Application of recent developments of molecular tools in the conservation of cheetahs

  • David Thuo

Student thesis: Doctoral Thesis


Paradigm shifts in the field of conservation biology along with continuous decline in biodiversity in the past few decades have elicited the need to develop and apply robust, cheap, and easily available tools in conservation planning. Among the recent technological tools, advances in molecular techniques have presented a multitude of opportunities in the studies of biodiversity and nature conservation. The research presented in this thesis investigates the potential of two different emerging molecular techniques; DNA metabarcoding and single nucleotide polymorphisms as conservation and management tools for cheetahs Acinonyx jubatus, Africa’s most threatened big cat. There are only 7,100 cheetahs left in the wild, reduced from over 100,000 a century ago, existing only in 9% of their historical distributional range. This range-wide decline is largely associated to habitat loss and fragmentation, prey base decimation and persecutions. The majority of the 7,100 individuals occur outside government protected areas, therefore I have used this species as a case study for managing human-carnivore conflict. In these non-protected areas, there is a high likelihood of human-carnivore conflicts with the repercussions being meted on cheetahs as they are easy to sight and kill regardless of their involvement in livestock predation. Moreover, modern cheetahs are threatened by the lack of genetic diversity linked with the population collapse more than 12,000 years ago, making them especially prone to diseases and poor reproduction. I review the current state of biodiversity loss especially in relation to carnivores and highlight different molecular techniques and approaches that have so far been used to underpin the diet and patterns of genetic variation of wild species. Next, I validate the potential of DNA metabarcoding in dietary analysis of cheetahs using captive individuals and then I apply this technique to characterise the diet of free-ranging cheetahs in Kenya to assess the level of livestock predation. Finally, I examine the potential of cheetah-specific single nucleotide polymorphism (SNPs) markers generated using genome-complexity reduction approach to describe evidence of population and regional substructure.
The results demonstrate that DNA metabarcoding provides a sensitive method of prey detection in cheetah scats and highlights the need to account for systematic biases to control for possible scat degradation, feeding day, meal size and prey species consumed. Also, the results showed that cheetahs in Kenya prey on a diverse range of taxa and domestic animals form a small component of their diet. Finally, the SNP data showed low values across all samples, suggesting limited genetic diversity in Kenyan cheetahs but they provided evidence for genetic differentiation between the southern population (Maasai Mara) and northern population (Laikipia). This thesis describes all of the methods used and provides a useful resource for further research that involves elusive and endangered species.
Date of Award2021
Original languageEnglish
SupervisorDianne Gleeson (Supervisor) & Elise Furlan (Supervisor)

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