Since I was working in the wildlife sanctuary which harbours about 25 markhor and 30 individuals of musk deer . Besides this 70000 domestic sheep and goat are grazing their for a period of five months. I was working on all the hosts. But for collection of faecal samples I divided the sampling into two periods. Fir the five months when their were large number of domestic animals I usually collected the fresh faecal samples of goat and sheep following the herds. But it was very much difficult to collect the fresh faecal samples of wild ungulates because I was not able to differentiate the faecal samples of wild ungulates during this period. But after the domestic animals leave the wildlife Sanctuary I was able to collect the fresh faecal samples because they usually migrate downwards and I were easily able to collect fresh faecal samples during post grazing period . Can I justify it
Yes, you can justify it, since this approach is more certain than, as you said, trying to collect samples from the ungulates during the first period since you couldn't distinguish the difference. However, it will also depend on what you are actually measuring/collecting/observing within these samples. Perhaps there are temporal differences in what you are observing, so you need to keep this is mind if you are comparing these samples between the domestic and wild animals.
I think your problem will be in the change of season and vegetation. If the vegetation is not affected by season you are O.K. ,but if the vegetation is affected by season you will not be justifiable in my opinion.
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