The Tree Skip is a way to jump over the river without having to climb up the tree and push off the log to form a bridge. This skip can save up to 35 seconds, or 50 million years in Limbo speedrunning time.
To do the Tree Skip, you need to use the crate to boost yourself over the river. First and foremost, the crate needs to be positioned correctly. A reference point can be to have the left side of the crate touch the very last piece of grass that's in the water. This only takes one normal step and one tiny step.
After that, jump on the crate and perform a crate boost. If you get it right, you'll be launched far enough to grab the ledge over the river and continue.
Controller vs Keyboard
If using a PlayStation or Xbox controller with a joystick, it is crucial to roll the stick quickly upwards from north-west to north-east position and press jump at the same time. The momentum from a 'fast-stick-roll' will consistently transfer to the box, causing it to spin out of control. Whether or not this amounts to Limboy climbing out of the pond on the other side depends on the starting position of the box and the timing of the jump.
If using a keyboard the skip is executed by turning on the left top corner of the box and pressing jump. The console controller 'fast-stick-roll' is replicated with the following inputs on the keyboard: left, up, then right + jump. Importantly the 'up' input must be made fractionally before the 'right + jump' input. Again, if the box position and jump timing is right, Limboy will make it across the pond safely.