When bugs reveal biodiversity


  • Kristine Bohmann,

    1. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
    2. School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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  • Ida Bærholm Schnell,

    1. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
    2. Copenhagen Zoo, Frederiksberg, Denmark
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  • M. Thomas P. Gilbert

    Corresponding author
    • Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Correspondence: M. Thomas P. Gilbert E-mail: mtpgilbert@gmail.com


One of the fundamental challenges of conservation biology is gathering data on species distribution and abundance. And unless conservationists know where a species is found and in which numbers, it is very difficult to apply effective conservation efforts. In today's age of increasingly powerful monitoring tools, instant communication and online databases, one might be forgiven for thinking that such knowledge is easy to come by. However, of the approximately 5,400 terrestrial mammals on the IUCN Red List, no fewer than 789 (ca. 14%) are listed as ‘Data Deficient’ (IUCN 2012) – IUCN's term for ‘haven't got a clue’. Until recently, the only way to gather information of numbers and distribution of terrestrial mammals (and many other vertebrates) was through observational-based approaches such as visual records, the presence of tracks or spoor or even identification from bushmeat or hunters' trophies pinned to the walls in local villages. While recent technological developments have considerably improved the efficacy of such approaches, for example, using remote-sensing devices such as audio- or camera-traps or even remote drones (Koh & Wich 2012), there has been a growing realization of the power of molecular methods that identify mammals based on trace evidence. Suitable substrates include the obvious, such as faecal and hair samples (e.g. Vigilant et al. 2009), to the less obvious, including environmental DNA extracted from sediments, soil or water samples (e.g. Taberlet et al. 2012), and as recently demonstrated, the dietary content of blood-sucking invertebrates (Gariepy et al. 2012; Schnell et al. 2012). In this issue of Molecular Ecology, Calvignac-Spencer et al. (2013) present a potentially powerful development in this regard; diet analysis of carrion flies. With their near global distribution, and as most field biologists know, irritatingly high frequency in most terrestrial areas of conservation concern (which directly translates into ease of sampling them), the authors present extremely encouraging results that indicate how carnivorous flies may soon represent a strong weapon in the conservation arsenal.

Globally, biodiversity is declining at an unprecedented rate, and unless vigorous conservation initiatives are urgently implemented, much of our diversity may soon be lost forever (Butchart et al. 2010). Acknowledging the key role played by biodiversity-related information in feeding decision-making processes, ‘Parties to the Convention on Biological Diversity’ made the improvement of ‘knowledge, the science base and technologies relating to biodiversity’ one of the Aichi Biodiversity Targets (CoP10 2010). This is an objective of tremendous importance as, even for comparatively well-studied groups of animals such as mammals, future efforts to assess biodiversity may not only document temporal changes in recognized species' ranges, but are also predicted to unveil the existence of more than 300 new species in the next 20 years (Jones & Safi 2011). Thus, any methodological breakthroughs that increase the ease of data collection, and/or reduce financial and physical costs, are extremely valuable.

Broad biodiversity assessment (e.g. depiction of vertebrate or mammal communities) as well as targeted species monitoring (e.g. determination of endangered species population densities) traditionally relies on classical ecological methods such as capture-recapture experiments or line-transect surveys (N'Goran et al. 2012). These approaches are obviously useful, but are also extremely laborious, often requiring the involvement of trained people and highly qualified specialists (e.g. taxonomists). In addition, they often fail to detect elusive and/or low-density animals, as exemplified by the relatively recent discoveries of a new primate species in Africa (Hart et al. 2012).

Mammals, birds and amphibians detected in carrion flies

The genotyping of host DNA in invertebrates (iDNA), such as mosquitoes (Kent 2009), is a well-established technique for use in characterization of host–parasite transmission networks. Only recently, however, has the use of such invertebrates been proposed as a method for assaying vertebrate presence itself (Gariepy et al. 2012; Schnell et al. 2012). Although in hindsight a remarkably obvious proposition (as many of the best ideas always are), in this issue of Molecular Ecology, Calvignac-Spencer et al. (2013) demonstrate an exciting new addition to the iDNA sampling platter, to include the ‘carrion’ flies (defined as the blow and flesh flies of the Calliphoridae and Sarcophagidae families, respectively) that feed on the live flesh of open wounds, carrion or faeces (Fig. 1). In initial validation experiments, the authors captured flies present under dissection nets that were feeding around known mammalian carcasses. From 63% of the flies, the authors were able to generate assignable mammal mitochondrial DNA sequences. Interestingly, DNA from mammals different to the carcass bait (thus, were not derived from immediate feeding) were revealed in 13% of the flies. Subsequently, using home-made collection traps (Fig. 2), the authors collected 40 additional flies in a dry deciduous forest in Madagascar and 75 flies in a tropical moist forest in Ivory Coast, none of which were associated with known carcasses. 42% and 39% of the flies, respectively, contained identifiable mammal sequences originating from four and 16 different mammal taxa. Notably, the authors also occasionally detected birds and amphibians, hinting at a wider yet unexplored usage of the method. Remarkably, the taxa identified in the just 40 analysed Malagasy carrion flies represented 13% of the mammal species known to be in that area, while the 75 analysed Ivorian flies revealed six of the nine local primate species, as well as the rare and endangered Jentink's duiker (Cephalophus jentinki). Given that these results are based on relatively small sample sizes, represented both large and small mammal species and include some species not easily observed in the areas, the results are remarkable and highlight how the power of invertebrates should not be underestimated.

Figure 1.

Carrion flies feeding on the carcass of a red colobus monkey in the Ivory Coast (photo courtesy of Kathrin Nowak).

Figure 2.

An example of a home-made carrion fly trap used by Calvignac-Spencer et al. (2013), constructed from a soft drink bottle and plastic plate – easy to assemble and effective at attracting the flies (photo courtesy of Kathrin Nowak).

Challenges ahead

Invertebrates that feed on mammals, their decaying rem-ains or their faeces can be found (and thus collected) over large geographical areas (in particular carrion flies with their near global distribution) and can be collected en masse, either by offering oneself as bait (e.g. leeches) or with traps that are both easy to construct and use. Visual transects are limited to medium- to large-size diurnal species, it may require hundreds of kilometres of censusing effort per site, and it is especially difficult to carry out in areas with hunting where game species are shy, whereas collection of host DNA from invertebrates is rapid, requires limited manpower, and as demonstrated in this study is capable of detecting even species that are small, nocturnal and cryptic.

This is not to say that iDNA-based sampling is without its limitations. First, not all species may have a generalist diet. Some mosquitos, for example, have been demonstrated to have host preferences (Lyimo & Ferguson 2009), and the task of fully investigating the dietary preferences (if any) of other invertebrates is often challenged by a poor understanding of the taxonomic diversity of the group and may even be yet further complicated by preferences linked to time of year, stage of life and so on. Thus, without fully understanding whether such biases exist, false conclusions may be made on the presence/absence of target species in the area. Second, postfeeding, host DNA survival will vary considerably between invertebrates, from the very short term (days) in tsetse flies (e.g. Steuber et al. 2005), to much longer term (months) in leeches (Schnell et al. 2012), which when combined with the mobility of the different species, will add uncertainty to the geographic and even temporal proximity of the last meal to the point of invertebrate capture. Third, the results of relevant iDNA-based studies published to date have relied on identification through mitochondrial DNA (mtDNA). While in general an excellent means with which to generate basic presence/absence data for a species (as long as reference databases of comparative sequence are relatively complete, something which is far from true in most cases), mtDNA lacks the power of nuclear DNA (nuDNA)-based analyses for discriminating between individuals within a species, a key requisite should information such as population size estimates be needed. Thus, until evidence is provided for survival of nuDNA of sufficient quality in such samples, the wider-scale applications of the invertebrates, whether leech, mosquito, tick or fly will remain limited. Lastly, of course, iDNA analyses require specialized laboratory facilities tailored to minimize the chance of extract/sample cross-contamination, as well as the molecular biology expertise to undergo the research.

A powerful supplementary tool

Nevertheless, despite these potential limitations, the prospective power offered by iDNA is considerable, and once coupled to second-generation sequencing as a means to increase the sample flow-through, it represents an economical means to survey large numbers of samples. It would be a mistake, however, to view iDNA as a competitor to other established techniques and advocate their replacement. In contrast, what is urgently needed now is the allocation of research funding to enable a focused effort on determining which strategies and combinations of methods, drawn from the full biodiversity assessment tool-box, would be the most efficient. This would need to take into account biodiversity assessment accuracy and comprehensiveness, cost-effectiveness and other practical aspects and might best be undertaken through direct comparison of methods by focusing on predefined study sites chosen due to the thoroughness at which they can be studied. With such data helping guide future biodiversity assessment, it can be hoped that the number of IUCN's ‘Data Deficient’ species (IUCN 2012) might be rapidly reduced for a reason other than extinction.

All three authors contributed equally to this perspective.