Evaluating the use of non‐invasive hair sampling and ddRAD to characterize populations of endangered species: Application to a peripheral population of the European mink

The application of next‐generation sequencing (NGS) to non‐invasive
samples is one of the most promising methods in conservation genomics, but
these types of samples present significant challenges for NGS. The
European mink (Mustela lutreola) is critically endangered throughout its
range. However, important aspects such as census size and inbreeding
remain still unknown in many populations, so it is crucial to develop new
methods to monitor this species. In this work, we placed hair tubes along
riverbanks in a border area of the Iberian population, which allowed the
genetic identification of 76 European mink hair samples. We then applied a
reduced representation genomic sequencing (ddRAD) technique to a subset of
these samples to test whether we could extract sufficient genomic
information from them. We show that several problems with the DNA,
including contamination, fragmentation, oxidation, and possibly sample
mixing, affected the samples. Using various bioinformatic techniques to
reduce these problems, we were able to unambiguously genotype 19 hair
samples belonging to six individuals. This small number of individuals
showed that the demographic status of the species in this peripheral
population is worse than expected. The data obtained also allowed us to
perform preliminary analyses of relatedness and inbreeding. Although
further improvements in sampling and analysis are needed, the application
of the ddRAD technique to non‐invasively obtained hairs represents a
significant advance in the genomic study of endangered species.