Timber Tracking of Jacaranda copaia from the Amazon Forest Using DNA Fingerprinting
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sampling
2.2. DNA Extraction and SNP Analysis
2.3. Genetic Diversity Analysis
2.4. Bayesian Clustering Analysis
2.5. Genetic Differentiation among Populations, Countries, and Crusters
2.6. Genetic Assignment Analysis
3. Results
3.1. Genetic Diversity
3.2. Bayesian Cluster
3.3. Population Differentiation
3.4. Isolation by Distance
3.5. Genetic Assignment
4. Discussion
4.1. Genetic Diversity
4.2. Population Genetic Differentiation
4.3. Genetic Assignment and Practical Applications
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Country | Sampling Site/Population Sample | n | Latitude | Longitude | Abbrev | n1 |
---|---|---|---|---|---|---|
1-F. Guiana | Counami | 30 | 5.41543 | −53.175 | 1FG-Co | 32 |
2-F. Guiana | Sinnamary | 2 | 5.2884 | −52.916 | ||
3-F. Guiana | Piste de Paul Isnard | 27 | 5.33216 | −53.957 | 2FG-Is | 29 |
4-F. Guiana | Apatou | 2 | 5.27343 | −54.218 | ||
5-F. Guiana | Route de Cacao | 30 | 4.56779 | −52.406 | 3FG-Ro | 32 |
6-F. Guiana | Regina | 2 | 4.13118 | −52.088 | ||
7-F. Guiana | Saut Maripa | 28 | 3.87833 | −51.857 | 4FG-Ma | 28 |
8-Brazil | ESEC de Maraca-RR | 31 | 3.37032 | −61.444 | 5BW-Ma | 31 |
9-Brazil | Flona de Anauá e arredores-Rorainópolis-RR | 28 | −0.9339 | −60.451 | 6BW-An | 28 |
10-Brazil | AMATA Flona do Jamari-RO | 8 | −9.4014 | −62.911 | 7BW-Ja | 8 |
11-Brazil | ESEC do Jarí | 15 | −0.4955 | −52.829 | 8BW-Jr | 15 |
12-Brazil | Resex Chico Mendes-Xapuri-AC (AMATA-Flona do Jamari) | 16 | −10.504 | −68.595 | 9BW-Xa | 16 |
13-Brazil | Resex Chico Mendes-Comunidade Cumaru-Assis-AC | 15 | −10.772 | −69.647 | 10BW-Co | 15 |
14-Brazil | FLONA Amapá-AP | 20 | 0.52785 | −51.128 | 11BE-Am | 20 |
15-Brazil | PARNA da Ana Avilhanas-AM | 11 | −2.5345 | −60.837 | 12BE-Av | 11 |
16-Brazil | Flona de Tapajós-PA | 27 | −2.8687 | −54.92 | 13BE-Ta | 27 |
17-Brazil | Resex Tapajós-Arapins-PA | 11 | −3.0792 | −55.278 | 14BE-Ar | 11 |
18-Brazil | FLONA Tefé-AM | 4 | −3.5248 | −64.972 | 15BE-Te | 4 |
19-Brazil | FLONA do Carajás | 23 | −6.0628 | −50.059 | 16BE-Ca | 23 |
20-Peru | Dpto Loreto, Maynas, El Napo, Huiririma Native Community | 26 | −2.4761 | −73.744 | 17PN-Hu | 26 |
21-Peru | Huaman Urco | 27 | −3.3128 | −73.198 | 18PN-Ur | 27 |
22-Peru | Dpto Loreto, Maynas, Las Amazonas, Est. Biológica Madreselva | 28 | −3.6312 | −72.233 | 19PN-Ma | 28 |
23-Peru | Dpto Loreto, Mayna, Iquitos, Comunidad Campesina Yarina | 28 | −3.827 | −73.567 | 20PN-Ya | 28 |
24-Peru | Allpahuayo | 2 | −3.9544 | −73.422 | ||
25-Peru | Dpto Loreto, Mar. Ramón Castilla, C. Poblado Unión Progresista | 27 | −3.9727 | −70.841 | 21PN-Pr | 29 |
26-Peru | Dpto Loreto, Requena, Jenaro Herrera Research Centre | 11 | −4.8966 | −73.646 | 22PN-Re | 11 |
27-Peru | Jenaro Herrera | 25 | −4.9158 | −73.649 | 23PN-He | 25 |
28-Peru | Dpto Loreto, Alto Amazonas, Jeberos, Centro Poblado Jeberos | 26 | −5.2598 | −76.317 | 24PN-Je | 26 |
29-Peru | Shucushuyacu | 27 | −6.0199 | −75.854 | 25PN-Sh | 27 |
30-Peru | Dpto Ucayali, Cor. Portillo, Con. Forestal-Oxigeno para el Mundo | 29 | −8.8869 | −74.034 | 26PS-Po | 29 |
31-Peru | Dpto Ucayali, Padre Abad, Macuya Forestry Research Station | 30 | −8.8766 | −75.014 | 27PS-Pa | 30 |
32-Peru | Dpto Ucayali, Atalaya, Tahuania, Concesión Forestal-Javier Díaz | 29 | −9.9803 | −73.817 | 28PS-Di | 29 |
33-Peru | Dpto Ucayali, Atalaya, Raymondi, Comunidad San Juan de Inuya | 12 | −10.582 | −73.071 | 29PS-In | 12 |
34-Peru | Dpto Madre de Dios, Tahuamanu, Concesión Forestal Maderacre | 31 | −11.145 | −69.758 | 30PS-Md | 33 |
35-Peru | Ibéria | 2 | −11.299 | −69.524 | ||
36-Peru | Dpto Madre de Dios, P.N. Manu, Est. Biológica Cocha Cashu | 15 | −11.903 | −71.403 | 31PS-Ca | 15 |
37-Peru | Dpto Madre de Dios, Manu, Estación Biológica Los Amigos | 30 | −12.565 | −70.088 | 32PS-Am | 30 |
38-Peru | Dpto Madre de Dios, R. Nac. Tambopata, La Torre-Sandoval | 24 | −12.832 | −69.284 | 33PS-Ta | 24 |
39-Bolivia | Riberalta, MABET | 15 | −10.442 | −65.55 | 34Bo-Ri | 15 |
40-Bolivia | Riberalta, El Desvelo | 11 | −11.093 | −65.746 | 35Bo-De | 11 |
41-Bolivia | Cobija, Road—Bella Vista | 13 | −11.198 | −68.287 | 36Bo-Vi | 13 |
42-Bolivia | Riberalta, El Chorro | 5 | −11.514 | −66.327 | 37Bo-Ch | 5 |
43-Bolivia | Rurrenabaque, Área Protegida Madidi | 29 | −14.162 | −67.905 | 38Bo-Ma | 29 |
Sample | n | nSNPs | CpMtSNPs | nCpMtSNPs | ||||||
---|---|---|---|---|---|---|---|---|---|---|
1FG-Co | 32 | 6.6 | 122 | 50.4 | 0.023 | 0.028 | 0.005 | 16 | 6.7 | 45.3 |
2FG-Is | 29 | 4.9 | 190 | 69.0 | 0.109 | 0.197 | 0.25 * | 17 | 13.3 | 62.5 |
3FG-Ro | 32 | 5.7 | 196 | 71.7 | 0.094 | 0.202 | 0.295 * | 16 | 6.7 | 64.1 |
4FG-Ma | 28 | 3.5 | 195 | 72.6 | 0.148 | 0.254 | 0.286 * | 16 | 13.3 | 65.7 |
5BW-Ma | 31 | 2.4 | 193 | 82.3 | 0.299 | 0.309 | 0.005 | 16 | 6.7 | 73.4 |
6BW-An | 28 | 1.5 | 195 | 70.8 | 0.291 | 0.292 | −0.022 | 15 | 0 | 72.7 |
7BW-Ja | 8 | 32.3 | 207 | 80.5 | 0.194 | 0.298 | 0.198 * | 17 | 13.3 | 72.6 |
8BW-Jr | 15 | 4.3 | 207 | 83.2 | 0.205 | 0.287 | 0.057 | 16 | 13.3 | 75.0 |
9BW-Xa | 16 | 4.5 | 204 | 72.6 | 0.278 | 0.290 | −0.021 | 16 | 6.7 | 75.0 |
10BW-Cu | 15 | 1.8 | 147 | 83.2 | 0.261 | 0.275 | 0.016 | 15 | 0 | 73.5 |
11BE-Am | 20 | 1.1 | 204 | 75.2 | 0.215 | 0.231 | 0.052 | 15 | 0 | 66.4 |
12BE-Av | 11 | 7.5 | 207 | 61.9 | 0.278 | 0.290 | −0.021 | 15 | 0 | 64.8 |
13BE-Ta | 27 | 2.8 | 197 | 83.2 | 0.261 | 0.275 | 0.016 | 15 | 0 | 74.2 |
14BE-Ar | 11 | 3.1 | 183 | 69.0 | 0.238 | 0.276 | 0.078 | 15 | 0 | 68.0 |
15BE-Te | 4 | 1.4 | 207 | 83.2 | 0.141 | 0.257 | 0.057 | 15 | 0 | 73.5 |
16BE-Ca | 23 | 5.3 | 190 | 81.4 | 0.275 | 0.282 | −0.019 | 15 | 0 | 75.0 |
17PN-Hu | 26 | 2.4 | 149 | 30.1 | 0.053 | 0.059 | 0.017 | 17 | 13.3 | 28.1 |
18PN-Ur | 27 | 5.0 | 147 | 31.9 | 0.060 | 0.066 | 0.018 | 17 | 13.3 | 29.7 |
19PN-Ma | 28 | 4.4 | 147 | 30.1 | 0.054 | 0.066 | 0.031 | 19 | 20.0 | 28.9 |
20PN-Ya | 28 | 2.5 | 147 | 30.1 | 0.059 | 0.064 | 0.024 | 16 | 6.7 | 27.4 |
21PN-Pr | 29 | 4.7 | 142 | 30.1 | 0.065 | 0.069 | 0.016 | 19 | 26.7 | 29.7 |
22PN-Re | 11 | 1.8 | 146 | 25.7 | 0.043 | 0.065 | 0.072 | 15 | 0 | 22.7 |
23PN-He | 25 | 3.8 | 145 | 29.2 | 0.050 | 0.056 | 0.018 | 16 | 20 | 28.1 |
24PN-Je | 26 | 7.9 | 142 | 28.3 | 0.041 | 0.061 | 0.087 * | 19 | 26.7 | 28.1 |
25PN-Sh | 27 | 3.2 | 147 | 26.5 | 0.047 | 0.053 | 0.028 | 14 | 0 | 23.4 |
26PS-Po | 29 | 13.9 | 146 | 30.1 | 0.046 | 0.075 | 0.087 * | 16 | 6.7 | 27.4 |
27PS-Pa | 30 | 3.1 | 140 | 30.1 | 0.063 | 0.064 | 0.020 | 14 | 0 | 26.6 |
28PS-Di | 29 | 4.9 | 139 | 23.9 | 0.054 | 0.061 | 0.024 | 15 | 0 | 21.1 |
29PS-In | 12 | 4.8 | 213 | 23.0 | 0.056 | 0.061 | 0.017 | 15 | 0 | 20.3 |
30PS-Ma | 33 | 4.5 | 206 | 88.5 | 0.297 | 0.315 | 0.045 | 15 | 0 | 78.1 |
31PS-Ca | 15 | 2.4 | 213 | 82.3 | 0.271 | 0.310 | 0.073 | 15 | 0 | 72.7 |
32PS-Am | 30 | 4.5 | 209 | 88.5 | 0.312 | 0.317 | −0.010 | 15 | 0 | 78.1 |
33PS-Ta | 24 | 3.2 | 209 | 85.0 | 0.284 | 0.314 | 0.080 | 15 | 0 | 75.0 |
34Bo-Mb | 15 | 2.8 | 207 | 84.1 | 0.321 | 0.324 | −0.026 | 16 | 6.7 | 75.0 |
35Bo-De | 11 | 1.3 | 206 | 84.1 | 0.297 | 0.312 | −0.012 | 16 | 6.7 | 75.0 |
36Bo-Vi | 13 | 0.8 | 205 | 82.3 | 0.313 | 0.313 | −0.023 | 15 | 0 | 72.7 |
37Bo-Ch | 5 | 1.4 | 212 | 82.3 | 0.340 | 0.348 | −0.086 | 19 | 26.7 | 75.8 |
38Bo-Ma | 29 | 1.3 | 226 | 87.6 | 0.322 | 0.313 | −0.032 | 15 | 0 | 77.3 |
Overall | 832 | 4.4 | 183 | 100 | 0.178 | 0.204 | 0.086 * | 15.9 | 6.7 | 55.9 |
French Guiana | 121 | 5.2 | 200 | 76.1 | 0.095 | 0.192 | 0.506 * | 18 | 20.0 | 69.5 |
Brazil | 209 | 4.2 | 226 | 100 | 0.261 | 0.354 | 0.264 * | 30 | 100 | 100 |
Peru | 429 | 4.7 | 217 | 92.9 | 0.111 | 0.222 | 0.498 * | 23 | 53.3 | 88.3 |
Bolivia | 73 | 1.5 | 218 | 92.9 | 0.319 | 0.359 | 0.113 * | 20 | 33.3 | 85.9 |
Sample | nCpMtSNPs (128) | nSNPs (113) | CpMtSNPs (15) | |
---|---|---|---|---|
All population samples | 38 | 0.484 ± 0.043 * | 0.415 ± 0.032 * | 0.942 ± 0.042 * |
Genetic groups | 8, 9, and 4 | 0.401 ± 0.044 * | 0.315 ± 0.03 * | 0.896 ± 0.094 * |
Countries | 4 | 0.295 ± 0.036 * | 0.233 ± 0.022 * | 0.695 ± 0.144 * |
French Guiana | 4 | 0.120 ± 0.017 * | 0.117 ± 0.017 * | 0.011 ± 0.002 |
Brazil | 12 | 0.299 ± 0.049 * | 0.224 ± 0.03 * | 0.925 ± 0.103 * |
Peru | 17 | 0.466 ± 0.056 * | 0.456 ± 0.056 * | 0.741 ± 0.267 * |
Bolivia | 5 | 0.142 ± 0.034 * | 0.107 ± 0.024 * | 0.735 ± 0.383 * |
Reporting Groups | Self-Assignment Test of Grouped Individuals | Self-Assignment Test of Individuals | ||||
---|---|---|---|---|---|---|
Rate | Score | Rate | Score | Rate: Score > 80% | Rate: Score > 95% | |
1 | 100 | 100 | 100 | 99.9 | 100 | 99.4 |
2 | 100 | 100 | 100 | 100 | 100 | 100 |
3 | 100 | 100 | 98.6 | 99.8 | 100 | 98.6 |
4 | 100 | 100 | 96.0 | 93.2 | 89.7 | 69.2 |
5 | 100 | 100 | 100 | 100 | 100 | 100 |
6 | 100 | 100 | 94.5 | 91.7 | 82.6 | 67.4 |
7 | 100 | 100 | 100 | 98.2 | 96.5 | 94.7 |
Overall | 100 | 100 | 98.4 | 97.5 | 95.5 | 89.9 |
Country | ||||||
French Guiana | 100 | 100 | 87.6 | 98.1 | 99.1 | 99.1 |
Brazil | 100 | 100 | 98.1 | 99.9 | 100 | 98.5 |
Peru | 100 | 100 | 98.1 | 93.4 | 87.8 | 72.8 |
Bolivia | 100 | 100 | 100 | 99.9 | 100 | 100 |
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Capo, L.F.M.; Degen, B.; Blanc-Jolivet, C.; Tysklind, N.; Cavers, S.; Mader, M.; Meyer-Sand, B.R.V.; Paredes-Villanueva, K.; Honorio Conorado, E.N.; García-Dávila, C.R.; et al. Timber Tracking of Jacaranda copaia from the Amazon Forest Using DNA Fingerprinting. Forests 2024, 15, 1478. https://doi.org/10.3390/f15081478
Capo LFM, Degen B, Blanc-Jolivet C, Tysklind N, Cavers S, Mader M, Meyer-Sand BRV, Paredes-Villanueva K, Honorio Conorado EN, García-Dávila CR, et al. Timber Tracking of Jacaranda copaia from the Amazon Forest Using DNA Fingerprinting. Forests. 2024; 15(8):1478. https://doi.org/10.3390/f15081478
Chicago/Turabian StyleCapo, Lorena Frigini Moro, Bernd Degen, Celine Blanc-Jolivet, Niklas Tysklind, Stephen Cavers, Malte Mader, Barbara Rocha Venancio Meyer-Sand, Kathelyn Paredes-Villanueva, Eurídice Nora Honorio Conorado, Carmen Rosa García-Dávila, and et al. 2024. "Timber Tracking of Jacaranda copaia from the Amazon Forest Using DNA Fingerprinting" Forests 15, no. 8: 1478. https://doi.org/10.3390/f15081478