For decades we were taught to prune all limbs, big or small, at the branch collar. However, over the past few years a debate has been growing about what to do when pruning large limbs. Some would argue that when removing large branches or stems it is better practice to leave a stub. The thought is by leaving a stub, decay organisms would take more time to enter the parent stem, thus offsetting internal decay and structural weakness for some time.
I have debated this in my head for years, but recently while reading Fungal Strategies of Wood Decay in Trees by Schwartze, Engels, and Mattheck, I came across these lines. "After removal of a branch, this cut surface is like a chemical battlefield, as not only spores of wood decay fungi germinate there but also the spores of many other fungi, e.g. the mold fungi. Because of the competitive pressure and interplay of different fungi, it is much more difficult for wood decay fungi to become established on such a substraight..." It goes on to say that leaving a large stub allows more potential for wood decay to become established, and once established, wood decay is difficult to slow down.
Now of course, tree species and specific wood decay organisms all play a part. From the conservation biology point of view, large declining stubs are also home for many species of arthropods and fungi that would otherwise not have a home, so there may be some intrinsic value. With that in mind, site use and targets may come in to play.
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