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

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...

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Bibliographic Details
Published in:	Ecology and evolution Vol. 8; no. 1; pp. 185 - 196
Main Authors:	Robeson, Michael S., Khanipov, Kamil, Golovko, George, Wisely, Samantha M., White, Michael D., Bodenchuck, Michael, Smyser, Timothy J., Fofanov, Yuriy, Fierer, Noah, Piaggio, Antoinette J.
Format:	Journal Article
Language:	English
Published:	England John Wiley & Sons, Inc 01-01-2018 John Wiley and Sons Inc Wiley
Subjects:	Agricultural economics Agricultural ecosystems blocking primer CO1 Deoxyribonucleic acid Diet DNA DNA sequencing Feeders Feeding behavior feral swine Food availability Food resources Hogs Hunting Introduced species Invasive species metabarcoding Nucleotide sequence Original Research Primers Stomach Suidae Sus scrofa Swine trnL blocking primer metabarcoding trnL diet CO1 feral swine
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Summary:	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. We developed a DNA sequencing‐based protocol to describe the plant and animal diet composition of wild pigs from three eco‐regions within the United States: California, Texas, and Florida. We show that the overall plant and animal diet composition is significantly different between these eco‐regions. By applying the protocol, we describe here, assessing the diet composition of wild pigs through DNA analysis will increase management efficacy by allowing control efforts to be focused in landscapes supporting seasonally preferred diet items.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	2045-7758 2045-7758
DOI:	10.1002/ece3.3638