Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA

Abstract

Population genetics is essential for understanding and managing marine ecosystems, but sampling remains challenging. We demonstrate that high-throughput sequencing of seawater environmental DNA can provide useful estimates of genetic diversity in a whale shark (Rhincodontypus) aggregation. We recover similar mitochondrial haplotype frequencies in seawater compared to tissue samples, reliably placing the studied aggregation in a global genetic context and expanding the applications of environmental DNA to encompass population genetics of aquatic organisms.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Results from seawater environmental DNA analyses of a whale shark aggregation in the Arabian Gulf.

References

  1. 1

    Pierce, S. J. & Norman, B. Rhincodon typus. http://dx.doi.org/10.2305/IUCN.UK.2016-1.RLTS.T19488A2365291.en (IUCN, 2016).

  2. 2

    Rowat, D. & Brooks, K. S. J. Fish Biol. 80, 1019–1056 (2012).

    CAS  Article  Google Scholar 

  3. 3

    Robinson, D. P. et al. PLoS ONE 8, e58255 (2013).

    CAS  Article  Google Scholar 

  4. 4

    Dicken, M. L., Booth, A. J. & Smale, M. J. ICES J. Mar. Sci. 63, 1640–1648 (2006).

    Article  Google Scholar 

  5. 5

    Ficetola, G. F., Miaud, C., Pompanon, F. & Taberlet, P. Biol. Lett. 4, 423–425 (2008).

    Article  Google Scholar 

  6. 6

    Thomsen, P. F. et al. Mol. Ecol. 21, 2565–2573 (2012).

    CAS  Article  Google Scholar 

  7. 7

    Port, J. A. et al. Mol. Ecol. 25, 527–541 (2016).

    CAS  Article  Google Scholar 

  8. 8

    Thomsen, P. F. et al. PLoS ONE 7, e41732 (2012).

    CAS  Article  Google Scholar 

  9. 9

    Thomsen, P. F. & Willerslev, E. Biol. Conserv. 183, 4–18 (2015).

    Article  Google Scholar 

  10. 10

    Robinson, D. P. et al. PLoS ONE 11, e0158593 (2016).

    Article  Google Scholar 

  11. 11

    Castro, A. L. F. et al. Mol. Ecol. 16, 5183–5192 (2007).

    CAS  Article  Google Scholar 

  12. 12

    Schmidt, J. V. et al. PLoS ONE 4, e4988 (2009).

    Article  Google Scholar 

  13. 13

    Vignaud, T. M. et al. Mol. Ecol. 23, 2590–2601 (2014).

    CAS  Article  Google Scholar 

  14. 14

    Kondrashov, F. A. & Kondrashov, A. S. Phil. Trans. R. Soc. B. 365, 1169–1176 (2010).

    Article  Google Scholar 

  15. 15

    Valentini, A. et al. Mol. Ecol. 25, 929–942 (2016).

    CAS  Article  Google Scholar 

  16. 16

    Fontes, J., McGinty, N., Machete, M. & Afonso, P. in QScience Proc. (The 4th Int. Whale Shark Conf.) Vol. 2016, iwsc4.17 (2016).

  17. 17

    Meekan, M., Speed, C., Planes, S., McLean, C. & Bradshaw, C. Population Monitoring for Whale Sharks (Rhincodon typus) (Australian Institute of Marine Science, 2008).

  18. 18

    Librado, P. & Rozas, J. Bioinform. 25, 1451–1452 (2009).

    CAS  Article  Google Scholar 

  19. 19

    Meyer, M., Stenzel, U. & Hofreiter, M. Nat. Protoc. 3, 267–278 (2008).

    CAS  Article  Google Scholar 

  20. 20

    Boyer, F. et al. Mol. Ecol. Resour. 16, 176–182 (2016).

    CAS  Article  Google Scholar 

  21. 21

    Drummond, A. J., Suchard, M. A., Xie, D., Rambaut, A. Mol. Biol. Evol. 29, 1969–1973 (2012).

    CAS  Article  Google Scholar 

  22. 22

    Watterson, G. A. Theor. Popul. Biol. 7, 256–276 (1975).

    CAS  Article  Google Scholar 

  23. 23

    Tajima, F. Genetics 105, 437–460 (1983).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. 24

    Nei, M. & Li, W.-H. Proc. Natl Acad. Sci. USA 76, 5269–5273 (1979).

    CAS  Article  Google Scholar 

  25. 25

    Alam, M. T., Petit R. A. III, Read, T. D. & Dove, A. D. M. Gene 539, 44–49 (2014).

    CAS  Article  Google Scholar 

  26. 26

    Schmidt, J. V. et al. Endang. Species Res. 12, 117–124 (2010).

    Article  Google Scholar 

Download references

Acknowledgements

We thank the Qatar Ministry of Environment for their collaboration and invaluable support. In particular, the crew on board R/V Saqt Al Khaleej is thanked for help with logistics for the water sampling. We thank the Maersk Oil Research and Technology Centre (MO-RTC) in Doha, Qatar, for being the main sponsor of the project. Special thanks to A. S. Al-Emadi (Head of MO-RTC) and J. Al-Khori (Technical Manager of MO-RTC) for supporting the project. The Danish National Research Foundation and the Natural History Museum of Denmark are thanked for additional funding. We thank T. B. Brand and the rest of the staff at the Centre for GeoGenetics, University of Copenhagen, as well as K. Magnussen and the Danish National Sequencing Centre for laboratory support. M. Krag is thanked for help with tissue samples. L. Olsen and P. Gravlund, National Aquarium Denmark (Den Blå Planet), provided a Stegostoma fasciatum tissue sample. J. V. Schmidt, University of Illinois at Chicago; R. W. Jabado, UAE University, Abu Dhabi, United Arab Emirates; and N. S. Blom, Danish Technical University, are thanked for scientific input. E. Vissing is thanked for the custom Python script.

Author information

Affiliations

Authors

Contributions

P.F.T., E.E.S., I.B.N., P.R.M. and S.S.B. conceived and designed the experiments. E.E.S., I.B.N., P.F.T., P.R.M. and S.S.B. performed the experiments. E.E.S., I.B.N., P.F.T. and M.W.P. analysed the data. E.E.S., P.F.T., P.R.M., S.S.B., E.D.L., D.P.R., S.W.K., M.W.P., M.A.J., L.O. and E.W. contributed materials or analysis tools. E.E.S., P.F.T., P.R.M., I.B.N., E.D.L. and S.W.K. wrote the paper.

Corresponding author

Correspondence to Philip Francis Thomsen.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary information

Supplementary Figures 1–11, Supplementary Experimental Procedures, Supplementary References. (PDF 1557 kb)

Supplementary Table 1

Overview of water samples used in this study. Related to Fig. 1c-f, and main text experimental procedures. Seawater eDNA samples collected for this study in the Arabian Gulf, off Qatar. Table includes sampling sites, collection dates, shark observations during eDNA sampling, total number of DL1 and DL2 sequences obtained from each water sample after data cleaning, haplotypes (DL1 and DL2) recovered from each water sample, and results from qPCR (number of positive qPCR replicates, average cycle threshold, average estimated eDNA concentration, and standard deviation of estimated eDNA concentration). (XLSX 20 kb)

Supplementary Table 2

Overview of tissue samples used in this study. Related to Fig. 1c-f, and main text experimental procedures.Whale shark tissue samples from Al Shaheen, Arabian Gulf, included in the study. Table includes tissue sample ID numbers, WildBook photo ID numbers (http://www.whaleshark.org), sex and size of sampled sharks, and haplotypes (DL1 and DL2) for the samples. *Bold red = individual was confirmed present on one or more of the eDNA sampling days: 27 May 2013, 28 May 2013, 19 May 2014, or 20 May 2014. (XLSX 13 kb)

Supplementary Table 3

Haplotype sequences used in this study. A list of all DL1 and DL2 haplotype sequences used in this study. Haplotype sequences include both the ones obtained from tissue and water samples as well as those retrieved from NCBI. For the DL2 sequences, they do not represent the complete fragment amplified by the primers, since the middle part has been removed bioinformatically due to low sequence quality (see Supplementary Experimental Procedures). *Indicates that the haplotype was recovered from one or more water samples. (XLSX 12 kb)

Supplementary Data 1

Input file for phylogenetic analysis of the DL2 fragment in BEAST. (XML 33 kb)

Supplementary Data 2

Input file for phylogenetic analysis of the DL2 fragment in BEAST, including only priors and no sequence data. (XML 22 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Sigsgaard, E., Nielsen, I., Bach, S. et al. Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA. Nat Ecol Evol 1, 0004 (2017). https://doi.org/10.1038/s41559-016-0004

Download citation

Further reading