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For the stomach content data, the mass of prey groups present within each sample was converted to percentage composition.
The 2-dimensional nMDS plot based on weights of prey groups by location and month revealed clear separation of the diets of FA and UA fish for both saithe (Fig. 2a) and cod (Fig. 2b).
Applying group/species-specific methods in many situations may also require considerable methodological development, as at present assays have only been designed for a limited number of prey groups or species [e.g. 4], [7], [17], [18], may not be useful to identify lower taxa [e.g. 8] or are only applicable to specific predators [6], [19], [20].
To quantify whether the gudgeons from different habitat types differed in diet, we conducted non-parametric MANOVA [42], [43] on Bray Curtis distances for the proportions of prey groups with habitat type and local populations as factors, testing the significance by permuting the raw data (1000 permutations) using function adonis in the R package vegan version 1.17-4 1.17-4 [44]
For example, only morphology can efficiently allow us to distinguish different life stages of prey groups, for example the apparent consumption of adult versus pupal forms of Chironomidae, which represent subtle niche differentiation in trawling Myotis bats (Krüger et al. 2014).
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The same ranking of relative importance of these prey groups was obtained based on the frequency of occurrence data, although the importance of prey items present in small amounts in some samples was exaggerated (e.g. cephalopods and euphausiids during crèche stage) (Table 3).
A total of 5273 individual prey of 111 prey groups were identified, having a total weight of 36.8 kg (Appendix S1).
Slightly less than half of the faecal samples (39 out of 88) tested positive for one or more of the prey groups targeted with PCR tests (Figure S1).
Out of these prey groups especially insects are thought to be rich carotenoid sources, whereas the mammal prey items have low value as sources of carotenoids [19], [23].
The mean percentage contribution of the prey groups identified by SIMPER were plotted to show the main differences in dietary composition between bins.
Of the 88 faecal samples collected, 39 contained detectable DNA from one or more of the prey groups targeted with PCR tests.
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