Blow flies as urban wildlife sensors

Abstract

Wildlife detection in urban areas is very challenging. Conventional monitoring techniques such as direct observation are faced with the limitation that urban wildlife is extremely elusive. It was recently shown that invertebrate-derived DNA (iDNA) can be used to assess wildlife diversity in tropical rainforests. Flies, which are ubiquitous and very abundant in most cities, may also be used to detect wildlife in urban areas. In urban ecosystems, however, overwhelming quantities of domestic mammal DNA could completely mask the presence of wild mammal DNA. To test whether urban wild mammals can be detected using fly iDNA, we performed DNA metabarcoding of pools of flies captured in Berlin, Germany, using three combinations of blocking primers. Our results show that domestic animal sequences are, as expected, very dominant in urban environments. Nevertheless, wild mammal sequences can often be retrieved, although they usually only represent a minor fraction of the sequence reads. Fly iDNA metabarcoding is therefore a viable approach for quick scans of urban wildlife diversity. Interestingly, our study also shows that blocking primers can interact with each other in ways that affect the outcome of metabarcoding. We conclude that the use of complex combinations of blocking primers, although potentially powerful, should be carefully planned when designing experiments.

Female Blow Flies As Vertebrate Resource Indicators

“…Vertebrate DNA detected by flies approximated the mammal richness in the sampled regions. Using vertebrate-specific primers producing short (<250 bp) amplicons, we were able to detect the same number of wild animal species in our urban samples (S = 6, excluding four domestic animal species) as a recent study in Germany, though without the use of blocking primers or next generation sequencing 13 . Similarly, richness values, as well as vertebrate detection rates, from flies captured at the national parks were comparable to previous studies investigating carrion DNA from flies in pristine tropical habitats 11,14,15 .…”

“…If implemented for iDNA studies, passive traps should be checked frequently to avoid degradation of DNA and potential disturbance by other animals. In terms of preparation of flies, some studies pool samples prior to molecular diet analysis 13,15 . Though this method may be more cost-efficient when performing next generation sequencing to quickly asses biodiversity of an area, it has been shown that pooling can reduce the number of detectable vertebrate species in a sample 14 .…”

“…Recent studies suggest utilizing invertebrates, such as blow flies (Diptera: Calliphoridae), to indirectly monitor vertebrates 11–13 , with evidence that flies out-perform traditional survey methods in detecting animal richness 14,15 . Many blow fly species are necrophagous, requiring an animal carcass as a larval developmental substrate 16 .…”

Vertebrate diversity revealed by metabarcoding of bulk arthropod samples from tropical forests

“…Since the field of iDNA originated, targeted collection followed by iDNA analyses of gut contents has been carried out on different invertebrate taxa such as leeches (Drinkwater et al, 2019;Pérez-Flores, Rueda-Calderon, Kvist, Siddall, & Oceguera-Figueroa, 2016;Schnell et al, 2018;Weiskopf et al, 2018), sand flies (Kocher, De Thoisy, et al, 2017), blow and flesh flies Hoffmann et al, 2018;Lee, Gan, Clements, & Wilson, 2016;Lee, Sing, & Wilson, 2015;Rodgers et al, 2017;Schubert et al, 2015), mosquitoes (Kocher, De Thoisy, et al, 2017), ticks (Gariepy et al, 2012), marine copepods (Meekan et al, 2017), and shrimps (Siegenthaler et al, 2019). This has offered a new and promising tool to complement traditional vertebrate monitoring methods, something of great value in the ongoing biodiversity monitoring efforts (Bohmann et al, 2013).…”

Monitoring Mammal Community Shifts Across Silvicultural Treatments Utilizing Camera Traps and the Development of Invertebrate- Derived Dna in Hardwood Forests of North America

“…In the tropics, iDNA has been used to monitor mammal diversity (Lee et al 2015). For iDNA studies, invertebrates are mass captured, the targeted vertebrate DNA is isolated, and then it is sequenced (Hoffmann et al 2018). The sequenced DNA is matched with known sequences of a specific species from public databases, which provides evidence that the species is present within a site (Rodgers et al 2017).…”