Cloacal swabbing as a tool to study diet in migrating raptors using DNA metabarcoding

Abstract

While much research has gone into understanding the timing and patterns of migration, little has been done to understand the diet of raptors during migration. Most raptor dietary studies focus on the breeding season or winter, but migratory diet may be quite different due to differences in habitat type and prey availability along migration flyways. Here, we tested the efficacy of DNA metabarcoding to detect prey DNA on cloacal swabs. In 2019, we collected cloacal swabs from raptors during spring and fall migration in Duluth, MN. We analyzed 287 cloacal swabs from 11 species of raptors. We hypothesized that detection of dietary DNA on cloacal swabs would be influenced by the species of raptor swabbed, the size of the raptor, and migratory flight strategy (passive/soaring flight vs. active flight). Prey DNA was detected on 18.46% of cloacal swabs. Using a generalized linear model, we found that neither species, size, nor migratory flight strategy were better than the null model at explaining differences in detection of dietary DNA. To our knowledge, this is the first study to use cloacal swabbing and DNA metabarcoding to detect dietary DNA and our results indicate that this method has potential for further use.