Hmmm I see what you're saying. It's a mess but I optimistically think it's still something we will be able to tease out, by looking at many genes in a genome.

Hmmm I see what you're saying. It's a mess but I optimistically think it's still something we will be able to tease out, by looking at many genes in a genome. FWIW, It was recently estimated that 2% of core genes per genome are from HGT. https://en.wikipedia.org/wiki/Horizontal_gene_transfer_in_evolution#Resolution_of_uncertainty_with_phylogenomics https://en.wikipedia.org/wiki/Horizontal_gene_transfer_in_ev... It makes HGT fairly identifiable and gives us a lot of non-transfered genes to work with when reconstructing a tree.