This week, David O’Neill had an opportunity to suggest a paper for Journal Club. For his choice, he selected a non-invasive genetic study of otters. I should say that David is currently working on a similar themed subject, using samples collected from Ireland and Wales for the MISE project.
David’s paper of choice was by Bonesi et al. (2012) “Lessons from the use of non-invasive genetic sampling as a way to estimate Eurasian otter population size and sex ratio”, recently published in Acta Theriologica.
A bit of Background
The Eurasian otter is a difficult species to survey visually due to its elusive behaviour and trapping puts the animal and indeed the surveyor under a lot of stress. Trapping is also labour intensive and generally expensive. An alternative approach is the use of DNA extracted from otter spraints, which can be used as a non-invasive source of DNA to obtain a DNA fingerprint from individual otters and give an estimate of the number of otters in the study area.
In a European context, the species is considered “near threatened” due to a European wide decline of the species, which is now steadily recovering in Western Europe. The status of the species has instigated a lot of research and a number of reintroduction projects have taken place across Europe, in an attempt to help the species to recover in areas where it was once established. One such re-introduction took place in the late 1990’s on the River Thames catchment, Britain.
Bonesi et al. (2012) presented a non-invasive approach to sample otters from this reintroduction site on the Thames. 121 otter spraints were collected over a seven month period with 19% of spraints amplifying for five loci or more, the minimum required for the identification of an individual. Of the 17 otters introduced in this study, only six otters were detected using this non-invasive approach.
This study had the advantage of obtaining a genetic profile for some of the individuals prior to the introduction and allowed the comparison of genotypes obtained from spraints with reference to the known genotype of the individual. Of the 17 otters reintroduced to the area, only six were discovered using this approach which underrepresented the known population. However, only 23 DNA preps yielded sufficient DNA to generate a genotype.
Due to the limitations experienced in this study, the authors wrote conclusions from their experience which could be incorporated in future studies. Non-invasive genetic sampling may not capture all the individuals and in this study some otters were more territorial than others and their spraints may be more commonly found than else dominant otters, resulting in an underestimation of the population. There also appeared to be a sex bias in the results, but this may also be attributed to the number of males that were released in the study.
Some of the author’s conclusions and future recommendations:
- This study looked at otters that were released into an area and territories may not have been established during the seven months that sampling was conducted post-release. A follow up survey could have addressed this
- Future studies should invest resources early in the study and try the following suggestions
- Optimise the storage of spraints for DNA extraction
- Extract the DNA as soon as possible to avoid long term storage
- Increase the quantity of DNA in the DNA extract (perhaps by using a DNA extraction kit)
- Increase the sampling area so capture the otters that may have established themselves outside the core study/release area
- Increase the time frame for otter spraint collection
Our general consensus from this paper was that the authors wrote an interesting paper about a fairly small study. However, the authors wrote a good discussion and produced a good review of previously published non-invasive genetic otter studies, making this paper a good source of relevant literature for researchers who may be beginning a similar study. The shortfalls in the study have been addressed and valuable lessons were learned with possible ways to address them recommended to the reader, resulting in a practical addition to the literature.