Genetic tools for the study and conservation of forest elephants with potential application to the geographical assignment of ivory

Abstract

Elephant ivory is one of the most traded products and directly threatens the survival of this charismatic taxon. In Central African rainforests, alarming rates of decline of the elusive forest elephant (Loxodonta cyclotis) have been reported over the last fifteen years. There is a crucial need to develop novel tools to underpin traditional approaches that have failed to provide timely information for the rapid intervention of national wildlife law enforcement agencies to hinder the slaughter and stop fuelling the global illegal market. Genetic data are appealing because they can provide real-time, reliable and shareable information for immediate response on the ground and increased collaboration between countries involved along the global ivory trade chain. Genetic resources for forest elephants are scarce and the available nuclear microsatellite genetic markers present limited opportunities for capacity building and data sharing due to the need for sophisticated equipment and calibration among laboratories. In chapter 2, I present the first genome wide set of 1,365 SNP markers generated for forest elephants and validate genotyping assays for a subset of 107 SNP loci. In chapter 3, I develop two new simple, inexpensive and reliable sexing assays that are suitable for non-invasive DNA samples and can be incorporated into larger SNP panels. These new genetic resources offer ease of data sharing and technical portability and thus present great potential to provide routine tools. However, wildlife managers are often still reluctant to rely on faecal DNA surveys because there remains the uncertainty of success in recovering sufficient good quality data, while a high investment into fieldwork and laboratory costs is required. In chapter 4, I provide new tools and guidelines for sample collection, storage and preparation in order to increase the quality and cost-efficiency of non-invasive DNA genotyping. In chapter 5, using an extensive elephant SNP dataset derived from elephant faecal DNA, I investigate the genetic structure of elephants in Gabon. I find that SNP markers reveals the existence of four groups, with additional patterns of genetic differentiation within one group. Moreover, by combining SNP genotyping data with hypervariable mitochondrial DNA control region sequences, I show that it is possible to increase the resolution of geographical assignment to populations defined by a combination of observed genetic differentiation and investigative needs. This thesis links genetic approaches and management needs, in order to provide fast, accurate, cost-efficient and needs-driven tools to support National wildlife law enforcement agencies into elephant population management and investigation of the illegal ivory trade at the intra-national level.