iDNA from terrestrial haematophagous leeches as a wildlife surveying and monitoring tool – prospects, pitfalls and avenues to be developed

Abstract

Invertebrate-derived DNA (iDNA) from terrestrial haematophagous leeches has recently been proposed as a powerful non-invasive tool with which to detect vertebrate species and thus to survey their populations. However, to date little attention has been given to whether and how this, or indeed any other iDNA-derived data, can be combined with state-of-the-art analytical tools to estimate wildlife abundances, population dynamics and distributions. In this review, we discuss the challenges that face the application of existing analytical methods such as site-occupancy and spatial capture-recapture (SCR) models to terrestrial leech iDNA, in particular, possible violations of key assumptions arising from factors intrinsic to invertebrate parasite biology. Specifically, we review the advantages and disadvantages of terrestrial leeches as a source of iDNA and summarize the utility of leeches for presence, occupancy, and spatial capture-recapture models. The main source of uncertainty that attends species detections derived from leech gut contents is attributable to uncertainty about the spatio-temporal sampling frame, since leeches retain host-blood for months and can move after feeding. Subsequently, we briefly address how the analytical challenges associated with leeches may apply to other sources of iDNA. Our review highlights that despite the considerable potential of leech (and indeed any) iDNA as a new survey tool, further pilot studies are needed to assess how analytical methods can overcome or not the potential biases and assumption violations of the new field of iDNA. Specifically we argue that studies to compare iDNA sampling with standard survey methods such as camera trapping, and those to improve our knowledge on leech (and other invertebrate parasite) physiology, taxonomy, and ecology will be of immense future value.

iDNA at Sea: Recovery of Whale Shark (Rhincodon typus) Mitochondrial DNA Sequences from the Whale Shark Copepod (Pandarus rhincodonicus) Confirms Global Population Structure

“…Invertebrate-derived DNA (iDNA) is an offshoot of this approach that involves the extraction of genetic material of animals via the flesh-eating or haematophagous invertebrates that parasitise them (Schnell et al, 2015;Schubert et al, 2015;Lee et al, 2016). To date, most iDNA studies have focused on terrestrial vertebrates and have extracted host DNA from insects, ticks, or leeches.…”

Field calibration of blowfly-derived DNA against traditional methods for assessing mammal diversity in tropical forests

“…Frequently used methods include live trapping, such as cage traps (Hanif-Ridzuan et al 2010;Madinah et al 2011), mist nets, and harp traps (Kingston et al 2003;Sing et al 2013), camera traps (Clements 2013;Hedges et al 2015a), indirect signs such as tracks or scat (Daim 2002), interviews with local communities (Sharma et al 2005), direct observations by researchers (Syakirah et al 2000;Jayaraj et al 2013), and hair traps (Castro-Arellano et al 2008;Hedges et al 2015b). Recent additions to the toolbox are secondary sources of mammal DNA, for example, mammal DNA detected from owl-pellet bones (Rocha et al 2015) and invertebrate gut contents (Calvignac-Spencer et al 2013a, 2013bSchnell et al 2012Schnell et al , 2015Lee et al 2015). These methods can provide accurate identification of mammal species, are not stressful to the mammals themselves, require the least ecological and taxonomic expertise, and yet have the potential to detect rare and cryptic species (Calvignac-Spencer et al 2013a;Schnell et al 2012;Lee et al 2015).…”

“…Blowflies (Diptera: Calliphoridae) have shown promising potential as sources of mammal DNA due to their presence in all habitats (Norris 1965) and broad host preferences as saprophagous and coprophagous generalists (Calvignac-Spencer et al 2013a, 2013bAzwandi et al 2013; Lee et al 2015;Schnell et al 2015). Chrysomya bezziana has been reported feeding on mammal species from the orders Artiodactyla (7 spp.…”

“…Standardised methods for sampling of blowflies have been developed that take into account the persistence period of mammal DNA in blowfly guts . Despite the increasing interest in invertebrate-derived mammal DNA for mammal diversity assessments, field calibrations of the performance of invertebrate-derived mammal DNA against traditional methods have yet to be conducted (Schnell et al 2015).…”

Barcoding the food chain: from Sanger to high-throughput sequencing

“…Some studies have shown that eDNA extracted from water is a good indicator of relative species abundance in aquatic systems (Lodge et al 2012;Thomsen et al 2012;Pilliod et al 2014), and while this provides a good starting point, it remains a thorny issue for terrestrial systems (Saitoh et al 2016), for invertebrate species (due to primer bias), or when degraded DNA is used (King et al 2008). One solution is to model occupancy (species-level) or spatial mark-recapture (individual-level) data, although careful experimental designs are needed before data collection can begin (Schnell et al 2015). Finally, barcoding techniques can always be used in parallel with a subsample of traditional trapping methods and morphological analysis of samples (Furlong 2015).…”