Extended Data Fig. 5: Results of phylogenetic tests of gene flow direction.

The schematic at the top of the figure shows topologies informative on gene flow from Eurasian into Iberian lynx. An excess of genomic windows returning topologies where the ancient Iberian lynx is in a basal position relative to the number of genomic windows retuning topologies where the contemporary Iberian lynx is basal indicates gene flow from Eurasian lynx onto the modern Iberian lynx population, above that occurring into the ancient Iberian lynx population. The lower part of the figure shows individual results (points) generated using each combination of one contemporary Iberian lynx (30 individuals total) and one of the two Eurasian lynx as representative for the two main Eurasian clades. An excess (mean 1.84-fold higher) of topologies with the ancient Iberian lynx in the basal position in all comparisons indicates that the admixture inferred using D statistics can be attributed, at least in part, to gene flow from Eurasian lynx into ancestors of contemporary Eurasian lynx.