[Bioperl-l] Comparative genomics - regions of synteny and whole genome duplication

[Ian Korf]

> Another point that also concers the discussion on gene
> families/clustering/orthologues/paralogues: the real biological criterium
> for orthology and paralogy is not sequence similarity, it's
> common pathway of molecular evolution!

The definition of orthology and paralogy has nothing to do with function.
Orthologs are genes that are separated by a speciation event. Paralogs are
genes that are separated by a gene duplication. It is possible that
orthologous genes do not have the same function. Suppose you have the
orthologous genes A B C in two species s1 and s2. In s2, C gets
duplicated to C'.

s1:  A B C
s2:  A B C   C'

Suppose that after the duplication, either C or C' has more freedom to
diverge. If C retains its original function, then a functional
classification (or similarity-based classification) will put s2:C as the
ortholog of s1:C, and a synteny argument will agree. But, if C' retains
the original function, the functional and syntenic classifications will
disagree. But really, both s2:C and s2:C' are both orthologs of s1:C.

-Ian