Computational protocol: Diet analysis in piscivorous birds: What can the addition of molecular tools offer?

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Protocol publication

[…] Fish prey detection rates obtained from the three sample types using molecular or morphological analysis and each fish species’ share of the total number of detected individuals resulting from morphological analysis of the pellets were calculated using MS Excel 2010 (Microsoft). Sample‐based rarefraction curves were calculated using EstimateS Version 9.1.0 (Colwell, ) with 500 randomized runs without replacement and extrapolation for feces and fish samples to 588 samples. Graphs were plotted using SigmaPlot 12.0 (Systat Software, Inc.) which was also used for calculations of chi‐square tests including Yates corrections testing for differences in order‐level prey detection between molecular and morphological analysis for each sample type.As a statistical test for differences in variability/dispersion (i.e., the variation in co‐occurrence of species) between sample types, multivariate dispersion was tested using the betadisper routine in the R (R Development Core Team, ), package “vegan” (Oksanen et al., ), implementing the “permdisp2” routine (Anderson, ). Per sample type, the centroid of multivariate dispersion was depicted. Additionally, PERMANOVA (9,999 permutations) was used to test for significant differences in average prey species composition between the sample types. […]

Pipeline specifications

Software tools SigmaPlot, vegan
Application Miscellaneous