Phylogeny between monocot and eudicot

Question

[Mohammed]

Hello everyone

I'm working on a project about phylogeny and I chose to make a NJ tree between Oryza sativa subsp. japonica and Arabidopsis thaliana.

But the groups aren't aligning correctly (As I thought)

The OsbZIP groups are found in other groups of AtbZIPs as in the image attached.

Is this right?

Answer 1

[Kevin Blighe]

Hello Mohammed,

Your NJ tree's "misalignment" (OsbZIPs scattering into non-matching AtbZIP clades) is totally expected and correct for bZIP phylogenetics between rice (monocot) and Arabidopsis (eudicot). Here's why, briefly:

• Divergence & Duplications: Deep split (~140–200 Mya) + lineage-specific WGDs cause paralog expansions, spilling OsbZIPs across clades (e.g., monocot-specific in Group 2).
• Method Artifacts: NJ struggles with rate variation; ~70–80% orthologs align, but the rest reflect rice innovations.

Kevin