Phylogenetic Comparative Methods: PGLS
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4.9 years ago

Hey guys, I have a a 13 columns 58 row table, where each row is a species and each column represents the number of genes in a gene family (numerical data). Numerical data is normalized by the sum total for that species and hence is continuous, containing some 0 values. I would like to remove any effects of phylogeny before analyzing my data using PGLS. I am not particularly statistics savvy, so I have a few phylogenetic/stats related questions:

1). Due to having 0 in some entries in the data table, should I increase all by one, and perhaps log transform the data?

2). I am going to use a species tree, but don't have branch lengths, is it ok to add a branch length of 1 to each branch for PGLS? There are no polytomies and the species tree is unrooted.

3). If PGLS confirms signal, what is the next step? Can you use the residuals for further analyses, or can the original trait data be corrected using the residuals somehow? The reason I ask is because I wish to group species into sub-categories (such as nocturnal, diurnal) to investigate group patterns rather than individual species patterns.

Can anyone please help here?

Thank you!!

genome R alignment sequence • 1.4k views

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