Theory question on dN/dS values for phylogeny
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3.6 years ago
DNAngel ▴ 240

Hi all,

This might be a noob question but I was just wondering, what does it mean if an internal branch has a higher dN/dS ratio but the tips leading from that branch have low dN/dS values. I ran the M0 model for a gene just to test things and understand the output data.

Here's an example of what I'm talking about (not showing the entire tree here but this is one small clade example where dN/dS values are shown right after the #):

((A #0.153, B #0.52) #0.22, C #0.105) #1.67) ...


So the branch leading to species A,B,C has a higher dN/dS (1.67) value but why wouldn't it also be above 1 for species A,B, and C? How can M0 determine that an internal branch evolved at a higher rate than the species at the tips?

Thank you!

dNdS paml codeml • 787 views