Above I have a close up focusing on a fallen tree partially covered with mud. Roots are exposed with chunks of mud still clinging on. This is my now typical way of building trees using mostly cylinder hinges (30554 and 30554b) for bark texture and rigid hoses of various lengths for branches and roots. Off of the hose branches I use Battle Droid Arms (30377), Robot Arm bar 1 x 3 (4735) and Clips with mechanical claw (48729). I have various techniques for thickening the branch as it comes of the tree, but generally the hose goes right through to the end. Various cylinders, cones and 2x2 round plates help to give texture and an appropriate thinning of the branch until you get down to bare hoses. Unfortunately, the angle the tree ended up at did not really show the roots very well. It all sort of looked like a bush. Oh well, that's the way it goes.
(a) Cylinder hinge for bark (b) 3mm Rigid hoses for branches (c) Droid arms for branches (d) Robot Arms work great as a start of branches off of the hoses (e) Mechanical claws work great to attach to hoses as small branch growths or on the end of (c) Droid arms to finish a branch. There is a bit more than this going on here, but this should give the general idea.
In the image above, you can see how the overall plains of the mud swell like waves. As described in the previous "making of" post, the suspended plates that are underneath the visible mud pieces allow for great control in articulating direction while also providing a spongy give and take each time plates were added to the matrix.