[NiCkMiLnE]

tone specifically in the wood is from the density, weight and finish.

with neck thru, you want to use stronger woods for the neck portion, as they are tighter for the tone usually and reduce mud, as well as give the neck stability.
then if you use somthing like mahogany for the wings it gives the tone that girth, as the resonance of the body also affects how the pickup will magnetise the string.

good combinationm and you will see is very common is maple laminates with magohany wings.