Population Genetic Diversity and Structure of Ancient Tree Populations of Cryptomeria japonica var. sinensis Based on RAD-seq Data
Abstract
:1. Introduction
2. Materials and Methods
2.1. Population Sampling
2.2. DNA Extraction and RAD Sequencing
2.3. SNP Calling and Filtering
2.4. Genetic Diversity and Genetic Differentiation
2.5. Population Structure
2.6. Demographic History
3. Results
3.1. Genetic Diversity and Differentiation
3.2. Genetic Structure
3.3. Demographic History
4. Discussion
4.1. An Old Plantation Derived from Japanese Origin
4.2. Low Genetic Diversity and High Genetic Differentiation in Chinese Cryptomeria
4.3. Specific Genetic Structure with an Absence of IBD
4.4. Continuous Decline of Population Size without Postglacial Recolonization
4.5. Conversation Considerations
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Populations | Longitude (E) | Latitude (N) | Altitude (m) | n | |
---|---|---|---|---|---|
Province | location | ||||
Jiangxi | Lushan (LS) | 115.5801 | 29.3259 | 895 m | 22 |
Anhui | Huangshan (WT) | 118.1600 | 29.2743 | 436 m | 17 |
Fujian | Tianbaoyan (TBY) | 117.3044 | 25.5756 | 1132 m | 17 |
Nanping (YTG) | 118.0848 | 26.4418 | 846 m | 10 | |
Wuyishan (WYS) | 117.4136 | 27.4535 | 892 m | 18 | |
Zhejiang | Tiantaishan (TT) | 121.0541 | 29.1458 | 897 m | 17 |
Tianmushan (XTM) | 119.2608 | 30.2017 | 1089 m | 21 | |
Total | 122 |
Pop | N | Na | Ne | Ho | He | F | Ar | pAr | |
---|---|---|---|---|---|---|---|---|---|
LS | Mean | 16 | 1.939 | 1.532 | 0.307 | 0.316 | 0.023 * | 1.77 | 0.03 |
SE | 0.008 | 0.011 | 0.006 | 0.005 | 0.009 | ||||
WT | Mean | 11 | 1.550 | 1.309 | 0.187 | 0.174 | 0.023 * | 1.42 | 0.00 |
SE | 0.016 | 0.013 | 0.009 | 0.007 | 0.015 | ||||
TBY | Mean | 15 | 1.900 | 1.458 | 0.286 | 0.277 | −0.023 | 1.70 | 0.01 |
SE | 0.010 | 0.011 | 0.006 | 0.005 | 0.009 | ||||
YTG | Mean | 8 | 1.614 | 1.351 | 0.239 | 0.209 | −0.123 * | 1.53 | 0.00 |
SE | 0.016 | 0.012 | 0.008 | 0.006 | 0.011 | ||||
WYS | Mean | 11 | 1.871 | 1.466 | 0.306 | 0.279 | −0.087 * | 1.71 | 0.00 |
SE | 0.011 | 0.011 | 0.007 | 0.006 | 0.009 | ||||
TT | Mean | 17 | 1.838 | 1.429 | 0.266 | 0.257 | −0.033 | 1.64 | 0.01 |
SE | 0.012 | 0.011 | 0.007 | 0.006 | 0.08 | ||||
XTM | Mean | 15 | 1.807 | 1.427 | 0.279 | 0.257 | −0.082 * | 1.64 | 0.01 |
SE | 0.013 | 0.011 | 0.007 | 0.006 | 0.007 | ||||
Total | Mean | 13.3 | 1.789 | 1.424 | 0.267 | 0.253 | −0.042 | 1.63 | 0.0086 |
SE | 0.005 | 0.004 | 0.003 | 0.002 | 0.004 |
Source | df | SS | MS | Est. Var. | % |
---|---|---|---|---|---|
Among Pops | 6 | 4033.190 | 672.198 | 18.885 | 12% |
Among Indiv | 89 | 14,142.633 | 158.906 | 18.552 | 12% |
Within Indiv | 96 | 11,693.000 | 121.802 | 121.802 | 76% |
Total | 191 | 29,868.823 | 159.239 | 100% | |
FST | 0.119 | ||||
Nm | 1.858 |
LS | WT | TBY | YTG | WYS | TT | XTM | |
---|---|---|---|---|---|---|---|
LS | - | 1.014 | 2.460 | 1.251 | 2.630 | 1.533 | 1.963 |
WT | 0.198 *** | - | 1.296 | 0.696 | 1.293 | 0.995 | 1.047 |
TBY | 0.092 *** | 0.162 *** | - | 1.927 | 7.846 | 2.902 | 3.259 |
YTG | 0.167 *** | 0.264 *** | 0.115 *** | - | 2.287 | 1.282 | 1.490 |
WYS | 0.087 *** | 0.162 *** | 0.031 ** | 0.099 *** | - | 2.780 | 4.953 |
TT | 0.140 *** | 0.201 *** | 0.079 *** | 0.163 *** | 0.083 *** | - | 4.788 |
XTM | 0.113 *** | 0.193 *** | 0.071 *** | 0.144 *** | 0.048 ** | 0.050 *** | - |
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Cai, M.; Wen, Y.; Uchiyama, K.; Onuma, Y.; Tsumura, Y. Population Genetic Diversity and Structure of Ancient Tree Populations of Cryptomeria japonica var. sinensis Based on RAD-seq Data. Forests 2020, 11, 1192. https://doi.org/10.3390/f11111192
Cai M, Wen Y, Uchiyama K, Onuma Y, Tsumura Y. Population Genetic Diversity and Structure of Ancient Tree Populations of Cryptomeria japonica var. sinensis Based on RAD-seq Data. Forests. 2020; 11(11):1192. https://doi.org/10.3390/f11111192
Chicago/Turabian StyleCai, Mengying, Yafeng Wen, Kentaro Uchiyama, Yunosuke Onuma, and Yoshihiko Tsumura. 2020. "Population Genetic Diversity and Structure of Ancient Tree Populations of Cryptomeria japonica var. sinensis Based on RAD-seq Data" Forests 11, no. 11: 1192. https://doi.org/10.3390/f11111192