Blood, sweat and tears: a review of non-invasive DNA sampling

Abstract

The use of DNA data is ubiquitous across animal sciences. DNA may be obtained from an organism for a myriad of reasons including identification and distinction between cryptic species, sex identification, comparisons of different morphocryptic genotypes or assessments of relatedness between organisms prior to a behavioural study. DNA should be obtained while minimizing the impact on the fitness, behaviour or welfare of the subject being tested, as this can bias experimental results and cause long-lasting effects on wild animals. Furthermore, minimizing impact on experimental animals is a key Refinement principle within the ‘3Rs’ framework which aims to ensure that animal welfare during experimentation is optimised. The term ‘non-invasive DNA sampling’ has been defined to indicate collection methods that do not require capture or cause disturbance to the animal, including any effects on behaviour or fitness. In practice this is not always the case, as the term ‘non-invasive’ is commonly used in the literature to describe studies where animals are restrained or subjected to aversive procedures. We reviewed the non-invasive DNA sampling literature for the past six years (380 papers published in 2013-2018) and uncovered the existence of a significant gap between the current use of this terminology (i.e. ‘non-invasive DNA sampling’) and its original definition. We show that 58% of the reviewed papers did not comply with the original definition. We discuss the main experimental and ethical issues surrounding the potential confusion or misuse of the phrase ‘non-invasive DNA sampling’ in the current literature and provide potential solutions. In addition, we introduce the terms ‘non-disruptive’ and ‘minimally disruptive’ DNA sampling, to indicate methods that eliminate or minimise impacts not on the physical integrity/structure of the animal, but on its behaviour, fitness and welfare, which in the literature reviewed corresponds to the situation for which an accurate term is clearly missing. Furthermore, we outline when these methods are appropriate to use.

Emerging indicators of fish welfare in aquaculture

“…No fixed definitions exist for the terms ‘invasive’ and ‘non‐invasive’ when applied to animal‐based methods 55,56 . Non‐invasive sampling may refer to methods which avoid any direct physical contact including handling, capture and restraint 57,58 .…”

A New Non-invasive Method for Collecting DNA From Small Mammals in the Field, and Its Application in Simultaneous Vector and Disease Monitoring in Brushtail Possums

“…Several techniques have been developed to collect DNA from marine and terrestrial animals. The common objective of these methods is to obtain high-quality template DNA from biological materials without the need for sedation or the risk of causing significant injury, and to minimize interfering with the target animals' natural behaviour (Lefort et al, 2018).…”

Metabarcoding faecal samples to investigate spatiotemporal variation in the diet of the endangered Westland petrel (Procellaria westlandica)

“…However, this methodology usually requires that gut content is obtained by stimulating regurgitation after capturing individual birds through a technique that has been called “lavage” (Barrett et al, 2007; Ryan and Jackson, 1986; Wilson, 1984). Such an invasive sampling method (Lefort et al, 2019) is not only unethical, but also potentially dangerous for the birds. Furthermore, the efficiency of this method is usually limited because many individuals would have empty stomachs at the moment of sampling, and highly digested prey items may not be identifiable to genus or species level.…”