Supplementary Information

Supplementary Information for

Repping S, van Daalen SKM, Brown LG, Korver CM, Lange J, Marszalek JD, Pyntikova T, van der Veen F, Skaletsky H, Page DC, Rozen S.

High mutation rates have driven widespread architectural polymorphism among human Y chromosomes. Nature Genetics 38, 463 (2006)

Tables

Supplementary Table 1 Summary of samples and experimental results.
Supplementary Table 2 AZFc architectures that can be generated from the reference sequence in three or fewer homologous recombination events.

Figures

Figure S1 Y-chromosome genealogical tree and structural polymorphisms identified, with sample identifiers and haplotype designations.
Figure S2 AZFc architectures that can be generated from the reference sequence in three or fewer homologous recombination events.
Figure S3 Deletion at center of palindrome P3 in sample PD339.
Figure S4 Structural variant in sample YCC038.
Figure S5 Mutational event that can generate AZFc architecture c6.
Figure S6 Mutational pathway that can generate AZFc architecture c36.
Figure S7 Mutational pathways that can generate AZFc architecture c38.
Figure S8 Copy number of BPY2 and CDY1 genes.

Files

Supplementary Methods" Includes:

Assays for potential structural polymorphisms
Non-ampliconic structural differences from chimpanzee are not polymorphic
Reproducibility of measurements of distal-Yq heterochromatin length
Verification of TSPY array-size results
STSs and probes used to investigate PD339 and YCC038
Minimum-mutation histories of structural polymorphisms
Total branch length in genealogical tree of 47 Y chromosomes
Maximum likelihood analysis of rate of IR3/IR3 inversion events
Haplotype of the human Y-chromosome reference sequence
Rates of large-scale structural mutations compared to other kinds of mutations
Assaying distal-Yq heterochromatin length in WHT3299
Assaying the number of gray amplicons in WHT2426
Availability of cell lines
References