We aim to identify rapidly evolving genes on two branches connected to the root node across 3,000 single-copy gene families. Our assumption is that some genes experienced rapid evolution on each ancestral branch following the divergence between groups A and B.
Here are the rooted tree structures we used:
We employed the two-ratio branch model to analyze these trees and calculated p-values using likelihood ratio tests (LRT). However, we observed that the rapidly evolving genes identified on branch A are exactly the same as those identified on branch B. Similarly, we obtained identical results using the branch-site model.
For reference, the outputs from CodeML for one gene family are attached. These include:
Based on my understanding of the two-ratio branch model, the results for the two branches should differ. Could you kindly clarify if I might be misunderstanding the model, or if there is another explanation for these observations?
Thank you very much for your time and assistance.
Best regards,
Wenqiang