What Does Elevation Of Dn/Ds Ratio Indicate?
Entering edit mode
9.1 years ago
qiyunzhu ▴ 430

Hello folks,

I am writing a paragraph regarding a gene family, in which a specific clade has increased dN/dS ratio comparing to other clades. I know this because I did PAML analysis using both one-ratio model and two-ratio model and then did likelihood ratio test and get a significant answer. We all know that dN/dS > 1 indicates positive selection, < 1 suggests stabilizing selection, = 1 means neutral. That's not my question.

My situation is: the dN/dS ratio is around 0.1 for the whole tree and is 0.2 for this specific clade. What does an increase from 0.1 to 0.2 mean, biologically? That's what I am wondering.

I tried to write "this indicates that the evolutionary rate (is this a proper term?) is elevated in this clade, meaning there is some sort of positive evolution operating on this clade, despite the overall stabilizing selection. I further deduce that the protein is generally conserved and functional, but it needs some tuning-up." I also did branch-model test and found a couple of positive sites.

Is my intepretation sane? Or should I choose some more proper phrasing? Or I'm totally misunderstanding the topic? I searched the web a little bit but so far couldn't find any literature discussing this. If you happen to know some literatures please share. Thank you!

paml selection evolution • 3.2k views

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