Can I Study Selection Pressure On Multigene Family Using Codeml Or Hyphy?

Question

[GR]

Dear all,

I have the following query re the selection analysis using codeml/HyPhy.

The objective of my work is to test whether the set of genes are under selection pressure or not. I have used orthomcl to extract orthology clusters for my dataset.

Most of the literature I have seen study selection pressure on single-copy orthologs ( gene that have 1-1 orthologs in the species of interest). What should I do in case of multigene families? Does HyPhy/Codeml works well in case of multi gene families? Do I have to extract 1-1 relations from these families and then input to codeml/hyphy or the orthomcl cluster directly can go as input to HyPhy?

Many thanks, Rtu

Answer 1

[Joseph Hughes]

Different genes are likely to have different functions and different selection pressures but this is what paml or hyphy will enable you to detect. For example, it is often thought that following duplication, there is strong positive selection on the duplicates and this can be detected in codeml. Here is a practical exercise that illustrates the use of PAML on the family of Lactate Dehydrogenase following duplication. Your dataset is probably larger but the same approach would apply.

There is probably a limit to the size of the multigene family that would be feasible to analyse and if the functions of the different genes are very different, it would probably make more sense to analyse each gene separately because selection signatures could be drowned out.