use codeml to investigate positive selection in xenologs

Question

[Elahe Rabiei-Motlagh]

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

[Andrzej Zielezinski]

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.

Answer 1

[Andrzej Zielezinski]

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:

• Treangen et al. (2011)
• Sun et al. (2013),
• Sun et al. (2016).

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

Answer 2

[Elahe Rabiei-Motlagh]

Thank you. I really appreciate your help.