I am trying to compare and determine if there are differences in the compositions of specific chemicals in plant species that are or are not eaten by an insect species. I was imagining defining the chemical composition of all plant species that are palatable as one "chemical community" and the composition of plant species that are not palatable as another and then applying Simpson's or some other index of dissimilarity. However, I haven't seen this kind of analysis done in the context of chemical composition before. I was also hoping to somehow account for genetic relatedness of the plant species in my analysis, but I have no idea of how to approach that or if it would be possible.
Is there a better way to be thinking about the assemblages of compounds or different statistical methods that would be better for this application? I'm also open to any suggestions of how to account for genetic relatedness.
Beta diversity will show differences or you can do canonical ordination
Yes, I can imagine a matrix where chemicals are the variables and plant species are the samples. This could be either presence/absence (1 = chemical in plant, 0 = it isn't) or more quantitative, but I'd imagine the presence/absence would be fine to get started. Whether plants are eaten or not is then a factor grouping sets of plants. Such a matrix is easily analysed using a host of methods. My preference is for non-parametric multivariate analysis, and you can look at my profile for publications on this. There's even a resemblance measure that can incorporate information about distances (genetic or otherwise) in calculating dissimilarities between samples (Clarke KR, Somerfield PJ, Chapman MG (2006) On resemblance measures for ecological studies, including taxonomic dissimilarities and a zero-adjusted Bray-Curtis measure for denuded assemblages. J. Exp. Mar. Biol. Ecol. 330:55-80).
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