trnL outperforms rbcL as a DNA metabarcoding marker when compared with the observed plant component of the diet of wild white-faced capuchins (Cebus capucinus, Primates)

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.

Advances and prospects of environmental DNA in neotropical rainforests

“…By contrast, only few diet studies have been performed on neotropical organisms, i.e. on tapirs from French Guiana (Hibert et al 2013), on white-face capuchins from Costa Rica (Mallott et al 2018), on neotropical vampire bats (Bohmann et al 2018) and rodents (Lopes et al 2015), and on particular arthropods (Paula et al 2016;Kocher, de Thoisy, François Catzeflis, et al 2017;Rodgers et al 2017). New protocols of diet assessment based on faeces or gut contents are now available and optimized to reduce host DNA concentration in DNA extracts (e.g.…”

Methodological trends and perspectives of animal dietary studies by noninvasive fecal DNA metabarcoding

“…This may be due to the suitability of the P6 loop region for fecal metabarcoding because of its high conservativeness of primer sequences, short fragment size and moderate variation. The P6 loop has been documented as performing better in terms of plant detection and quantification through fecal metabarcoding than the standard region used in plant DNA barcoding: rbc L (Mallott, Garber, Malhi, & Doi, 2018). However, species‐level identification using only the P6 loop is often difficult because some related plant species share the same sequences (Ando et al., 2013; Rayé et al., 2011).…”

“…Some studies have indicated a positive correlation between RRA and the mass percentage of tissue mixture (Thomas, Deagle, Paige Eveson, Harsch, & Trites, 2015) or consumed plants (Willerslev et al., 2014) and observed percentages of feeding behavior (Mallott et al., 2018). Deagle et al.…”

“…Some studies have indicated a positive correlation between RRA and the mass percentage of tissue mixture (Thomas, Deagle, Paige Eveson, Harsch, & Trites, 2015) or consumed plants (Willerslev et al, 2014) and observed percentages of feeding behavior (Mallott et al, 2018). Deagle et al (2018) conducted a simulation to show that RRA can be more accurate than FOO in the quantification of diet even with moderate recovery biases.…”

Diet composition of reintroduced Red-and-Green Macaws (Ara chloropterus) reflects gradual adaption to life in the wild

“…Observational data can be subject to observer bias or inability to record feeding signs correctly (Shrestha andWegge 2006, Matthews et al 2020). Macroscopic fecal inspection is limited by the fact that mastication and digestion by the consumer can render dietary elements unidentifiable (Tutin andFernandez 1993, Hayward 2013) while DNA-based studies are susceptible to inadequate reference databases and amplification biases (Piñol et al 2015, Mallott et al 2018, McClenaghan et al 2019, Scasta et al 2019). In the present study, we corroborate that single techniques are more limited than a combined approach in which the observation and metabarcoding of feces complement each other.…”