In article <313E139B.176F at pc029.pharm.nwu.edu>, John Hogenesch <john at pc029.pharm.nwu.edu> writes:
|> Molecular evolutionary biologists,
|> I'm writing a paper where we identify five new members
|> of a gene family. This brings the total number of identified
|> proteins in vertebrates to eight. In addition there are five
|> Drosophila members of this family and one bacterial. What
|> characteristics would make these proteins a superfamily, family,
|> or subfamily? They all contain a conserved domain, and all but
|> two contain a second domain shared by bunches of proteins. The
|> splicing patterns of a couple of these proteins have been
|> determined, and they are also conserved (in the conserved
|> domains).
|> Any insight would be appreciated, as I can't seem to
|> find a cogent definition of these terms. I get the feeling
|> people throw them around a lot.
|>|> John Hogenesch
|>john at pc029.pharm.nwu.edu
There is no current "laws" about the rank terminology of
multigene families. It depends on the phylogeny and on the
physiology, but also on the field history.
For instance, in the ligand-gated ion channel field, it is now
widely accepted that nicotinic, GABAa, glycine, 5HT3 and gutamate
chloride channel form a SUPERFAMILY. All the receptors are
pentamers forming a pseudosymetric channel. The sequence off all
subunits are phylogenetically related.
I think it could be better to call this "supergroup" a CLASS.
Inside this CLASS, there is several SUPERFAMILY, such as the subunits
of chloride channels.
I proposed to call FAMILY a monophyletic group containing subunits
forming receptors for the same ligand, such as nicotinic receptors.
Inside a FAMILY, I decided to call SUBFAMILY a monophyletic group
of subunits forming receptors only with subunits of the same group.
Example: the alpha-bungarotoxin insensitive receptors of the brain.
Finally, I called TRIBE a monophyletic group containing subunits
with the same role in the oligomer (GABAa alpha subunit...).
CLASS SUPERFAMILY FAMILY SUBFAMILY TRIBE member
nicotinicoid
excitatory
nicotinic
alpha-BGT-
alpha
a2
a3
...
These divisions may represent split between two phyla:
example: for the nAChR FAMILY
_______________________ vertebrates neuronal BGT+ subunits
|
| _______________ "protostomia" subunits
| |
|_______|
| _______ vertebrates muscle subunits
|_______|
|______ vertebrates neuronal BGT-
Similarly, in the "protostomia" FAMILY, we find three TRIBES of insect subunits
and one TRIBE which is the nematode homolog of the first three.
I think you can find your own criteria. There is only three laws.
If we suppose that a careful phylogenetic analysis was performed:
LAW 1: ALL GROUPS HAVE TO BE MONOPHYLETIC
Since new members are regularly cloned, the classification has to be
able to evolve in a logical manner, and without changing the name of
the menbers:
LAW 2: ONE CAN SPLIT A GROUP INTO TWO GROUPS OF THE SAME RANK
LAW 3: ONE CAN FUSE TWO GROUPS IN A GROUP OF HIGHER RANK
good luck,
Nicolas
