Conservation Genetics of the Rare and Endangered Tree Species, Camellia nitidissima (Theaceae), Inferred from Microsatellite DNA Data
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. DNA Extraction and Microsatellite Analysis
2.3. Data Analysis
3. Results
3.1. Test of Neutrality
3.2. Genetic Diversity
3.3. Test for Bottleneck Effects
3.4. Genetic Structure
4. Discussion
4.1. Genetic Variation of C. nitidissima
4.2. Genetic Differentiation and Population Genetic Structure
4.3. Conservation Implications for C. nitidissima
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Region and Population | Location | Altitude (m) | Sample Size (Count as Individual) | Estimated Population Size (Count as Individual) | |
---|---|---|---|---|---|
Nanning | |||||
ZZC | Zhongzhencun, Gutan, Longan | 230 | 36 | 170 | |
BLS | Boluoshan, Fushu, Xixiangtang | 240 | 33 | 190 | |
GMS | Gengmaoshan, Fushu, Xixiangtang | 380 | 30 | 160 | |
ZD | Zhongdong, Fusui | 280 | 11 | 140 | |
Fangcheng | |||||
FL | Fulong | 170 | 31 | 39 | |
BLC | Bailicun, Dalu | 20 | 31 | 180 | |
NLP * | Niulanping, Nasuo | 178 | 20 | 63 | |
PTC * | Paotaicun, Nasuo | 165 | 17 | 120 | |
NZS * | NZS-1 | Mount Nazi, Nasuo | 120 | 30 | 70 |
NZS-2 | Mount Nazi, Nasuo | 250 | 29 | 100 | |
NZS-3 | Mount Nazi, Nasuo | 306 | 30 | 40 | |
total | 89 | 210 | |||
DWJ | Dawangjiang, fucheng | 70 | 30 | 150 | |
DYC | Diaoyingcun, Malu, Dongxing | 410 | 30 | 32 | |
JDC | Jiaodongcun, Jiangping, Dongxing | 130 | 27 | 37 |
Population | NA | NE | NP | P(%) | AR | HO | UHE | FIS-GenALEx | p-Value of HWE Test | FIS-INest | FIS-INest 95% HDPI | FST | FST (ENA) | BOTTLENECK Test (p Value) | |||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
IAM | SMM | TPM | |||||||||||||||
ZZC | 5.857 | 2.888 | 3 | 100.00 | 2.871 | 0.606 | 0.603 | −0.031 | 0.4673 | 0.121 | 0.083–0.162 | 0.05469 | 0.03906 *a | 0.68750 | |||
BLS | 4.857 | 2.335 | 0 | 100.00 | 2.478 | 0.353 | 0.482 | 0.307 | 0.0005 * | 0.289 | 0.224–0.352 | 1.00000 | 0.03906 *a | 0.10938 | |||
GMS | 7.000 | 4.065 | 5 | 85.714 | 3.235 | 0.589 | 0.649 | 0.069 | 0.0071 * | 0.087 | 0.063–0.127 | 0.04688 *a | 1.00000 | 0.43750 | |||
ZD | 6.857 | 4.783 | 2 | 100.00 | 3.679 | 0.494 | 0.757 | 0.324 | 0.0005 * | 0.188 | 0.049–0.414 | 0.37500 | 0.57813 | 1.00000 | |||
FL | 6.429 | 3.638 | 1 | 85.714 | 2.932 | 0.498 | 0.603 | 0.148 | 0.0005 * | 0.066 | 0.004–0.137 | 0.01563 *a | 0.07813 | 0.43750 | |||
BLC | 8.429 | 4.137 | 2 | 100.00 | 3.409 | 0.608 | 0.684 | 0.077 | 0.0026 * | 0.064 | 0.002–0.144 | 0.81250 | 0.01563 *a | 0.10938 | |||
NLP | 5.000 | 2.813 | 0 | 85.714 | 2.749 | 0.513 | 0.560 | 0.054 | 0.0658 | 0.115 | 0.038–0.192 | 0.68750 | 0.15625 | 0.56250 | |||
PTC | 4.286 | 2.779 | 2 | 85.714 | 2.662 | 0.485 | 0.533 | 0.098 | 0.0709 | 0.135 | 0.051–0.221 | 0.01563 *a | 1.00000 | 0.01563 *a | |||
NZS | NZS-1 | 7.143 | 3.929 | 100.00 | 3.194 | 0.604 | 0.667 | 0.108 | 0.0077 * | 0.00781 *a | 0.07813 | 0.93750 | |||||
NZS-2 | 8.571 | 4.486 | 100.00 | 3.492 | 0.608 | 0.691 | 0.130 | 0.0005 * | 0.37500 | 0.03906 *a | 0.68750 | ||||||
NZS-3 | 8.429 | 4.983 | 100.00 | 3.415 | 0.560 | 0.645 | 0.192 | 0.0005 * | 0.10938 | 0.29688 | 0.93750 | ||||||
Population level | 11.857 | 6.056 | 5 | 100.00 | 3.588 | 0.590 | 0.694 | 0.169 | 0.0006 * | 0.129 | 0.102–0.157 | 0.29688 | 0.07813 | 0.93750 | |||
DWJ | 6.571 | 3.922 | 3 | 100.00 | 3.081 | 0.656 | 0.657 | −0.028 | 0.5046 | 0.073 | 0.032–0.111 | 0.02344 *a | 0.10938 | 0.29688 | |||
DYC | 6.143 | 2.736 | 1 | 100.00 | 2.797 | 0.545 | 0.614 | 0.110 | 0.0087 * | 0.128 | 0.068–0.205 | 0.93750 | 0.05469 | 0.68750 | |||
JDC | 5.714 | 3.145 | 3 | 100.00 | 2.920 | 0.490 | 0.609 | 0.200 | 0.0005 * | 0.143 | 0.083–0.206 | 0.29688 | 0.46875 | 0.93750 | |||
Mean b | Mean c | 6.583 | 3.608 | 95.238 | 3.033 | 0.536 | 0.620 | 0.126 | |||||||||
Mean d | 6.558 | 3.501 | 94.805 | 2.975 | 0.539 | 0.608 | 0.107 | ||||||||||
Species c | 0.199 | 0.190 | |||||||||||||||
Species d | 0.203 | 0.194 |
Nanning Group Population | Mean | Fangcheng Group Population | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ZZC | BLS | GMS | ZD | FL | BLC | NLP | PTC | NZS | DWJ | DYC | JDC | |||||||
NZS-1 | NZS-2 | NZS-3 | Population level | |||||||||||||||
Nanning group population | ZZC | — | 0.2002 B | |||||||||||||||
BLS | 0.2332 * | — | ||||||||||||||||
GMS | 0.1598 * | 0.2076 * | — | |||||||||||||||
ZD | 0.2360 * | 0.2822 * | 0.2046 * | — | ||||||||||||||
Mean | 0.2206 a | |||||||||||||||||
Fangcheng group population | FL | 0.2598 * | 0.3129 * | 0.2583 * | 0.0793 * | 0.2304 a | — | |||||||||||
BLC | 0.2124 * | 0.2546 * | 0.2024 * | 0.0760 * | 0.0886 * | — | ||||||||||||
NLP | 0.3463 * | 0.3919 * | 0.3000 * | 0.0781 * | 0.2099 * | 0.2012 * | — | |||||||||||
PTC | 0.3290 * | 0.3845 * | 0.3002 * | 0.1066 * | 0.2034 * | 0.1852 * | 0.0745 * | — | ||||||||||
NZS | NZS-1 | 0.2163 * | 0.2946 * | 0.1895 * | 0.0670 * | 0.1510 * | 0.1248 * | 0.1043 * | 0.0901 * | — | ||||||||
NZS-2 | 0.2071 * | 0.2581 * | 0.1965 * | 0.0534 * | 0.1153 * | 0.1083 * | 0.0888 * | 0.0878 * | 0.0656 * | — | ||||||||
NZS-3 | 0.2298 * | 0.2878 * | 0.2139 * | 0.0779 * | 0.1336 * | 0.1353 * | 0.0999 * | 0.0646 * | 0.0539 * | 0.0282 * | — | |||||||
Popu-lation level | 0.2000 * | 0.2509 * | 0.1844 * | 0.0507 * | 0.1163 * | 0.1114 * | 0.0769 * | 0.0597 * | — | — | — | — | ||||||
DWJ | 0.2795 * | 0.2886 * | 0.2694 * | 0.0489 * | 0.1514 * | 0.1523 * | 0.1412 * | 0.1428 * | 0.1258 * | 0.1126 * | 0.1199 * | 0.1034 * | — | |||||
DYC | 0.2733 * | 0.3087 * | 0.2579 * | 0.0944 * | 0.1761 * | 0.1972 * | 0.1345 * | 0.1608 * | 0.1508 * | 0.1097 * | 0.1433 * | 0.1153 * | 0.1580 * | — | ||||
JDC | 0.2901 * | 0.3224 * | 0.2740 * | 0.0860 * | 0.1686 * | 0.1605 * | 0.1243 * | 0.1064 * | 0.1237 * | 0.1022 * | 0.0996 * | 0.0904 * | 0.1103 * | 0.1511 * | — | |||
Mean | 0.2813 A | 0.1383 bC |
Source of Variation | d.f. | Sum of Squares | Variance Components | Percentage of Variation | |
---|---|---|---|---|---|
with ZD population | Between regional groups | 1 | 105.083 | 0.27423 | 16.14 ** |
Among populations within regional groups | 10 | 163.984 | 0. 24829 | 14.61 ** | |
Within populations | 758 | 891.677 | 1.17636 | 69.24 ** | |
Total | 769 | 1160.744 | 1.69887 | ||
after excluding ZD population | Between regional groups | 1 | 129.538 | 0.36877 | 16.73 ** |
Among populations within regional groups | 9 | 177.470 | 0.27863 | 12.64 ** | |
Within populations | 737 | 1147.375 | 1.55682 | 70.63 ** | |
Total | 747 | 1454.383 | 2.20422 |
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Chen, Z.; Wang, J.; Tang, J.; Wang, Z.; Chai, S.; He, X.; Wei, X. Conservation Genetics of the Rare and Endangered Tree Species, Camellia nitidissima (Theaceae), Inferred from Microsatellite DNA Data. Forests 2022, 13, 1662. https://doi.org/10.3390/f13101662
Chen Z, Wang J, Tang J, Wang Z, Chai S, He X, Wei X. Conservation Genetics of the Rare and Endangered Tree Species, Camellia nitidissima (Theaceae), Inferred from Microsatellite DNA Data. Forests. 2022; 13(10):1662. https://doi.org/10.3390/f13101662
Chicago/Turabian StyleChen, Zongyou, Junfang Wang, Jianmin Tang, Zhengfeng Wang, Shengfeng Chai, Xingjin He, and Xiao Wei. 2022. "Conservation Genetics of the Rare and Endangered Tree Species, Camellia nitidissima (Theaceae), Inferred from Microsatellite DNA Data" Forests 13, no. 10: 1662. https://doi.org/10.3390/f13101662