Fig. 3.

Genealogical discordance in Chromosome X. a The D-statistic for testing introgression for 100-kb windows on chromosome X for tree topology (((ISEA, X), pygmy hog), warthog) (X = EUWB, MS, and XI). Excesses of BABA in 46–86 Mb indicated higher genetic similarity between ISEA and pygmy hog. See supplementary Figs. 9–14 for D-statistic testing introgression for 100-kb windows on autosome chromosomes. b SAGUARO plot illustrating the distribution of the five frequent rooted local topologies over the X chromosome. The red unrooted topologies support introgression from a missing linage into European/North China wild boar. Note that the blue unrooted topology includes the discrepant haplotype within Chinese population (see text for further explanation). ISEA = Islands of Southeast Asia Sus; MS = Meishan; XI = Xiang; EUWB = European wild boar; See Supplementary data 3 for further details and supplementary Figure 8 for results for autosomal chromosomes