Is it possible or acceptable to tell that a gene may be older than its homologues only from the observation that it contains relatively more GC % ? How much difference in GC content qualifies to tell a gene is a younger/older acquisition ?
Can the phylogenetic age be inferred from GC content? I do not think so. In bacteria, e.g., GC content is often a useful characteristics for inferring evolutionary relationships and genomic islands of markedly different GC content point to 'recent' horizontal gene transfer events, but the bacterium can acquire two genes "at the same time" (either from one source or two different sources): one gene with high GC content and another one with low GC content . . .
Thank you Martin. Also when we look at a family of gene present in both Gram positive and negative and if the average GC content in Gram negative homologue is higher than that of Gram positive examples, still we cannot conclude the gene originated from Gram negative and transferred to Gram positive ?
Is the assumption of "higher GC content means phylogenetically older gene" valid?
The phylogeny is just one of the four aspects of a bacterium; the other three are morphology, physiology and ecology; everything depends on everything else.
Yes. I am trying to select the oldest member among members of an enzyme family to make rooted phylogenetic tree.