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Carrion flies’ suppers reveal secrets of forest biodiversity

January 15, 2013Kate0 Comments

Picture the scene: you’re standing deep in a rainforest, gazing around you at the lush green scenery. In the depths of this tangled mass of tree trunks live a multitude of mammal species – from fruit-feasting bats, to dainty duikers. -  Your task is to find out exactly which species are found here.

Traditional methods have had biologists traipsing through the dense forest searching for footprints, droppings, burrows and other traces – great for adventure, but not quite so efficient and cost-effective. Many of the animals are shy and elusive creatures, and the area far-reaching and difficult to navigate. Camera traps are a more recent and less labour-intensive method, but can fail to capture animals below a certain size.

So why not employ an army of winged minions to gather the information for you?

A recent paper, published in the journal Molecular Ecology, by Calvignac-Spencer et al. (2013) explores a new technique in estimating biodiversity – by capturing carrion flies and analysing the DNA present in their stomachs from their last supper, we can gain an invaluable snapshot of the different kinds of animals present in the surrounding area.

Carrion flies (those of the blow, and flesh fly families of Calliphoridae and Sacophagidae) are found in a huge variety of habitats worldwide, feeding on the carrion, open wounds, and/or faeces of a plethora of species. They’re also a lot more abundant and easier to catch than the majority of mammals. Many species on the IUCN red list are currently “data deficient” in their distribution and abundance due to the challenge of collecting information on such rare and elusive species. This method could therefore revolutionise the monitoring of animal populations or habitats that have previously been difficult to assess using traditional means.

Calvignac-Spencer and colleagues collected 115 flies randomly in two forest locations: the Taï National Park, Côte d’Ivoire, and Kirindy Forest in western Madagascar. 40% of the flies captured contained identifiable DNA after extraction, from which the team were able to identify 20 mammalian species, 2 bird species (a water rail – Rallus aquaticus and a type of hornbill – Bycanistes sp.) and 1 amphibian (a species of Screeching frog – Arthroleptis sp.). Considering the relatively modest sample size, the mammal species identified for Kirindy Forest represented an impressive 13% of the documented mammal community for this area.

By far the most exciting find was the endangered Jentink’s duiker (Cephalophus jentinki) – a type of small antelope, of which only 2,000 are estimated to remain.

Among the other animals found were little collared fruit bats (Myonycteris torquata), porcupines (either Atherurus africanus or Hystrix cristata), a pygmy hippo (Hexaprotodon liberiensis) and various species of monkeys and lemurs such as the Western red colobus (Piliocolobus badius badius) and grey mouse lemur (Microcebus murinus). The species’ accumulation curve analysis that Calvignac-Spencer et al. carried out on the Taï flies data indicates that continued sampling would likely have yielded an even greater number of mammal species’ DNA.

Whilst this is the first use of carrion flies to assess mammalian biodiversity in a given area, previous studies have identified vertebrate DNA in the bloodmeals of mosquitoes, ticks and tsetse flies. Last year a study by Schnell et al. used leeches to detect mammal species in Vietnam, yielding evidence for the presence of the rare Annamite striped rabbit. However, both mosquitoes and leeches have been shown to exhibit host preferences, with the latter only revealing proof of terrestrial mammals species. Whilst it has also been suggested that carrion flies may be selective in their feeding, Calvignac-Spencer et al. argue that their results show little sampling bias, with both terrestrial and arboreal mammals, ranging in size from <0.1kg to 235kg, being discovered.

With the detection of bird and amphibian species as well as mammals, it may be possible to extend the use of carrion fly DNA analysis to other animal groups. It is even conceivable that such methods could be used to identify individuals, allowing population sizes to be estimated. But for now, it’s most important application will be for the early stages of assessment – in determining whether a particular species is present in the first place

With their global distribution, greater ease of capture, and lesser degree of host preference, carrion flies are likely to become one of the key tools of DNA-based evaluation of mammalian diversity. However, Calvignac-Spencer et al. propose the concept of a vertebrate sampling “toolbox” of haematophagous insects and leeches from which the most suitable tool can be chosen depending on the specific requirements of the study and habitat in question. The wealth of potential data sets that these methods could provide in the future suggests an exciting step forward for conservation biology in practice.


Calvignac-Spencer, S., Merkel, K., Kutzner, N., Kühl, H., Boesch, C., Kappeler, P. M., Metzger, S., Schubert, G. and Leendertz, F. H. (2013), Carrion fly-derived DNA as a tool for comprehensive and cost-effective assessment of mammalian biodiversity. Molecular Ecology. doi: 10.1111/mec.12183

Schnell, I. B., Thomsen, P. F., Wilkinson, N., Rasmussen, M., Jensen, L. R. D., Willerslev, E., Bertelsen, M. F., Gilbert M. T. P. (2012) Screening mammal biodiversity using DNA from leeches. Current Biology 22 (8) pp. R262-R263.

Townzen, J. S., Brower, A. V. Z. and Judd, D. D. (2008), Identification of mosquito bloodmeals using mitochondrial cytochrome oxidase subunit I and cytochrome b gene sequences. Medical and Veterinary Entomology, 22 pp.386–393.

Madagascan rainforest – Frank Vassen
Carrion fly – Bob Peterson

Jentink’s duiker illustration – Kate Whittington

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