Using genetics of captive and wild meta-populations of mega-herbivores (elephants and rhinos) to inform conservation planning initiatives

Additional Supervisors:
Dr Sue Walker, Chester Zoo
Prof Graham Kerley, Centre for African Conservation Ecology

Wild populations of large herbivores play a vital role to the functioning of African ecosystems but are increasingly endangered as a result of poaching and loss and fragmentation of their habitat (Ripple et al. 2015). The International Union for Conservation of Nature (IUCN) Conservation Breeding Specialist Group (CGSG) highlights that to achieve viable populations of species thriving in healthy ecosystems conservation planning initiatives must involve integrated species conservation planning that considers all populations of the species (inside and outside the natural range) under all conditions of management. Therefore, prior to implementing gene flow between in situ and ex situ populations, it is key that we characterise genetic diversity and understand the likely consequences of gene flow within and among captive and wild populations. It is essential to avoid: inbreeding depression due to the breeding of closely related animals; loss of genetic distinctiveness and loss of local adaptation due to the interbreeding of genetically distinct subspecies; and adaptation to captivity that results in individuals poorly adapted to natural conditions (Frankham 2008). Any of these can result in reducing the fitness of managed populations, making matters worse rather than better. However, knowledge of the genetic composition of potential donor and recipient populations can ensure that introduced individuals enhance and complement local genetic variation boosting the success of that population and so the whole species. This project will focus on the population genetics of two African large herbivores; the eastern black rhino and the African elephant with the aim to integrate genetic information into population management and improve overall viability of endangered species.

Currently within Europe there is extensive detailed pedigree information and breeding records for the captive eastern black rhino including numbers of offspring borne to different individuals. The genetics of this meta-population across European zoos will be genetically characterized using microsatellite and mtDNA markers which will also allow comparison with wild populations genotyped for the same markers (Moodley et al. 2017). Information from the pedigrees and breeding records will also allow the student to compare the expected and observed effects on genetic diversity in the zoo population potentially allowing the detection of a genetic signal of adaptation to captivity. A comparison between wild and captive populations will indicate how diverse the captive population is and how it could best be used to complement wild populations. Additionally, a genomics approach will be explored to evaluate its potential to better understand genome wide effects of the breeding programme and to characterize genetic differences among subspecies of rhinos.

Additionally, detailed information is available on translocations, breeding and survival in another meta-population of a large herbivores; the African elephant in South Africa. The student will also gather and analyse genetic information from these populations to infer patterns of gene flow, introgression, heterozygosity and selection and from these evaluate the impact of past management decisions on the genetic health of small populations. The understanding gained from comparisons of the genetic dynamics of the wild and captive populations will be used to inform conservation planning initiatives and improve long-term viability of species.

Research Questions:
1. How genetically diverse is the EU eastern black rhino population and how do they compare to wild populations?
2. Is there any evidence of genetic adaptation to captivity in rhino zoo populations and if so what are the consequences of this on loss of genetic diversity?
3. What are the genetic and demographic effects of translocations of elephant populations in South Africa and how overall can this be used to inform genetic management of conservation planning initiatives?