Figure 3.
Proportions of Deleted and Undeleted Chromosomes by Y Haplogroup
(A) Proportions of chromosomes in each Y haplogroup within four deletion classes: undeleted (purple), gr/gr (green), b2/b3 (orange), and b1/b3 (blue). Haplogroups are defined in (B). The height of each bar indicates the proportion of Y chromosomes in that haplogroup within a particular deletion class. For example, the prevalence of gr/gr-deleted chromosomes across haplogroups in the United States sample mirrors that of nondeleted chromosomes, as shown by the fact that the heights of green columns (gr/gr-deleted chromosomes) are similar to the heights of purple columns (nondeleted chromosomes). By contrast, in the Polish sample, the column representing gr/gr-deleted chromosomes in haplogroup F∗xK is lower than the column representing nondeleted chromosomes, but for haplogroup R1a, the gr/gr-deletion column is higher than the column representing nondeleted chromosomes. This indicates that gr/gr-deleted chromosomes are underrepresented in F∗xK and overrepresented in R1a. As discussed in the text, branch N1 was excluded from the analysis. Triangles mark haplogroups that make major contributions to variation in prevalence across haplogroups on the basis of their standardized residuals.20Table S6 provides statistical details, including counts.
(B) Genealogical tree of human Y chromosomes used in determining Y haplogroups for this study. Branch tips are labeled with haplogroup designations with the use of terminology from Karafet et al.19 SNPs shown along branches are summarized in Karafet et al.19 Three haplogroups are defined by a single variant and are monophyletic (E, N1, and R1a); remaining haplogroups are paraphyletic (Table S5). The SRY10831 polymorphism reflects an A>G mutation early in the history of extant Y chromosomes; its reversion in an M207-derived chromosome defines branch R1a.