Conservation Genetic Assessment of Savannah Elephants (Loxodonta africana) in the Greater Kruger Biosphere, South Africa
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Area and Sample Collection
2.2. Laboratory Procedures and Microsatellite Quality Control
2.3. Genetic Diversity and Structure
2.4. Effective Population Size (Ne) and Demographic History
3. Results
3.1. Microsatellite Data Validation
3.2. Genetic Diversity and Structure
3.3. Effective Population Size and Demographic History
4. Discussion
4.1. Genetic Diversity and Structure
4.2. Demographic History and Effective Population Size
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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APNR | KNP | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Locus | NA | He | Ho | FIS | AR | PAR | NA | He | Ho | FIS | AR | PAR |
FH1 | 5 | 0.711 | 0.702 | 0.013 | 4.936 | 0.012 | 5 | 0.712 | 0.717 | −0.007 | 4.987 | 0.063 |
FH19 | 8 | 0.724 | 0.673 | 0.070 | 6.796 | 0.077 | 8 | 0.759 | 0.739 | 0.026 | 7.877 | 1.157 |
FH39 | 12 | 0.715 | 0.750 | −0.049 | 8.261 | 0.847 | 10 | 0.731 | 0.717 | 0.019 | 9.439 | 2.025 |
FH40 | 6 | 0.512 | 0.548 | −0.070 | 4.673 | 0.676 | 4 | 0.557 | 0.533 | 0.042 | 4.000 | 0.003 |
FH48 | 8 | 0.596 | 0.605 | −0.015 | 6.342 | 0.651 | 7 | 0.639 | 0.652 | −0.021 | 6.509 | 0.818 |
FH60 | 4 | 0.427 | 0.444 | −0.039 | 3.113 | 0.153 | 3 | 0.369 | 0.348 | 0.058 | 2.988 | 0.027 |
FH67 | 8 | 0.666 | 0.625 | 0.062 | 7.006 | 2.035 | 5 | 0.646 | 0.605 | 0.064 | 4.999 | 0.028 |
FH71 | 3 | 0.564 | 0.500 | 0.114 | 2.998 | 0.000 | 3 | 0.525 | 0.478 | 0.089 | 3.000 | 0.002 |
FH94 | 6 | 0.700 | 0.671 | 0.042 | 5.034 | 1.034 | 4 | 0.564 | 0.630 | −0.120 | 4.000 | 0.000 |
FH103 | 5 | 0.353 | 0.339 | 0.040 | 4.896 | 0.240 | 5 | 0.328 | 0.370 | −0.127 | 4.758 | 0.102 |
LA5 | 7 | 0.570 | 0.581 | −0.018 | 4.729 | 0.803 | 5 | 0.555 | 0.565 | −0.019 | 4.521 | 0.595 |
LA6 | 4 | 0.463 | 0.492 | −0.062 | 2.901 | 0.094 | 5 | 0.484 | 0.478 | 0.013 | 4.510 | 1.703 |
LaT06 | 13 | 0.649 | 0.539 | 0.171 * | 8.590 | 2.715 | 7 | 0.448 | 0.324 | 0.279 | 6.937 | 1.062 |
LaT08 | 14 | 0.845 | 0.863 | −0.022 | 11.188 | 0.849 | 13 | 0.861 | 0.870 | −0.010 | 12.148 | 1.809 |
LaT13 | 11 | 0.800 | 0.742 | 0.073 | 7.520 | 0.933 | 8 | 0.753 | 0.761 | −0.010 | 7.411 | 0.824 |
LaT18 | 10 | 0.775 | 0.781 | −0.008 | 7.182 | 1.586 | 6 | 0.795 | 0.486 | 0.393 * | 6.000 | 0.404 |
LaT24 | 13 | 0.851 | 0.834 | 0.020 | 9.947 | 2.648 | 8 | 0.827 | 0.658 | 0.206 | 7.916 | 0.617 |
LaT25 | 8 | 0.673 | 0.558 | 0.170 * | 6.458 | 0.647 | 7 | 0.764 | 0.783 | −0.025 | 6.746 | 0.935 |
Overall | 8.06 | 0.644 ± 0.142 | 0.625 ± 0.140 | 0.030 * | 6.25 | 0.89 | 6.28 | 0.629 ± 0.158 | 0.595 ± 0.158 | 0.054 * | 6.04 | 0.68 |
Even Sample Classes | Even Distance Classes (5 km) | |||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
D | r | U | L | Ur | Lr | P | ω | Pω | C | r | U | L | Ur | Lr | P | ω | Pω | |
APNR + KNP adults | 2 | 0.019 | 0.013 | −0.013 | 0.034 | 0.004 | 0.003 | 188.700 | 0.000 | 1663 | 0.004 | 0.006 | −0.006 | 0.012 | −0.003 | 0.080 | 224.281 | 0.000 |
3 | 0.012 | 0.010 | −0.009 | 0.023 | 0.001 | 0.011 | 115.622 | 0.000 | - | - | - | - | - | - | - | - | - | |
4 | 0.008 | 0.008 | −0.007 | 0.017 | −0.001 | 0.020 | 74.778 | 0.000 | - | - | - | - | - | - | - | - | - | |
APNR + KNP adult females | 3 | 0.040 | 0.024 | −0.021 | 0.068 | 0.013 | 0.001 | 125.857 | 0.000 | 320 | 0.024 | 0.015 | −0.013 | 0.042 | 0.007 | 0.001 | 263.182 | 0.000 |
9 | 0.014 | 0.007 | −0.007 | 0.025 | 0.003 | 0.000 | 37.493 | 0.000 | - | - | - | - | - | - | - | - | - | |
APNR + KNP adult males | 2 | −0.001 | 0.020 | −0.019 | 0.022 | −0.023 | 0.533 | 180.299 | 0.000 | 604 | −0.001 | 0.011 | −0.010 | 0.011 | −0.013 | 0.583 | 212.809 | 0.000 |
3 | 0.004 | 0.016 | −0.015 | 0.022 | −0.013 | 0.290 | 100.978 | 0.002 | - | - | - | - | - | - | - | - | - | |
APNR adults | 2 | 0.018 | 0.014 | −0.013 | 0.033 | 0.003 | 0.006 | 116.296 | 0.001 | 1639 | 0.004 | 0.006 | −0.006 | 0.011 | −0.003 | 0.122 | 81.399 | 0.002 |
3 | 0.011 | 0.010 | −0.009 | 0.022 | −0.001 | 0.023 | 75.154 | 0.001 | - | - | - | - | - | - | - | - | - | |
APNR adult females | 3 | 0.038 | 0.023 | −0.021 | 0.065 | 0.011 | 0.001 | 58.721 | 0.000 | 316 | 0.023 | 0.014 | −0.013 | 0.040 | 0.005 | 0.002 | 40.909 | 0.004 |
8 | 0.017 | 0.008 | −0.007 | 0.029 | 0.005 | 0.000 | 25.058 | 0.001 | - | - | - | - | - | - | - | - | - | |
9 | 0.011 | 0.007 | −0.006 | 0.022 | 0.000 | 0.002 | 23.625 | 0.004 | - | - | - | - | - | - | - | - | - | |
APNR adult males | 2 | 0.000 | 0.021 | −0.020 | 0.023 | −0.023 | 0.516 | 85.590 | 0.015 | 596 | −0.001 | 0.011 | −0.010 | 0.011 | −0.013 | 0.573 | 67.208 | 0.028 |
3 | 0.004 | 0.017 | −0.015 | 0.022 | −0.014 | 0.300 | 74.756 | 0.018 | - | - | - | - | - | - | - | - | - |
Overall | Adults | Adult Males | Adult Females | |
---|---|---|---|---|
Fst | 0.004 ± 0.002 * | 0.004 ± 0.003 * | −0.001 ± 0.003 | 0.014 ± 0.007 * |
G’’st | 0.011 ± 0.007 * | 0.010 ± 0.007 * | −0.003 ± 0.007 | 0.039 ± 0.018 * |
Jost’s Dest | 0.007 ± 0.004 * | 0.006 ± 0.004 * | −0.002 ± 0.005 | 0.025 ± 0.012 * |
APNR | APNR+KNP | |
---|---|---|
LD Method | 388.3 [245.2–809.3] | 510.2 [319.9–1091.4] |
EPA | 197 [83–436] | 692 [109–743] |
VarEff | ||
Harmonic mean | 343.8 | 339.3 |
Median | 454.7 | 443.5 |
90% central range | 160.9–970.9 | 157.5–920.8 |
Migraine | 737 [590–915]; 7370 [5900–9150] | 723 [581–895]; 7230 [5810–8950] |
ΘF | 618.5; 6185 | 614.7; 6147 |
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Santos, T.L.; Fernandes, C.; Henley, M.D.; Dawson, D.A.; Mumby, H.S. Conservation Genetic Assessment of Savannah Elephants (Loxodonta africana) in the Greater Kruger Biosphere, South Africa. Genes 2019, 10, 779. https://doi.org/10.3390/genes10100779
Santos TL, Fernandes C, Henley MD, Dawson DA, Mumby HS. Conservation Genetic Assessment of Savannah Elephants (Loxodonta africana) in the Greater Kruger Biosphere, South Africa. Genes. 2019; 10(10):779. https://doi.org/10.3390/genes10100779
Chicago/Turabian StyleSantos, Teresa L., Carlos Fernandes, Michelle D. Henley, Deborah A. Dawson, and Hannah S. Mumby. 2019. "Conservation Genetic Assessment of Savannah Elephants (Loxodonta africana) in the Greater Kruger Biosphere, South Africa" Genes 10, no. 10: 779. https://doi.org/10.3390/genes10100779
APA StyleSantos, T. L., Fernandes, C., Henley, M. D., Dawson, D. A., & Mumby, H. S. (2019). Conservation Genetic Assessment of Savannah Elephants (Loxodonta africana) in the Greater Kruger Biosphere, South Africa. Genes, 10(10), 779. https://doi.org/10.3390/genes10100779