Phylogeography of the Chinese Beard Eel, Cirrhimuraena chinensis Kaup, Inferred from Mitochondrial DNA: A Range Expansion after the Last Glacial Maximum
Abstract
:1. Introduction
2. Results
2.1. Genetic Diversity
Populations (Abbreviation) | Sample Size (n) | Haplotype Numbers | Haplotype Diversity (h) | Nucleotide Diversity (π) | Tajima’s D | Fu’s Fs | Ramos–Onsins & Rozas’ R2 | SSD | Raggedness Index |
---|---|---|---|---|---|---|---|---|---|
cyt b | 266 | 64 | 0.700 | 0.002 | −2.569 ** | −28.372 ** | 0.010 ** | 0.000 | 0.022 |
CR | 266 | 112 | 0.916 | 0.003 | −2.340 ** | −26.782 ** | 0.010 ** | 0.001 | 0.044 |
Ningde(ND) | 49 | 45 | 0.997 | 0.003 | −2.164 ** | −25.812 ** | 0.032 ** | 0.008 | 0.033 |
Xiamen(XM) | 37 | 24 | 0.943 | 0.002 | −2.663 ** | −20.242 ** | 0.035 ** | 0.001 | 0.020 |
Shantou(ST) | 30 | 27 | 0.991 | 0.002 | −2.062 ** | −25.791 ** | 0.043 ** | 0.010 | 0.041 |
Yangjiang(YJ) | 50 | 36 | 0.964 | 0.002 | −2.521 ** | −26.174 ** | 0.024 ** | 0.001 | 0.025 |
Beihai(BH) | 35 | 28 | 0.978 | 0.003 | −1.932 ** | −25.372 ** | 0.044 ** | 0.001 | 0.016 |
Haikou(HK) | 37 | 24 | 0.929 | 0.002 | −1.893 ** | −18.808 ** | 0.044 ** | 0.104 | 0.020 |
Sanya(SY) | 28 | 7 | 0.915 | 0.002 | −1.808 * | −12.332 ** | 0.057 ** | 0.098 | 0.026 |
Total | 266 | 160 | 0.967 | 0.002 | −2.538 ** | −25.652 ** | 0.012 ** | 0.001 | 0.017 |
2.2. Population Structure Pattern
cyt b + CR | ND | XM | ST | YJ | BH | HK | SY |
---|---|---|---|---|---|---|---|
ND | |||||||
XM | 0.00216 | ||||||
ST | −0.00717 | −0.00612 | |||||
YJ | 0.00359 | −0.00241 | 0.00158 | ||||
BH | −0.00492 | −0.00350 | −0.01347 | 0.00157 | |||
HK | 0.00754 | 0.00423 | −0.00378 | 0.00535 | 0.00391 | ||
SY | 0.00407 | 0.00458 | −0.00086 | 0.00663 | 0.01164 | 0.01176 |
cyt b + CR | Sum of Squares | Percentage of Variation | Fixation Indices | Significance Tests |
---|---|---|---|---|
Groups: Taiwan strait (ND) (XM, ST, YJ, BH, HK, SY) | ||||
Among groups | 2.178 | 0.18 | ФCT = 0.00182 | p = 0.580 |
Among populations within groups | 9.447 | 0.11 | ФSC = 0.00125 | p = 0.264 |
Within populations | 469.925 | 99.70 | ФST = 0.00297 | p = 0.277 |
Groups: Pearl River (ND, XM, ST) (YJ, BH, HK, SY) | ||||
Among groups | 1.463 | −0.28 | ФCT = −0.00283 | p = 0.906 |
Among populations within groups | 10.161 | 0.33 | ФSC = 0.00324 | p = 0.130 |
Within populations | 469.925 | 99.96 | ФST = 0.00042 | p = 0.236 |
Groups: Leizhou Peninsula (ND, XM, ST, YJ, HK, SY) (BH) | ||||
Among groups | 2.010 | 0.09 | ФCT = 0.00085 | p = 0.390 |
Among populations within groups | 9.614 | 0.16 | ФSC = 0.00156 | p = 0.223 |
Within populations | 469.925 | 99.75 | ФST = 0.00242 | p = 0.213 |
Groups: Qiongzhou Strait (ND, XM, ST, YJ, BH) (HK, SY) | ||||
Among groups | 2.170 | 0.16 | ФCT = 0.00159 | p = 0.246 |
Among populations within groups | 9.454 | 0.11 | ФSC = 0.00110 | p = 0.359 |
Within populations | 469.925 | 99.73 | ФST = 0.00269 | p = 0.247 |
2.3. Historical Demography
3. Discussion
3.1. Population Genetic Structure and Phylogeographic Pattern
3.2. Historical Demography and Population Expansion
4. Materials and Methods
4.1. Sample Collection
4.2. DNA Extraction, Amplification and Sequencing
4.3. Data Analysis
5. Conclusions
Supplementary Files
Supplementary File 1Acknowledgments
Author Contributions
Conflicts of Interest
References
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Li, H.; Lin, H.; Li, J.; Ding, S. Phylogeography of the Chinese Beard Eel, Cirrhimuraena chinensis Kaup, Inferred from Mitochondrial DNA: A Range Expansion after the Last Glacial Maximum. Int. J. Mol. Sci. 2014, 15, 13564-13577. https://doi.org/10.3390/ijms150813564
Li H, Lin H, Li J, Ding S. Phylogeography of the Chinese Beard Eel, Cirrhimuraena chinensis Kaup, Inferred from Mitochondrial DNA: A Range Expansion after the Last Glacial Maximum. International Journal of Molecular Sciences. 2014; 15(8):13564-13577. https://doi.org/10.3390/ijms150813564
Chicago/Turabian StyleLi, Hai, Hungdu Lin, Jianlong Li, and Shaoxiong Ding. 2014. "Phylogeography of the Chinese Beard Eel, Cirrhimuraena chinensis Kaup, Inferred from Mitochondrial DNA: A Range Expansion after the Last Glacial Maximum" International Journal of Molecular Sciences 15, no. 8: 13564-13577. https://doi.org/10.3390/ijms150813564