Author: Edel Sheerin, MISE Project Assistant, WIT

Introduction: So, you’ve searched woodland trails, hiked up mountains and scrutinized grassy river banks, in sometimes rather unforgiving weather conditions with the goal of collecting as much poo as possible for the MISE project. The last time you saw those samples they were in small plastic tubes or bags, and were sent off to the laboratory at Waterford Institute of Technology. Have you wondered what exactly happens next? How do we get all the information we need from the poo or hair samples collected during our surveys?

Throughout the lifetime of the project, our dedicated volunteers in both Ireland and Wales have collected thousands of samples. From otter and forest mammal surveys to red squirrel and pine marten hair tube surveys, the samples also include some unfortunate animals killed on our roads. See the examples below: Following a survey, all details such as the GPS co-ordinates, field observations, tests required and sample IDs are recorded on our online databases. This enables those of us in the lab to view incoming samples from all project partners, in both Ireland and Wales, and allows us to prepare by keeping the lab fully stocked. Once the samples reach the lab they are stored in our giant walk-in freezer at WIT, which is kept at minus 20 degrees Celsius.

Getting DNA from the sample: The first step in the lab is to extract DNA from the sample, and this method varies slightly depending on the sample type. For example, if the sample is hair, first we need to break it down in order to release the cells that contain the DNA. With faecal samples, we use the cells that are rubbed off the intestine as the faecal material passes through the animal’s gut, these cells coat the outer surface of the poo. A short protocol to liberate the DNA from the cells is then followed and the end result looks like this photo.  (If you wish to read further details on the DNA techniques please follow this link.) Each sample we process is given a unique DNA extraction code. This enables us to quickly search our internal database, locate the sample (we have an archive of boxes containing almost 7,000 samples) and track its progress within the lab.

So we have the DNA…. Next? Once DNA has been made from all the samples of a given survey, we then test them to find out what animal it was from, if it was male or female, and in some cases we can also determine the DNA fingerprint to identify an individual. This information can be combined to tell us about the local animals in a particular survey area.  We use the sex test as an indicator of the quantity and quality of DNA present in each sample, as a cost-effective and time saving measure, so that only the best samples are subsequently used to obtain a genetic fingerprint. All of this data is then plugged into statistics programs which enable us to study the genetic health of the animals and estimate the number of animals present in an area, sometimes we can even tell which animals are related to each other!

This information will be used to advise conservation strategies for future management. When all the results have been uploaded to the shared online database, the MISE Project Officers can then access them to use in survey reports and scientific peer-reviewed publications, these are made available online through the MISE website. We also submit records to data centres whose aim is to record and monitor the biological diversity within Ireland and Wales. In Ireland the records are sent to the National Biodiversity Data Centre (NBDC) and in Wales the MISE Project Officers contribute data to  Cofnod (the North West Wales local records centre) and WWBIC (West Wales Biodiversity and Information Centre).

Lab training:   We have provided lab training for volunteers from Ireland and Wales, where they learned the different DNA techniques and applied them to samples from our surveys. In keeping with our cross-border collaboration, we share our skills and expertise with our colleagues from Wales who have also visited the lab to learn about and carry out the DNA tests.