The application of non- and minimally-invasive biological and environmental samples in wildlife surveillance and genetic research

Abstract

Increased anthropogenic activities lead to severe global biodiversity loss, requiring effective conservation and management, particularly for terrestrial animals. Long-term wildlife monitoring and genetic research associated are of paramount importance, allowing for characterizing how and why a given ecosystem and wildlife inhabiting it are changing in response to environmental changes and conservation interventions applied. A variety of information thus is needed, such as population dynamics, species distribution, genetic variation, and disease cross-species transmission. However, in-field monitoring and biological sample collection are often hindered due to logistic barriers and ethical issues, especially for rare and threatened species. In my doctoral work, I evaluated the applicability of non-invasive environmental DNA (eDNA) based methods in terrestrial wildlife monitoring in combination with target capture and metabarcoding. Furthermore, I investigated the nucleic acid preservation of minimally-invasive dried blood spots (DBS) samples stored for up to 15 years in sub-standard storage conditions in comparison with blood samples stored in a cold chain. In the meanwhile, I explored the applications of DBS samples in genomic research and viral pathogen surveillance. I revealed sampling from waterholes during the dry season in tropical forests can provide representative environmental samples to apply eDNA-based methods for terrestrial animal monitoring. Target capture prior to sequencing retrieved more genomic information, while metabarcoding tend to be more sensitive to species shedding large amounts of DNA in terms of species detection. Integration of target capture and metabarcoding should be considered to improve the overall performance of eDNA-based methods. In terms of DBS sampling strategy, I provided evidence showing although nucleic acid degradation persisted in comparison to blood samples stored in a cold chain, relatively large DNA fragments (~20,000 bp) were preserved in DBS samples even for over 9 years of storage. DBS samples were suitable for complete mitochondrial genome related research for various species, while its application in viral pathogen research may be limited, particularly RNA viruses. Overall, my work emphasized the value of eDNA-based methods in terrestrial animal surveys and demonstrated the great promise of DBS samples in wildlife genetic or genomic research even for those being stored over a decade.