How to Handle Incorrect Clade Grouping of a Reference Genome in a Phylogenetic Tree?

Question

[oasiswho]

Hi everyone,

I encountered an issue while building a phylogenetic tree and would appreciate some guidance or discussion.

I used a reference genome to annotate my target genome, but during the phylogenetic analysis, I found that the reference genome was incorrectly grouped into the same clade as my target genome. Biologically, this reference genome should be much more distant from my species.

Here are my questions:

Has anyone experienced a similar issue? If I want to build a robust phylogenetic tree, should I remove this reference genome and reconstruct the tree? Alternatively, should I keep the reference genome in the tree and describe this anomaly in my discussion section? Any insights or advice on how to handle this situation would be greatly appreciated!

Thank you!

Answer 1

[Mensur Dlakic]

Has anyone experienced a similar issue?

I am sure many people have gotten the trees they didn't expect.

Assuming you know how to do a tree reconstruction, the obtained tree doesn't lie. Either the two species are more related than you think, or something went wrong upstream of tree reconstruction.

You didn't give us enough information to offer more than this general conclusion. We don't know: 1) is this is a single-gene or concatenated tree? 2) DNA or protein? 3) how did you align the sequences? 4 were the alignments trimmed? 5) what were you expecting in terms of tree distances and what did you get? 6) what are other tree members and how are their distances relative to your species of interest?

[oasiswho]

Dear Mensur Dlakic Thank you very much for your response. I am currently working on constructing a phylogenetic tree based on mitochondrial genomes. I included five existing mitochondrial genomes along with two outgroup species to build the tree.

Here is my results:

Figure 1

A. sachalinensis is my target genome, and A. alba is my reference genome. After annotation, I blasted all genes, and corrected it manually.

(1)I used two methods: one is a concatenated multi-gene tree constructed with IQ-TREE2, as Figure 1 shown (a), and the other is a coalescent-based species tree constructed using ASTRAL(Figure 1 (B)). (2)The analysis was performed using DNA sequences. (3)I aligned the sequences using MAFFT. (4)The alignments were not trimmed and were directly used for tree construction after alignment. (5)My primary goal is to compare the placement of species in the mitochondrial tree with that in the chloroplast tree. However, I found discrepancies between the placement of species in the mitochondrial tree and the chloroplast tree. (6)The tree members and the two reference papers for comparison are provided in the attached image. The I would like to refer to the chloroplast phylogenetic tree illustrated in Figure 2 of Semerikova et al., 2018, as well as the chloroplast and mitochondrial phylogenetic trees presented in Figures 3 and 4 of Park et al., 2024. Thank you so much!

Figure 2

Figure 3 Figure 4