I created a phylogeny using sequences from 4 different genes, in order to use it in comparative phylogenetic analysis. The initial unconstrained tree had some weird paraphylies, which could not be supported by the existing literature, so I used constrains in order to fix them, as I had done succesfully in the past. The problem is that the statistical tests I did using IQ-TREE to check the validity of the constrained topology doesn't support it. I was wondering if I could still use the constrained topology, which makes a lokt more sense when compared with existing phylogenies of the same animal group and how could I justify it. Many thanks in advance!
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