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Supplementary Figure S1 Distribution of observed (blue) and Poisson
expected (red) standard deviation of human-chimpanzee divergence over
different window sizes. The observed variation is consistently larger than
expected, but sample variance starts to increase rapidly in windows less
than ~ 250kb.
Supplementary Figure S2 Co-variation of the divergence rate of different
sequence classes in sliding 1 Mb windows. CpG and non-CpG divergence is
highly correlated. As is repetitive and non-repetitive sequence divergence.
Supplementary Figure S3 Correlation between human-chimpanzee
divergence and distance to the closest telomere for 1 Mb windows on
metacentric (a) or acrocentric (b) chromosomes. Each dot corresponds to a
unique 1 Mb window. The color of the dots represent their mean
recombination rate (red = highest, dark blue = lowest).
Supplementary Figure S4 The ratio of human-chimpanzee non-CpG
divergence over mouse-rat divergence vs. the ratio of human GC-content
over mouse GC-content across 199 syntenic blocks greater than 1 Mb.
Hominid-specific acceleration in subtelomeric blocks is evident even when
ignoring CpG sites.
Supplementary Figure S5 Length distribution of small indels (< 15kb)
detected within scaffolds (a and d) or contigs only (b and c). For chimpanzee
“insertions”, the former is a over-estimate of the number of actual indels due
to assembly artifacts, whereas the latter is a under-estimate, due to the
small contig size.
Supplementary Figure S6 Size distribution of segmental duplications
detected in the chimpanzee genome.
Supplementary Figure S7 Cumulative distribution of Ka/Ki values for
13,454 orthologs as observed (blue), as expected if all orthologs evolved at
Ka/Ki = 0.23 (green), and as expected if 23% of the codons evolved at K a/Ki
= 1 and the rest at Ka/Ki = 0 (red). There is a small excess of orthologs with
Ka/Ki > 1 in the observed distribution, possibly indicating an enrichment of
genes under strong positive selection.
Supplementary Figure S8 Median Ka/Ki over sliding 10-gene windows
across chromosome 1. Three peaks, corresponding to the indicated gene
clusters are visible.
Supplementary Figure S9 Fraction of ancestral (blue) and derived (green)
alleles by frequency in the sample. More ancestral alleles are at high
frequency and more derived are at low frequency. The precise distributions
are skewed by the minor allele frequency distribution and the ascertainment
method for the SNPs, which favored moderate (5-25%) variants over very
low or very high frequency variants.
Supplementary Figure S10 Probability of an allele being ancestral vs
frequency calculated for a constant-size population (no bottleneck), shown
in red, a population having just undergone a bottleneck with b = 0.2, shown
in green, and one have just undergone a bottleneck with b = 0.3, shown in
blue.
Supplementary Figure S11 Distribution of observed pa(x) for samples from
European (CEPH, red), Asian (Japanese and Han Chinese, blue), and West
African (Yoruba, green) HapMap samples in the ENCODE regions. Due to
the small number of variants sampled, the scatter is large, but the trendlines
for Europeans and Asians clearly have slope < 1 while that for West Africans
is ~1.
Supplementary Figure S12 Distribution of diversity-divergence scores
(blue) sorted from highest to lowest along with their high frequency derived
allele skew p-values (green, negative log converted and scaled). Note the
large separation in score of the first six regions from the remainder of the
distribution. Dashed horizontal line shows the score cutoff for skews of pvalue < 0.1.