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

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.

Demographic and environmental drivers of metagenomic viral diversity in vampire bats

“…In Peru, increasing longitude corresponds to a northwest-southeast gradient, such that sites in the northwest (Cajamarca and Amazonas Departments) had the highest saliva viral diversity. While these sites do not correspond to a single ecoregion, our previous work has highlighted northwest Peru as a corridor for gene flow of vampire bats and rabies virus between the Coast and Andes/Amazon and as a hotspot of mitochondrial haplotype richness (Bohmann et al, 2018). We therefore hypothesize that unusually high mixing of bats from different ecoregions creates a melting pot for saliva viruses.…”

“…Livestock densities around each site were downloaded from the FAO GLiPHA database for the predominant prey of vampire bats in Peru including cows, pigs, sheep and goats (Bohmann et al, 2018;Food & Agriculture Organization of the United Nations, 2012). The densities for each species were combined and extracted within a 10-km buffer of each site, as movements between sites have been reported over lesser distances (Trajano, 1996), using the packages maptools (Bivand & Lewin-Koh, 2017), rgDal (Bivand et al, 2017) and raster.…”

An appetite for pests: Synanthropic insectivorous bats exploit cotton pest irruptions and consume various deleterious arthropods

“…Furthermore, all negative extraction controls were screened for contamination. Quantitative PCR screenings followed Alberdi et al (2018), Bohmann et al (2018), and Murray, Coghlan, and Bunce (2015). All qPCR settings and reagent concentrations are provided in Supporting Information 2: Table S2.…”

DNA metabarcoding in diet studies: Unveiling ecological aspects in aquatic and terrestrial ecosystems

“…However, generally, these studies are mostly descriptive, and only about one third (47 out 150) addressed impacts of human‐mediated changes in diets (37% of the studies on terrestrial organisms and 22% of the studies on aquatic taxa, see Table S1). For terrestrial species, most of these studies focused on the impacts of urbanized areas (Bohmann et al, ; Coghlan et al, ; Cravens et al, ; Forin‐Wiart et al, ; Groom et al, ; Khanam, Howitt, Mushtaq, & Russell, ; Lim, Ramli, Bhassu, & Wilson, ; Quéméré et al, ; Smith, Thomas, Levi, Wang, & Wilmers, ; Sullins et al, ) and landscape changes due to agriculture (e.g., Branco et al, ; Clare et al, , ; Sugimoto et al, ) in trophic interactions. Importantly, the results obtained so far provide substantial knowledge toward effective conservation planning and management, by identifying the impacts of introduced species, both revealing competition with native fauna (Brown et al, ; Egeter, Bishop, & Robertson, ; Robeson II et al, ; Zarzoso‐Lacoste et al, ) and uncovering the importance of introduced plant species to the diet of endangered species (Ando et al, ).…”

“…Favoring their place as good biological models in the assessment of vertebrates' diets, bat species have distinct feeding and foraging habits, and different ecologic requirements and are widely distributed across a variety of terrestrial ecosystems, even in human-altered habitats (Kemp et al, 2019;Long, Kurta, & Clemans, 2013). Moreover, the possibility to concomitantly explore both the diet of a species and its population structure was recently explored using the common vampire bat Desmodus rotundus as focal species (Bohmann et al, 2018). Thus, bats might be highlighted as model species for the investigation of the diet of vertebrates in terrestrial ecosystems.…”