From faeces to species: genetic identification of otters from spraints

Non-invasive genetic monitoring  involves the use of DNA  to survey a target species without directly trapping or observing it. The technique is particularly useful for rare, elusive or secretive animals. This is especially true for the otter (Lutra lutra), as it is a shy animal, rarely seen by people. The non-invasive tracking of otters is by no means a new concept; C.B Moffatt wrote in 1927 that “the otter’s presence on a small stream or on a pond is, however, often not suspected except by those who are accustomed to track him by his “seal” or his “spoor””. Nowadays, we call otter faeces “spraints”, and it is the otter DNA that is available in the spraint that we can use for genetic analysis.

Otter spraint. Image from the MISE Project on Facebook

At the Mammals in a Sustainable Environment (MISE) Project, we have organised a number of volunteer surveys where we get the public involved in otter tracking. We get people together and talk to them about otters and how to look for their signs such as slides, holts, sign heaps, foot-prints and spraints. The volunteers are trained how to collect otter spraints in zip-lock bags, and how to record co-ordinates using GPS units. The surveys are good fun, an interesting way to get involved in citizen science, and have been a great success in both Ireland and Wales, throughout the INTERREG IVA Region.

A team of volunteers surveying for otter spraints

But in order to deal with the DNA in the spraint (known to be of very low quality and quantity), a number of molecular techniques needed to be developed. David O’Neill, a recent PhD graduate in Waterford Institute of Technology  has been leading the study. O’Neill firstly developed a test that would ensure that the DNA present in the spraint was actually that of an otter.  A second set of tests were developed to test for the X and Y chromosome of the otter to find out if the otter was male or female. Finally, a panel of microsatellite markers were optimised to work in conjunction with the spraint DNA in order to obtain a unique genetic fingerprint of individual otters.

Collecting otter spraints in the field

O’Neill isn’t the first scientist to identify otters from spraint DNA, however the techniques he has developed are designed to be used with real-time PCR, a platform designed to detect minute or trace quantities of DNA. Earlier this year when the horse meat scandal broke out, trace quantities of horse meat DNA were detected using this sensitive and accurate technique. O’Neill’s work is also novel as he can use the results he obtains from both the species and gender test to select the spraint DNAs that have the best quality DNA and are subsequently more likely to yield a full genetic fingerprint. One of the main drawbacks with the use of otter spraint DNA is that the success of identifying individual otters is quite low. However, when the spraints are first screened using O’Neill’s strategy, he can discard the samples that are unlikely to work, and thus save time and resources. O’Neill was also able to sequence other samples that did not amplify as otter. Some of the other samples collected during volunteer surveys included pine marten, fox and mink.

O’Neill et al’s paper “Development of novel real-time TaqMan PCR assays for the species and sex identification of otter (Lutra lutra) and their application to non-invasive genetic monitoring” has just appeared under early view in Molecular Ecology Resources. The techniques are currently being used for a long term monitoring project in Ireland and Wales, and are also being applied to smaller scale studies.  The study is proving to be very useful to screen large numbers of spraints prior to subsequent individual analysis.
David O’Neill, Peter D. Turner, Denise B. O’Meara, Elizabeth A. Chadwick, Lee Coffey, Catherine O’Reilly (2013). Development of novel real-time TaqMan® PCR assays for the species and sex identification of otter (Lutra lutra) and their application to noninvasive genetic monitoring Molecular   Ecology Resources DOI: 10.1111/1755-0998.12141