1
Supporting Information
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Supporting Tables
Table S1: Strains and Sequence Data Used in This Study
Strain Name
CCMV strain
Heberling
RhCMV strain 68-1
RhCMV Strain 180.92
Strain 3301
Strain 6397
Strain BE/9/2010
Strain BE/10/2010
Strain BE/11/2010
Strain BE/21/2010
Strain BE/27/2010
Strain Davis
Strain HAN
Strain HAN1
Strain HAN2
Strain HAN3
Strain HAN8
Strain HAN12
Strain HAN16
Strain HAN19
Strain HAN22
Strain HAN28
Strain HAN31
Strain JHC
Strain JP
Strain PAV16
Strain PAV18
Strain PAV21
Strain Toledo
Strain TR
Strain U01 FINAL
Organism
GenBank
Accession
Number
Panine herpesvirus 2
NC_003521.1
Macacine herpesvirus
3
Macacine herpesvirus
3
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
NC_006150.1
DQ120516
GQ466044.1
JX512197.1
KC519319.1
KC519320.1
KC519321.1
KC519322.1
KC519323.1
JX512198.1
KJ426589.1
JX512199.1
JX512200.1
JX512201.1
JX512202.1
JX512203.1
JX512204.1
JX512205.1
JX512206.1
JX512207.1
JX512208.1
HQ380895.1
GQ221975.1
KJ872539.1
KJ872540.1
KJ872542.1
GU937742.1
KF021605.1
JN379814
Source
Throat Swab
Urine
Lung Tissue
Urine
Urine
Urine
Urine
Urine
Urine
Urine
Liver
Unknown
Bronchoalveolar Lavage
Bronchoalveolar Lavage
Bronchoalveolar Lavage
Bronchoalveolar Lavage
Bronchoalveolar Lavage
Urine
Bronchoalveolar Lavage
Bronchoalveolar Lavage
Bronchoalveolar Lavage
Bronchoalveolar Lavage
Blood
Prostate
Amniotic Fluid
Amniotic Fluid
Amniotic Fluid
Urine
Vitreous Humor
Urine
1
Strain U04 FINAL
Strain U33 FINAL
Strain UKNEQAS1
Strain VR1814
Strain Merlin
Strain HAN20
Strain HAN38
Strain 3157
Strain HAN13
Strain PAV20
Strain TB/40E
Strain AF1
Strain U11
Strain U8
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
Human herpesvirus 5
JN379815
JN379816
KJ361971.1
GU179289.1
NC_006273.2
GQ396663.1
GQ396662.1
GQ221974.1
GQ221973.1
KJ872541.1
EF999921
GU179291.1
GU179290.1
GU179288.1
Urine
Urine
Urine
Cervical Secretions
Urine
Bronchoalveolar Lavage
Bronchoalveolar Lavage
Urine
Bronchoalveolar Lavage
Amniotic Fluid
Throat Wash
Amniotic Fluid
Urine
Urine
3
2
Table S2: Linear model fit of intraspecies diversity modela
Estimate
Standard Error
4
t
Pr(>|t|)
Intercept
-1.87962
0.06348
-29.61
2 x 10-16
Divergence
0.66219
0.10703
6.187
1.71 x 10-09
Recombination Rate
0.16581
0.03164
5.241
2.75 x 10-07
-16
2
a. F-statistic: 45.75 on 2 and 470 DF, p-value < 2.20 X 10 , Adjusted R = 0.2018
3
5
6
7
Figure S1: HCMV genome-wide recombination rates. Population-scaled recombination rates
(2Ner) were calculated in 500 base pair windows, log transformed and plotted by genomic
coordinate.
8
4
9
10
11
Figure S2: Log transformation of intraspecies diversity (π). Distribution of intraspecies
diversity (π) prior to (A) and after log transformation (C). Normal Q-Q Plots of untransformed (B)
and log transformed (D) intraspecies diversity.
12
5
13
14
15
16
Figure S3: Log transformation of population-scaled recombination rates (2Ner).
Distribution of population-scaled recombination rates (2Ner) prior to (A) and after log
transformation (C). Normal Q-Q Plots of untransformed (B) and log transformed (D) populationscaled recombination rates (2Ner).
17
6
18
19
20
Figure S4: Log transformation of interspecies divergence (Dxy). Distribution of interspecies
divergence (Dxy) prior to (A) and after log transformation (C). Normal Q-Q Plots of
untransformed (B) and log transformed (D) interspecies divergence (Dxy).
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7
22
23
24
25
26
27
28
29
Figure S5: CLR values from neutral simulations. Presented are results from two sets of
neutral simulations. The first set consisted of 1000 simulations performed with the ms program,
with values of theta and rates of recombination set equal to the HCMV genome wide averages
and a constant population size. The second set of simulations was similar to the first but
included a 99% reduction of population size 500 generations in the past followed by exponential
growth to the current size. Both sets of results are presented on the same scale for ease of
comparison. Red lines indicate the 99% significance threshold obtained from the simulated
data.
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8
31
32
33
34
35
36
37
38
39
40
41
42
Figure S6: Correlation of HCMV intraspecies diversity, interspecies divergence and
recombination rates from a thinned dataset. Intraspecies diversity (π), interspecies
divergence (Dxy), and population recombination rates (2Ner) were calculated in 500 bp. A
thinned dataset was selected by including only windows located every 5,000 bps across the
genome. Scatter plots of (A) population recombination rates (2Ner) and intraspecies diversity (π)
(Pearson’s R = 0.44, P = 1.6 x 10-03) (B) interspecies divergence (Dxy) and intraspecies diversity
(π) (Pearson’s R = 0.49, P = 2.8 x 10-04) (C) population recombination rates (2Ner) and
interspecies divergence (Dxy) (Pearson’s R = 0.35, P = 1.3 x 10-02) and (D) the corrected levels
of intraspecies diversity (π/Dxy) and population recombination rates (2Ner) (Pearson’s R = 0.28,
P = 6.0 x 10-02). Blue lines represent linear regressions of the data and grey shading indicates
the 95% confidence intervals. All statistics are log transformed prior to calculation of correlations
and plotting.
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9
44
45
46
47
48
49
50
Figure S7: Haplotype Maps of Putative Regions of Selective Sweeps. Shown are haplotype
maps of 100 bp regions within the putative selective sweep regions identified in Figure 6. The
maps are shown for the regions corresponding to (A) lncRNA2.7, (B) lncRNA4.9, and (C)
lncRNA5. For each panel, the top sequence is CCMV and all sequences below are the HCMV
sequences analyzed. Mismatches within the alignment are colored (G = Yellow, C = Blue, A =
Red, T = Green).
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