Phylogeny between monocot and eudicot
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?
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Kevin Blighe
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Mohammed •
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Mohammed •
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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
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