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

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 sub-tropical forests and have focused on the use of a
single category of invertebrates, this study compares the use of flies-
and mosquito-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 12S rRNA (12S-V5) and 94 bp
mammal-specific 16S rRNA (16Smam) mitochondrial markers, and individual
bloodfed mosquitoes were sequenced using the 340 bp vertebrate-specific
12S rRNA fragment (Mam-12S-340). From the fly pools, we detected 10 mammal
species using 16Smam, while 12S-V5 detected four bird, two amphibian and
six mammal species. 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 and one
bird species. Focusing on mammal species, we did not find significant
differences in the proportion of 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.