Fig. 1

a Structure of the hg19 Y chromosome showing the different sequence classes using coordinates from [20]. The black vertical lines represent the uniquely mappable positions used for the analysis (see the “Materials and methods” section). The legend indicates the number of uniquely mappable positions and the proportion of each sequence class included in the analysis. b Neighbor-joining tree of a Y chromosome phylogeny comprising two Neandertals [1, 15], four ancient humans [11,12,13,14] and twenty nine present-day humans [7, 9, 10] with associated relative branch length differences (i.e., the difference in branch length normalized by the total number of sites used for the comparison) compared to a present-day non-African Y chromosome (R1b1a2a1a2b). The haplogroup names are taken from the respective publications. The colors indicate the population of origin. The ancient individuals and their estimated ages are marked in bold. The crosses denote the expected relative branch length differences for the ancient individuals based on their estimated ages and assuming a constant mutation rate of \(7.34 \times 10^{-10}\) mutations/bp/year [1]. The error bars represent 95% confidence intervals (CIs) computed by resampling branch lengths from a Poisson distribution as described in Petr et al. [1]