This is a test version of Biostars. For the public version, visit https://www.biostars.org.
use codeml to investigate positive selection in xenologs

Hi,

I have a collection of genes that are xenolog (not ortholog). Can I use CODEML program of the PAML software package (v4.4) to investigate the presence of positive selection at individual amino acid codons?

Can I investigate changes in evolutionary pressure in the collection of xenologs? In all articles I've read, changes in evolutionary pressure were investigated in the collection of orthologs.

Kind regards, Elahe

codeml xenolog
• 1,920 views • link
written by Elahe Rabiei-Motlagh • Elahe Rabiei-Motlagh

I'm glad I could help. Please use ADD COMMENT when responding to existing posts to keep threads logically organized. If my solution below is useful then "accept" (green check mark) the answer to provide closure to this thread.

• 0 views • link
written by Andrzej Zielezinski Andrzej Zielezinski

2 answers

Yes, you can investigate the presence of positive selection acting on horizontally transferred genes.

Newly acquired genes have higher rates of evolution than other genes in the genome. For example, Hao & Golding (2006) found that within the Bacillaceae, recently transferred genes had higher Ka/Ks ratios than native genes, showing rapid evolution. As transferred genes persist in the genome, the Ka/Ks ratio decreases, suggesting adaptation of the new genes to the new environment of the host.

Here are papers that used CODEML (from PAML package) to calculate Ka/Ks ratio in xenologs:

I'm sure you will find more papers on this topic.

• 0 views • link
written by Andrzej Zielezinski Andrzej Zielezinski

Thank you. I really appreciate your help.

• 0 views • link
written by Elahe Rabiei-Motlagh • Elahe Rabiei-Motlagh

Log in to answer this question.

More posts like this