What's causing this discoloration of a shake roof?

Most of this slope looked like this, and it was just this slope. Dark discoloration of the shingles just below the butts of overlapping shingles. No evidence of fire anywhere and it didn’t come off on your fingers like soot.

I’m stumped. Anyone know?

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My guess would be a reaction to the flashing.

What type of cedar is it and what was the flashing material.

Iron Stains
Iron stains may appear in two forms: the reddish brown discoloration caused by rust, and blue-black discoloration caused by the reaction of iron from nails and other metal objects with extractives from the cedar. To prevent these stains, use only hot-dipped galvanized, aluminum or stainless steel nails when fastening cedar.

It looks to be pretty standard “aging” to me. Most wood-shake roofing material I see looks like this.

How old is the roof?

http://www.cedarbureau.org/faq/product.htm

EXTRACTIVE BLEEDING
What is extractive bleeding and how does one clean it off?
Extractive bleeding is characterized by the tannins in the wood being dissolved in moisture and migrating to the surface of the product. Rain will sometimes wash these stains away; however if left to weather, the sun can cause polymerization, thus requiring the addition of a tannin blocker and new top coat finish (ensure proper surface preparation before applying new top coat) once the moisture problem has been solved. Compounds containing oxalic acid appear to be the most effective at removing extractive bleeding stains: ensure you use proper safety precautions and follow the oxalic acid compound manufacturer’s application directions. Extractive bleeding does not signify failure of the applied finish, but instead is found in applications where a source of moisture is present. Extractive bleeding is not a manufacturing defect nor is it a finish defect; it is a natural phenomenon that occurs in applications. Tannin blocking products help, however, the CSSB does not provide any finish warranty. Check with your sidewall product manufacturer, finish manufacturer, Approved Installer, or professional contractor for more assistance.

I would have thought it was staining due to fungal growth in the areas that don’t dry as fast, but I don’t see many cedar roofs around here.

shakes under the flashing…moisture, combined with no sun turns them black

We had that type of leaching from the cedar in the log homes we built. It comes out of the wood and is left when the water evaporates…Tannin, I think. It’s been a while.

Almost looks like creosote that they used to put on telephone poles as a wood preservative. It caused a dark staining in cracks and crevices, but would fade due to UV deterioration.

I agree, I think it is the tannin’s in the cedar, leaching down

North side of the roof??

Flashing material.