Why does wood become darker when it ages?
While most wood we see comes from stain or oils, wood left on its own will darken.  As far as this article suggests, this is caused by the polymerization of polyphenols from lignin into tannins which are dark red or brown in color when they are highly polymerized.  

The specific content of the lignin in different woods will affect the density, strength and color of the wood.  

This woodworking reference shows that intense UV exposure to wood will darken it to give it an aged look.