Homology/similarity/identity: proper usage.

[ahouse at BINAH.CC.BRANDEIS.EDU]

>	orthology - where the two sequences encode the same protein,
>	e.g. a myoglobin in a human and a myoglobin in a whale
>
>	paralogy - where the relationship between the two sequences
>	is not consistent with the phylogeny, e.g. myoglobin in a human
>	and beta-globin in a human (here, the ancestor of myoglobin
>	and hemoglobin is much older than recent ancestors of humans).
>

I think that you might what to distinguish these terms not with respect to
phylogentic consistency but rather in terms of genetic events.  A gene
duplication (that gives rise to a pair of paralogous genes) may happen before a
linneage split.  If the 2 genes become functionally diiferent in the 2
linneages you may be fooled into imagining a homology that is due to a shared
derived gene when in fact you don't have orthologous genes because of the
paralogy in the ancestor.

Jeremy Ahouse
Brandei