Positive Selection Of Multiple Copies Of A Gene Within The Same Genome

Question

[Dejian]

My colleague and I are holding different opinions about positive selection. The major issue is whether positive selection can be done among multiple copies of a gene within the same species. I think it can. But I cannot find suitable cases to prove it. The papers I have got mainly deal with positive selection among species. Some papers conducted positive selection within species. However, they used cDNA information and SNP from multiple species. For example, Moy etal. (2008) analyzed intraspecific diversity in oyster sperm bindin. Ramensky etal. (2008) found that alternatively spliced exons of human genes were under positive selection. I wonder whether there is an example that analyzed the multiple copies of a certain gene within the same genome (without using multiple individuals) and found the genomic copies were under positive selection. Do you know such examples? If any, please share with me. I will continue to search for such examples, and will share it with you if any. Thanks!

[Dejian]

Hi, I am back with two examples. Both are from MBE. (1) Large Gene Family Expansions and Adaptive Evolution for Odorant and Gustatory Receptors in the Pea Aphid, Acyrthosiphon pisum (2)Positive Selection and Expression Divergence Following Gene Duplication in the Sunflower CYCLOIDEA Gene Family

Answer 1

[Philippe]

Hi,

I didn't know any cases so far but I was curious about this question and found some evidence in the litterature. The mammalian PRAME gene family has been studied in different species and several group showed that part of the family members evolved under positive selection:

• Chang et al, 2011
• Birtle et al, 2005

Before finding these examples I was thinking that there are no reason it could not happened. If a gene is highly duplicated and at least one copy (or more) keep the ancestral function, then the other genes are free to evolve any new function and this can potentially be achieved by positive selection of some copies. I didn't look further but I am quite sure we can find other references.

[Dejian]

Yes, you are right. I shared two examples above.

Answer 2

[Larry_Parnell]

Selection to maintain multiple copies of a given gene is a type of selection acting upon all members, and this could be distinct from forces acting to different degrees upon different copies of that gene. With this as background, I offer the case of human amylase 1 (AMY1) and copy number affected by starch in the diet. Neighboring but distinct populations in Africa have different AMY1 copy numbers, different AMY1 expression levels and different amounts of starch in their diets. The authors report "(h)igher AMY1 copy numbers and protein levels probably improve the digestion of starchy foods and may buffer against the fitness-reducing effects of intestinal disease."

[Dejian]

Positive selection often occurs to genes involved in immunity, reproduction and dietary system. Your example about AMY1 is based on comparison between multiple individuals. In fact, it is not what I want. But, thank you all the same for sharing your knowledge. I have found two suitable cases and listed them in the comment to my question.

Answer 3

[Bill Pearson]

Here is an example of identification of positive selection in an enzyme, using several genes in the same species (paralogs).

Y. Ivarsson, A. J. Mackey, A M. Edalat, W. R. Pearson and B. Mannervik "Identification of residues in glutathione transferase capable of driving functional diversification in evolution - a novel approach to protein redesign" J Biol Chem (2003) 278:8733-8738