Promise and limitations of 18S genetic screening of extracted DNA from wild primates

Abstract: Genomic screening of fecal DNA provides insight into diet, parasite infection dynamics, and other aspects of the ecology and pathogens of wild populations. Here, we amplify and sequence the V4/V5 regions of the eukaryotic 18S ribosomal RNA gene from fecal DNA of wild capuchin monkeys (Cebus imitator). We examined the eukaryotic diversity of fecal DNA collected from 26 individuals, each sampled 1-4 times across a 19 month period, for a total sample of 94 fecal DNA extracts. We found a total of 3110 distinct amplicon sequence variants (ASVs) classified as Eukaryotes. Of these, 2174 ASVs were unknown, 405 were assigned to Metazoa, and 54 were assigned to the phylum Nematoda . We found 18 ASVs of nematodes that possibly parasitize monkeys: 10 are assigned to lungworm taxa (Superfamily Metastrongyloidae; genus Angiostrongylus), six to the genus Strongyloides, and two to the genus Austrostrongylus. Additionally, we found 36 ASVs that were assigned to nematodes that likely parasitize plants and/or invertebrates that the monkeys consume. Taken together with past dietary and coprological study of the same primate population, our results suggest that invertebrate consumption and parasitic infection, especially by lungworms, is common and widespread among this population of wild monkeys. Future contributions to genomic reference databases will allow these results to be revisited and refined. We conclude by discussing the promise and limitations of 18S sequencing for ecological surveys based on genetic screening of feces.