DNA metabarcoding reveals the influence of crops on the diet of a large group-living Neotropical ungulate

Abstract

The expansion of agricultural lands is a major driver of habitat loss, impacting biodiversity and contributing to human-wildlife conflicts, notably through crop-raiding by species like the threatened white-lipped peccary (Tayassu pecari). This study aimed to assess the plant diet of white-lipped peccaries in the Emas National Park (ENP) and its surrounding areas in the Brazilian Cerrado using DNA metabarcoding of fecal samples to uncover the diversity of native plants consumed and the incorporation of cultivated ones. We analyzed 35 fecal samples from three areas in ENP (east, south, and within). Using the trnL and rbcL markers for DNA metabarcoding, we identified 37 species-level and 86 genus-level Operational Taxonomic Units (OTUs), revealing a diet comprising native, exotic, and cultivated plants. Poaceae, Fabaceae, and Annonaceae were the predominant families regarding read proportion, and Poaceae, Fabaceae, and Euphorbiaceae regarding the number of OTUs. Alpha diversity of plants indicated significant spatial variation in diet composition, with the southern area showing the lowest diversity, while the within and eastern areas showed similarly higher values. Beta diversity also revealed a dissimilarity in OTUs composition among the three sampling areas. Our findings highlight the peccaries’ preference for native vegetation, such as Fusaea longifolia, and their reliance on crop species like Zea mays (flour corn) and Glycine max (soybean), particularly in areas with limited natural resources. This study underscores the value of DNA metabarcoding in providing detailed dietary insights and facilitating the identification of native species for habitat restoration. Conservation strategies should focus on promoting the regeneration of native vegetation to reduce crop-raiding and conflicts with farmers. These efforts are crucial for maintaining ecosystem balance and supporting the conservation of the white-lipped peccary and the associated species in the region.