Abstract
DNA metabarcoding is a powerful tool for assessing the diets of wild animals, but there is no clear consensus on which proposed plant barcoding marker is most suitable for dietary analysis. This study compares two DNA plant barcoding markers that are commonly used for dietary analyses from degraded DNA, rbcL and trnL, to detailed dietary observations of wild white-faced capuchins (Cebus capucinus). Observational dietary data and fecal samples (n = 170) were collected for one year from a group of individually recognizable monkeys at La Suerte Biological Field Station, Costa Rica. DNA was extracted and portions of the rbcL and trnL chloroplast were amplified and sequenced on the Illumina MiSeq platform. Sequences were analyzed using obitools. Of the two barcoding markers tested, trnL yielded greater numbers of sequences with equal sequencing effort, higher resolution taxonomic identifications (albeit with a larger reference database), and identified a greater number of families also found in the observed diet. There was no relationship between observed capuchin feeding behavior and dietary composition based on either sequence occurrence or relative abundance of sequences using rbcL as a marker. However, dietary composition based on the relative abundance of trnL sequences was significantly positively associated with the observed percentage of feeding and foraging time capuchins’ spent on each plant species. Additionally, in 35% of cases, the relative abundance of trnL sequences assigned to particular plant families in fecal samples was highly positively correlated with time spent consuming plants from those same families. Our results indicate that trnL is a more robust DNA metabarcoding marker for plant dietary analysis and may potentially be used to quantitatively assess differences in diet within or between species.
Highlights
DNA metabarcoding is quickly becoming a powerful tool in ecology for understanding trophic interactions and non-invasively assessing the diets of wild animals, with the increasing availability of high-throughput sequencing technologies [1,2]
Target regions must be variable enough to discriminate between closely related animal and plant species, yet flanking regions should be conserved enough to be less variable within a single species
Even though there is a consensus for some taxonomic groups as to which standardized DNA region should be used for metabarcoding, including dietary analysis (e.g., COI for invertebrates) [4,5], multiple barcoding target regions have been proposed for other taxonomic groups, such as plants [1,3,6,7]
Summary
DNA metabarcoding is quickly becoming a powerful tool in ecology for understanding trophic interactions and non-invasively assessing the diets of wild animals, with the increasing availability of high-throughput sequencing technologies [1,2]. DNA barcoding marker genes must be chosen carefully to provide meaningful results [3]. The choice of marker depends on the biology of the study species, the questions being asked, the quality of the DNA sample, and completeness of reference databases [2]. Target regions must be variable enough to discriminate between closely related animal and plant species, yet flanking regions should be conserved enough to be less variable within a single species. Even though there is a consensus for some taxonomic groups as to which standardized DNA region should be used for metabarcoding, including dietary analysis (e.g., COI for invertebrates) [4,5], multiple barcoding target regions have been proposed for other taxonomic groups, such as plants [1,3,6,7]
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