We believe that this in most cases reflect the evolutionary relationship between the different sequences although exceptions will be, and has already, been found. It may be necessary to set arbitrary levels of identity to establish the nomenclature. In higher plants, it is clear that specific LHC proteins exhibits specific functions within the general function of light-harvesting. We do not know to which extent this is true for algae. We also realize the problems in these assignments since the precise functions of the different genes are very hard to elucidate.
All designations have to be based on intelligent guesses by the researchers in the particular field.
A second problem arise when genes, encoding similar proteins, are sequenced from many species within a phylogenetic group. Again, we have to rely on guesses and assumptions made by the researcher. It is also likely that some of the green algal LHC proteins will be the functional homologues to some of the higher plant proteins, but about this we know nothing at the moment so we have chosen to give their genes names different from the higher plant genes. In our opinion, the fact that a given gene of Chlamydomonas might turn out to have identical function to a higher plant gene does not represent a problem for the nomenclature. In the future, it will hopefully be possible to functionally correlate some of the LHC proteins from green algae and higher plants.