Quick edit-
1. When you're choosing colors, try to avoid that limbo of greyish brown colors. Even though they are technically very tree-like colors, pixeling is always more about implication rather than recreation. The edited palette isn't awfully different but note the shift from the violet darkest shade to the more yellow lightest, and how the middle ones are a little more reddish brown than grey.
2. When you want to shade organic forms, one of the best ways is to start with the most common shadow as a base and "pull" the lighter parts out like clay. So this here is the foundation. I'm using your line art because I'm lazy, although there are a few issues with it that someone else can cover if they want.
3. Starting to pull out light areas. Pay attention to what the line art implies, especially in the trunk. The outline makes it look like there are three big ridges that make it up, so shade those ridges accordingly.
4. Adding shadows, following the rays that the highlights follow. Don't be afraid to make big fields of shadows, too.
5. Highlights and details. Always try to avoid single-pixel noise, so when you're making bark, do it in short lines.
6. Having a little more fun with the palette, just because you can.
