Phylogeny differences between gene and orthologs

Question

[Mehmet]

Dear All:

I would like to ask you. What is difference between two phylogenies? First phylogeny is based on a gene sequence (18 S), second phylogeny is based on ortholog proteins (~75 single copy orthologs)?

I found two different results. My species is a sister species to A phylum based on 18 S (This is based on previous papers). But it is sister to B phylum based on orthologs (based on my work)?

what can make this difference?

Thank you.