Methods

The alignments were constructed using the program CLUSTALW:

THOMPSON et al. (1994). CLUSTALW: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680

The "hypervariable" portions, of variable lengths in different subunits, were removed, in order to avoid bias, particularly with distance-methods. The phylogenetic inferences were computed using the package PHYLIP:

FELSENSTEIN, J (1993). PHYLIP, phylogenetic inference package. Distributed by the author, department of Genetics, University of Washington, Seattle.

according to the methods presented in:

Nicolas Le Novère and Jean-Pierre Changeux (1995). Molecular evolution of the nicotinic acetylcholine receptor: an example of multigene family in excitable cells. J Mol Evol 40: 155-172.
(HTML version, Postscript version)

Above the branches are the bootstrap scores (each alignment is bootstrapped 1000 times) of the Maximum Parsimony (rounded to the nearest integer). Under the branches are the bootstrap scores of the Neighbor-Joining. The triplications denote uncertainties, i.e. total opposition of the methods, or the two methods providing bootstrap scores below 50 %. When the topology obtained contradicts the species systematic, the trees are corrected, the new branches being annotated "syst".

The position of subunits linked by dotted line have been determined with an independant alignment (because the sequence is very short and could distort the general result).

Those trees were experimentally designed. They do not fully represent the personal opinion of the author, and they are surely not fully identical to the actual evolutionary history of the subunits.

Comments

This tree is preliminar. I put it here to provide an overview, waiting for a more thorough analysis.

For more information see:

Chiu J., DeSalle R., Lam H.-M., Maisel L., Coruzzi G. (1999). Molecular evolution of glutamate receptors: A primitive signaling mechanism that existed before plants and animals diverged. Mol Biol Evol 16 : 826-838.

Last modification: Wed Nov 24 10:59:05 GMT 2004 | Nicolas Le Novère