I need to determine the diet composition and relative proportion of plant species in mule deer diet. What I currently understand is that fecal samples need to be fresh in order to accurately sequence plant DNA in them. Unfortunately, the deer I am studying live deep in the wilderness and are difficult to spot and watch poop, so I've had trouble getting enough fresh samples.
Does anyone have experience collecting older fecal samples for genetic analysis of diet, and how well did plant DNA amplify?
One thing I know is that it also is dependent on the read length. This is also dependent on the brand/type of sequencer (ion torrent, Illumina etc) you will use.
Fecal samples are tough matter to do DNA analyis on, thats for sure.
You might also want to make sure that the way you isolate and analyze does not create some kind of bias towards plants with large amounts of DNA or DNA that is easily degraded because of leaf structure.
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