adding phy_tree reduces number of ASVs

[MCK-sketch]

Hi, I am new to using phyloseq and wanted some help with the following. When I build my phyloseq object with the phy_tree slot empty the number of ASVs is >5000, but when I add the phy_tree (constructed followin this https://f1000research.com/articles/5-1492/v2) to the phyloseq object the number of ASVs reduces to ~200. Can someone let me know why this might be? Thank you