One idea would be to reserve three letter names for elegans and let everyone else go wild with names of the form:   abcdefghi-n. The choice of using Cbr-unc-4 would still be open.
My main motivation was having unique names and not hurting the C. elegans nomenclature.

Paul

I guess I'm okay with this, as long as we keep the three-letter species prefix.

Eric:  ...And as we heard in LA, there is no clear fog-2 orthologue, but many FTR genes in both species.  How do we handle these?

--Well, at the moment it is not possible to tell which of all those C. briggsae FTR genes are ortholog(s) of fog-2, because there are only 2 species represented (we will need 4 species represented to make this determination).  But if there have been independent duplications of FTR genes in each lineage, then there will be MULTIPLE ORTHOLOGS for fog-2 (i.e., all the genes in C. briggsae that share a common ancestral gene from which fog-2 derived in the briggsae-elegans ancestor).

Given that, I'm willing to consider the idea of parallel naming--one specifically relative to elegans, another independent. ...  Do we really want to have to look at a correspondence table to see what a gene does?

--God no, not parallel naming.  We want to avoid synonymization problems AT ALL COSTS.  A correspondence table for orthologs would not in any way tell you what a gene does.  But it provides an efficient database-friendly method for determining orthologs.

(Even though a good prediction is that orthologs will share function because they share ancestry, one can only determine function by some kind of empirical work, and orthologs could well have changed function during evolution, or at least developmental role.  Note: contrary to popular belief systems, "COGs" are not necessarily orthologs.  Deletions of a different paralog in each genome could easily lead (and HAS led) to mistaking a reciprocal highest BLAST pair for orthologs.)