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Genetic structure of Patagonian toothfish populations from otolith DNA

Published online by Cambridge University Press:  19 May 2016

Lola Toomey ,
Dirk Welsford ,
Sharon A. Appleyard ,
Andrea Polanowski ,
Cassandra Faux ,
Bruce E. Deagle ,
Mark Belchier ,
James Marthick  and
Simon Jarman
Lola Toomey*
Affiliation:
Australian Antarctic Division, 203 Channel Highway, Kingston, TAS 7050, Australia
Dirk Welsford
Affiliation:
Australian Antarctic Division, 203 Channel Highway, Kingston, TAS 7050, Australia
Sharon A. Appleyard
Affiliation:
CSIRO National Research Collections Australia, GPO Box 1538, Hobart, TAS 7001, Australia
Andrea Polanowski
Affiliation:
Australian Antarctic Division, 203 Channel Highway, Kingston, TAS 7050, Australia
Cassandra Faux
Affiliation:
Australian Antarctic Division, 203 Channel Highway, Kingston, TAS 7050, Australia
Bruce E. Deagle
Affiliation:
Australian Antarctic Division, 203 Channel Highway, Kingston, TAS 7050, Australia
Mark Belchier
Affiliation:
British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 0ET, UK
James Marthick
Affiliation:
Menzies Institute for Medical Research, 17 Liverpool St, Hobart, TAS 7000, Australia
Simon Jarman
Affiliation:
Australian Antarctic Division, 203 Channel Highway, Kingston, TAS 7050, Australia CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, no 7, 4485-661 Vairão, Portugal
*
lolatoomey@gmail.com
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Abstract

The Patagonian toothfish, Dissostichus eleginoides, is a valuable fishery species and has a discontinuous distribution across the Southern Ocean. Identification of the genetic stock structure of toothfish would allow evaluation of the suitability of the spatial scale at which fisheries management operates. Genetic subdivision seems likely given the species distribution. Population genetics studies of this species have been performed; however, they have been limited by sample size, spatial coverage and/or the type of markers investigated. As a potential solution, we developed methods for extracting toothfish DNA from otoliths that are available in large numbers from collections held at several research institutes. Genetic differentiation between the three oceanic sectors was investigated. Four mitochondrial and four nuclear markers with multiple single nucleotide polymorphisms were sequenced by high throughput sequencing for samples from six locations. Genetic differentiation was found between three sectors with nuclear markers. However, only the Pacific sector was differentiated from other sectors with mitochondrial markers. This study demonstrates the usefulness of otolith DNA as a means of increasing sample sizes for population genetics research of fish. Additionally, the combination of nuclear and mitochondrial markers may allow insight into how the observed differences in movements between male and female toothfish impact population structure.

Keywords

AntarcticDissostichus eleginoideshigh throughput sequencingpopulation geneticssingle nucleotide polymorphisms
Type
Biological Sciences
Information
Antarctic Science , Volume 28 , Issue 5 , October 2016 , pp. 347 - 360
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Copyright
© Antarctic Science Ltd 2016 

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References

Appleyard, S.A., Ward, R.D. & Williams, R. 2002. Population structure of the Patagonian toothfish around Heard, McDonald and Macquarie islands. Antarctic Science, 14, 364–373.CrossRefGoogle Scholar
Appleyard, S.A., Williams, R. & Ward, R.D. 2004. Population genetic structure of Patagonian toothfish in the West Indian Ocean sector of the Southern Ocean. CCAMLR Science, 11, 21–32.Google Scholar
Ashford, J.R., Jones, C.M., Hofmann, E.E., Everson, I., Moreno, C.A., Duhamel, G. & Williams, R. 2008. Otolith chemistry indicates population structuring by the Antarctic Circumpolar Current. Canadian Journal of Fisheries and Aquatic Sciences, 65, 135–146.Google Scholar
Ballard, J.W.O. & Rand, D.M. 2005. The population biology of mitochondrial DNA and its phylogenetic implications. Annual Review of Ecology Evolution and Systematics, 36, 621–642.Google Scholar
Benjamini, Y. & Hochberg, Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society - Methodological, B57, 289–300.Google Scholar
Brown, J., Brickle, P. & Scott, B.E. 2013. Investigating the movements and behaviour of Patagonian toothfish (Dissostichus eleginoides Smitt, 1898) around the Falkland Islands using satellite linked archival tags. Journal of Experimental Marine Biology and Ecology, 443, 65–74.CrossRefGoogle Scholar
CCAMLR. 2014. Toothfish fisheries Available at: https://www.ccamlr.org/en/fisheries/toothfish-fisheries. Accessed 7 May 2015.Google Scholar
Collins, M.A., Brickle, P., Brown, J. & Belchier, M. 2010. The Patagonian toothfish: biology, ecology and fishery. Advances in Marine Biology, 58, 227–300.Google Scholar
Cuveliers, E.L., Bolle, L.J., Volckaert, F.A.M. & Maes, G.E. 2009. Influence of DNA isolation from historical otoliths on nuclear-mitochondrial marker amplification and age determination in an overexploited fish, the common sole (Solea solea L.). Molecular Ecology Resources, 9, 725–732.CrossRefGoogle Scholar
Diniz-Filho, J.A.F., Soares, T.N., Lima, J.S., Dobrovolski, R., Landeiro, V.L., Telles, M.P.D., Rangel, T.F. & Bini, L.M. 2013. Mantel test in population genetics. Genetics and Molecular Biology, 36, 475–485.CrossRefGoogle ScholarPubMed
Duhamel, G. & Williams, R. 2011. History of whaling, sealing, fishery and aquaculture trials in the area of the Kerguelen Plateau. In Duhamel, G. & Welsford, D.C., eds. The Kerguelen Plateau: marine ecosystem and fisheries. Paris: Société Française d’Ichtyologie, 15–28.Google Scholar
Eastman, J.T. 2005. The nature of the diversity of Antarctic fishes. Polar Biology, 28, 93–107.CrossRefGoogle Scholar
Edgar, R.C. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 26, 2460–2461.Google Scholar
Hall, T.A. 1999. Bioedit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95–98.Google Scholar
Holm, S. 1979. A simple sequentially rejective multiple test procedure. Scandinavian Journal of Statistics, 6, 65–70.Google Scholar
Kalish, J. & Timmiss, T. 2000. Determination of Patagonian toothfish age, growth and population characteristics based on otoliths. Final report, FRDC Project 97/123. Canberra: Fisheries Research and Development Corporation, 22 pp.Google Scholar
Knowlton, N. 2000. Molecular genetic analyses of species boundaries in the sea. Hydrobiologia, 420, 73–90.CrossRefGoogle Scholar
Kuhn, K.L. 2007. Assessment of genetic structure in three Southern Ocean fishes revealed by mitochondrial and nuclear single nucleotide polymorphisms (SNPs). PhD thesis, University of Delaware, 252 pp. [Unpublished].Google Scholar
Librado, P. & Rozas, J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451–1452.CrossRefGoogle ScholarPubMed
Marlow, T.R., Agnew, D.J., Pruves, M.G. & Everson, I. 2003. Movement and growth of tagged Dissostichus eleginoides around South Georgia and Shag Rocks (subarea 48.3). CCAMLR Science, 10, 101–111.Google Scholar
Møller, P.R., Nielsen, J.G. & Fossen, I. 2003. Fish migration: Patagonian toothfish found off Greenland. This catch is evidence of transequatorial migration by a cold-water Antarctic fish. Nature, 421, 599.Google Scholar
Morin, P.A., Leduc, R.G., Archer, F.I., Martien, K.K., Huebinger, R., Bickham, J.W. & Taylor, B.L. 2009. Significant deviations from Hardy-Weinberg equilibrium caused by low levels of microsatellite genotyping errors. Molecular Ecology Resources, 9, 498–504.CrossRefGoogle ScholarPubMed
Peakall, R. & Smouse, P.E. 2012. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research – an update. Bioinformatics, 28, 2537–2539.Google Scholar
Poulsen, N.A., Nielsen, E.E., Schierup, M.H., Loeschcke, V. & Grønkjaer, P. 2006. Long‐term stability and effective population size in North Sea and Baltic Sea cod (Gadus morhua). Molecular Ecology, 15, 321–331.Google Scholar
Prost, S. & Anderson, C.N.K. 2011. TempNet: a method to display statistical parsimony networks for heterochronous DNA sequence data. Methods in Ecology and Evolution, 2, 663–667.CrossRefGoogle Scholar
Rogers, A.D., Morley, S., Fitzcharles, E., Jarvis, K. & Belchier, M. 2006. Genetic structure of Patagonian toothfish (Dissostichus eleginoides) populations on the Patagonian Shelf and Atlantic and western Indian Ocean Sectors of the Southern Ocean. Marine Biology, 149, 915–924.CrossRefGoogle Scholar
Seeb, J.E., Carvalho, G., Hauser, L., Naish, K., Roberts, S. & Seeb, L.W. 2011. Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms. Molecular Ecology Resources, 11, 10.1111/j.1755-0998.2010.02979.x.Google Scholar
Shaw, P.W., Arkhipkin, A.I. & Al-Khairulla, H. 2004. Genetic structuring of Patagonian toothfish populations in the southwest Atlantic Ocean: the effect of the Antarctic Polar Front and deep-water troughs as barriers to genetic exchange. Molecular Ecology, 13, 3293–3303.Google Scholar
Smith, P. & McVeagh, M. 2000. Allozyme and microsatellite DNA markers of toothfish population structure in the Southern Ocean. Journal of Fish Biology, 57, 72–83.Google Scholar
Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution, 30, 2725–2729.Google Scholar
Ward, R.D., Appleyard, S.A. & Williams, R. 2002. Population structure of the Patagonian toothfish (Dissostichus eleginoides) in Australian waters. Final report, FRDC Project 2000/108. Hobart, TAS: CSIRO Division of Marine Research, 67 pp.Google Scholar
Welsford, D.C., Nowara, G.B., Candy, S.G., McKinlay, J.P., Verdouw, J.J. & Hutchins, J.J. 2009. Evaluating gear and season specific age - length keys to improve the precision of stock assessments for Patagonian toothfish at Heard Island and the McDonald Islands. Final report, FRDC Tactical Research Fund Project 2008/046. Kingston: Department of Environment, Water, Heritage and the Arts, Australian Antarctic Division, 125 pp.Google Scholar
Welsford, D.C., Candy, S.G., Lamb, T.D., Nowara, G.B., Constable, A.J. & Williams, R. 2011. Habitat use by Patagonian toothfish (Dissostichus eleginoides Smitt 1898) on the Kerguelen Plateau around Heard Island and the McDonald Islands. In Duhamel, G. & Welsford, D.C., eds. The Kerguelen Plateau: marine ecosystem and fisheries. Paris: Société Française d’Ichtyologie, 125–136.Google Scholar
Welsford, D.C., McIvor, J., Candy, S.G. & Nowara, G.B. 2012. The spawning dynamics of Patagonian toothfish in the Australian EEZ at Heard Island and the McDonald Islands and their importance to spawning activity across the Kerguelen Plateau. Final report, FRDC Project TRF 2010/064. Kingston: Australian Antarctic Division, 60 pp.Google Scholar
Williams, R., Tuck, G.N., Constable, A.J. & Lamb, T. 2002. Movement, growth and available abundance to the fishery of Dissostichus eleginoides Smitt, 1898 at Heard Island, derived from tagging experiments. CCAMLR Science, 9, 33–48.Google Scholar