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Sample analyses

The following microsatellite loci will be utilised to generate genetic data: FCA001, FCA008, FCA026, FCA031, FCA057, FCA069, FCA075, FCA085, FCA096, FCA097, FCA105, FCA113,  FCA126, FCA193, FCA224, FCA230, FCA240, FCA272, FCA275, FCA310, FCA391, FCA441, FCA453, FCA506, F115, F37, F41, F42 (primer sequences in Menotti-Raymond et al. 1999), ZnF (sex marker, primer sequence in Pilgrim et al. 2005) and KCH (king cheetah marker: Forward primer 5’-GTTGGAAGAGCACCAGAAGC-3’; reverse primer 5’-CAAAACCCTCAGCCATCACT-3’, Kaelin et al. 2012).

Heterozygosity and Hardy-Weinberg equilibrium values will be calculated using Cervus (Kalinowski et al. 2007) and inbreeding coefficients (Fis) will be calculated in GenePop using Weir & Cockerham (1984) methods (Raymond & Rousset 1995). These values will be used in conjunction with known origin (free roaming Cheetah caught on commercial farmland versus metapopulation Cheetah immobilised on small fenced reserves) to assess the current level of biodiversity of the cheetah metapopulation in relation to other wild Cheetah populations in South Africa. STRUCTURE (Pritchard et al. 2000) will be used to determine if there is more than one genetically distinguishable population within the samples. The GenAlEx macro for Excel (Peakall & Smouse 2006) will be used to look for rare alleles within the population.  Coancestry (Wang 2011) will be used to determine the relatedness between individuals.

Based on the information determined from the above analyses, it will be possible to make conclusions regarding the overall genetic health of the metapopulation as well as recommendations regarding movement of individual animals to conserve heterozygosity and rare alleles, and to prevent inbreeding.