In the 1980's Asphalt Roofing Manufacturers began to use limestone as a filler to combat rising oil prices.  So to cut down on the amount of oil used limestone was used as a filler in asphalt shingles.  There's just one problem with that idea.  Limestone is made from calcium and bacteria can use it as a food source.  One in particular named Gloeocapsa Magma is what plagues most roofs with black staining.  Because this bacteria is airborne it affects many homes.  When it lands on a roof and the conditions are right and a food source is present.  You will have black stains in due time.  This process generally takes 5-7 years with our Delaware climate depending on many factors.  One major factor is the quality of your shingle.  Some lower quality shingles will have visible staining in 3 years.  Older shingles, before the addition of limestone rarely become dirty.  Shade is another major factor.  Roofs below substantial tree cover are more likely to develop staining as well.