022; 13(10):1908. https://doi.org/10.3390/genes13101908
Chicago/Turabian StyleWang, Junjie, Wenjun Zhang, Jinxian Wu, Chao Li, Yu-Min Ju, Hung-Du Lin, and Jun Zhao. 2022. "Multilocus Phylogeography and Population Genetic Analyses of Opsariichthys hainanensis Reveal Pleistocene Isolation Followed by High Gene Flow around the Gulf of Tonkin" Genes 13, no. 10: 1908. https://doi.org/10.3390/genes13101908
APA StyleWang, J., Zhang, W., Wu, J., Li, C., Ju, Y.-M., Lin, H.-D., & Zhao, J. (2022). Multilocus Phylogeography and Population Genetic Analyses of Opsariichthys hainanensis Reveal Pleistocene Isolation Followed by High Gene Flow around the Gulf of Tonkin. Genes, 13(10), 1908. https://doi.org/10.3390/genes13101908