Neighbor joining trees of population samples, based on Manhattan distances.

<p>The scale bars refer to the number of substitutions per SNP genotyped. (A) For all autosomal SNPs in the study, grouped by sample and rooted by outgroup species. The shorter branch lengths for the <i>M. m. musculus</i> populations as well as the outgroups reflect the ascertainment bias for polymorphic SNPs in these subspecies and species. (B) For all haplotypes of a 6MB region on chromosome 6. Some haplotypes of Kaz group with <i>M. m. domesticus</i> due to introgression. The Cze population is partially introgressed by shorter fragments of <i>M. m. domesticus</i> haplotypes in this region (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002891#pgen.1002891.s001" target="_blank">Figure S1</a> for depiction of haplotype tracks of this region), which results in some paraphyletic groupings for some haplotypes.