Phylogenetic Analysis and Genetic Structure of Schlegel’s Japanese Gecko (Gekko japonicus) from China Based on Mitochondrial DNA Sequences
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sampling
2.2. DNA Extraction and Sequencing
2.3. Sequence Alignment and Phylogenetic Analyses
2.4. Population Genetic Analysis
3. Results
3.1. Sequence Information
3.2. Phylogenetic Analysis
3.3. Genetic Diversity, Genetic Structure and Historical Demography of G. japonicus Population
3.3.1. Genetic Diversity
3.3.2. Genetic Structure
3.3.3. Historical Demography
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Species | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 |
---|---|---|---|---|---|---|---|---|---|---|---|
1. G. japonicus | 0.6 ± 0.2 | ||||||||||
2. AHAQ06 | 12.0–12.9 | - | |||||||||
3. G.wenxianensis | 21.7–23.5 | 23.6–24.1 | 1.0 ± 0.3 | ||||||||
4. G. chinensis | 31.7–33.3 | 28.3–31.0 | 25.4–28.7 | 3.4 ± 0.6 | |||||||
5. G. swinhonis | 30.0–34.4 | 27.2–31.6 | 29.2–32.8 | 25.1–30.0 | 9.1 ± 0.9 | ||||||
6. G. subpalmatus | 31.6–33.0 | 32.1–33.0 | 28.4–30.6 | 29.1–30.2 | 22.5–25.8 | 1.3 ± 0.4 | |||||
7. G.auriverrucosus | 30.2–31.4 | 30.5–31.3 | 31.5–32.7 | 30.2–33.0 | 24.0–27.2 | 24.5–26.2 | 0.3 ± 0.2 | ||||
8. G. hokouensis | 33.5–35.4 | 29.8–31.3 | 28.7–30.8 | 30.6–33.7 | 28.9–31.4 | 27.9–30.1 | 30.5–33.1 | 0.9 ± 0.3 | |||
9. G. scabridus | 31.4–35.2 | 33.8–36.2 | 26.8–30.7 | 24.1–29.3 | 23.2–29.5 | 25.3–29.0 | 27.3–31.7 | 29.2–33.0 | 4.3 ± 0.6 | ||
10. G.gecko | 36.2–38.6 | 35.1–35.8 | 35.4–37.3 | 36.4–38.5 | 34.2–37.8 | 42.0–44.9 | 39.1–40.7 | 37.0–40.8 | 35.3–38.5 | 2.1 ± 0.4 | |
11. G.kikuchii | 33.0–35.2 | 35.5 | 37.3–38.1 | 28.7–30.4 | 28.2–33.6 | 28.1–28.2 | 36.1–37.3 | 36.2–37.8 | 28.5–29.7 | 32.6–33.4 | - |
Population | Number of Samples | Segregating Site (S) | Haplotypes | Haplotype Diversity (h) | Nucleotide Diversity (π) | Average Number of Difference (K) |
---|---|---|---|---|---|---|
Anqing, Anhui (AHAQ) | 11 | 2 | Hap1, 2, 3 | 0.473 | 0.00093 | 0.618 |
Lin’an, Anhui (AHLA) | 1 | 0 | Hap1 | NA | NA | NA |
Wuhu, Anhui (AHWH) | 12 | 2 | Hap1, 4 | 0.167 | 0.00050 | 0.333 |
Yong’an, Fujian (FJYA) | 3 | 3 | Hap1, 5 | NA | NA | NA |
Nanping, Fujian (FJNP) | 1 | 0 | Hap1 | NA | NA | NA |
Guilin, Guangxi (GXGL) | 19 | 3 | Hap1, 5 | 0.105 | 0.00047 | 0.316 |
Longsheng, Guangxi (GXLS) | 14 | 1 | Hap1, 6 | 0.264 | 0.00040 | 0.264 |
Yongfu, Guangxi (GXYF) | 5 | 3 | Hap1, 5 | 0.400 | 0.00180 | 1.2 |
Guiding, Guangzhou (GZGD) | 2 | 0 | Hap1 | NA | NA | NA |
Libo, Guizhou (GZLB) | 3 | 0 | Hap1 | NA | NA | NA |
Huaxi, Guizhou (GZHX) | 1 | 0 | Hap1 | NA | NA | NA |
Longli, Guizhou (GZLL) | 2 | 0 | Hap1 | NA | NA | NA |
Wuhan, Hubei (HBWH) | 13 | 3 | Hap1, 4, 5 | 0.590 | 0.00197 | 1.308 |
Hubeijing (HBJM) | 1 | 0 | Hap1 | NA | NA | NA |
Chengbu, Hunan (HNCB) | 13 | 0 | Hap1 | 0 | 0 | 0 |
Changde, Hunan (HNCD) | 8 | 2 | Hap1, 7 | 0.250 | 0.00075 | 0.5 |
Daoxian, Hunan (HNDX) | 19 | 4 | Hap1, 5, 6 | 0.556 | 0.00237 | 1.579 |
Huaihua, Hunan (HNHH) | 15 | 3 | Hap1, 5 | 0.248 | 0.00112 | 0.743 |
Huitong, Hunan (HNHT) | 16 | 2 | Hap1, 8, 9 | 0.542 | 0.00091 | 0.583 |
Huayuan, Hunan (HNHY) | 16 | 3 | Hap1, 5 | 0.233 | 0.00105 | 0.7 |
Shuangpai, Hunan (HNSP) | 4 | 4 | Hap1, 5, 10 | NA | NA | NA |
Shaoyang, Hunan (HNSY) | 5 | 1 | Hap1, 11 | 0.400 | 0.00060 | 0.4 |
Tongdao, Hunan (HNTD) | 6 | 2 | Hap1, 4 | 0.333 | 0.00100 | 0.667 |
Xinkou, Hunan (HNXH) | 20 | 3 | Hap1, 5 | 0.521 | 0.00235 | 1.563 |
Xinning, Hunan (HNXN) | 4 | 0 | Hap1 | NA | NA | NA |
Yueyang, Hunan (HNYY) | 12 | 0 | Hap1 | 0 | 0 | 0 |
Yongzhou, Hunan (HNYZ) | 12 | 3 | Hap1, 4, 5 | 0.591 | 0.00232 | 1.545 |
Zhuzhou, Hunan (HNZZ) | 7 | 4 | Hap1, 5, 6 | 0.524 | 0.00172 | 1.143 |
Rugao, Jiangsu (JSRG) | 2 | 0 | Hap1 | NA | NA | NA |
Longnan, Jiangxi (JXLN) | 24 | 6 | Hap1, 12 | 0.159 | 0.00144 | 0.957 |
Yueyan Forestry, Qingtang, Yongzhou, Hunan (QTYY) | 5 | 3 | Hap1, 5 | 0.400 | 0.00188 | 1.200 |
Yangxian, Shaanxi (SXYX) | 15 | 3 | Hap1, 5 | 0.533 | 0.00241 | 1.600 |
Lingshutan, Yongzhou, Hunan (YZLST) | 12 | 2 | Hap1, 4 | 0.303 | 0.00091 | 0.606 |
Hangzhou, Zhejiang (ZJHZ) | 8 | 5 | Hap1, 5, 13 | 0.464 | 0.00188 | 1.25 |
Zhoushan, Zhejiang (ZJZS) | 11 | 4 | Hap1, 4, 14 | 0.564 | 0.00208 | 1.382 |
Lishui, Zhejiang (ZJLS) | 1 | 0 | Hap1 | NA | NA | NA |
Yangshuo, Guangxi (GXYS) | 1 | 0 | Hap1 | NA | NA | NA |
Overall | 324 | 16 | 14 | 0.453 | 0.00176 | 1.171 |
Source of Variations | Sum of Squares | Variance Components | Percentage of Variation | Fixation Indices | Significance Tests |
---|---|---|---|---|---|
Among groups | 47.762 | 0.57420 | 39.53 | FCT = 0.39527 | 0.00000 |
Among populations within groups | 32.026 | 0.01214 | 0.84 | FSC = 0.01382 | 0.02639 |
Within populations | 252.108 | 0.86635 | 59.64 | ||
Total | 333.896 | 1.45269 | FST = 0.40362 | 0.03030 |
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Xia, L.; Cai, F.; Chen, S.; Cai, Y.; Zhou, K.; Yan, J.; Li, P. Phylogenetic Analysis and Genetic Structure of Schlegel’s Japanese Gecko (Gekko japonicus) from China Based on Mitochondrial DNA Sequences. Genes 2023, 14, 18. https://doi.org/10.3390/genes14010018
Xia L, Cai F, Chen S, Cai Y, Zhou K, Yan J, Li P. Phylogenetic Analysis and Genetic Structure of Schlegel’s Japanese Gecko (Gekko japonicus) from China Based on Mitochondrial DNA Sequences. Genes. 2023; 14(1):18. https://doi.org/10.3390/genes14010018
Chicago/Turabian StyleXia, Longjie, Fengna Cai, Shasha Chen, Yao Cai, Kaiya Zhou, Jie Yan, and Peng Li. 2023. "Phylogenetic Analysis and Genetic Structure of Schlegel’s Japanese Gecko (Gekko japonicus) from China Based on Mitochondrial DNA Sequences" Genes 14, no. 1: 18. https://doi.org/10.3390/genes14010018
APA StyleXia, L., Cai, F., Chen, S., Cai, Y., Zhou, K., Yan, J., & Li, P. (2023). Phylogenetic Analysis and Genetic Structure of Schlegel’s Japanese Gecko (Gekko japonicus) from China Based on Mitochondrial DNA Sequences. Genes, 14(1), 18. https://doi.org/10.3390/genes14010018