ASVs of the same genus in different branches on the phylogenetic tree


I constructed my phylogenetic tree using "qiime phylogeny align-to-tree-mafft-fasttree", and exported rooted tree. For taxonomic assignment of the ASVs, I produced weighted classifier of SILVA 138 SSURef NR99. After creating a phyloseq object with feature counts, taxa table, and rooted phylogenetic tree in R, using the "subset_taxa" function of phyloseq package, I selected all the ASVs using the genus names that I am interested in. When I draw the phylogenetic tree using those ASVs of the genera of interest, ASVs of the two genera were in different branches. What may cause the issue?

Due to confidentiality, I cannot share the files.

Thank you in advance


There are different algorithms underlying tree-building and taxonomy assignment, and this result highlights where these methods disagree.

It's also possible that Barnesiella are polyphyletic! In this case, both methods are right! :thinking:


Dear Colin,

Thank you for your response, and the information. That what I thought, as the tree generation is produced by the amplified 16S region only, but not sure. Good to hear expert opinions.

Best regards


This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.