Focal vs. fecal: Seasonal variation in the diet of wild vervet monkeys from observational and DNA metabarcoding data

Abstract

Assessing the diet of wild animals reveals valuable information about their ecology and trophic relationships that may help elucidate dynamic interactions in ecosystems and forecast responses to environmental changes. Advances in molecular biology provide valuable research tools in this field. However, comparative empirical research is still required to highlight strengths and potential biases of different approaches. Therefore, this study compares environmental DNA and observational methods for the same study population and sampling duration. We employed DNA metabarcoding assays targeting plant and arthropod diet items in 823 fecal samples collected over 12 months in a wild population of an omnivorous primate, the vervet monkey ( Chlorocebus pygerythrus ). DNA metabarcoding data were subsequently compared to direct observations. We observed the same seasonal patterns of plant consumption with both methods; however, DNA metabarcoding showed considerably greater taxonomic coverage and resolution compared to observations, mostly due to the construction of a local plant DNA database. We found a strong effect of season on variation in plant consumption largely shaped by the dry and wet seasons. The seasonal effect on arthropod consumption was weaker, but feeding on arthropods was more frequent in spring and summer, showing overall that vervets adapt their diet according to available resources. The DNA metabarcoding assay outperformed also direct observations of arthropod consumption in both taxonomic coverage and resolution. Combining traditional techniques and DNA metabarcoding data can therefore not only provide enhanced assessments of complex diets and trophic interactions to the benefit of wildlife conservationists and managers but also opens new perspectives for behavioral ecologists studying whether diet variation in social species is induced by environmental differences or might reflect selective foraging behaviors.

Molecular assessment of dietary variation in neighbouring primate groups

“…Behavioural diversity can be a product of both ecological factors and of cultural traits and it is very difficult to distinguish the effect of even small‐scale variation (Brakes et al, 2021; Samuni et al, 2020). We have shown previously that there are strong seasonal patterns in the diet of our population, thus being strongly correlated with resource availability (Brun, Schneider, Mas Carrió, Dongre, van de Waal, et al, 2022). Therefore, to assess IGV, we focused here on one season to reduce environmental variation, selecting summer when food resources are more abundant as it increases individuals' opportunities to select food according to their preferences.…”

“…DNA extraction of scat samples was performed using a phosphate buffer‐based approach (Taberlet et al, 2018) following a modified protocol of the NucleoSpin Soil Kit (Macherey‐Nagel, Düren, Germany), as described in (Brun, Schneider, Mas Carrió, Dongre, van de Waal, et al, 2022). Extractions were performed in a pre‐PCR laboratory exclusively dedicated to low DNA‐content analyses (Laboratory for Conservation Biology, University of Lausanne, Switzerland).…”

“…Bioinformatic processing of raw sequences was conducted with the OBITools package (Boyer et al, 2016) and in R (version 4.0.2). All details of experimental conditions and sequence alignment, filtering, clustering, data cleaning based on controls and taxonomic assignments are described in (Brun, Schneider, Mas Carrió, Dongre, van de Waal, et al, 2022).…”

“…We have shown previously a strong seasonal effect on vervet monkeys' diet analysing 823 faecal samples collected over a year, and a strong correlation between plant RRA and observational data, validating the use of RRA as a semi‐quantitative measure of consumption in this system. The results indicate that selective feeding behaviours are more likely to occur in summer when resources are more abundant than in scarcer seasons (Brun, Schneider, Mas Carrió, Dongre, van de Waal, et al, 2022). The current study therefore focuses on assessing IGV between four neighbouring groups of vervets during the summer season.…”

“…Depending on the studied organism and field conditions, observations on broad temporal and spatial scales are complicated. Recently, the use of DNA metabarcoding in the field of primatology has enabled new insights, in particular regarding the consumption of arthropods (Lyke et al, 2018; Mallott et al, 2015, 2017; Rowe et al, 2021) but also plants (Brun, Schneider, Mas Carrió, Dongre, van de Waal, et al, 2022; Mallott et al, 2018; Quéméré et al, 2013). The sampling procedure of eDNA promises new opportunities to investigate behavioural plasticity through the study of foraging behaviour of species that are challenging to observe but for which faecal samples can be obtained.…”