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The CHAIC classification tree tested the efficiency of the variables; area of harvest, season, and sex to predict the gonad and fat stages of SA sardines. Figure 5.6 represents the bar chart for the gonad stages (as defined in Table 5.1) of SA sardines, showing the split at each node where separation took place. It was observed that at each split, the majority of samples were classified into gonad stage 3 (early development of gonads), followed by stages 2 (inactive gonads) and 4 (gonads close to maturity). These stages were represented by 85% of the samples, while only 8% of the samples were classified into gonad stage 1 (immature or inactive gonads), and 9% into gonad stages 5, 6 and 7 (stages 5 and 6 = maximum gonad maturity before spawning, stage 7 = condition of gonads just after spawning). Due to limited number of samples showing maximum gonad maturity, these

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gonad stages were poorly represented in this study. This may result into bias conclusions about the relationships between K. thyrsites presence and gonad maturity stage of sardines.

For the fat stages (as defined in Table 5.2), 77% of the samples were classified into fat stages 1, 2 and 3, with fat stage 4 represented by only 11% of the samples, and fat stages 5, 6 and 7 by only 12% of the SA sardine samples. This trend continued with each split (area, season and sex) through the CHAIC classification tree for fat stage.

The independent association between the prevalence of K. thyrsites (taking only qPCR results into account) and gonad and fat stage, respectively, was investigated. It was found that K. thyrsites presence was independent of both gonad and fat stage (P-values for Chi-square tests were > 0.05). In contrast to the gonad results for SA sardines, studies by St-Hilaire et al. (1998) and Levsen et al. (2008) showed that sexually mature Atlantic salmon (Salmo salar) are more likely to be infected with K. thyrsites than their sexually immature counterparts, possibly due to depressed host immunity (St- Hilaire et al., 1998; Jones et al., 2016).

The independence of the prevalence of K. thyrsites and gonad and fat stages could in part be explained by the high prevalence of K. thyrsites in the SA sardine samples used in this study. With a prevalence of 91% for the sardine samples, only a small number of samples were not infected, therefore, the number of infected samples in the different gonad and fat stages was not significantly different. However, in the present study, the stages within the gonad and fat stage classifications were not represented by equal number of samples. The gonad and fat stages of SA sardines were therefore not considered in further statistical analysis by GLMs.

98 Figure 5.6 CHAID classification and regression tree for gonad stage (g1 to g7 represents gonad stages as explained in Table 5.1) of SA sardines with area (east, south and west coast), season (summer, autumn, winter and spring) and sex (m – male and f – female) as classification variables.

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5.3.1.4 Correlation between size and weight of fish samples

Table 5.5 summarises the Pearson’s correlations between size and weight for the SA sardine and SA kingklip samples, respectively. For both species, a significant (P < 0.0001) linear positive correlation (r = 0.928 for sardines, r = 0.957 for kingklip) was found between size and weight. This indicated that as the size of the fish increased, the weight also increased. Therefore, the relationship between K. thyrsites prevalence was investigated for size only, allowing for better comparison between the three species of fish investigated in this study.

Figure 5.7 shows that the average (± standard deviation) size of fish was significantly different (P < 0.001) for the four species of fish. Kingklip was significantly larger in size (75.94 ± 10.10 cm) compared to SA sardine (17.97 ± 1.72 cm), M. capensis (38.61 ± 1.22 cm) and M. paradoxus (39.88 ± 1.00 cm). The average size for sardines was the smallest amongst the four species. The significant difference in size between SA kingklip, SA sardine, and Cape hake was expected since SA sardine is small pelagic fish typically ranging in caudal length between 12 and 25 cm (Van der Lingen et al., 2006; Reed et al., 2012). Cape hake and SA kingklip are demersal fish species; where Cape hake may range in length between 10 and > 95 cm (Botha, 1986), and SA kingklip between 20 and > 130 cm (Payne, 1986). There was, however, no significant difference in the average size between M. capensis and M. paradoxus. The average size for all the Cape hake samples combined was calculated as 39.37 ± 9.97 cm, which fell within the typical size range for Cape hake of 40 to 60 cm (Cohen, 1990). The relationship between K. thyrsites prevalence and the size was therefore calculated for the combined Cape hake size data.

Table 5.5 Mean (± standard deviations) size (cm) and weight (g) of SA sardine and SA kingklip samples, with Pearson’s correlation coefficient (R-value), correlation coefficient of determination (R2_{-value) and P-value for}

correlation between size and weight

SA sardine SA kingklip

Variables Means and

standard deviation Pearson’s correlation test Means and standard deviation Pearson’s correlation test *_{Size (cm) 17.97 ± 1.72 R = 0.928} R2 _{= 0.860} P < 0.0001 75.95 ± 10.10 R = 0.957 R2 _{= 0.915} P < 0.0001 Weight (g) P-value 88.67 ± 22.70 2 258.09 ± 1 078.97

*_{Size refers to caudal length in cm}

R - correlation coefficient measures the strength and the direction of a linear relationship between the two variables size and weight

R2 _{- correlation coefficient of determination represents the percent of the data that is the closest to the regression}

equation (linear association between size and weight) P-value with a significance level at 0.05

100 Figure 5.7 Means (± standard deviation), with standard error bars, for the size (cm) of the four species of fish: SA kingklip, SA sardine, and Cape hake (mc - M. capensis and mp - M. paradoxus). abc_{Different superscripts}

indicate significant differences at P < 0.05. Size refers to caudal length in cm. Total number of samples: SA kingklip = 70, SA sardine = 267, Cape hake = 57 (number of samples of mc = 22 and number of samples of mp = 35).