I found the homology ratio* for all protein coding genes between several organisms and mouse using a phylogenetic-based approach. I have noticed that the ratio found between an organism and mouse is greater than the ratio between another organism and mouse! On the other hand the second is evolutionary closer to mouse than the first.
As the topic of homology analysis is non that trivial, I have a couple of questions:
- Can we compare the ratio of homology between the above 2 couples or such a comparison is biased - non scientific and why(even though I have seen studies where the ratio of homology found between different organisms and an organism of reference are compared)?
- Shouldn't the ratio of homology be proportional to the evolutionary distance of the organisms (according to conservation)?
I am looking for an article/research that clarifies the matter but cannot really find one!
Thanks in advance for any suggestions!
*When I am talking about homology ratio above, I mean protein coding genes of the organism with an homolog in mouse / all protein coding genes in the organism. x 100 :-)
RE-EDIT:
The way I calculate the above ratio, I dont take into acount the one-to-many or many-to many relationships! I just find the genes that have at least one homolog in mouse..i think that might be the bias of my calculation, right?
Hi,
welcome to Biostars. My comment is about a pet peeve of mine. Homology implies shared common descent. So percent homology is meaningless, really. It would be like saying "my wife is 85% pregnant". You either are or, you are not! I believe you mean percent sequence similarity?
As for your question. I appears that you stumbled on the difference between gene trees and species trees. It is very possible that in your analysis of gene X, species A is closest to mouse, while for gene Y species is B is closest to mouse.
Relevant humor:
Evolutionist Loses It As Colleague Conflates Homology and Similarity Yet Again
You are right and i clarify. So i am not talking about the sequence similarity neither.When i am saying "homology percentage" , i mean the ratio :
protein coding genes of the organism with an homolog in mouse / all protein coding genes in the organism. x 100 :-)