I am confused by a phylogenetic analysis. My gene phylogeny is shown as the following figure (assume all nodes are well supported). Most species in firmicutes form a clade. However, the gene also shows sporadic distribution in a few distantly related genus including E coli, Thermus Aquaticus, Bartonella, Methanococcu (Archaea), seemingly indicating a result of LGT (lateral gene transfer. However, none of them group with firmicutes, which contradicts the hypothesis of LGT. Could it be because of the accelerated evolution after LGT?
Does anyone have any ideas on how I should explain this phenomenon? LGT, massive loss or others?
How did you build your tree: neighbour joining, maximum likelihood, parsimony? Do you have a species tree of the taxa the way they should be related? Can you show a tree with branch lengths?