Hi Massimo,

Looks really interesting study!

I just need some details for my correct understanding.

What you want to show?

I mean, are you working at a protein level (to explain the mutations at the origin of the switch in function) or at a genetic level (show that you get a gene duplication followed by a neofunctionalization)?

Because for my point, if you showed that your genes have direct ancestry and then the 2 copies have different function (produce different products), this is matching already the definition of neofunctionalization...

Best

Guillaume

Dear Guillaume,

I have both protein and CDS sequences. Previous studies had demonstrated that gene B evolved from gene A and that gene B had a different function. I found that gene A and B are located in tandem so it is likely that a tandem gene B evolved from a tandem duplication. My doubt is how do I test my hypothesis? 

Thank you for your answer

Hi Massimo,

You may want to check this link if it can be helpful: https://www.researchgate.net/post/How_to_detect_paralogs_in_a_list_of_protein_pairs_in_a_high-throughput_manner;

Hi Massimo,

Okay. For my point, you have sufficient data in hand.

You can tell me

1/Gene B evolve from gene A (previous work)

2/ Function of B is slightly different

3/Gene A and B are organized in tandem.

For testing if it's a tandem duplication that give the gene B, I have now idea on how people do... I guess that showing a tandem is already a "proof" of tandem duplication??

If your gene organisation and cis elements are conserve, how to explain this without a duplication event?

Hope i help...

Best

Guillaume

If understood correct neo-functionalization originally was proposed and predicted using the tools to detect positive selection...

http://www.sciencemag.org/content/290/5494/1151.full?sid=7a51c659-ac74-474f-96ea-f10a2b8592f4

Thank you Olga,