Figure S1 Maximum likelihood tree of SCCmec type I elements in ...

12 00 06 RH RH 59 1 0 RH 12 RH _74 00 12 00 11 E 01 03 00 06 RH 7 0 26 7 9 3 06 6 6 8 _ 7 D 0 0 5 00X0 4 RH 120 12 00 RH _7 40 2 6 07 00 20 11 40 16 0 5 06 9_ 0 17 94 RH 57 74 00 1 120 _7 01 50 7 002 4 1 RH 1 4 _ D 10 1 67 4 8 120 8 R RH1 0 0 2 H 1 07 4 0 19 4 5 50 R H 1 2 0 0 0 1 2 4 _ 7 0 0 0 37 0 1 4 9 R H 1 2 0 0 0 1 9 4 _ 7 4 00 1 7 2863 2000 7_7 167 208_ 4017 5 7401 11 RH12 736 00019 5 _ 7 4 0E 2 9 0 0 1687 D 87 63 RH 10 00 03 97 RH 12 00 01 99 _7 40 17 35 RH1 200 020 1_7 401 664 RH12000 663_740 1752

H

CSA RH7 CS 5 RH A 120 CS RH72 006 AR 87_ RH H0 740 6 1 CS 2 0 0 173 1 CS ARH 0 6 8 8 8 _ A 0 7 CS RH 40 1 1 A 74 CS RH 1 3 R H ARH 65 R H 1 2 40 12 000 00 69 C 06 1_ CS SAR 86 74 AR H2 _7 01 40 68 H7 7 4 17 8 CS 1 9 AR H5 8

01 H R SA C 2 68 8 01 66 3 _74 01 0 4 05 75 _7 00 06 36 11 00 2 5 H 12 000 8 71 R H 2 3 7 01 R H 1 RH 23 74 0172 3 R SA RH 4 2_ C SA H3 0 2 3 3 _ 7 4 0 1 7 0 0 C SAR 0 0 2 3 _ 7 4 1 7 4 C H12 000 231 740 28 R H12 000 62_ 4017 2 R 12 006 1_7 0169 H 6 0 4 6 R 12 00 _7 RH 120 0658 671 RH 1200 0 401 R H ARH1 6 8 2 _ 7 0 1 7 1 6 CS 1 2 0 0 0 6 0 _ 7 4 679 RH 20006 9_7401 RH1 200022 _7401691 1 0 3 H 8 2 R 000 40171 RH12 000678_7 42 R H 1 2 06 80 _7 40 17 R H 12 00 03 76 RH 10 00 CSARH30 RH1 000 037 8 CSARH67 RH12000693_7401708 RH120 00690_ 740167 2 CSARH79 CSARH39 CSARH8 3

RH CS 1 1 0 0 0 CSA R H ARH82 4 9 1 RH4 9 RH 1000 RH 1200 0402 1 RH 20 023 5 0 10 00 0685 _740 1 03 _ 89 740 751 17 07 D7 CS 44 AR 1 H5 9

C C SA C SAR RH7 SA H 1 R 43 H 14

2 H0 6 AR H3 3 CS SAR H1 C AR CS

01 04 00 1 03 1 0RH30 0 4 9 3 63 RH A 00 04 16 3 4 CSH 11 1 0 0 5 40 R H 4 5 0 0 5 09 2 _ 7 4 0 1 7 R 43 1 0 0 1 1 _ 7 E H1 200 067 1 R 1 0 2 RH 120 0039 2 170 R HH 1 0 00 0 0 3 9 2 _ 7 4 0 1 7 3 8 R H10 0022 _740 R H120 0226 R 1200 677 RHA H44 _7401 CS 1R2 0 0 0 2 1 1 R H 25_=_C0X E21 00 05 06 R H 11 E3 18 3 005 10 RH 110 E3015 E3520

R

CSA RH 16

RH10000 375 690 RH1 200 022 1_7 401 RH 11 00 05 00 5 CSARH388 40 16 02 03 _7 1 6 6 5 R H 12 000 0 2 1 0 _ 7 4 00 1 7 1 2 4 0 0 R H 1 2 0 0 2 0 6 _ 7 SARH60 9 C 0 5 0 RH12 100 730 RH1 401 00 9 _ 77 4 0 1 74 9 6 067 0 3 2 0 0 0 2 0 5 _1 1 0 00 1 7 204 0 H RH1 H 60 4 R 7 R 120 9 8 _ SA 3 71 5 06 RH C E 001 E 34 6 73 7 120 E 17 05 RH 4 0 1 7 8 66 _7 40 03 9 7 17 _7 00 03 8 5 02 67 10 00 03 39 0 00 06 H 10 00 0 40 1 2 0 0 RR H 1 0 0 0 0 0 0 0 H R HH 1 2 R H1 10 R R H R

R R H1 R H1 20 H 2 0 12 00 0 R 00 02 20 02 19 0_ R HH 1 2 12 00 R 07 _7 74 0 00 2 H _7 40 01 02 15 10 40 1 74 1 _ 0 1 6 R 8_ 74 00 72 66 7 R HH 1 07 4 00 1 7 3 8 0 4 11 00 17 13 RH 120 C 0 0 0 3 74 9 006 R H CSSAR0 4 9 29 89_ RH1 1 1 AR H08 740 200 0 H 175 5 0 2 0 2 _ E0 0 4 928 7 4 0 371 9 E44 167 7 RH1 2 6 RH1 3 000 2000 039 223_ 4 R H 1 07 4 0 1 7 1 4 RH120 0 00234 0 _ 7 4 0 10 3 9 0 73 RH 12 00 06 E 26 689 84 RH 120 002 28__7 40 16 95 740 166 7 CSARH33 RH11000494 RH12000666 _7401693 RH1 0000 398 CSARH66 81 65 _7 40 16 RH 12 00 06R H 11 00 04 98 00377 R H 1 0704 0 1 6 7 80 2 0 _ 7 4 0 1 6 76 9 0002 R H 1 2 0 0 0 6 7 2 __ 7 4 0 1 66 8 3 1 2 4 R H 1 2 0 0 0 6 6 3 _ 7 4 0 COL9 8 72 RH1 20006 4 0 1_ D 0 X0 7 1 _ H R 6 9 _= 1 7 5 5 0 0 6 4 2 7 87 4 0 0 4 98 2 0 2 0 E _ 1 2 7 1 1 00 0 0 37 2 55 RH 02 0 0 R HH 1 07 4 0 10 5 0 12 R 6_ 100 RH 21 1 00 RH 9 20 1 39 RH 00 99 00 1 6 25 1 0 H H 74 R 6 6 R 6 _ SA 2 2 5 4 19 C D 1 17 85 0 03 00 4 0 12 _7 00 81 10 RH 06 RH 00 2 1 H R

RH12000694_7401720 RH10 00038 1 RH 120 RH 11 006 77_ 740 170 6 E2 77 900 05 11 RH E2 1 1 0 0 0 5 1 2 R H9 4 0 R H 11 2 0 0 0 2 0000 12_7 4016 384 89



CSARH 61 CSAR H09 CSAR H68 CSA RH6 9

CS A CS RH2 CS ARH 2 A CS RH 12 45 AR H4 2

3 H0 AR CS

Additional file 3: Figure S1 Maximum likelihood tree of SCCmec type I elements in historic MRSA isolates. The tree was constructed using variation in 38 SNP core sites identified in 192 isolates. The coloured 0.02 branch labels indicate the isolates used in the parsimonious minimal spanning tree of SCCmec type I elements illustrated in Figure 3A and the temporal analysis illustrated in Figure 3B (also included in Supplementary Figures 1, 2 and 3), and are colour coded according to the genotypes displayed in this figure. The isolates not included in the temporal analysis are in indicated in black text.



RH11000509 RH10000385

posterior 1

RH12000681_7401754 RH10000398 RH11000504 RH12000672_7401670 RH12000202_7401676 RH12000221_7401690 RH12000220_7401678 RH12000217_7401737 RH12000211_7401677 RH12000197_7401711 RH12000194_7401675 RH12000195_7401687 RH11000510 RH12000218_7401749 RH12000234_7401739 RH12000666_7401693 RH10000392 RH11000506 RH11000507 RH12000694_7401720 RH12000689_7401755 RH12000684_7401695 RH12000670_7401741 RH12000669_7401729 RH12000663_7401752 RH12000676_7401694 RH12000679_7401730 RH12000671_7401753 RH12000667_7401705 RH12000657_7401680 RH12000668_7401717 RH12000216_7401725 RH12000210_7401665 RH12000215_7401713 RH12000664_7401669 RH12000677_7401706 RH12000219_7401666 RH12000226_7401738 RH12000222_7401702

0.06

RH10000401 RH11000492 RH11000493 RH10000399 RH10000390 RH11000494 RH10000380 RH10000379 RH11000501 RH10000391 RH11000496 RH10000388 RH10000387 RH10000386 RH10000375 RH12000212_7401689 RH12000205_7401700 RH12000665_7401681 RH12000214_7401701 RH12000203_7401688 RH12000206_7401712 RH12000209_7401748 RH12000208_7401736 RH12000207_7401724 RH10000397 RH11000505 RH12000196_7401699 RH10000384 RH10000381 RH12000683_7401683 RH12000201_7401664 RH11000498 RH12000198_7401723 RH12000200_7401747 RH12000199_7401735 RH10000396 RH10000394 RH11000500 RH11000499 RH10000400 RH10000382 RH10000383 RH12000223_7401714 RH12000224_7401726 RH12000192_7401663 RH10000403 RH12000659_7401704 RH12000227_7401750 RH12000228_7401667 RH10000395 RH10000393 RH10000389 RH12000685_7401707 RH12000690_7401672 RH12000693_7401708 RH12000235_7401751 RH11000491 RH10000402 RH12000687_7401731 RH12000678_7401718 RH11000503 RH12000660_7401716 RH12000232_7401715 RH12000682_7401671 RH12000662_7401740 RH12000229_7401679 RH12000680_7401742 RH12000675_7401682 RH12000233_7401727 RH12000236_7401668 RH12000661_7401728 RH12000658_7401692 RH12000230_7401691 RH12000231_7401703 RH12000688_7401743 RH12000686_7401719 RH12000691_7401684 RH10000377 RH11000495 RH10000376 RH10000378

1945

1945

1950

1950

1955

1955

1960

1960

1965

1965

1970

1970

Additional file 4: Figure S2 Posterior support of maximum clade credibility trees of the historic MRSA population based on BEAST analysis (as illustrated in Figure 3B). Internal branches are colored according to their posterior support (see figure for key).

0.6

Root to tip divergence

0.5

0.4

0.3

0.2

0.1

0 1940

1945

1950

1955

1960

1965

1970

Years

Additional file 5: Figure S3 Linear of the root-to-tip distances of historic MRSA SCCmec type I Supplementary Figure regression 3 elements. The isolates used (n=122) are those indicated in the Additional file 6: Figure S4 and used for the BEAST analysis (Figure 3B). The analysis was carried out using Path-O-Gen v1.4 (http://tree.bio.ed.ac.uk/software/pathogen/) with a best-fit root from the maximum likelihood tree and the dates of isolation. The plot contains straight-line best fit of the root-to-tip divergence for each of the isolates, with a correlation coefficient of 0.5408 and an R2 of 0.2925. The time to most recent common ancestor for the SCCmec type I elements in the archaic clone isolates examined is 1941.



0.12

Root to tip divergence

0.1

0.08

0.06

0.04

0.02

0 1945

1950

1955

1960

1965

1970

Years

Additional file 6: Figure S4 Linear regression of the root-to-tip distances of the archetypal MRSA clone population usedFigure for BEAST analysis. Supplementary 4 The analysis was carried out using Path-O-Gen v1.4 (http://tree.bio.ed.ac.uk/software/pathogen/) with a best-fit root from the maximum likelihood tree and the dates of isolation. The plot contains straight-line best fit of the root-to-tip divergence for each of the isolates, with a correlation coefficient of 0.7907 and an R2 of 0.6525. The time to most recent common ancestor for the whole population was estimated to be 1947, consistent with the Bayesian analyses (as illustrated in Figure 3B).