Establishing SNPSTR Markers to Fight Illegal Wildlife Trade

Abstract

One of the causes of the loss of biodiversity on this planet is the over-exploitation by humans. Even though laws and policies are in place for the protection of endangered species, illegal wildlife trade remains an attractive and lucrative market: Nearly 6,000 species of animals and plants have been documented to be traded illegally. To help raise awareness and shed light on this serious issue, this thesis provides a detailed overview of the illegal wildlife trade and its effects on biodiversity and society. <br /> In wildlife forensics, DNA markers frequently form the basis of a molecular approach to effectively detect and prove illegal wildlife trade. This thesis establishes SNPSTR markers in order to fight illegal wildlife trade. SNPSTRs combine short tandem repeats (STRs) with at least one flanking single nucleotide polymorphism (SNP) within one amplicon. Such a combination offers many advantages. For instance, the average number of alleles per locus is increased compared to a length-based detection of the STRs alone, thus allowing the resolution of STR isoalleles and more refined analyses. <br /> In this thesis, an efficient workflow for the development of SNPSTR markers is presented. Using this workflow, 74 animal species from a variety of taxa have been covered. A total of 1365 SNPSTR markers have been developed, forming the core work of this thesis. However, as STR markers without a flanking SNP also contain valuable information and may reveal a SNP in future studies, a further 314 pure STR markers were included. On average, each species set contains 18 SNPSTR markers (and four STR markers) that can be amplified in a single, multiplexed PCR reaction, allowing subsequent wildlife forensic analysis for the species. <br /> The applicability of SNPSTRs in wildlife forensics is demonstrated by showing that individual identifications and parent-offspring tests can be carried out to prove illegal wildlife trade. Moreover, it is also possible to determine the geographical as well as the population origin of specimens so that they can be returned and poaching hotspots can be identified. Furthermore, SNPSTRs also allow the genetic diversity of populations to be assessed, providing a basis for future conservation legislation. In addition, it is shown exemplarily that SNPSTR markers can be partially applied to other species within the same (taxonomic) family, thus saving a lot of resources in solving wildlife crimes. Moreover, SNPSTR profiles can also be obtained from material that is highly trafficked but still challenging for DNA analysis. Furthermore, while more research is needed, it appears that cultured cells may provide an additional and sustainable resource for establishing new SNPSTR markers. Overall, although some limitations remain, particularly in terms of sample size, the versatile usability of SNPSTR has been proven. <br /> This work is meant to make a significant contribution in the fight against illegal wildlife trade by providing SNPSTR markers for a wide range of applications and by proving the suitability and advantages of these viable tools. Primer sequences and allele information from the SNPSTRs are publicly available on a data portal (https://fogs-portal.de/data) to researchers, forensic scientists, government agencies, and authorities worldwide. Therefore, the SNPSTR markers can be used for research, monitoring, and, not least, detecting, proving and preventing illegal wildlife trade. In this way, the work of this thesis aims to help save protected wildlife from overexploitation - and species from extinction.