Evidence for admixture within Panthera genome sequences. (A) Species tree topology of the three Panthera species defined by black outline. Blue lines represent coalescent patterns of tiger + snow leopard shared alleles, green indicates lion + tiger shared alleles, and red represents lion + snow leopard shared alleles. (B) Distribution of trees supporting each topology from the genome-wide sliding window analysis (y-axis) plotted against divergence time (x-axis), shown for autosomes and the X Chromosome (see Supplemental Fig. S9 for individual chromosome plots). (C) Mean and standard error for divergence times for each category of sister-species relationship within the three taxa. (D) Phylogeny and relative divergence time (y-axis, in millions of years ago) for each window plotted along the largest autosome (Chromosome A1, above) and the X Chromosome (below). Dots are color-coded for each of the three sister-species relationships (see legend). The gray dots indicate the age of the base of Panthera. Note the drop in divergence times for both internal and basal nodes in regions corresponding to extremely low recombination rates (bottom). Recombination data are from the domestic cat linkage map (Schmidt-Kuntzel et al. 2009).