In the Weeds
There are some deep botanical & philosophical questions that piqued my curiosity. In finding some answers, I am sharing these here:
When you air layer or propagate by cutting, are we “training” those features to be more trunk-like, or does the tree naturally adapt? For us, an arm is always an arm. (Trunks often have characteristics and patterns different than their branches. For example a trunk may have radial branches and frequency and spacing, while some branches display their tertiary (?) branches and leaves to maximize photosynthesis.)
You can clone a tree using nothing more than a tiny piece of tissue (“tissue culture propagation”), and it ultimately works because trees don’t really have a firm body plan like mammals do, they’re fractals that can re-initiate the entire thing from anywhere that you have cells that can differentiate. Cells capable of doing this exist throughout the limb structure.
Once you have the opposing poles of vegetative bud on one end and root production on the other, and are able to transport substances between those two poles (nutrients, sugar, hormones, water), the rest is really a story about sugar production/demand and hormone exchange between those poles. Morphology springs out of all that and is an interplay between auxin/cytokinin as well as sugar productivity (shaded shoots lose out to lit ones) causing some shoots to simply suck on the straw harder.
When we air layer or make a cutting we are tipping the balance of cells spontaneously deciding to differentiate into root cells by flooding a region (the callus formed at the cut site) with auxin and sugar from above. Cells are receiving a signal that there is productive foliage above while surrounded by an increasing pile of sugars (the accumulating mass of callus). Typically auxin and sugars would just fly right by the cut site and head down to the roots or diffuse into the tree, but we’ve cut that flow off and it all bunches up at the cut site instead. The cells observe an unusually high quantity of auxin in relation to cytokinin and start producing roots, which soon begin signaling upwards with cytokinin again.
The hormones and photosynthetic productivity then help determine a morphology or “habit” for the tree, but in bonsai we often hasten some of these balances either by allowing light to penetrate into a canopy (shifting productivity to the interior) or by lowering branches (eg in conifers) to make it harder for auxin to march up from the tips of branches and into the trunk (once again shifting the probability of budding to the interior — auxin “doesn’t like to go uphill” and so the interior dormant buds lose the signal that the tip is productive, and are more likely to start growing in response).
A good search query to start with on google scholar is “apical dominance”
—MaciekA (r/Bonsai)