Using DNA metabarcoding for simultaneous inference of common vampire bat diet and population structure.

Kristine Bohmann,Gareth Jones,Martin Nielsen,Luisa Dos Santos Bay Nielsen,Daniel G Streicker,Shyam Gopalakrishnan,M Thomas P Gilbert

doi:10.1111/1755-0998.12891

Abstract

Metabarcoding diet analysis has become a valuable tool in animal ecology; however, co‐amplified predator sequences are not generally used for anything other than to validate predator identity. Exemplified by the common vampire bat, we demonstrate the use of metabarcoding to infer predator population structure alongside diet assessments. Growing populations of common vampire bats impact human, livestock and wildlife health in Latin America through transmission of pathogens, such as lethal rabies viruses. Techniques to determine large‐scale variation in vampire bat diet and bat population structure would empower locality‐ and species‐specific projections of disease transmission risks. However, previously used methods are not cost‐effective and efficient for large‐scale applications. Using bloodmeal and faecal samples from common vampire bats from coastal, Andean and Amazonian regions of Peru, we showcase metabarcoding as a scalable tool to assess vampire bat population structure and feeding preferences. Dietary metabarcoding was highly effective, detecting vertebrate prey in 93.2% of the samples. Bats predominantly preyed on domestic animals, but fed on tapirs at one Amazonian site. In addition, we identified arthropods in 9.3% of samples, likely reflecting consumption of ectoparasites. Using the same data, we document mitochondrial geographic population structure in the common vampire bat in Peru. Such simultaneous inference of vampire bat diet and population structure can enable new insights into the interplay between vampire bat ecology and disease transmission risks. Importantly, the methodology can be incorporated into metabarcoding diet studies of other animals to couple information on diet and population structure.

Highlights

Vampire bats occur in Central and South America and are exceptional among mammals in that they subsist exclusively on blood (Greenhall, Joermann, & Schmidt, 1983; Greenhall, Schmidt, & Joermann, 1984; Greenhall & Schutt, 1996)
Bloodmeal and faecal samples were collected from common vampire bats (Desmodus rotundus) caught between 2009 and 2013 at 15 sites across three ecoregions in Peru; Andes, Amazon and Pacific coast (Figure 1a; Table S1a)
Our results show clear phylogeographic structure of the mitochondrial COI and 16s markers in the common vampire bat in Peru: the 16s and COI haplotype 2 were restricted to the coastal sites, while at the nine southern collection sites in the Andes and Amazon, the 16s and COI haplotype 1 co-occurred in all bats (Figure 4)

Summary

Introduction

Vampire bats occur in Central and South America and are exceptional among mammals in that they subsist exclusively on blood (Greenhall, Joermann, & Schmidt, 1983; Greenhall, Schmidt, & Joermann, 1984; Greenhall & Schutt, 1996). Other studies using DNA markers have been more specific, but failed to identify prey in large proportions of samples and used time-consuming approaches that do not scale to large data sets (Bobrowiec, Lemes, & Gribel, 2015; Carter, Coen, Stenzler, & Lovette, 2006; Ito, Bernard, & Torres, 2016). This illustrates that while genetic approaches offer an attractive solution to reconstruct vampire bat diets with high specificity, existing methods have not yet reached a technical level that would make them costeffective and efficient for large-scale applications

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Conclusion