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This tree is about 6 years old. Every year, I have to trim off a couple branches which contain plain green leaves. It seems to be worse this year. I was under the impression that these mutant shoots only occur below the grafting and were a result of the root ball plant. Why am I seeing these shoots higher up in the tree?

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What you have here is variegation, you have a variegated Japanese maple. In genetics it is called chimera, it means that a mutation occurred only in a part of the organism (plant in your case), other cells are still not mutated (wild type). So the organism is a mix of mutated and non mutated cells. In your plant it shows as variegated leaves, so healthy green tissue (cells) with a mutated colored tissue (the edge of the leaves). The green tissue is doing the photosynthesis part, since the mutated cells do not have chlorophyll anymore (hence the different color). It is important to know that the mutated cells (which cause the nice color around the leaves), won't survive without the healthy green cells because they are not able to do photosynthesis themselves.

Variegation is nice for us, it looks nice, however it is for the plant not so efficient. See it as a handicap for the plant. That's why some of the branches get rid of the mutated cells and become normal healthy again. A bit like natural selection within the plant. So it is actually the other way around, the green leaves are the original healthy one, and the variegated leaves contain mutated cells.

I am afraid you can do nothing more as you do already, cut of the branches with healthy green leaves.

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