Genetic Structure and Population Demographic History of a Widespread Mangrove Plant Xylocarpus granatum J. Koenig across the Indo-West Pacific Region
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection and DNA Extraction
2.2. Chloroplast DNA Sequencing and Data Analysis
2.3. Nuclear SSR Genotyping and Data Analysis of X. Granatum
2.4. Inference of Demographic History
- Scenario 1—Constant population size model: The effective population size of Pop# was constant at N1 from the past to the present.
- Scenario 2—Population shrinkage model: The effective population size of Pop# reduced from Na to N1 at t1.
- Scenario 3—Population expansion model: The effective population size of Pop# increased from Nb to N1 at t1.
- Scenario 4—Bottleneck model: The effective population size of Pop# experienced a bottleneck from Nd to Nc at t2 followed by population size recovery from Nc to N1 at t1.
3. Results
3.1. Phylogenetic Relationships of the cpDNA Haplotypes in Xylocarpus
3.2. Geographical Distribution of cpDNA Haplotypes
3.3. Genetic Structure Revealed by SSR Markers
3.4. Inferences of Demographic History
4. Discussion
4.1. Genetic Structure of a Widespread Mangrove Plant, X. granatum, across the IWP Region
4.2. Inferences of the Demographic History of X. granatum
4.3. Malay Peninsula as a Common Barrier to Widespread Mangrove Plants
4.4. Relationships with Other Xylocarpus Species
5. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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ID | Country | Locality | Coordinate | Chloroplast DNA | h | Nulcear SSRs | ||
---|---|---|---|---|---|---|---|---|
n | H | n | Voucher | |||||
Xylocarpus granatum J. Koenig | ||||||||
1 | Mozambique | Maputo | 25.85° S, E32.696° E | 9 | 2 | 0.198 | - | TK10122702 |
2 | Mozambique | Quelimane | 17.883° S, 36.861° E | 4 | 1 | 0.000 | 4 | TK10122504 |
3 | Seychelles | Mahe | 4.654° S, 55.403° E | 6 | 1 | 0.000 | - | KT12022201 |
4 | Myanmar | Ayeyarwady | 15.95° N, 95.357° E | 6 | 1 | 0.000 | 4 | TK11100805 |
5 | Thailand | Phuket | 8.204° N, 98.442° E | 4 | 2 | 0.375 | 4 | KT09121701 |
6 | Malaysia | Klang | 2.988° N, 101.355° E | 7 | 2 | 0.245 | 4 | TK11121403 |
7 | Malaysia | Kemaman | 4.65° N, 103.427° E | 6 | 1 | 0.000 | 4 | TK11121603 |
8 | Malaysia | Sabah | 5.945° N, 118.022° E | 6 | 1 | 0.000 | 4 | TK11072202 |
9 | Singapore | Sungei Buloh | 1.448° N, 103.73° E | 5 | 1 | 0.000 | - | KT09111202 |
10 | Indonesia | Java | 7.709° S, 108.9° E | 6 | 1 | 0.000 | - | KT09111508 |
11 | Indonesia | Bali | 8.734° S, 115.197° E | 8 | 1 | 0.000 | 4 | KT09111704 |
12 | Vietnam | Dong Rui | 21.226° N, 107.375° E | 3 | 2 | 0.444 | - | TK10050104 |
13 | Philippines | Panay | 11.802° N, 122.207° E | 11 | 1 | 0.000 | 4 | TK11062404 |
14 | Palau | Airai | 7.368° N, 134.576° E | 5 | 2 | 0.320 | 4 | YT60917 |
15 | Micronesia | Kosrae | 5.279° N, 162.973° E | 8 | 1 | 0.000 | 3 | TK11121601 |
16 | Vanuatu | Malatie | 17.55° S, 168.341° E | 3 | 1 | 0.000 | 4 | KT10073101 |
17 | New Caledonia | Baie de Taare | 22.259° S, 167.013° E | 7 | 1 | 0.000 | 4 | KT13022607 |
18 | Australia | Daintree River | 16.258° S, 145.399° E | 7 | 1 | 0.000 | 3 | KT13031902 |
Total 111 | Total 50 | |||||||
Xylocarpus moluccensis M.Roem. | ||||||||
19 | India | Pichavaram | 11.431° N, 79.794° E | 2 | 1 | 0.000 | - | TK10112308 |
20 | Thailand | Trat | 12.165° N, 102.482° E | 2 | 2 | 0.500 | - | KT09121902 |
21 | Malaysia | Klang | 3.038° N, 101.264° E | 7 | 1 | 0.000 | - | TK11121404 |
22 | Vietnam | Ca Mau | 8.716° N, 104.814° E | 1 | 1 | 0.000 | - | TK10042705 |
23 | Philippines | Panay | 11.802° N, 122.2° E | 4 | 1 | 0.000 | - | TK11062405 |
24 | Myanmar | Ayeyarwady | 15.95° N, 95.357° E | 1 | 1 | 0.000 | - | KK09122608 |
Total 17 | ||||||||
Xylocarpus rumphii (Kostel.) Mabb. | ||||||||
25 | Malaysia | Kilim | 6.42° N, 99.417° E | 1 | 1 | 0.000 | - | KLG20130620 |
trnD–trnT | trnL–trnF | accD–psaI | |||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Haplotype | Accession No. | 4 | 185 | 191 | 196–201 | 202 | 223 | 231 | 232 | 404 | Accession No. | 946 | 950 | 979 | Accession No. | 1222 | 1266 | 1325 | 1525 |
Xylocarpus granatum J. Koenig | |||||||||||||||||||
XG1 | LC217845 | C | A | A | - | T | T | A | A | T | LC217851 | C | C | C | LC217857 | G | C | A | - |
XG2 | LC217846 | C | A | C | - | T | T | A | A | T | LC217851 | C | C | C | LC217857 | G | C | A | - |
XG3 | LC217846 | C | A | C | - | T | T | A | A | T | LC217851 | C | C | C | LC217858 | G | C | G | - |
XG4 | LC217846 | C | A | C | - | T | T | A | A | T | LC217852 | T | A | C | LC217858 | G | C | G | - |
Xylocarpus moluccensis M. Roem. | |||||||||||||||||||
XM1 | LC217847 | T | C | C | AAAGGA | A | G | A | A | G | LC217853 | T | C | G | LC217859 | G | G | G | - |
XM2 | LC217847 | T | C | C | AAAGGA | A | G | A | A | G | LC217854 | C | C | C | LC217859 | G | G | G | - |
XM3 | LC217848 | T | C | C | AAAGGA | A | G | G | A | G | LC217854 | C | C | C | LC217860 | A | G | G | T |
XM4 | LC217848 | T | C | C | AAAGGA | A | G | G | A | G | LC217855 | T | A | C | LC217860 | A | G | G | T |
XM5 | LC217849 | T | C | C | AAAGGA | A | G | G | G | G | LC217855 | T | A | C | LC217860 | A | G | G | T |
Xylocarpus rumphii (Kostel.) Mabb. | |||||||||||||||||||
XR (XM4) | LC217850 | T | C | C | AAAGGA | A | G | G | A | G | LC217856 | T | A | C | LC217861 | A | G | G | T |
Source of Variation | Total Variance (%) | F-Statistics | p-Value | F'-Value |
---|---|---|---|---|
13 populations | ||||
Among populations | 40.4% | FST = 0.404 | 0.001 | F'ST = 0.802 |
Among individuals within populations | 59.6% | - | - | - |
K = 2 | ||||
Among group | 19.8% | FRT = 0.198 | 0.001 | F'RT = 0.748 |
Among population within groups | 27.2% | FSR = 0.339 | 0.001 | F'SR = 0.678 |
Among individuals within populations | 53.0% | FST = 0.470 | 0.001 | - |
K = 3 | ||||
Among group | 18.3% | FRT = 0.183 | 0.001 | F'RT = 0.648 |
Among population within groups | 24.9% | FSR = 0.302 | 0.001 | F'SR = 0.610 |
Among individuals within populations | 56.8% | FST = 0.432 | 0.001 | - |
Between the Indian Ocean (Pop 2,4,5 and 6) and the South China Sea (Pop 7,8,11,13 and 14) | ||||
Among group | 10.4% | FRT = 0.104 | 0.001 | F'RT = 0.389 |
Among population within groups | 23.9% | FSR = 0.266 | 0.001 | F'SR = 0.577 |
Among individuals within populations | 65.8% | FST = 0.342 | 0.001 | - |
Between the Indian Ocean (Pop 2,4,5 and 6) and Oceania (Pop 15,16,17 and 18) | ||||
Among group | 11.6% | FRT = 0.116 | 0.001 | F'RT = 0.416 |
Among population within groups | 23.5% | FSR = 0.266 | 0.001 | F'SR = 0.567 |
Among individuals within populations | 64.9% | FST = 0.351 | 0.001 | - |
Between the South China Sea (Pop 7,8,11,13 and 14) and Oceania (Pop 15,16,17 and 18) | ||||
Among group | 25% | FRT = 0.246 | 0.001 | F'RT = 0.815 |
Among population within groups | 21% | FSR = 0.283 | 0.001 | F'SR = 0.572 |
Among individuals within populations | 54% | FST = 0.459 | 0.001 | - |
ABC1 | Posterior Probability (95% Confidence Interval (Lower–Upper)) | ||
---|---|---|---|
Scenario | Region 1 | Region 2 | Region 3 |
1 | 0.2640 (0.2586–0.2693) | 0.2564 (0.2477–0.2651) | 0.2554 (0.2500–0.2607) |
2 | 0.2543 (0.2491–0.2596) | 0.2645 (0.2482–0.2660) | 0.3917 (0.3858–0.3977) |
3 | 0.2340 (0.2288–0.2392) | 0.2221 (0.2136–0.2305) | 0.1624 (0.1579–0.1669) |
4 | 0.2477 (0.2420–0.2533) | 0.2571 (0.2482–0.2660) | 0.1905 (0.1858–0.1952) |
ABC2 | |
---|---|
Scenario | Posterior Probability (95% Confidence Interval: Lower–Upper) |
1 | 0.3794 (0.3712–0.3877) |
2 | 0.0839 (0.0784–0.0893) |
3 | 0.3111 (0.3031–0.3190) |
4 | 0.0877 (0.0821–0.0934) |
5 | 0.0590 (0.0541–0.0639) |
6 | 0.0789 (0.0734–0.0844) |
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Tomizawa, Y.; Tsuda, Y.; Saleh, M.N.; Wee, A.K.S.; Takayama, K.; Yamamoto, T.; Yllano, O.B.; Salmo III, S.G.; Sungkaew, S.; Adjie, B.; et al. Genetic Structure and Population Demographic History of a Widespread Mangrove Plant Xylocarpus granatum J. Koenig across the Indo-West Pacific Region. Forests 2017, 8, 480. https://doi.org/10.3390/f8120480
Tomizawa Y, Tsuda Y, Saleh MN, Wee AKS, Takayama K, Yamamoto T, Yllano OB, Salmo III SG, Sungkaew S, Adjie B, et al. Genetic Structure and Population Demographic History of a Widespread Mangrove Plant Xylocarpus granatum J. Koenig across the Indo-West Pacific Region. Forests. 2017; 8(12):480. https://doi.org/10.3390/f8120480
Chicago/Turabian StyleTomizawa, Yuki, Yoshiaki Tsuda, Mohd Nazre Saleh, Alison K. S. Wee, Koji Takayama, Takashi Yamamoto, Orlex Baylen Yllano, Severino G. Salmo III, Sarawood Sungkaew, Bayu Adjie, and et al. 2017. "Genetic Structure and Population Demographic History of a Widespread Mangrove Plant Xylocarpus granatum J. Koenig across the Indo-West Pacific Region" Forests 8, no. 12: 480. https://doi.org/10.3390/f8120480
APA StyleTomizawa, Y., Tsuda, Y., Saleh, M. N., Wee, A. K. S., Takayama, K., Yamamoto, T., Yllano, O. B., Salmo III, S. G., Sungkaew, S., Adjie, B., Ardli, E., Suleiman, M., Tung, N. X., Soe, K. K., Kandasamy, K., Asakawa, T., Watano, Y., Baba, S., & Kajita, T. (2017). Genetic Structure and Population Demographic History of a Widespread Mangrove Plant Xylocarpus granatum J. Koenig across the Indo-West Pacific Region. Forests, 8(12), 480. https://doi.org/10.3390/f8120480