The question came up on whether we can sequence lichens in animal diets.

It’s a bit of extra work, but we think so.

Lichens are symbioses between fungi and either algae or cyanobacteria (or both).  As such, identifying them requires a decision on whether to go after the fungi or the photobionts.

Newmaster et al. (2013) reported that they were able to use ITS to identify the fungi in lichens in the diets of woodland caribou. Seemed to work pretty well.

We need to do some more reading on the relative benefits of identifying lichens by their fungi or the alga/cyanobacteria, but it seems like, at the very least, identifying the fungi would work.