Comparison of mosquito and fly derived DNA as a tool for sampling vertebrate biodiversity in suburban forests in Berlin, Germany

Abstract

The use of invertebrate-derived DNA (iDNA) is a promising non-invasive tool to monitor wildlife. While most studies have been carried out in dense tropical and subtropical forests and have focused on the use of a single category of invertebrates, this study compares the use of flies and mosquitoes-derived DNA to assess vertebrate diversity in semi-urban environments. We conducted our sampling in four different forest plots in Berlin, Germany. Pools of flies and non-bloodfed mosquitoes were metabarcoded using 108-bp vertebrate-specific 12 S rRNA (12 S-V5) and 94-bp mammal-specific 16 S rRNA (16Smam) mitochondrial markers, and individual bloodfed mosquitoes were sequenced using the 340-bp vertebrate-specific 12 S rRNA fragment (Mam-12 S-340). Most sequencing was only successful for mammal species.From the fly pools, we detected 10 mammal species using 16Smam, and six species using 12 S-V5. From the non-bloodfed mosquito pools, we only amplified putative contaminant DNA, indicating that mosquito females without visual signs of a blood meal carry no traces of vertebrate DNA. Finally, in the bloodfed mosquitoes, we identified four mammal species. We did not find significant differences in the proportion of mammal species detected regarding the total available number of species between sampling localities. Fly samples were easier to obtain and more abundant over the sampled localities compared to mosquito samples. We conclude that, while there are a few advantages in using mosquito blood meals, the use of flies in the detection of wildlife in a suburban environment is more effective in terms of collection of samples and detection of vertebrates, although this technique is limited to few mammal species in the urban environment.

Comparing iDNA from mosquitoes and flies to survey mammals in a semi‐controlled Neotropical area

“…In our study, approximately 50% (42% from mosquitoes and 58% from flies) of the retained sequences, considering both genes, were from human, likely due to the daily presence of the PESC staff, despite the zoo closure to the public. The higher human detection by flies than mosquitoes could be explained by the presence of human leftovers that are visited by the flies within the PESC and in the urban areas surrounding it, promoting a higher detection of human in the fly iDNA (Danabalan et al, 2023). Although the use of blocking primers is often adopted to minimize this problem (Calvignac‐Spencer et al, 2013; Rodgers et al, 2017), we opted to deal with human contamination only in bioinformatic steps.…”

Using eDNA for mammal inventories still needs naturalist expertise, a meta‐analysis

“…Finally, a third group of DNA originates from invertebrates—iDNA—that are ectoparasites of the targeted taxa and blood/fecal meals are used as DNA sources (Calvignac‐Spencer et al., 2013). Among them are leeches (Hanya et al., 2019; Schnell et al., 2012), flies (Fernandes et al., 2023; Schubert et al., 2015), mosquitoes (Danabalan et al., 2023; Massey et al., 2022), and dung beetles (Drinkwater et al., 2021).…”

Corrigendum

“…In Environmental DNA 5:3, for the article by Danabalan, L. R., et al (2023) entitled “Comparison of mosquito and fly derived DNA as a tool for sampling vertebrate biodiversity in suburban forests in Berlin, Germany” (pages 476–487), the authors would like to update the Acknowledgments section as follows:…”