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

Abstract

Severely fragmented habitats increase the risks towards native mammal populations through isolation, increased edge effects, and predation. Therefore, monitoring the movement of mammal populations through anthropogenically-altered landscapes can be a valuable tool for conservation. Here we use metabarcoding of invertebrate-derived DNA (iDNA) from carrion flies (Calliphoridae and Sarcophagidae) to track mammal populations in the Wheatbelt Region of southwestern Australia, where widespread clearing for agriculture has removed most of the native perennial vegetation and replaced it with an agricultural system. Using this technique, we investigated whether the localization of the iDNA signal reflected the predicted distribution of four native species - echidna (Tachyglossus aculeatus), numbat (Myrmecobius fasciatus), woylie (Bettongia penicillata), and chuditch (Dasyurus geoffroii) - and two non-native, invasive mammal species - fox (Vulpes vulpes) and feral cat (Felis catus). We collected bulk iDNA samples (n = 150 samples, totalling 3,428 carrion flies) at a single time point from three conservation reserves and road edges between them. We detected 14 of the 40 mammal species known from the region, including our target species. Detections of target native taxa were centered on conservation reserves, with some detections from road edges nearby. We detected foxes and feral cats throughout the study area, including all conservation reserves. There was a significant difference between the diversity (F(3, 98) = 5.91, p<0.001) and composition (F(3, 43) = 1.72, p<0.01) of taxa on road edges and conservation reserves: conservation reserves hosted more native biodiversity than did road edges. Our data 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 non-invasive monitoring for mammals. With further development, iDNA metabarcoding could assist in decision-making surrounding the conservation of endangered taxa, invasive species management and impacts of habitat fragmentation. Article Impact Statement: Carrion fly iDNA metabarcoding can be used to monitor mammalian distribution at a fine scale. This article is protected by copyright. All rights reserved.