You may read Karp et al., 2013 in Ecology letters: Forest bolsters bird abundance, pest control and coffee yield.
But what are you searching? Studying populations of the "producer" of faeces or search for preys/alimentation ?
In this study, these authors were able (with anyway a low rate of success) to determine which birds were eating a specific pest (coleoptera) of coffee.
For deer I would imagine that fecal would be the best source, unless the species is very cryptic about where it defecates. Fecal samples definitely work; the biggest problem for them can be finding the dung/scat for certain species (and of course some samples may not work, dropout occurs). For some species like cats, people often use detection dogs to find the samples for them. As long as you can find the samples easily, fecal seems like the best way to to. Nicola Anthony at the University of New Orleans uses dung samples as a source for DNA for duiker species in Central Africa.
No it will not like that. it is not so simple. first of all take blood samples and isolate the DNA from blood either using kits or other protocol for DNA isolation blood then PCR for specific sequence which you need and then define your particular sequence and design your own primers and isolate DNA from faecal matter and find out the perticular Sequences. then it may be reliable source.
Hi, are you working on population study of endangered species? Non invasive samples have been a quite good source for DNA genotyping when collected fresh. You can see some examples on the elephant study by Lori Eggert (University of Missoury).