I'm late to this thread, but if I recall correctly, the chocolate allele in Yorkies was bred in from another breed. The chocolate allele has a very specific DNA sequence, and it's been proven beyond a shadow of a doubt that it did not occur spontaneously in Yorkies and had to have been bred in from another breed carrying the chocolate allele. I believe that this is the relevant article:
Coat color DNA testing in dogs: Theory meets practice