A new tool in the toolbox for large-scale, high-throughput fisheries mark-recapture studies using genetic identification
Russell W. Bradford A B , Peta Hill A , Campbell Davies A and Peter Grewe A
+ Author Affiliations
- Author Affiliations
A CSIRO Wealth from Oceans Flagship, Marine and Atmospheric Research, GPO Box 1538, Hobart, Tas. 7001, Australia.
B Corresponding author. Email: russ.bradford@csiro.au
Marine and Freshwater Research 67(8) 1081-1089 https://doi.org/10.1071/MF14423
Submitted: 23 December 2014 Accepted: 13 April 2015 Published: 16 September 2015
Journal Compilation © CSIRO Publishing 2016 Open Access CC BY-NC-ND
Abstract
The lack of independently verifiable estimates of catches and fisheries independent estimates of abundance and fishing mortality are major sources of uncertainty in the management of many fisheries. DNA profiling provides the potential to substantially improve the quality of data for assessments and act as an additional deterrent to illegal, unreported, and unregulated (IUU) fishing. Barriers to the implementation of this technology include cost of sample collection and processing, forensic grade quality control, and the ability to apply undetectable tags. We present the results of a comparison of two current and one new (gene tag tool, GTT) sampling techniques, using the highly valued southern bluefin tuna as an example. We demonstrate that fish sampled with two techniques are highly unlikely to be recognised as ‘tagged’, whereas one technique was easily recognisable after 73 days. The GTT reduced handling before DNA extraction, whereas both other techniques require additional labour, adding to cost and potential contamination of the evidentiary chain. Evidence of cross-contamination in the Whatman FTA Elute samples suggests they may not be as suitable for at-sea field applications. Two of the three sampling techniques are capable of obtaining high quality tissue samples for stock assessment and chain of custody purposes in a cost-effective and unidentifiable manner.
Additional keywords: biopsy, fishery-independent, genetic tag, mark-recapture.
References
Anon. (2011). ‘Your Forensic Samples, Our Experience.’ (General Electric Healthcare, General Electric Company: Little Chalfont, UK.)Beacham, T. D., Wetklo, M., Wallace, C., Olsen, J. B., Flannery, B. G., Wenburg, J. K., Templin, W. D., Antonovich, A., and Seeb, L. W. (2008). The application of microsatellites for stock identification of Yukon River Chinook salmon. North American Journal of Fisheries Management 28, 283–295.
| The application of microsatellites for stock identification of Yukon River Chinook salmon.Crossref | GoogleScholarGoogle Scholar |
Bert, T. M., Tringali, M. D., and Seyoum, S. (2002). Chapter 3: Development and application of genetic tags for ecological aquaculture. In ‘Ecological Aquaculture: The Evolution of the Blue Revolution’. (Ed. B.A. Costa-Pierce.) pp. 47–76. (Blackwell Publishing Ltd: Melbourne.)
Bravington, M., Grewe, P., and Davies, C. (2014). Fishery-independent estimate of spawning biomass of southern bluefin tuna through identification of close-kin using genetic markers. FRDC Report 2007/034, Hobart, Tas., Australia.
Carruthers, T. R., and McAllister, M. K. (2010). Quantifying tag reporting rates for Atlantic tuna fleets using coincidental tag returns. Aquatic Living Resources 23, 343–352.
| Quantifying tag reporting rates for Atlantic tuna fleets using coincidental tag returns.Crossref | GoogleScholarGoogle Scholar |
Davies, C., Preece, A., and Basson, M. (2007). A review of the Southern Bluefin Tuna Commission’s Scientific Research Program and considerations of current priorities and way forward. In ‘12th Meeting of the Extended Scientific Committee’, 4–8 September and 10–14 September 2007, Hobart, Tas., Australia. CCSBT-ESC/0709/16. (CSIRO Oceans & Atmosphere Flagship: Hobart.)
Davies, C., Moore, A., Grewe, P., Bradford, R., and Basson, M. (2008). Report on the potential and feasibility of genetic tagging of SBT. In ‘13th Meeting of the Extended Scientific Committee’, 8–12 September 2008, Rotorua, New Zealand. CCSBT-ESC/0809/14. (CSIRO Oceans & Atmosphere Flagship: Hobart, Tas., Australia.)
Eggen, A. (2012). The development and application of genomic selection as a new breeding paradigm. Animal frontiers 2, 10–15.
| The development and application of genomic selection as a new breeding paradigm.Crossref | GoogleScholarGoogle Scholar |
Eriksen, T. B., Fraser, T., Gregersen, H., Kristiansen, M., Olufsen, M., Rajan, B., Ramirez, R., Raungsri, J., Ron, O., and Sarmiento, M. G. (2011). Should fin clipping be used as a method for identification of fish? Available at http://norecopa.no/student-essays [Verified 24 June 2015].
Fleming, N. (2011). DNA chip test will track down illegal fish. Available at http://www.newscientist.com/article/mg21028125.100-dna-chip-test-will-track-down-illegal-fish.html#.VYnvWEa0Lfc [Verified 24 June 2015].
Fontenot, D. K., and Neiffer, D. L. (2004). Wound management in teleosts fish: biology of the healing process, evaluation, and treatment. The Veterinary Clinics Exotic Animal Practice 7, 57–86.
| Wound management in teleosts fish: biology of the healing process, evaluation, and treatment.Crossref | GoogleScholarGoogle Scholar |
Glover, K. A. (2010). Forensic identification of fish farm escapees: the Norwegian experience. Aquaculture Environment Interactions 1, 1–10.
| Forensic identification of fish farm escapees: the Norwegian experience.Crossref | GoogleScholarGoogle Scholar |
Graves, J. E., and McDowell, J. R. (2003). Stock structure of the world’s istiophorid billfishes: a genetic perspective. Marine and Freshwater Research 54, 287–298.
| Stock structure of the world’s istiophorid billfishes: a genetic perspective.Crossref | GoogleScholarGoogle Scholar |
Harley, S., Bradford, R., and Davies, C. (2008). Using passive integrated transponder (PIT) technology to improve performance of CCSBT’s conventional tagging programme. In ‘CCSBT 5th Management Procedure Workshop/13th Meeting of the Extended Scientific Committee’, 2–7 September and 8–12 September 2008, Rotorua, New Zealand. CCSBT-ESC/0809/14. (CSIRO Oceans & Atmosphere Flagship: Hobart, Tas., Australia.)
Hearn, W. S., Polacheck, T., Pollock, K. H., and Whitelaw, W. (1999). Estimation of tag reporting rates in age-structured multicomponent fisheries where one component has observers. Canadian Journal of Fisheries and Aquatic Sciences 56, 1255–1265.
| Estimation of tag reporting rates in age-structured multicomponent fisheries where one component has observers.Crossref | GoogleScholarGoogle Scholar |
Hearn, W., Polacheck, T., and Stanley, C. (2008). Estimates of reporting rate from the Australian surface fishery based on previous tag seeding experiments and tag seeding activities in 2007/2008. In ‘CCSBT 5th Management Procedure Workshop/13th Meeting of the Extended Scientific Committee’, 2–7 September and 8–12 September 2008, Rotorua, New Zealand. CCSBT-ESC/0809/21. (CSIRO Oceans & Atmosphere Flagship: Hobart, Tas., Australia.)
Hilborn, R., and Walters, C. J. (1992). ‘Quantitative Fisheries Stock Assessment and Management: Choices, Dynamics and Uncertainty.’ (Chapman and Hall: New York.)
ISOFISH (1998) The involvement of Mauritius in the trade in Patagonian toothfish from illegal and unregulated longline fishing in the Southern Ocean and what might be done about it. ISOFISH Occasional Report 1, 3rd edn, Hobart, Australia.
Kuhne, S., Schroeder, C., Holmquist, G., Wolf, G., Horner, S., Brem, G., and Ballagi, A. (2005). Detection of bovine viral diarrhoea virus infected cattle – testing tissue samples derived from ear tagging using an Erns capture ELISA. Journal of Veterinary Medicine B 52, 272–277.
| Detection of bovine viral diarrhoea virus infected cattle – testing tissue samples derived from ear tagging using an Erns capture ELISA.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BD2Mrktlygtw%3D%3D&md5=351cacebbe8bc467e1021420228b9336CAS |
McKenzie, J. R., Parsons, B., Seitz, A. C., Kopf, R. K., Mesa, M., and Phelps, Q. (Eds) (2012). ‘American Fisheries Society Symposium 76. Proceedings of the Symposium Advances in Fish Tagging & Marking Technology’, 24–28 February 2008, Auckland, New Zealand. (American Fisheries Society: Bethesda, MD, USA.)
Nagy, Z. T. (2010). A hands-on overview of tissue preservation methods for molecular genetic analyses. Organisms, Diversity & Evolution 10, 91–105.
| A hands-on overview of tissue preservation methods for molecular genetic analyses.Crossref | GoogleScholarGoogle Scholar |
Nguyen, N. H., Ponniah, A. G., and Ponzoni, R. W. (2006). Potential applications of reproductive and molecular genetic technologies in the selective breeding of aquaculture species. In ‘Development of Aquatic Animal Genetic Improvement and Dissemination Programs: Current Status and Action Plans. World Fish Centre Conference Proceedings 73’, 21–22 September 2005, Penang, Malaysia. (Eds R. W. Ponzoni, B. O. Acosta, and A. G. Ponniah.) pp. 15–21. (WorldFish: Penang, Malaysia.)
Ogden, R., Dawnay, N., and McEwing, R. (2009). Wildlife DNA forensics – bridging the gap between conservation genetics and law enforcement. Endangered Species Research 9, 179–195.
| Wildlife DNA forensics – bridging the gap between conservation genetics and law enforcement.Crossref | GoogleScholarGoogle Scholar |
Polacheck, T., and Davies, C. (2008). Considerations of implications of large unreported catches of southern bluefin tuna for assessments of tropical tunas, and the need for independent verification of catch and effort statistics. CSIRO Marine and Atmospheric Research Paper 23, Hobart, Australia.
Polacheck, T., Eveson, J. P., Laslett, G. M., Pollock, K. H., and Hearn, W. S. (2006). Integrating catch-at-age and multiyear tagging data: a combined Brownie and Petersen estimation approach in a fishery context. Canadian Journal of Fisheries and Aquatic Sciences 63, 534–548.
| Integrating catch-at-age and multiyear tagging data: a combined Brownie and Petersen estimation approach in a fishery context.Crossref | GoogleScholarGoogle Scholar |
Pollock, K. H., Hoenig, J. M., Hearn, W. S., and Caligaert, B. (2001). Tag reporting rate estimation: 1. An evaluation of the high-reward tagging method. North American Journal of Fisheries Management 21, 521–532.
| Tag reporting rate estimation: 1. An evaluation of the high-reward tagging method.Crossref | GoogleScholarGoogle Scholar |
Preece, A., Davies, C., Bravington, M., Hillary, R., Eveson, P., and Grewe, P. (2013). Preliminary cost and precision estimates of sampling designs for gene tagging for SBT. CCSBT-ESC/1309/18. Commission for the Conservation of Southern Bluefin Tuna.
Smith, L. M., and Burgyone, L. A. (2004). Collecting, archiving and processing DNA from wildlife samples using FTA databasing paper. BMC Ecology 4, 4–11.
| Collecting, archiving and processing DNA from wildlife samples using FTA databasing paper.Crossref | GoogleScholarGoogle Scholar | 1:STN:280:DC%2BD2czpvFaksQ%3D%3D&md5=04a7b9d602da4d9265e3f3f628500399CAS | 15072582PubMed |
Smith, P., and McVeagh, M. (2000). Allozyme and microsatellite DNA markers of toothfish population structure in the Southern Ocean. Journal of Fish Biology 57, 72–83.
| Allozyme and microsatellite DNA markers of toothfish population structure in the Southern Ocean.Crossref | GoogleScholarGoogle Scholar | 1:CAS:528:DC%2BD3cXot1ylt78%3D&md5=59acb6b1ad714814085d17e8572c9d56CAS |
Stokstad, E. (2010). News focus: to fight illegal fishing, forensic DNA gets local. (American Association for the Advancement of Science: Washington, DC, USA.) Available at www.sciencemag.org./10.1126/science.330.6010.1468 [Verified 18 June 2012].
Thorsteinsson, V. (2002). Tagging methods for stock assessment and research in fisheries, report of Concerted Action FAIR CT.96.1394 (CATAG). Marine Research Institute Technical Report 79, Reykjavik.
Ward, D. L. (2003). Effects of marking techniques and handling on swimming ability of bonytail chub. Journal of the Arizona-Nevada Academy of Science 36, 34–36.
