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

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Hello,

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

tree
tree1596×1046 163 KB

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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:

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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