The demographic history of the brown hyena was calculated using only the autosomal chromosomes in PSMC (Li and Durbin 2011 (link)). Scaffolds representing the X chromosome of the striped hyena were determined through a synteny analysis to the cat X chromosome (CM001396.2) using Satsuma synteny (Grabherr et al. 2010 (link)). These scaffolds were then removed along with any scaffold shorter than 1 Mb. A consensus diploid sequence was constructed using Samtools (Li et al. 2009) to be used as input for PSMC. PSMC was implemented using parameters previously shown to be meaningful when considering human data. One hundred bootstrap analyses were undertaken. When plotting, we assumed a generation time of 6 years and a mutation rate of 7.5 ×10−9 per generation for autosomes. Generation time was estimated based off of the estimated breeding ages of a number of Namibian brown hyena based on tooth wear. The ages of these individuals being ∼12, 14, 9–11, 4–5, 3–4, and 6 years of age.
In order to estimate the mutation rate, we carried out a pairwise distance analysis on the striped and brown hyena’s autosomes using a consensus base IBS approach in ANGSDv0.913. We then calculated the average per generation mutation rate assuming the divergence date of the two species to be 4.2Ma (Koepfli et al. 2006 (link)), a genome-wide strict molecular clock and a generation time of 6 years. Additional analyses utilizing different mutation rates based on the 95% confidence interval of the brown and striped hyena divergence from Koepfli et al. 2006 (link) (2.6 and 6.4 Ma) can be seen in supplementary figure S3, Supplementary Material online.