Multiple Dataset-Based Insights into the Phylogeny and Phylogeography of the Genus Exbucklandia (Hamamelidaceae): Additional Evidence on the Evolutionary History of Tropical Plants
Abstract
1. Introduction
2. Results
2.1. Haplotype Network of the Combined Chloroplast Regions
2.2. Population Genetics Based on SSR Loci
2.3. Phylogenetic Trees and Divergence Time Estimation
3. Discussion
3.1. The Origin and Dispersal History of Exbucklandia by Seed Dispersal
3.2. The Southward Expansion of E. populnea and E. tonkinensis Through Pollen Dispersal
3.3. Taxonomic Implication of Exbucklandia Species
3.4. The Genetic Diversity and Conservation of Exbucklandia Species
4. Materials and Methods
4.1. Sample Collection and DNA Extraction
- To construct a plastid tree with high support, 1 representative individual per population was selected for plastid genome sequencing, so that we could assemble complete chloroplast genome sequences to construct a plastid tree.
- To construct a plastid haplotype network, we amplified four cpDNA fragments in 8 individuals per population, and the results showed that most populations harbored only one haplotype, suggesting that 8 individuals per population were sufficient.
- For obtaining nuclear data, we selected populations containing ≥10 individuals to amplify with SSR primers to ensure the reliability of genetic diversity and population structure analyses.
4.2. Plastid Region Amplification and Haplotype Network Construction
4.3. SSR Amplification, Inspection, and Diversity Analysis
4.4. Shallow Plastid Genome Sequencing and Assembly
4.5. Phylogenetic Tree Construction and Divergence Time Estimation
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Species | Pop ID | NT | I | HO | HE | F |
---|---|---|---|---|---|---|
E. tricuspis | IN | 33 | 0.334 | 0.211 | 0.218 | 0.034 |
MAFH | 25 | 0.168 | 0.105 | 0.106 | 0.054 | |
VMBM | 98 | 1.118 | 0.360 | 0.588 | 0.347 | |
VNBHH | 40 | 0.379 | 0.244 | 0.238 | 0.044 | |
VNBNB | 98 | 1.056 | 0.297 | 0.524 | 0.387 | |
VNKB | 80 | 0.897 | 0.289 | 0.464 | 0.422 | |
E. populnea | NP | 38 | 0.428 | 0.277 | 0.271 | −0.031 |
XZ01 | 23 | 0.200 | 0.115 | 0.121 | −0.010 | |
XZ02 | 34 | 0.393 | 0.222 | 0.241 | 0.051 | |
YNBLF | 53 | 0.649 | 0.347 | 0.383 | 0.105 | |
YNDWS | 48 | 0.561 | 0.310 | 0.340 | 0.029 | |
YNJTC | 57 | 0.616 | 0.360 | 0.367 | 0.017 | |
YNMBZ | 46 | 0.556 | 0.276 | 0.343 | 0.149 | |
YNPMZ | 47 | 0.536 | 0.280 | 0.321 | 0.098 | |
YNQTZ | 45 | 0.594 | 0.314 | 0.386 | 0.201 | |
YNXLS | 54 | 0.590 | 0.267 | 0.333 | 0.190 | |
GZLB | 66 | 0.777 | 0.357 | 0.441 | 0.192 | |
GZGHX | 46 | 0.479 | 0.273 | 0.290 | 0.025 | |
GXBXS | 49 | 0.592 | 0.290 | 0.362 | 0.157 | |
GXWDX | 61 | 0.663 | 0.254 | 0.382 | 0.326 | |
GXYRT | 37 | 0.319 | 0.221 | 0.201 | −0.087 | |
VNSL | 47 | 0.409 | 0.207 | 0.225 | 0.064 | |
VNNCS | 41 | 0.380 | 0.226 | 0.220 | −0.017 | |
VNSSH | 106 | 1.220 | 0.386 | 0.613 | 0.371 | |
VNTPO | 90 | 0.920 | 0.300 | 0.482 | 0.355 | |
E. longipetala | GZLGS | 39 | 0.429 | 0.324 | 0.278 | −0.158 |
GXSW | 50 | 0.687 | 0.375 | 0.436 | 0.147 | |
HNQJD | 50 | 0.542 | 0.202 | 0.326 | 0.344 | |
HNBMS | 69 | 0.779 | 0.315 | 0.434 | 0.266 | |
E. tonkinensis | GXGPS | 60 | 0.684 | 0.321 | 0.393 | 0.265 |
HNJQS | 62 | 0.675 | 0.392 | 0.387 | 0.063 | |
HNMJX | 78 | 0.946 | 0.369 | 0.522 | 0.339 | |
GDBJ | 50 | 0.581 | 0.315 | 0.355 | 0.072 | |
GDZMP | 84 | 0.940 | 0.338 | 0.500 | 0.344 | |
GDCDD | 58 | 0.618 | 0.383 | 0.358 | −0.096 | |
GDBX | 90 | 1.017 | 0.476 | 0.543 | 0.129 | |
GDDDS | 45 | 0.492 | 0.255 | 0.300 | 0.192 | |
GDFXC | 67 | 0.740 | 0.264 | 0.413 | 0.324 | |
GDHSD | 73 | 0.904 | 0.342 | 0.513 | 0.337 | |
GDNL | 56 | 0.775 | 0.424 | 0.475 | 0.131 | |
HK | 57 | 0.717 | 0.387 | 0.421 | 0.072 | |
HAIDLS | 87 | 1.106 | 0.397 | 0.600 | 0.307 | |
HAIJFL | 79 | 0.971 | 0.419 | 0.526 | 0.233 | |
HAILMS | 67 | 0.789 | 0.410 | 0.448 | 0.089 | |
FJCBC | 35 | 0.356 | 0.164 | 0.235 | 0.246 | |
FJDYS | 47 | 0.427 | 0.193 | 0.250 | 0.229 | |
FJGYS | 64 | 0.652 | 0.296 | 0.354 | 0.128 | |
FJMHS | 41 | 0.445 | 0.267 | 0.277 | 0.024 | |
JXJPS | 46 | 0.586 | 0.341 | 0.367 | 0.060 | |
JXWZF | 61 | 0.763 | 0.427 | 0.455 | 0.081 | |
Total | 0.649± | 0.303± | 0.372± | 0.152± | ||
0.242 | 0.079 | 0.118 | 0.141 |
FIS | FIT | FST | NM | |
---|---|---|---|---|
E. populnea | 0.126 ± 0.026 | 0.609 ± 0.041 | 0.557 ± 0.04 | 0.248 ± 0.035 |
E. tonkinensis | 0.18 ± 0.038 | 0.533 ± 0.031 | 0.432 ± 0.023 | 0.367 ± 0.037 |
E. tricuspis | 0.283 ± 0.07 | 0.643 ± 0.045 | 0.507 ± 0.032 | 0.283 ± 0.036 |
E. longipetala | 0.116 ± 0.063 | 0.584 ± 0.035 | 0.503 ± 0.042 | 0.321 ± 0.048 |
Genus Exbucklandia | 0.189 ± 0.033 | 0.621 ± 0.027 | 0.536 ± 0.022 | 0.232 ± 0.02 |
Pop ID | Country | Research Contents (Number of Individuals) | Pop ID | Country | Research Contents (Number of Individuals) | ||||
---|---|---|---|---|---|---|---|---|---|
A * | B ** | C *** | A * | B ** | C *** | ||||
E. tonkinensis | E. populnea | ||||||||
FJMHS | China | ★(8) | ●(15) | XZ01 | China | ★(8) | ●(22) | ||
FJGYS | China | ★(8) | ●(23) | XZ02 | China | ★(8) | ●(18) | ||
FJCBC | China | ★(8) | ●(27) | YNQTZ | China | ▲(1) | ★(8) | ●(20) | |
FJDYS | China | ★(8) | ●(17) | YNXLS | China | ▲(1) | ★(8) | ●(18) | |
GDBJ | China | ★(8) | ●(24) | YNDWS | China | ▲(1) | ★(8) | ●(16) | |
GDHSD | China | ▲(1) | ★(8) | ●(16) | YNMBZ | China | ▲(1) | ★(8) | ●(19) |
GDDDS | China | ▲(1) | ★(8) | ●(20) | YNJTC | China | ▲(1) | ★(8) | ●(23) |
GDWZS | China | ★(8) | YNQLD | China | ▲(1) | ★(8) | |||
GDNL | China | ▲(1) | ★(8) | ●(19) | YNGLG | China | ▲(1) | ★(8) | |
GDCDD | China | ★(8) | ●(19) | YNYFS | China | ★(8) | |||
GDZMP | China | ▲(1) | ★(8) | ●(20) | YNPMZ | China | ▲(1) | ★(8) | ●(23) |
GDFXC | China | ★(8) | ●(24) | YNHQZ | China | ★(8) | |||
GDBX | China | ★(8) | ●(24) | YNBLF | China | ▲(1) | ★(8) | ●(21) | |
GXLJ | China | ▲(1) | NP | Nepal | ★(8) | ●(16) | |||
GXGPS | China | ●(16) | VNTPO | Vietnam | ★(8) | ●(24) | |||
HAIJFL | China | ▲(1) | ★(8) | ●(19) | VNNCS | Vietnam | ★(8) | ●(20) | |
HAIJX | China | ▲(1) | ★(8) | VNSSH | Vietnam | ▲(1) | ★(8) | ●(19) | |
HAILMS | China | ▲(1) | ★(8) | ●(21) | VNSL | Vietnam | ▲(1) | ★(8) | ●(20) |
HAIDLS | China | ▲(1) | ★(8) | ●(15) | E. tricuspis | ||||
HK | China | ▲(1) | ★(8) | ●(15) | IN | Indonesia | ▲(1) | ★(8) | ●(16) |
HNMJX | China | ★(8) | ●(24) | MATR | Malaysia | ▲(1) | ★(8) | ||
HNQYF | China | ▲(1) | MAFH | Malaysia | ▲(1) | ★(8) | ●(14) | ||
HNJQS | China | ★(8) | ●(25) | VNKB | Vietnam | ★(8) | ●(16) | ||
JXWZF | China | ▲(1) | ★(8) | ●(20) | VNBNB | Vietnam | ▲(1) | ★(8) | ●(21) |
JXJPS | China | ★(8) | ●(19) | VNBHH | Vietnam | ▲(1) | ★(8) | ●(15) | |
E. populnea | VMBM | Vietnam | ★(8) | ●(25) | |||||
GXYRT | China | ★(8) | ●(20) | E. longipetala | |||||
GXBXS | China | ▲(1) | ★(8) | ●(20) | GXSW | China | ▲(1) | ★(8) | ●(20) |
GXWDX | China | ▲(1) | ★(8) | ●(21) | GZLGS | China | ▲(1) | ★(8) | ●(20) |
GZLB | China | ★(8) | ●(22) | HNQJD | China | ▲(1) | ★(8) | ●(20) | |
GZGHX | China | ▲(1) | ★(8) | ●(15) | HNBMS | China | ★(8) | ●(24) |
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Huang, C.; Fan, Q.; Xu, K.; Shi, S.; Meng, K.; Du, H.; Jin, J.; Guo, W.; Li, H.; Chen, S.; et al. Multiple Dataset-Based Insights into the Phylogeny and Phylogeography of the Genus Exbucklandia (Hamamelidaceae): Additional Evidence on the Evolutionary History of Tropical Plants. Plants 2025, 14, 1061. https://doi.org/10.3390/plants14071061
Huang C, Fan Q, Xu K, Shi S, Meng K, Du H, Jin J, Guo W, Li H, Chen S, et al. Multiple Dataset-Based Insights into the Phylogeny and Phylogeography of the Genus Exbucklandia (Hamamelidaceae): Additional Evidence on the Evolutionary History of Tropical Plants. Plants. 2025; 14(7):1061. https://doi.org/10.3390/plants14071061
Chicago/Turabian StyleHuang, Cuiying, Qiang Fan, Kewang Xu, Shi Shi, Kaikai Meng, Heying Du, Jiehao Jin, Wei Guo, Hongwei Li, Sufang Chen, and et al. 2025. "Multiple Dataset-Based Insights into the Phylogeny and Phylogeography of the Genus Exbucklandia (Hamamelidaceae): Additional Evidence on the Evolutionary History of Tropical Plants" Plants 14, no. 7: 1061. https://doi.org/10.3390/plants14071061
APA StyleHuang, C., Fan, Q., Xu, K., Shi, S., Meng, K., Du, H., Jin, J., Guo, W., Li, H., Chen, S., & Liao, W. (2025). Multiple Dataset-Based Insights into the Phylogeny and Phylogeography of the Genus Exbucklandia (Hamamelidaceae): Additional Evidence on the Evolutionary History of Tropical Plants. Plants, 14(7), 1061. https://doi.org/10.3390/plants14071061