DNA Census of African Savannah Elephant (Loxodonta africana) population in South Africa to mitigate inbreeding and poaching
We are in the process of creating a comprehensive national DNA database of the Southern African elephant population. As elephant populations in Africa continue to both decline and increase rapidly in different regions, it is vital to create a genetic landscape of the herds to monitor the levels of genetic variation in order to manage elephants wisely into the future using knowledge gained. This project will focus on inbreeding in overpopulated reserves and areas that may adversely impact the behavior, health and reproductive success of the species. With the threat of a genetic bottle neck, it is vital to understand the amount of inbreeding on local reserves to help managers make informed breeding and management decisions. The database will further allow for increased traceability of illegal ivory in the markets, as the information will be available to law enforcement for tracing confiscated ivory and help pinpoint poaching hot-spots in the country and to identify possible trafficking routes. The elephants’ DNA will be extracted and profiles created which will be used to measure inbreeding, relatedness, and innate immunity of the population. Reports of this information will be made available to owners to guide management decisions, and law enforcement will have access to the secure database for future criminal prosecutions.
Skin biopsy samples will be collected from elephants on private reserves, zoos, and parks in South Africa. For each animal darted, information on individual and family history as well as identifying characteristics will also be recorded e.g. tuskless. All samples will be collected following the chain of custody standard operating procedure (SOP), approved by the Scientific Authority as well as the police, and subsequently stored and processed at the genetics laboratory at the National Zoological Gardens in Pretoria. Each sample will be divided into two equal sections; one will be used immediately for analysis and the other will be stored for future use in research and criminal cases. The information collected will then be compiled onto the National Zoological Garden’s database and mirrored in a secure, online Cloud managed by North Carolina State University available to elephant managers, law enforcement, researchers, and law making organizations throughout the world.
Aim and objectives
The overall objective of this study is to create a DNA database of the South African elephant population to assist with elephant management practices in reserves, as well as to offer a deterrent/decrease the value of illegally obtained elephant ivory, which will link back to a specific population and thus identify origins. In addition to collecting individual information (physical features, history, location, and genetic information), the inbreeding coefficient, relatedness, and innate immunity of each herd will be calculated. This data will provide valuable indication of the extent to which populations on the small reserves throughout South Africa are inbred, and how many are related to the Kruger Park elephants as well as elephants in other countries. Since inbreeding can weaken disease resistance of mammals, the innate immunity of elephants sampled will be calculated to find the extent of influence, if any, that the segregation of the elephant population onto small reserves has had on their immune systems. Linking confiscated ivory to elephants in the database will further provide insight into the hot-spots and the rate of poaching in South Africa.
For the creation of the database, biological samples from African Elephants of both sexes and all ages on private and public reserves and in captive facilities in South Africa will be collected. The aim is to collect samples from roughly 80% of the 56 small parks and reserves in South Africa. Due to the size of some parts such as the Kruger population, bulls and matriarchs will be targeted for sample collection.
Identifying characteristics, including ear traits, tusk length, and tail traits will be photographed and noted on a data sheet. Skin biopsy samples (~200mg) will be collected by a veterinarian using a biopsy dart in the presence of a conservation officer. Samples will be placed in 80% ethanol for transport to the laboratory. Any captive animals or those already tranquilized for transport will also receive blood draws, saliva swabs, and hair draws, performed by the veterinarian (blood). All samples will be collected following chain of custody protocol approved by the Scientific Authority.
Darts made specifically for the project will collect a biopsy sample and mark the elephant so that it is not sampled twice. The dye will further contain an anti-biotic to prevent infection
Once a sampling event has taken place, samples are transferred to the National Zoological Gardens of South Africa (NZG) in Pretoria, where genetic analysis is conducted. Tissue samples are divided into 2 parts, one of which is analysed and the other which is stored for use in court cases or future research. DNA is extracted and genotyped at 30 microsatellite loci, which have been specifically designed for elephants. Innate immunity is tested using 9 toll-like receptor (TLR) genes, which are capable of viral and bacterial pathogen recognition.
Benefits of the project
The DNA database will allow reserve managers to make informed breeding and management decisions about their elephant populations. Information obtained during this study will be available to interested parties such as law enforcement agencies, vets, reserve owners and managers, conservation officials and researchers. Samples obtained and added to the database will allow for cross-referencing with future confiscated ivory and hopefully a reduction in poaching statistics. Further research into immunology will be possible, allowing for more informed management decisions regarding a facility’s elephant population. Problem elephants can be moved to reserves where they can contribute to genetic diversity which may also decrease behavioural problems often observed with young bulls becoming problematic and infantaside.
The Project Team
Collaborators and supporters
The National Zoological Gardens (NZG) of South Africa, Rory Hensman Conservation Research Unit (RHCRU), and the Animal Forensics Program of the North Carolina State University Forensics Sciences Institute (FSI) have partnered for this project to establish a dedicated genetics laboratory to process and database the DNA of South African elephant populations. Additional support is provided by The Department of Environmental Affairs (DEA), the South African National Biodiversity Institute (SANBI) and the Ecological Defense Group (EDGE), who have endorsed this project and the research being conducted by the team.