Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (Sus scrofa)

Abstract

Wild pigs (Sus scrofa) are an invasive species descended from both domestic swine and Eurasian wild boar that was introduced to North America during the early 1500s. Wild pigs have since become the most abundant free‐ranging exotic ungulate in the United States. Large and ever‐increasing populations of wild pigs negatively impact agriculture, sport hunting, and native ecosystems with costs estimated to exceed $1.5 billion/year within the United States. Wild pigs are recognized as generalist feeders, able to exploit a broad array of locally available food resources, yet their feeding behaviors remain poorly understood as partially digested material is often unidentifiable through traditional stomach content analyses. To overcome the limitation of stomach content analyses, we developed a DNA sequencing‐based protocol to describe the plant and animal diet composition of wild pigs. Additionally, we developed and evaluated blocking primers to reduce the amplification and sequencing of host DNA, thus providing greater returns of sequences from diet items. We demonstrate that the use of blocking primers produces significantly more sequencing reads per sample from diet items, which increases the robustness of ascertaining animal diet composition with molecular tools. Further, we show that the overall plant and animal diet composition is significantly different between the three areas sampled, demonstrating this approach is suitable for describing differences in diet composition among the locations.

Advancing the integration of multi‐marker metabarcoding data in dietary analysis of trophic generalists

“…Second, our study confirmed the value of using multiple markers, but suggests that previous studies based on a mix of nonoverlapping specific markers each targeting a particular dietary component (e.g., Coghlan et al, ; Groom et al, ; Robeson et al, ; Sullins et al, ) may not be sufficient to overcome marker biases and thus provide a reliable diet composition. This is because markers considered universal for a given taxonomic clade may still have considerable variations in affinity across taxa within that clade, and thus may not amplify some important items in the diet (Aizpurua et al, ; Alberdi et al, , ; Bowser et al, ; Clarke et al, ; Kaunisto et al, ; Piñol et al, ).…”

Using DNA Metabarcoding to Examine Wild Pig (Sus scrofa) Diets in a Subtropical Agro-Ecosystem

“…Animals are frequently consumed but at a lower total volume compared to plants (Ballari and Barrios-García 2014). A wide variety of invertebrates and vertebrates have been documented as diet items (Henry and Conley 1972, Wood and Roark 1980, Ditchkoff and Mayer 2009, Wilcox and Van Vuren 2009, Robeson et al 2018. Wild pigs are also important scavengers and are known to exhibit coprophagy (DeVault et al 2003, Selva et al 2003, Copado et al 2004.…”

DNA metabarcoding in diet studies: Unveiling ecological aspects in aquatic and terrestrial ecosystems

“…For terrestrial species, most of these studies focused on the impacts of urbanized areas (Bohmann et al, ; Coghlan et al, ; Cravens et al, ; Forin‐Wiart et al, ; Groom et al, ; Khanam, Howitt, Mushtaq, & Russell, ; Lim, Ramli, Bhassu, & Wilson, ; Quéméré et al, ; Smith, Thomas, Levi, Wang, & Wilmers, ; Sullins et al, ) and landscape changes due to agriculture (e.g., Branco et al, ; Clare et al, , ; Sugimoto et al, ) in trophic interactions. Importantly, the results obtained so far provide substantial knowledge toward effective conservation planning and management, by identifying the impacts of introduced species, both revealing competition with native fauna (Brown et al, ; Egeter, Bishop, & Robertson, ; Robeson II et al, ; Zarzoso‐Lacoste et al, ) and uncovering the importance of introduced plant species to the diet of endangered species (Ando et al, ). There have also been some studies focusing on the diets of reintroduced or recovering populations (Kowalczyk et al, ; Pansu et al, ; Pinho et al, ) and on the effects of hunting in niche partitioning between both herbivores (Pansu et al, ) and carnivores (Smith et al, ).…”