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And Movements of Yellowfin Tuna (Orange); Larger, Darker Arrows Indicate More Common Movements of Yellowfin

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And Movements of Yellowfin Tuna (Orange); Larger, Darker Arrows Indicate More Common Movements of Yellowfin John S. Gunn Naomi P. Clear Robert D. Ward Sharon A. Appleyard Peter M. Grewe Bronwyn H. Innes i The origin of recruits to the east coast yellowfin tuna fishery and delineation of the structure of yellowfin stocks in the western Pacific: final report to the Fisheries Research and Development Corporation Bibliography Includes index. ISBN 1 876996 02 1. 1. Yellowfin tuna fisheries – western Pacific Ocean. 2. Fishery resources – western Pacific Ocean. I. Gunn, John, 1956- . II. Fisheries Research and Development Corporation (Australia). III. CSIRO. Marine Research. 639.2758 Cover illustration of yellowfin tuna, Thunnus albacares, by Roger Swainston © CSIRO Marine Research, Australia Project No. 94/022 Final Report Table of Contents TABLE OF CONTENTS ................................................................................................ I LIST OF TABLES ....................................................................................................... III LIST OF FIGURES .................................................................................................... VII 1 NON-TECHNICAL SUMMARY .............................................................................. 1 Objectives ................................................................................................................ 1 Outcomes Achieved ................................................................................................ 1 KEYWORDS ................................................................................................................ 5 2 BACKGROUND..................................................................................................... 6 3 NEED ...................................................................................................................10 4 OBJECTIVES .......................................................................................................11 5 SAMPLE COLLECTION AND HANDLING ...........................................................12 5.1 Sample Collection ....................................................................................... 12 5.2 Handling of samples ................................................................................... 14 5.3 Data collection and storage ........................................................................ 15 5.4 Assigning individual fish to a cohort ......................................................... 15 6 GENETICS ...........................................................................................................18 6.1 Background ................................................................................................. 18 6.2 Methods ....................................................................................................... 19 6.3 Results ......................................................................................................... 23 6.4 Discussion ................................................................................................... 30 6.5 References ................................................................................................... 35 7 OTOLITH CHEMISTRY ........................................................................................44 7.1 Introduction ................................................................................................. 44 7.2 Otolith Elemental Chemistry (WD-EM and PIXE) ...................................... 45 7.3 Secondary Ion Mass Spectrometry (SIMS) ................................................ 92 8 SYNTHESIS OF GENETICS AND OTOLITH CHEMISTRY RESULTS .................. 110 8.1 Introduction ................................................................................................... 110 8.2 Biological and Oceanographic considerations........................................... 111 8.3 Conventional tagging data and movement patterns of yellowfin in the eastern AFZ ......................................................................................................... 113 8.4 Outcomes of the genetics study .................................................................. 117 8.5 How do tagging results aid in our interpretation of the genetics and otolith chemistry results? .............................................................................................. 118 i Project No. 94/022 Draft Final Report 8.6 Catch distribution and catch rates ........................................................... 119 8.7 References ................................................................................................. 125 9 BENEFITS ........................................................................................................... 128 10 FURTHER DEVELOPMENT ............................................................................... 129 11 PLANNED OUTCOMES ...................................................................................... 132 12 CONCLUSION .................................................................................................... 134 ACKNOWLEDGEMENTS ........................................................................................ 136 APPENDIX A - STAFF ............................................................................................. 137 APPENDIX B. INTELLECTUAL PROPERTY ........................................................... 137 APPENDIX C. DATABASE STRUCTURES FOR STORAGE OF PROJECT DATA 138 ii Project No. 94/022 Final Report List of Tables Table 5.1.1. The samples collected for this project from 1994 to 1999. Additional samples for genetics analyses included samples that had been collected in the early 1990s (see table 7.2.1). ................................................................................................................................... 13 Table 5.4.1. The growth equations used to calculate age from length. ...................................... 15 Table 5.4.2. Length-at-age calculated from Yamanaka (1990) and Yabuta et al. (1960), compared with Wild (1986) lengths-at-age for studies of eastern Pacific yellowfin tuna. 16 Table 6.2.1. Populations, sampling locations (approximate longitude and latitude) and sample sizes of yellowfin tuna examined for five microsatellite loci. ............................................. 19 Table 6.2.2. Microsatellite motif, primer sequences, number of alleles observed and allele size of yellowfin microsatellite loci. The motif listed is that obtained from the original yellowfin sequence used to generate amplification primers. ............................................... 22 Table 6.3.1. Homogeneity χ2 analysis for comparisons of microsatellite allele frequencies in temporal yellowfin tuna populations, bolded P values are significant after probability of H0 calculated from 5000 Monte Carlo runs, critical P=0.01b ................................................... 25 Table 6.3.2. Summary of genetic variability data per locus in each yellowfin tuna population 26 Table 6.3.3. Genetic variability at five loci in all yellowfin tuna populations (standard errors in parenthesis) .......................................................................................................................... 27 Table 6.3.4. χ2 analysis for differentiation of five microsatellite loci in eight yellowfin tuna populations, bolded P values are significant after probability of H0 calculated from 5000 Monte Carlo runs, critical P=0.01. ...................................................................................... 27 Table 6.3.5. Locus 161 pairwise comparisons of allele frequencies, χ2 values above the diagonal & P values below. P values in bold are significant after probability of H0 calculated from 5000 Monte Carlo runs ........................................................................................................ 28 Table 6.3.6. FST values obtained from AMOVA analysis of five microsatellite loci in eight yellowfin tuna populations, bolded P values are significant after Bonferroni correction. .. 28 Table 6.3.7. Matrix of genetic distance coefficients between yellowfin populations, below diagonal = Nei (1978) unbiased genetic distance, above diagonal = Cavalli-Sforza and Edwards (1967) chord distance ........................................................................................... 29 Table 7.2.1. Samples from 6 locations were analysed using WD-EM and PIXE probes. The WD-EM analysis was carried out on 4 occasions. .............................................................. 47 iii Project No. 94/022 Draft Final Report Table 7.2.2. Means table for sampling locations ........................................................................ 51 Table 7.2.3. Results from ANOVA between sampling locations. .............................................. 53 Table 7.2.4. Summary of ANOVA Bonferroni post-hoc tests indicating group (location) means that differ significantly. * indicates p<0.05; otherwise p<0.01. .......................................... 54 Table 7.2.5. Samples from each cohort analysed by WD-EM and PIXE analysis and included in statistical analysis. ............................................................................................................... 55 Table 7.2.6. Means table for cohorts (WD data not standardised to calcium) ............................ 56 Table 7.2.7. Means table for cohorts (WD data standardised) ................................................... 56 Table 7.2.8. Results of ANOVA for cohorts. ‘Std’ indicates the elements standardised
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