Fig. 1.

Y haplogroups present in HS founders and modern HS rats. a) NJ, unrooted tree using Y SNPs and indels in HS founders. Branch lengths correspond to genetic distance. b) Distribution of alleles by rat among Y SNPs passing filters (Supplementary Fig. S2). Plot shows count of reference alleles on X-axis and count of alternate alleles on Y-axis for each rat. Side plots are histograms of allele counts in modern HS rats (small dots). Missingness in low-coverage modern samples leads to scatter on the axes. Labeled large dots are HS founders. Y1 and Y2 haplogroups are labeled. c) Distribution of Y haplogroups in the HS rat population over time. Plot shows birth year on X-axis and haplogroup percentage on Y-axis. d) Pseudo-alignment of Y1 (top) or Y2 (bottom) founder haplotypes, at SNPs passing filters (Supplementary Fig. S2), where Y1 (left) or Y2 (right) founders have intragroup SNPs. Boxed founders have haplotypes present in modern HS rats.