Supplemental Material
Figure S1:
Figure S1 legend: Images of mixed monolayers with fluorescent staining. HeLa cells were
stained orange, BHK cells were stained green, and nuclei were stained blue. A) B1:H10 B)
B1:H1 c) B10:H1.
Figure S2:
0.2
0.3
0.1
0.2
0.3
40
0
0.0
0.4
20
Frequency
40
20
0
0.0
0.4
0.1
0.2
0.3
0.0
0.4
0.1
0.2
0.3
0.4
Percent of population
Percent of population
Frequency distribution of minority variants
B1:H0_A_1
Frequency distribution of minority variants
B1:H0_A_2
Frequency distribution of minority variants
B1:H10_A_1
Frequency distribution of minority variants
B1:H10_A_2
0.3
0.0
0.4
0.1
0.2
0.3
0
0.0
0.4
20
Frequency
40
0
0
0.2
20
Frequency
40
20
Frequency
40
20
0.1
40
Percent of population
0
0.1
0.2
0.3
0.0
0.4
0.1
0.2
0.3
0.4
Percent of population
Percent of population
Percent of population
Frequency distribution of minority variants
B5:H1_C_1
Frequency distribution of minority variants
B5:H1_C_2
Frequency distribution of minority variants
B1:H10_C_1
Frequency distribution of minority variants
B1:H10_C_2
0.2
0.3
Percent of population
0.4
0.0
0.1
0.2
0.3
Percent of population
0.4
0
20
Frequency
40
0
0
0.1
20
Frequency
40
Frequency
40
20
0
0.0
40
Percent of population
20
Frequency
Frequency
40
0
0.1
Percent of population
0.0
Frequency
20
Frequency
40
20
0
Frequency
0.0
Frequency distribution of minority variants
B1:H1_C_2
Frequency distribution of minority variants
B1:H1_C_1
Frequency distribution of minority variants
Ancestor_2
Frequency distribution of minority variants
Ancestor_1
0.0
0.1
0.2
0.3
Percent of population
0.4
0.0
0.1
0.2
0.3
0.4
Percent of population
Figure S2 legend: Distributions of minority allele frequencies in VSV populations. Alleles are
included in this analysis if they are >1% frequency and occur at a site with coverage >30. The
distributions above are a representative sample of the populations sequenced. These distributions
show that most minority alleles exist at low frequencies (>5%). Each population was sequenced
in duplicate, and the two technical replicates are shown side by side (e.g. Ancestor_1 and
Ancestor_2).
Appendix 1:
2661398
3218552
1448444
2811326
2412636
2041640
1464686
1836618
1822050
2921200
1029110
1905532
2365244
1049068
2811898
1789820
2355832
1185472
1804304
3221144
761840
1069158
1159400
2122722
1434992
2653084
1844706
1462548
2060884
2316164
1762744
2209128
1811072
1558068
1527012
2445994
2430000
1448534
1610804
870972
3119120
3431160
2423638
698446
2637826
3204428
1433914
2785988
2387198
2022292
1450612
1821066
1806728
2893096
999442
1886558
2345244
1022342
2784466
1761154
2332542
1173518
1781766
3194110
744256
1053136
98.8%
99.1%
98.8%
99.1%
98.7%
99.2%
98.9%
98.9%
98.9%
98.9%
98.8%
98.5%
98.2%
99.0%
99.0%
98.6%
98.2%
98.2%
99.2%
99.2%
99.0%
98.9%
99.1%
99.6%
99.0%
99.1%
98.9%
99.1%
99.0%
99.2%
99.2%
99.0%
97.1%
99.0%
99.2%
97.5%
99.0%
98.4%
99.0%
99.0%
98.8%
99.2%
97.7%
98.5%
5448
6582
5930
6723
6233
5855
6565
6524
6282
6655
6449
6574
6627
6816
6639
6031
6838
4633
6745
6775
7132
4048
7240
6786
5994
6651
6445
6602
6494
7118
6969
7452
4991
6533
6665
5044
7447
6949
6637
5856
6987
6720
4377
5238
Population Replicate 1 Replicate 2 Total Reads Rep 1 Total Reads Rep 2 Mapped reads Rep 1 Mapped reads Rep 2 Mapping percentage Rep1 Mapping percentage Rep2 Av Cov. Rep 1 Av Cov. Rep 1
1173656
2142486
1452904
2677216
1868860
1474180
2083058
2342388
1781630
2233018
1832996
1582500
1555408
2469762
2455302
1469104
1639678
887296
3145078
3459856
2447880
706018
Treatment
37
16
17
18
19
38
21
22
23
24
25
39
40
28
29
30
43
44
33
41
42
36
A
B
C
A
B
C
A
B
C
A
B
C
A
B
C
A
B
C
A
B
C
15
1
2
3
4
20
5
6
7
8
9
26
27
10
11
12
31
32
13
34
35
14
ANCESTOR
100% BHK
100% BHK
100% BHK
90% BHK, 10% HeLa
90% BHK, 10% HeLa
90% BHK, 10% HeLa
80% BHK, 20% HeLa
80% BHK, 20% HeLa
80% BHK, 20% HeLa
50% BHK, 50% HeLa
50% BHK, 50% HeLa
50% BHK, 50% HeLa
20% BHK, 80% HeLa
20% BHK, 80% HeLa
20% BHK, 80% HeLa
10% BHK, 90% HeLa
10% BHK, 90% HeLa
10% BHK, 90% HeLa
100% HeLa
100% HeLa
100% HeLa
Appendix 2:
Treatment
Population
ANCESTOR
100%/BHK
100%/BHK
100%/BHK
90%/BHK,/10%/HeLa
90%/BHK,/10%/HeLa
90%/BHK,/10%/HeLa
80%/BHK,/20%/HeLa
80%/BHK,/20%/HeLa
80%/BHK,/20%/HeLa
50%/BHK,/50%/HeLa
50%/BHK,/50%/HeLa
50%/BHK,/50%/HeLa
20%/BHK,/80%/HeLa
20%/BHK,/80%/HeLa
20%/BHK,/80%/HeLa
10%/BHK,/90%/HeLa
10%/BHK,/90%/HeLa
10%/BHK,/90%/HeLa
100%/HeLa
100%/HeLa
100%/HeLa
A
B
C
A
B
C
A
B
C
A
B
C
A
B
C
A
B
C
A
B
C
10%
5%
1%
4
5
2
5
4
6
9
7
7
5
5
4
5
3
10
5
5
5
11
5
8
5
9
10
9
12
8
13
17
20
13
14
15
10
13
9
20
11
15
12
23
13
16
12
112
94
80
191
301
111
181
243
102
181
135
227
214
174
210
309
277
125
235
247
239
122
Appendix 2 legend: For each sequenced population, this table lists the number of minority alleles
detected at each frequency cut-off. Each population was sequenced in duplicate, and only alleles
detected in both technical replicates were included in this analysis.
Appendix 3:
Appendix 3: Depth of coverage over the genome for each sample. Locations of primers and
amplicons used to amplify genome fragments shown by arrows and dotted lines above
reference genome. Coverage figures generated using BEDTools v2.25.0 (1) and Integrative
Genomics Viewer (IGV) v2.3.61 (2, 3). Continued on next page.
1.
2.
3.
Quinlan, Aaron R., Ira M. Hall. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26 (6).
841-842 (2010).
James T. Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P.
Mesirov. Integrative Genomics Viewer. Nature Biotechnology 29, 24–26 (2011).
Helga Thorvaldsdóttir, James T. Robinson, Jill P. Mesirov. Integrative Genomics Viewer (IGV): high-performance genomics data
visualization and exploration. Briefings in Bioinformatics 14, 178-192 (2013).
Appendix 3 (continued):
Appendix 3: Depth of coverage over the genome for each sample. Locations of primers and
amplicons used to amplify genome fragments shown by arrows and dotted lines above
reference genome. Coverage figures generated using BEDTools v2.25.0 (1) and Integrative
Genomics Viewer (IGV) v2.3.61 (2, 3). Continued on next page.
4.
5.
6.
Quinlan, Aaron R., Ira M. Hall. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26 (6).
841-842 (2010).
James T. Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P.
Mesirov. Integrative Genomics Viewer. Nature Biotechnology 29, 24–26 (2011).
Helga Thorvaldsdóttir, James T. Robinson, Jill P. Mesirov. Integrative Genomics Viewer (IGV): high-performance genomics data
visualization and exploration. Briefings in Bioinformatics 14, 178-192 (2013).
Primer Sequences
Primers used to generate amplicons for VSV consensus sequencing.
Forward Primer
Reverse Primer
CGAAGACAAACAAACCATTATTATC TGGTTCAGATTCTGTGTCAG
AATTGACAGCTCTTCTGCTC
CTTCTCTCTGAAATCAGA
GAAAAATGTTCCTTCCAATTACCA
GGGATTGGCTTGACATGATG
TCAGAACATACTCAGATGTGG
GTCCATGGAAATGAGGTT
TCATCTTAGCTCAAAGGCTC
TGGGTCTAGTAAGTCGGGTA
GACTCATTCAAAATTCTCGC
CAAGAGTCTAGCAAATGTCC
GCTCTCAATCAAATGGTTTC
AGGAATGGAGGTGATACACT
GTGGGGACAAGAGATAAAAC
ACGAAGACCACAAAACCAG
Fitness Data for evolved VSV populations
Treatment (% BHK)
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
100
91
91
91
91
91
91
91
91
91
91
91
91
91
91
91
91
91
91
83
83
83
83
83
83
83
83
83
83
83
83
83
83
83
83
83
83
50
50
50
50
50
50
50
50
50
Assayed Population log W relative to common competitor Assay Host
B1:H0 A
0.47778577 BHK
B1:H0 A
0.415515444 BHK
B1:H0 A
1.10219011 BHK
B1:H0 A
2.778819272 HeLa
B1:H0 A
0.621309357 HeLa
B1:H0 A
0.916290732 HeLa
B1:H0 B
1.360318875 BHK
B1:H0 B
1.570638163 BHK
B1:H0 B
-0.449916871 BHK
B1:H0 B
1.422012444 HeLa
B1:H0 B
1.094497555 HeLa
B1:H0 B
2.233646663 HeLa
B1:H0 C
1.037987667 BHK
B1:H0 C
-0.258583542 BHK
B1:H0 C
1.811866593 BHK
B1:H0 C
1.501721683 HeLa
B1:H0 C
0.644957797 HeLa
B1:H0 C
1.890258895 HeLa
B10:H1 A
0.463572739 BHK
B10:H1 A
0.550488326 BHK
B10:H1 A
-0.217218862 BHK
B10:H1 A
0.066609941 HeLa
B10:H1 A
0.344346293 HeLa
B10:H1 A
0.751763824 HeLa
B10:H1 B
-1.04668106 BHK
B10:H1 B
-0.064941017 BHK
B10:H1 B
-0.251314428 BHK
B10:H1 B
1.966980621 HeLa
B10:H1 B
1.458615023 HeLa
B10:H1 B
1.751174189 HeLa
B10:H1 C
1.007383276 BHK
B10:H1 C
2.784129019 BHK
B10:H1 C
1.439791108 BHK
B10:H1 C
0.346276237 HeLa
B10:H1 C
1.230695874 HeLa
B10:H1 C
1.097509753 HeLa
B5:H1 A
-1.08797389 BHK
B5:H1 A
-0.909370289 BHK
B5:H1 A
-1.225333931 BHK
B5:H1 A
1.993625622 HeLa
B5:H1 A
-0.120627988 HeLa
B5:H1 A
0.255055218 HeLa
B5:H1 B
0.225609644 BHK
B5:H1 B
1.17711974 BHK
B5:H1 B
0.657429098 BHK
B5:H1 B
0.785468509 HeLa
B5:H1 B
0.486306007 HeLa
B5:H1 B
0.449384342 HeLa
B5:H1 C
0.523498175 BHK
B5:H1 C
-0.136132174 BHK
B5:H1 C
0.332705754 BHK
B5:H1 C
0.772093998 HeLa
B5:H1 C
1.828844216 HeLa
B5:H1 C
0.275653497 HeLa
B1:H1 A
0.10336215 BHK
B1:H1 A
-0.73496247 BHK
B1:H1 A
0.345127472 BHK
B1:H1 A
0.754357912 HeLa
B1:H1 A
1.033097682 HeLa
B1:H1 A
0.236827471 HeLa
B1:H1 B
-1.024924573 BHK
B1:H1 B
0.878864326 BHK
B1:H1 B
-1.067170763 BHK
Treatment (% BHK)
50
50
50
50
50
50
50
50
50
17
17
17
17
17
17
17
17
17
17
17
17
17
17
17
17
17
17
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
9
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
0
Assayed Population log W relative to common competitor Assay Host
B1:H1 B
0.358212223 HeLa
B1:H1 B
0.830358662 HeLa
B1:H1 B
-0.405111188 HeLa
B1:H1 C
-1.149384614 BHK
B1:H1 C
-0.884202417 BHK
B1:H1 C
0.610478076 BHK
B1:H1 C
0.805065097 HeLa
B1:H1 C
1.735670003 HeLa
B1:H1 C
0.679416988 HeLa
B1:H5 A
0.014473165 BHK
B1:H5 A
-0.673729095 BHK
B1:H5 A
-0.898999235 BHK
B1:H5 A
0.865708422 HeLa
B1:H5 A
0.96192083 HeLa
B1:H5 A
0.470003629 HeLa
B1:H5 B
0.594707108 BHK
B1:H5 B
0.497872528 BHK
B1:H5 B
0.776911369 BHK
B1:H5 B
3.432435132 HeLa
B1:H5 B
1.187843422 HeLa
B1:H5 B
1.934671331 HeLa
B1:H5 C
-0.277319285 BHK
B1:H5 C
-4.239221605 BHK
B1:H5 C
-0.713950308 BHK
B1:H5 C
1.70296397 HeLa
B1:H5 C
2.261246436 HeLa
B1:H5 C
0.8940017 HeLa
B1:H10 A
0.630846154 BHK
B1:H10 A
-0.351186051 BHK
B1:H10 A
1.208746083 BHK
B1:H10 A
0.071188262 HeLa
B1:H10 A
0.303995648 HeLa
B1:H10 A
1.192426813 HeLa
B1:H10 B
-0.318817301 BHK
B1:H10 B
-0.855927002 BHK
B1:H10 B
-0.511549344 BHK
B1:H10 B
1.61485798 HeLa
B1:H10 B
1.735130857 HeLa
B1:H10 B
1.196791445 HeLa
B1:H10 C
-0.167838706 BHK
B1:H10 C
-0.429418349 BHK
B1:H10 C
-0.853489831 BHK
B1:H10 C
1.241713132 HeLa
B1:H10 C
2.915310706 HeLa
B1:H10 C
1.915951962 HeLa
B0:H1 A
0.020000667 BHK
B0:H1 A
0.746391695 BHK
B0:H1 A
0.232114817 BHK
B0:H1 A
1.351751064 HeLa
B0:H1 A
0.391024424 HeLa
B0:H1 A
1.727220948 HeLa
B0:H1 B
-0.215361411 BHK
B0:H1 B
-0.057238232 BHK
B0:H1 B
0.577892591 BHK
B0:H1 B
1.661139287 HeLa
B0:H1 B
1.081735418 HeLa
B0:H1 B
1.367062999 HeLa
B0:H1 C
1.196649403 BHK
B0:H1 C
0.760625218 BHK
B0:H1 C
1.200591975 BHK
B0:H1 C
0.853822403 HeLa
B0:H1 C
0.864597808 HeLa
B0:H1 C
0.971017534 HeLa