After blast and HMM search, I identified two set of homologous genes which are functionally different. I thought they might have come from gene duplication in the LCA. So I made the MSA where the alignment is excellent and the phylogenetic tree separates them in two clades with high topology support. Each clade contains genes from various species. Is this evidence good enough to show gene duplication?
The counter argument is that I can take two sets of somewhat similar genes from eukaryotes and prokaryotes and make tree out of that. But it does not mean they came from gene duplication.
1 answer
You answered your own question, because the two situations you describe aren't comparable. If your clades are distinct in their taxonomic affiliations (prokaryotic versus eukaryotic) this isn't the same thing as your situation at all, that is clearly "normal" phylogenetic signal. If however you have sequences from the same groups of species in two different clades, that is definitely evidence that those genes are paralagous (ie descended by gene duplication versus speciation).
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