New insights on diet variability revealed by DNA barcoding and high‐throughput pyrosequencing: chamois diet in autumn as a case study

Abstract

Characterizing the diet of large herbivores and the determinants of its variation remains a difficult task in wild species. DNA-based techniques have the potential to complement traditional time-consuming methods based on the microhistology of plant cuticle fragments in fecal or rumen samples. Recently, it has been shown that a short chloroplast DNA fragment, the P6 loop of the trnL (UAA) intron, can act as a minimalist barcode. Here, we used the trnL approach with high-throughput pyrosequencing to study diet from feces in a wild herbivore, the alpine chamois (Rupicapra rupicapra) and showed that the fine resolution in plant determination obtained with this method allows exploring subtle temporal shifts and inter-individual variability in diet composition. First, we built a DNA barcoding database of 475 plants species. Seventy-two percent of plant species can be unambiguously identified to species level, 79% to genus level and 100% to family level using the P6 loop. Second, we analysed 74 feces collected from October to November. Based on 47,896 P6 loop sequences, we identified a total of 110 taxa, 96 in October and 76 in November, with a clear diet shift between October and November. We recognized four and two clusters of feces composition in October and November, respectively, revealing different diet categories among individuals within each month. DNA-based diet analysis is faster and more taxonomically precise than studies based on microhistology, and opens new possibilities for analysing plant-herbivore interactions in the wild.

DNA metabarcoding diet analysis for species with parapatric vs sympatric distribution: a case study on subterranean rodents

“…The detection of DNA sequences of different food items and the sequence read counts observed can be subject to a number of methodological and biological bias (Deagle et al, 2013;Thomas et al, 2014). For example, biased amplification can occur when the primers match better sequences in certain species over others (Shehzad et al, 2012b), or because of preferential amplification of shorter sequences (Rayé et al, 2011). Biological factors, such as variation in the proportion of mitochondrial and chloroplast organelles among tissues and differential digestibility of foods, may also influence DNA quantity in the scats and therefore its detectability for diet analysis (Pegard et al, 2009;Deagle et al, 2010;Thomas et al, 2014).…”

Upscaling the niche variation hypothesis from the intra- to the inter-specific level

“…We considered each feces as an approximation of an individual's diet over several days (Castle 1956;Rayé et al 2011), although an individual diet is likely to be more diversified than the diet assessed from one of its feces. However, we assumed here that the possible underestimation of the individual diet's diversity was similar for all herbivore species.…”

“…The dietary composition of feces was investigated using DNA metabarcoding (Taberlet et al 2007). DNA sequences were obtained and analyzed following Rayé et al (2011). For each feces, the number of sequences was turned into proportions in order to confer the same weight to each feces (Willerslev et al 2014), and plants whose proportion was under 2.5 % were removed.…”

“…Large herbivores in general feed on a large number of plant items, but until recently, it remained difficult to assess the variety of plant species consumed in the wild (Rayé et al 2011). We therefore resorted to recently developed DNA metabarcoding methods (Pompanon et al 2012), which open new avenues to determine diet from easily collected materials (Rayé et al 2011) and estimate niche width for herbivores (Yoccoz 2012).…”

“…Large herbivores in general feed on a large number of plant items, but until recently, it remained difficult to assess the variety of plant species consumed in the wild (Rayé et al 2011). We therefore resorted to recently developed DNA metabarcoding methods (Pompanon et al 2012), which open new avenues to determine diet from easily collected materials (Rayé et al 2011) and estimate niche width for herbivores (Yoccoz 2012). The strong differences in sociality between the three herbivore species studied here allowed us to test whether the SH (at the inter-specific level) was supported, while the high seasonality observed in mountain environment, which is expected to lead to variation in niche breadth, allowed us to test whether NVH was supported at the intra-specific level.…”