Phylogenetic tree seems randomized

Question

[kutayozturk]

Hello,

I am a molecular biology PhD student who needs to do some basic bioinformatics work for my project. In my project, I was building phylogenetic trees for my GOI to see possible horizontal gene transfer and if any of the homologous proteins are identified in other organisms. In one of my trees, I have encountered an unusual pattern. It seemed like among whole tree, proteins belonging to species from two different genus were selected as homologous proteins. I used the same parameters for my other proteins, but never encountered such a situation. I have done reciprocal blast for some of the proteins and they were looking normal too. What possible explanations does such a pattern have?