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

Ecology and Evolution

Noah Fierer¹  Kamil Khanipov²  George Golovko²  Yuriy Fofanov²  Samantha M. Wisely³  Michael S. Robeson II⁴  Michael D. White⁵  Michael Bodenchuck⁶  Timothy J. Smyser⁷  Antoinette J. Piaggio⁷ 

[1] Department of Ecology and Evolutionary Biology Cooperative Institute for Research in Environmental Sciences University of Colorado Boulder CO USA;Department of Pharmacology The University of Texas Medical Branch Galveston TX USA;Department of Wildlife Ecology and Conservation USA5 USDA, Wildlife Services University of Florida Gainesville FL USA;Fish and Wildlife Conservation Biology Colorado State University Fort Collins CO USA;Tejon Ranch Conservancy Frazier Park CA USA;USDA, APHIS, Wildlife Services San Antonio TX USA;USDA, Wildlife Services National Wildlife Research Center Wildlife Genetics Lab Fort Collins CO USA;

关键词: blocking primer;    CO1;    diet;    feral swine;    metabarcoding;    trnL;   

DOI  :  10.1002/ece3.3638

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown