Fig. 2: Demographic history of Asian wild ass, Somali wild ass, and domestic donkeys.

a Demographic trajectories revealed by PSMC. The time scale on the x-axis is calculated assuming a mutation rate of 7.242 × 10⁻⁹ mutations per generation and site, while the assumed generation time is 8 years^11,87. Bootstrapping confidence intervals for each sample are shown in Supplementary Data 7. b Demographic history of Tropical African donkeys and North African & Eurasian donkeys revealed by SMC++. c Potential admixture events and corresponding times inferred with a model based on PSMC. Autosomal SNPs from randomly selected domestic donkeys (Ch-dz, Ir-3, Ky-7, and Sp-5) and the Somali wild ass were used in this analysis. The admixture events were indicated by crosses on the curves. d Phylogenetic tree based on Y chromosome SNPs from wild asses and domestic donkeys. Sample names in gold represent North African & Eurasian donkeys while sample names in red represent Tropical African donkeys. A total of 13,032 SNPs mapping to the Y chromosome were used to construct the tree. BEAST 2 was applied in this phylogenetic analysis. The parameters for generating the maximum clade credibility (MCC) tree are HKY for the site model, strict clock model for the clock model (clock rate = 1), and Yule model for tree priors. The phylogenetic tree was generated by Bayesian Markov chain Monte Carlo (MCMC) with 1000 simulations. The numbers beside the nodes indicate the estimated node height, the divergence time, and the corresponding 95% confidence intervals. Kya refers to 1000 years ago and Mya refers to million years ago. The node statistical support was assessed by MCMC posterior probability indicated by the edge color linked to the node. In Fig. 1c, d, the following acronyms have been used: Ke (Kenya), Ch (China), Ni (Nigeria), Ir (Iran), Sp (Spain), Eg (Egypt), Et (Ethiopia), Ti (Tibet), Au (Australia), and Don (the European donkey which sequence was reported in a previous study¹³).