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I have a dataset containing morphological and performance measures of species from various groups, including insects, lizards, frogs, spiders etc, and want to analyse the relationship between these measures and the animal's body size via regression methods, while controlling for common ancestry, similar to what has been done in this work:

Peattie, A. M. & Full, R. J. Phylogenetic analysis of the scaling of wet and dry biological fibrillar adhesives PNAS, 2007, 104, 18595-18600

For most of my species, statistically supported branch lengths are lacking, and I was thus wondering what the best way to conduct my analysis would be, and I would be grateful for any hint.

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Look also into PGLS. Either way, one thing you could do--it would be ugly--would be to set all branch lengths to 1. Additionally, you could smooth the tree with penalized likelihood, e.g. chronopl() function in ape package in R. Again, this is an ugly solution and look into PGLS (it won't solve the ugly phylogeny part).

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