I am wandering the biology meaning of pairwise dN/dS and what it can be used for. If I calculated a gene's pairwise dN/dS valuea between human and chimpanzee, and found it significantly higher than 1. What's that supposed to mean? This gene was positively selected in human lineage? or in chimpanzee lineage? or in both? Can anyone help me out here?
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dukecomeback •
A dN/dS significantly higher than 1 is indicative of positive selection. In the example you used, you cannot say if positive selection happened in human or chimp or both. To know this you should include an outgroup, which will inform on the ancestral states of (human,chimp) from which you could determine whether human or chimp have changed.
Thank you. I have another thought, hope for your opinion. Let's say we have ((human,chimp),mouse), for each of bunch genes, I calculate the pairwise dN/dS between human and mouse as w1, between chimp and mouse as w2, then I rank the genes according to difference of w1 and w2. Do you think the top 1% means something?
Nope. You have the same problem between chimp and mouse than between human and chimp, you cannot be sure which one accumulated substitutions, you can imagine complex scenarios (e.g. positive selection in chimp and mouse). That's the problem with pairwise comparisons.
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I assume you meant to say
pairwise? Can you correct the title/text in body of post?Soooooooo sorry for this, thank you for your correction.