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I am very new to phylogenetic comparative methods but I want to explore the evolutionary patterns of a number of quantitative traits I have across a small sample (5) of closely related species (between .45mya and 4.3mya divergence). I am confident in the structure of the tree, but I only have phenotypic data for a small sample of the tree. I want to measure how correlated the evolution of the traits are across this small phylogeny and test the traits to neutral evolutionary models.

Should I even attempt this? I know that there will be limits for what I can infer about evolution of these traits, but I’m not sure where to start in terms of identifying the specific weakness. I know it will depend closely on my trait measurements, some traits display notable divergence and others do not change much across the phylogeny.

Are there any approaches that would be useful for describing the evolutionary patterns for this small sample? What references would be useful for convincing me to hold off until I have a larger phylogenetic sample? Thanks in advance for any advice!

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  • $\begingroup$ Welcome to Bio.SE! It's early in the morning for me and I'm having a little difficulty understand the question. You have 5 species and you want to build a tree. If there is a clear progression of the phenotype through the divergences then you could infer the history of the phenotype and maybe pin it down at a genetic level? I don't see why there would be any problem with this as a preliminary study whilst you wait for larger datasets. $\endgroup$ – James Mar 11 '16 at 3:00
  • $\begingroup$ Are you saying that you have phenotypic data for 5 species in a much larger phylogenetic tree? This will clearly limit the types of conclusions you can draw, and all conclusions will be extremely uncertain. As a first step, it would probably be useful to estimate the phylogenetic signal in the different traits (Bloomberg's K, Pagel's lambda), to see what you have to work with. Plotting the traits on the tree is also useful, but I assume that you've already done this. $\endgroup$ – fileunderwater Mar 11 '16 at 9:10