Can you collect sculls from Tyto alba (or any other mammal-eating owl) pellets for the geometric analysis? You can also extract DNA from pellets and find hair in them. But don't you need P. maniculatus sculls for comparison?

The use of mosquitoes or other hematophagous arthropod then you do species identification on the blood collected from the mosquito

May be it exist (or could it be created easily?) a kind of ELISA test (or DNA specific probe test) to discriminate quickly the species on the field?

Barbazan P, Palabodeewat S, Nitatpattana N, Gonzalez JP. Detection of host virus-reactive antibodies in blood meals of naturally engorged mosquitoes. Vector Borne Zoonotic Dis. 2009 Feb;9(1):103-8. doi: 10.1089/vbz.2007.0242. Epub 2008 Oct 30.

We're also using hair traps for plucking hair samples of the common vole (Microtus arvalis); but DNA-based species identification is done in the lab during off-season.

I would use hair, extract DNA using protease-K or prepGEM, and develop species specific PCR in the thermo cycler, and run a PCR that produces different products that are species specific in length. Run the product out on a gel and you know who is who. That can be run in a matter of hours, so you can release the ones thata re of the wrong species.

I have wrestled with this issue for Peromyscus in a manuscript entitled "Habitat selection of rodents in a pinyon-juniper woodland" in J. Mammalogy available on my research gate profile (https://www.researchgate.net/publication/233935787_Habitat_Selection_of_Rodents_Along_a_Pinyon-Juniper_Woodland-Savannah_Gradient?ev=prf_pub). What I did was collect some vouchers and send them to a lab for DNA and prep/curation. This didn't resolve the "what about all the others" issue you are confronted with but it did allow me to gain additional confidence in the morphometric key characteristics we were using and I was able to report all this in the methods to strengthen the findings. In a similar vein, another paper I worked on with colleague Ted Weller and others (https://www.researchgate.net/publication/232663726_Field_identification_of_the_cryptic_vespertilionid_bats_Myotis_lucifugus_and_M._yumanensis?ev=prf_pub), we tackled more directly the cryptic field ID of two species of bats. We were able to develop a really nice matrix of echolocation call characteristics (frequency) and forearm length that effectively separated the two spp. In the paper we provide the matrix which can be used as a decision-matrix. We were able to confirm our work with non-lethal collection of tissue from wing membranes and get DNA lab confirmation of species. So that would be the kind of thing needed for your study taxa that you could develop with some extra work - of course the characteristics would be different. Hopefully these are good examples to look at for some ideas. Note on my profile there are two other papers where we tested some other morphometric characteristics of these same two cryptic bat species, using the post-hoc lab confirmation. So I would imagine that perhaps some protocol exists already to collect ear tissue or a toe perhaps of your Peromyscus and get a lab to confirm spp for you...Keep us posted with what you come up with, as it is an interesting field problem that doesn't always get the attention it deserves.

Article Habitat Selection of Rodents Along a Pinyon-Juniper Woodland...

Article Field identification of the cryptic Vespertilionid bats, Myo...

In New Zealand we regularly use the DNA from animal hairs to id species. These hairs are brushed off (fall off) when they enter feeding stations. Another method is to use tracking tunnels which captures footprints, these are very useful and with careful analyses can distinguish species.

I have also had great success identifying species (between closely related mustelids) by collecting scats using scent detection dogs.

You can measure your live animals (e.g. weight, head-tail, lenght of forelimb, hindlimb...and so on). Measure two populations of species of interest as control set...then see if there are some good discriminatory features (you can use Discriminant Analyses or simple box plot to see in what morphometric traits your species differ). Alternatively you can take pics of the head in lateral, dorsal and ventral view (not the skull!) of your trapped individuals and do morphometric on that. Many researchers apply this for lizards using a manual scanner....

It sounds like you are doing the simplest method I know of by following the protocol for assaying amylase from saliva using the technique Chip Aquadro and I developed many moons ago. Simple, cheap, and perfectly accurate. I know of no perfect, non-invasive technique that doesn't require analysis with some type of lab equipment. While you can take a power pack and gels etc. to the field it is usually easier to simply take the samples to the lab.

Very interesting new tool to consider: Carrion fly sentinels of mammalian diversity...

Article Carrion fly-derived DNA as a tool for comprehensive and cost...

We did capture-mark-recapture, measurement (full body, limbs, head, weight, tail, etc) took pictures, collected mouth swab as DNA sampling method, and released them.

I recently returned from the field, and it's good to see all of this great feedback. As I read the posted materials and delve into the literature, I'll update you on what I find.