Yo, I'm a PhD student and finishing up some data to publish. Working with 10 bacterial strains that are made up with 6 gamma-proteobacteria, 2 actinobacteria, 1 beta-proteobacteria and 1 sphingobacteria. I have 10 other strains that are references and 1 outgroup strain. I am using Mega5 to align with ClustalW and then I run Neighbor-Jointing and did bootstrapping. The strains connected with the reference strains perfectly and the outgroup has the shortest amount of branches but is yet still relatively associated with the rest of the bacteria.
However, when I bracket off the classes of bacteria, all of them are neatly segregated, however for some strange reason the gamma-proteobacteria sandwich the one beta-proteobacteria. I thought all the classes were supposed to be clearly segregated on a phylogenetic tree? Or is it because gamma and beta proteobacteria are so closely related that sometimes they do combine on a tree? I would like to know if I need to re-do because I don't want to be yelled at by the reviewers. Thank ya kindly.