Use of carrion fly iDNA metabarcoding to monitor invasive and native mammals

Abstract

Severely fragmented habitats increase the risk of extirpation of native mammal populations through isolation, increased edge effects, and predation. Therefore, monitoring the movement of mammal populations through anthropogenically altered landscapes can inform conservation. We used metabarcoding of invertebrate‐derived DNA (iDNA) from carrion flies (Calliphoridae and Sarcophagidae) to track mammal populations in the wheat belt of southwestern Australia, where widespread clearing for agriculture has removed most of the native perennial vegetation and replaced it with an agricultural system. We investigated whether the localization of the iDNA signal reflected the predicted distribution of 4 native species—echidna (Tachyglossus aculeatus), numbat (Myrmecobius fasciatus), woylie (Bettongia penicillata), and chuditch (Dasyurus geoffroii)—and 2 non‐native, invasive mammal species—fox (Vulpes vulpes) and feral cat (Felis catus). We collected bulk iDNA samples (n = 150 samples from 3428 carrion flies) at 3 time points from 3 conservation reserves and 35 road edges between them. We detected 14 of the 40 mammal species known from the region, including our target species. Most detections of target taxa were in conservation reserves. There were a few detections from road edges. We detected foxes and feral cats throughout the study area, including all conservation reserves. There was a significant difference between the diversity (F3, 98 = 5.91, p < 0.001) and composition (F3, 43 = 1.72, p < 0.01) of taxa detections on road edges and conservation reserves. Conservation reserves hosted more native biodiversity than road edges. Our results suggest that the signals from iDNA reflect the known distribution of target mammals in this region. The development of iDNA methods shows promise for future noninvasive monitoring of mammals. With further development, iDNA metabarcoding could inform decision‐making related to conservation of endangered taxa, invasive species management, and impacts of habitat fragmentation.

Analysing the effects of distance, taxon and biomass on vertebrate detections using bulk-collected carrion fly iDNA

“…The iDNA is increasingly used to assess vertebrate species diversity [19,[29][30][31]55]; therefore, it is vital to examine the factors that influence the detection of species using this technique. Here, we used the same bulk-collection method as in Fernandes et al [30] to collect and process flies, with two metabarcoding assays to detect vertebrate taxa from carrion flies collected from within the Perth Zoo and two transects extending away from the zoo.…”

“…The iDNA is increasingly used to assess vertebrate species diversity [19,[29][30][31]55]; therefore, it is vital to examine the factors that influence the detection of species using this technique. Here, we used the same bulk-collection method as in Fernandes et al [30] to collect and process flies, with two metabarcoding assays to detect vertebrate taxa from carrion flies collected from within the Perth Zoo and two transects extending away from the zoo. Despite the presumed mobility of carrion flies, we found that the signals from iDNA detections of zoo animals were predominantly geographically localized to the zoo, with much fewer sequences from zoo animals detected outside the zoo.…”

“…Furthermore, carrion flies are widespread in many different environments and are easy to sample [ 28 ]. Studies using carrion flies for vertebrate detection have so far been undertaken on mammal communities in Africa [ 15 , 29 ], Australia [ 30 ], South America [ 31 ] and Asia [ 25 , 32 ] and vertebrate communities in urbanized areas in Europe [ 33 ] and North America [ 34 ].…”

“…Firstly, carrion flies are very mobile, with some species of calliphorid flies documented dispersing up to 63.5 km from a source [ 35 ]. However, a recent study suggests that mammalian iDNA signals are localized around sources of mammalian biodiversity [ 30 ]. Furthermore, carrion flies are opportunistic feeders, and, unlike haematophagous invertebrates or mosquitoes, have yet to be shown to have species preference [ 15 , 19 ].…”

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).…”