Gladstone Fish Health Investigation 2011 - 2012 - Western Basin ...

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Appendix C – Statistical report: Histology results1. METHODSThere were 45 barramundi, 10 bull sharks, 25 grinner and 40 mud crabs submitted for histologicalanalyses . As each species had a different sampling scheme over locations, these were analysed separately.The statistical methods have been previously detailed; in summary: General linear models (GLMs; McCullagh and Nelder 1989) were adopted for the analyses, usingGenStat (<strong>2011</strong>). Each fish or crab was taken as an independent experimental unit. Weighting factors were used to adjust for the stratified sampling of both diseased and unaffectedanimals. As the grinner were all rated as ‘normal’ (not diseased), no weightings were adopted fortheir analyses. Length was generally significant for barramundi, bull sharks and grinner, so was retained in allanalyses to adjust for size (length being approximately the same as age). The primary variable of importance is cumulative score. Analyses are also conducted for eachindividual component of this score. These were all considered as continuous variables, as thesignificance‐difference testing and interpretation are more understandable on this basis. Liver lipid (fish) and hepatopancreas lipid (mud crabs) are categorical variables, so wereanalysed as counts in these classes under a Poisson GLM with a log‐link. The means, and significant differences between these, are primarily reported at the location bytrip level. These values are also then compared at the regional level. The pooled standard error wascalculated according to the usual sum‐of‐variances method (Raj 1968), and these were used toconduct a t‐test for the degree of difference between these regional means. Bull sharks (with fewer observations) were only analysed and reported at the regional level. Secondary analyses were also conducted, including ‘disease status’ in the model (except forgrinner, where all fish were rated as undiseased).2. RESULTS – BARRAMUNDISkin lesions were missing for 14 of the 45 observations, unfortunately including all five from Bundabergon trip 1. Muscle lesions were missing for two observations. This also results in missing values for thecumulative score for these fish. As shown in Figure 2.1, the distribution of the residuals justifies theanalyses using the assumptions of untransformed continuous data and the Normal distribution.129
Standardized residualsStandardized residualsStandardized residualsCumulative_score102816420-1-20-2-1012345678910Standardized residualsFitted values22.010-1-21.51.00.50.0-2-1 0 120.00.5 1.0 1.52.0Normal plotHalf-Normal plotFigure 2.1. Distr ibution of residuals for the analysis of the barramundi cumulative score data.Disease status – None of the ratings in Table 2.1 showed a significant (P < 0.05) difference betweennormal and diseased fish. Whilst cumulative score was close, note that the diseased fish had lower averages cores here.Table 2.1. Effects of disease stat us on the his tology ratingsfor barramundi.NormalDiseasedAverage s.e. Sig. level (P)Cumulative score 7.99 7.04 0.42 0.07Gill hyperplasia 2.39 2.37 0.14 0.49Gill parasites 2.00 1.93 0.22 0.69Liver MMCs 1.76 1.71 0.07 0.46Skin lesions 0.83 0.63 0.23 0.42Muscle lesions 0.35 0.17 0.11 0.17There was no significant effect (P = 0.20) of disease rating on the classification of liver lipid. Table 2.2showsthat the counts are well distributed across the liver lipid categories.130
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Department of Agriculture, Fisherie
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ContentsTable of tables 1Table of f
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Mullet (Mugilidae) 80Banana prawn (
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Figure 7. Barramundi caught in the
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Figure 38. Sharks caught in the Cal
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Phase 1 (August 2011-February 2012)
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The results in this study support t
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ecognised expertise and research pu
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Mr Mitchell reported high catches u
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Figure 2. Sampling sites within the
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Phase 2: Expanded Gladstone Fish He
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Mud crab (Scylla serrata): Mud crab
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For mud crabs, hepatopancreas, gill
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Table 2. The number of fish, crusta
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Significant findings and discussion
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Commercial barramundi catch and cat
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Figure 6. Eye condition observed in
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Conditions observed in barramundi s
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Figure 12. A barramundi caught in t
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provided another environmental stre
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was somewhat reduced because post-m
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4,000Commercial effort (days fished
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Size structure of mud crabs observe
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Figure 21. Examples of shell abnorm
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Of the 58 crabs observed to have sh
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HistopathologyLipid storage vacuola
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Commercial fishing effort for mulle
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Figure 28. (a) Mullet caught in Rod
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June/July: Mullet samples were coll
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Sharks and raysThe monitoring progr
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Observational findings Phase 1Phase
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Encysted larval parasites were foun
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in particular bull sharks, have bee
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Commercial banana prawn catch for t
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Observational findings Phase 2April
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Laboratory testing Phase 1Seven riv
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four displayed signs of redness. Th
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Conditions observed in pelagic fish
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FinfishObservational findingsDuring
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ConclusionsIn 2011, a wide range of
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Mud crabsFisheries Queensland did n
Page 83 and 84: Owens, L. 1983. Bopyrid isopod Epip
Page 85 and 86: Candidate speciesThe monitoring pro
Page 87 and 88: Table 1: Candidate species for each
Page 89 and 90: Sample processingSample processing
Page 91 and 92: Herring/grinner/Australian threadfi
Page 93 and 94: For example: the third specimen, re
Page 95 and 96: oooGonad - present/absentHepatopanc
Page 97 and 98: Cloudy eye,swollen,redness orhemorr
Page 99 and 100: Red pin pointmarks - nogeneral redn
Page 101 and 102: Lesion photos Description GradeThis
Page 103 and 104: L4continuedoperculumgrazing;cuts or
Page 105 and 106: Appendix A-3: Fish health assessmen
Page 107 and 108: Appendix B - Statistical report: Gl
Page 109 and 110: analyses, but this was not done for
Page 111 and 112: was a significant (P < 0.05) locati
Page 113 and 114: Percentage with fin condition > 015
Page 115 and 116: Table 3.6b. Effects of locations an
Page 117 and 118: Table 3.7d. Spleen categories - cou
Page 119 and 120: 32Bundy2Bundy1UpBoyne1UpBoyne2LwBoy
Page 121 and 122: Table 3.9c. Regional group means an
Page 123 and 124: Table 4.2c. Effects of locations an
Page 125 and 126: 4.5 Summarising by regionsThe means
Page 127 and 128: Ta ble 5.2a. Effects of locations a
Page 129 and 130: 5.5 Summarising by regionsThe means
Page 131 and 132: 6.3 ResultsThere was no significant
Page 133: Table 6.5 lists the mean values whe
Page 137 and 138: Table 2.3f. Muscle lesions.Lake Fit
Page 139 and 140: Table 4. 1f. Muscle lesions.Fitzroy
Page 141 and 142: Table 5.6. Regiona l m eans for the
Page 143 and 144: Contaminants in Tissue ofFish and C
Page 145 and 146: Contaminants in Tissue of Fish and
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Department of Science, Information
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Appendix E - Time line BarraBy John
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friends. Rapidly rising flood water
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To make note - condition loss was e
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May/June- FinsMy initial observatio
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Thes e escapee were now also in awo
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Figure N. Barramundi showing net ma
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September- Deaths and SicknessFigur
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There is numerous distinguishing fe
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Department of Agriculture, Fisherie
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