I am currently weighing the pros and cons of two methods for assessing the dietary preferences of a large carnivore, the spotted hyena. I have previously used microscopic hair root analysis (based on identification of prey hairs in faecal samples from a reference collection) to determine the dietary preferences of this species.
However, I am also considering using DNA metabarcoding to answer the same question by identifying the DNA of prey species in the hyena faecal samples. I know this method is newer and possibly more well-regarded, but it is also more expensive and complex.
Basically, is there any advantage to using metabarcoding over hair root analysis when assessing prey preference / dietary habits? Is one more accurate than the other when assessing the proportional contribution (or even just the presence) of different food sources in an animal's diet?
I have searched for papers comparing the two methods but as of yet have not seen any. If anyone has any literature that would help me with my decision that would be very helpful.
Many thanks!
Hi Arjun,
Although metabarcoding has its own limitations, it is for sure more taxonomically comprehensive than hair root analysis. Considering the efficiency of hyena’s digestive system and their scavenging behavior (might have scavenged/'kleptoparasited' on an almost finished carcass-without hair) you are highly likely to miss a prey species not because it is not there but because it was not morphologically represented. Another thing which might not apply to you is the taxonomic expertise, some hair might be wrongly assigned especially if the prey species in question are potential food item and exist within the study area. It doesn’t harm to do both-if you have time and resources.
Good luck!
David Njoroge Thuo Hi there, thanks a lot for the feedback. After consideration I am leaning towards going with metabarcoding. As you say it certainly can pick up things that morphological methods cannot.
I am still not totally clear if it is possible to measure proportional contribution of different prey species in their diet without doing a "feeding experiment" as Wachter et al. (2012) did for cheetahs. I am getting mixed feedback from different people. But anyway I will keep looking and see what can be done.
If the question is about 'preference' (rather than diet composition) you would also need to know the composition of the prey base they have access to. And with hyaenas readily feeding of carrion and kleptoparasitizing their diet is also influenced by what the kills from the predators they kleptoparasitize on and which carrion is available, ie they eat what's available to them, not what they pursue. Is direct observation an option?
Egil Droge Thanks for the feedback. To clarify, it's more about diet composition rather than preference -- i.e. I will not be looking at Jacob's index (for now). Direct observation is indeed possible as I work in the Ngorongoro Crater where hyenas are very well-habituated and the habitat is wide open, and we have a long-term dataset on both hyena and lion kills and kleptoparasitism events.
Nice! But do they allow night time work to observe hyaenas hunting? Or increase the amount of observed hunts.
Egil Droge No unfortunately nocturnal follows are not allowed here... the hyenas are very active in the morning and late afternoon, so I do see a decent number of hunts, but not as many as I'd want. However, faecal samples are very easy to collect (can readily get 1-2 fresh samples per day from known individuals)
Yes, it's usually very easy. If they rest, and you get a little too close, they often get up, defecate and move. At least, that's my experience from Liuwa.
Nice, that sure makes collecting fecal samples from known individuals a lot easier. Good luck with the study!
Will anyone tell me how to evaluate the predation pressure of carnivores on ungulates.
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