Fig. 3.

Multisite genotype structure. Each row refers to a multisite genotype of one rat. (A) At a randomly chosen locus, there is no clear clustering of multisite genotypes. (B) An example of a locus that was detected as a putative target of selection with H-scan, in which there is one multisite genotype frequent (11/29) in the NYC sample. This pattern is consistent with a hard selective sweep. (C) A candidate locus identified with G12 in which there are more than two frequent multisite genotypes—consistent with a soft selective sweep. (D) A comparison of the NYC samples to a sample of nine rats from the presumed ancestral range of the species in China, around the same focal site as in panel (C). Multisite genotypes are relatively heterogeneous in the Chinese sample where homogeneity is observed in the NYC sample. This observation is consistent with a recent onset of selection after the split from the ancestral population in China.