[BiO BB] orthologs vs in-paralogs

[Boris Steipe]

Phil Luo wrote:
> 
> Dear all,
> 
> As we know ,there are two kinds of homolog, ortholog and paralog. Genes in two
> species that have directly evolved from a single gene in the last common
> ancestor are called orthologs. A set of homologous genes that have diverged
> from each other as a consequence of genetic duplication are called paralogs.
> Sometime those paralogs which arose from a duplication after the speciation
> event are called in-paralogs.
> 
> My question is how to distinguish the in-paralogs from orthologs.

Paralogs have different functions. biochemistry, not bioinformatics.

> Which one is
> supposed to be more similar, in-paralogs or orthologs?


To the degree that the evolutionary rates remain the same, the difference will
be proportional to the time of separation from the common ancestor. For
orthologs this is the speciation event. For in-paralogs this is the duplication
event. Accordingly you would expect a situation in which pradoxically a protein
and it's paralog would be more similar than that protein and its ortholog in
another species.

That need not be universally true however, since the divergence of an in-paralog
(post-duplication) may occur under reduced selective pressure since the original
protein still fulfills its function. Thus the evolutionary rates need not be the same.

Accordingly: if you find paradoxical similarities as above, your best
explanation will be "in-paralogs". But if you have a duplication event in a
species (possible evidence could come from comparative genomics) you cannot
necessarily conclude that the proteins must be unusually similar. In fact,
looking for such events systematically and analysing divergence rates, would
make an interesting project to quantify the evolutionary pressure on genes after
duplication events.



Best regards,


Boris

---
Boris Steipe
University of Toronto
Program in Proteomics & Bioinformatics
Departments of Biochemistry & Molecular and Medical Genetics
http://biochemistry.utoronto.ca/steipe