DNA metabarcoding dietary analyses of the wood mouse Apodemus speciosus on Innoshima Island, Japan, and implications for primer choice

Abstract

We used DNA metabarcoding to assess the seasonal diets of the large Japanese wood mouse, Apodemus speciosus (Muridae, Rodentia), in forest edges adjacent to citrus orchards on Innoshima Island, Japan. We used one chloroplast and three mitochondrial DNA barcoding markers to determine mouse diets. Among the various plant and invertebrate diets, A. speciosus typically consumed Chinese cork oak (Quercus variabilis) in early spring (likely acorns preserved during winter) and gypsy moths (Lymantria dispar, a forest pest) in late spring and summer. In addition, we found that A. speciosus also preyed on orchard pests, including the gutta stink bug and other potentially harmful invertebrates. The season during which A. speciosus preyed on stink bugs corresponded with the harvest of orchard products. This study revealed several of the ecological roles of A. speciosus within the boundary zone between forest and human ecosystems. Furthermore, based on the performance of various mitochondrial markers in dietary profiling of invertebrate food items, we recommend the multi-locus DNA metabarcoding method to comprehensively assess the diet of A. speciosus.