I have a data set of chemical and physical traits (and herbivory data) from trees and vines at one of my study sites. Unfortunately, there was no overlap in the families trees vs vines came from at this study site. How do I account for the phylogenetic diversity in my analysis?
Trying to compare trees and vines.
Is phylogenetic generalised least squares the best or most appropriate method?
Is there phylogenetic data on australian plant families I can access to incorporate this into my analysis?
Any helpful links to tutorials
Dear Erica,
you can download phylogenies from https://tree.opentreeoflife.org/. They have a comprehensive set of phylogenies across the angiosperms. You can use the phytools and ape packages in R to load and manipulate the phylogenies. Regarding looking for phylogenetic signal in analyses, I would recommend using mcmcGLMM (in R as well). Here is a good tutorial that may apply in your case: http://www.mpcm-evolution.org/practice/online-practical-material-chapter-11/chapter-11-1-simple-model-mcmcglmm
I'm not shure that geografic criterion satisfies the task as in the intro to cladistic in trees at http://www.mobot.org/MOBOT/research/APweb/ and r-project has gota family of ready procedures. In order to separate clades from foreign sources other than Australia one should have composition lists for every group in and out of the source. Mantel test can assess if the difference is significant, but I do not have any idea about lists.
Phylogeny of R-project is introduced in http://www.phytools.org/eqg/Exercise_3.2/
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