We had a great start to the new year here at the project starting up with the publication of a methodological paper evaluating protocols for the collection and processing of pinniped samples for genetic analysis.
Genetic studies of elusive species such as pinnipeds are often limited by the number of samples available. This can lead to knowledge gaps because data may not be representative of the population and sample size is too low. Therefore, we evaluated different protocols for the collection and processing of samples from grey and harbor seals to see which ones are most suitable. This helped us to develop protocols that are able to provide data suitable for genetic analysis while at the same time being non-invasive (meaning that we do not have to capture and handle individual seals during sample collection). Optimising protocols for such non-invasive samples opens up the possibility of including these and increase sample size in conservation studies of seals. This means that a representative sample size for a particuclar population may be reached more easily than by purely relying on traditional samples such as skin biopsies. To do this, we analysed the performance of different protocols following successful DNA isolation, molecular sex identification and sequencing of a mitochondrial DNA fragment (control region).
It was shown that plucked hair, urine and buccal swabs were most effective for collection from individuals in captivity/rehabilitation centres, whereas the collection of scats (stool samples) was most appropriate for wild populations.
We also ran an experiment to look into how much DNA would degrade in stool samples when these are left out at ambient conditions. In order to do this, we took sub-samples weekly over a four week time period and assessed these. By doing so, we were able to show that DNA from these stool samples was still suitable for genetic analyses after four weeks at ambient conditions. This means that when we are out in the field collecting samples, it is indeed worth to also collect samples that look older because they can still have viable DNA and can be included for analyses.
By assessing the suitability of different sample types, this study provides important data that helps to effectively design future sampling strategies and helps to increase samples available for genetic analysis of seals.
This research is funded by the Galway-Mayo Institute of Technology, the Irish National Parks and Wildlife Service (Grant REF SPU G07-2017) and the Irish Department of Housing, Local Government and Heritage.
The paper was published in Conservation Genetics Resources and can be accessed via the DOI https://doi.org/10.1007/s12686-020-01182-4 or as a read-only version here.