For decades we've known when pruning the final cut should be at, or just outside, the branch collar. When trees shed branches naturally it's at this point. This is where the tree has the easiest time compartmentalizing and growing over the wound.
Now, it seems there's been some debate over the past few years about what to do when pruning larger branches back to parent stems on mature trees. Some seasoned arborists have insisted that leaving a stub is prudent when dealing with large branches. The idea is that by leaving a stub, decay will be slowed when moving into the stem.
What needs to be considered though, is in a short period of time the vascular system around this stub is going to die. This means any physiological process the tree has to fend off decay will cease, creating a corridor for decay to enter the parent stem through both heartwood rots and sapwood rots.
Below is a picture of a willow oak damaged in a storm 3 or 4 years ago. During the storm a large branch broke out leaving a substantial stub. In that time I've driven past this tree almost every day. A few weeks ago I noticed bark separating from the underside of the damaged limb. When I got out to look, it was obvious that sapwood decay had moved from the dead stub into the parent branch. Had a proper cut been made the tree would have had a better chance of reacting to the damage. Sure, decay still may have moved in to the stem, but the tree would have been putting on reaction wood to close the wound and reinforce the structural wood around the damage.
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