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

Abstract

The wild pig is well known for its generalist diet, a contributing factor to its successful invasion around the globe. We used DNA metabarcoding analyses of scat to examine wild pig diet on a cow-calf operation in south-central Florida. This 4,249-ha ranch is comprised of improved pastures and semi-native pastures that contain a mosaic of vegetation types. Both pasture types contain numerous wetlands and ditches as well as oak-palm woodlands. Fecal sampling was conducted along transects from March 2016 to February 2017. The study site was divided into five sampling areas to ensure dispersed sampling across the ranch. At least five freshly deposited scats were collected every two months from each sampling area and frozen. Regions of multiple genes that targeted either animal or plant DNA (CO1, trnL, and 12S rRNA marker genes) were selected for high throughput sequencing. Sequences were identified using the GenBank reference database. Two hundred nineteen fecal samples were collected and 196 were analyzed. Consensus lineages were retained if they could be confidently identified to family and were likely intentionally consumed by a pig. Between the three marker genes, 66 plant, 68 animal, and 12 fungal families were identified. Plant species dominated the diet with oak, torpedograss, joyweed, Bahiagrass, dayflower, and other grasses occurring in over half the samples analyzed. Animals were present across a wide taxonomic breadth, but encountered less frequently than plants with the exception of an exotic earthworm. Cattle, house mouse, cotton mouse, raccoon, mole cricket, Virginia opossum, and six species of fly were recorded from over 10% of fecal samples. This represents the first study to employ DNA metabarcoding to examine the dietary composition of this invasive vertebrate across an entire year.