Diet Assessment Based on Rumen Contents: A Comparison between DNA Metabarcoding and Macroscopy

Area of Science:

• Ecology and evolutionary biology
• Wildlife biology
• Molecular ecology

Background:

• Accurate dietary analysis is crucial for understanding ecology and evolution, but traditional methods are time-consuming and have limitations.
• DNA metabarcoding is a faster, cheaper alternative for diet analysis, but its accuracy compared to classic methods needs empirical validation.
• Wild ungulate dietary studies often rely on macroscopic identification of rumen contents, which can be labor-intensive and less precise.

Purpose of the Study:

• To empirically compare the accuracy and effectiveness of DNA metabarcoding against macroscopic identification for analyzing the diet of wild ungulates.
• To evaluate the performance of DNA metabarcoding in terms of taxa identification, taxonomic precision, and niche overlap analysis.
• To assess the potential of DNA metabarcoding for quantitative diet composition analysis in wildlife.

Main Methods:

• Comparison of DNA metabarcoding and macroscopic identification techniques using rumen contents from roe deer and fallow deer.
• Analysis of identified taxa, taxonomic precision (genus/species level identification), and niche overlap using both methods.
• Correlation analysis between macroscopic quantity and DNA sequence counts to evaluate quantitative accuracy.

Main Results:

• Both DNA metabarcoding and macroscopic methods yielded comparable results, with some discrepancies in item identification between techniques.
• DNA metabarcoding identified a higher total number of taxa and demonstrated substantially higher taxonomic precision (90% to genus/species level) than macroscopy (75%).
• Niche overlap analyses showed similar conclusions with presence/absence data, but DNA metabarcoding tended to show higher overlap with sequence count data compared to macroscopic weight.

Conclusions:

• DNA metabarcoding provides a valuable, cost-efficient alternative for quantitatively assessing ungulate diet composition, offering enhanced taxonomic precision and sensitivity.
• The significant correlation between macroscopic quantity and DNA sequence counts supports the use of metabarcoding for quantifying plant matter in diets.
• Integrating DNA metabarcoding into wildlife dietary studies can significantly improve the understanding of ecological and evolutionary processes driven by food choices.