I've recently wrapped up a large ecological study which determined species ID of large carnivores (black bear, wolves, coyotes, cougars, bobcats) and associated prey (mammals and birds) using mtDNA fragment analysis of the CytB region from scats. Interestingly, the cougars only had about 50% prey success and I am trying to figure out what may be the cause.
Inhibition seems unlikely since the same assay that identifies predator also indicates prey. However, we sample for DNA by thinly swabbing the inner and outer edges of the scat which theoretically pick up epithelial cells of the predator and whatever remains of the prey. Is there something about cougar scats which would inhibit the prey signal given that the predator DNA is not within the scat itself? Why are bobcats not similarly affected?
It may also be that the assay is missing a critical prey species but that also seems unlikely due to prey presence in the other species.
Any thoughts or insight would be appreciated.
Hey Misa - what a wonderful study and emerging question! A couple of things came to mind that you could test and help develop hypotheses to figure out what is going on with those cougars. One idea is that cougars might be more prone to using latrines or areas where the microhabitat (soil microbes specifically) could be a part of your inhibition problems. Simply the fact that those large predators have discrete areas where they poop might be enough to differentiate those microhabitats. This is of course, testable - just go out and characterize your microhabitats where you find different species' poops. Another idea is that the cougars do indeed have some endogenous inhibitors in their guts (like what you suggest, but are skeptical if bobcats do not have a similar things going on). My take on this hypothesis is that it is still viable because of the diversity of cougar prey (relative to bobcats). Providing them opportunities to eat a wide variety of prey might also have a tag-along gut fauna that includes more of the inhibitors, bacteria or fungi that can mess up your PCR or extractions. Again, this is testable - but you'd have to do a pretty good gut fauna inventory, not just the prey. Anyhow - those are a couple of competing hypotheses to test. Good luck! David
Thank you so much for your input Dr. Bickford. I believe your latrine hypothesis may by part of the problem and I am going to look into that a little further since there are many cases of clustering from the GPS data. Very appreciative of your suggestions and your awesome work in conservation biology!
Hi Misa,
If you don't already have them, these two sources may be helpful (including the authors themselves; re: M Culver):
Article Diet of pumas ( Puma concolor ) in Sonora, Mexico, as determ...
http://arizona.openrepository.com/arizona/bitstream/10150/253832/1/GPSC_NIG+Poster,+Naidu-Ashwin.pdf
good luck!
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