Figure S1: Maximum-parsimony tree showing sample ...

A B D

bkl-46 bkl-2

eng-GB1758 eng-GB1778 man-231

bak-41 bak-25 bak-20 mbu-29

kun-m82 mbu-33

mbu-5

bak-33

mbu-13 mbu-19 mbe-237P bkl-70

bak-35 mbe-164 bia-m47 bak-55 bhu-1561

bhu-1150 bhu-0957 JPT-NA18944 JPT-NA18940 YRI-NA19175 LWK-NA19380 YRI-NA18856 spa-20 spa-32 LWK-NA19334 gre-17 bhu-1164 bav-13 tur-4 spa-62 pal-4929 gre-78 ser-26 TSI-NA20510 gre-83m ser-2 fri-1320 eng-hgE nor-18 pal-5225 pal-5341 YRI-NA19098 YRI-NA19203 YRI-NA18504 YRI-NA19200 mbe-193P YRI-NA19223 YRI-NA19171 YRI-NA19207 YRI-NA18507 YRI-NA18516 YRI-NA19144 YRI-NA18501 ngo-98 pal-5365 YRI-NA18871 YRI-NA19153 YRI-NA19138 YRI-NA18853 YRI-NA18522 YRI-NA19160 YRI-NA19119 YRI-NA19130 bhu-1000

E CHB-NA18612 bhu-1606 CHB-NA18620 nep-0273

aus-m119 aus-m120

JPT-NA18974

nep-0172

nep-0186 bhu-1151 nep-0809 nep-0902 tur-8 nep-0171 eng-hgH nep-0191 bav-55 ire-0093 tur-1

bas-19 bas-16 pal-4919 pal-4918 hun-47 bas-17 eng-O69 eng-hgG hun-29 tur-2 pal-5047 pal-4940 pal-4922 pal-4921 pal-4947 pal-4941 pal-5048 pal-4942 pal-4943 tur-16 tur-6 eng-O36 TSI-NA20543 pal-5420 gre-3

tur-12 pal-5232 TSI-NA20588 ser-9 ser-13 gre-2 TSI-NA20525 fri-1784 bav-38

tur-13

pal-5257 gre-79

tur-7 tur-10 gre-85m tur-3 TSI-NA20805

gre-11

spa-15 gre-77 tur-14 TSI-NA20534 TSI-NA20765 TSI-NA20815 nep-0385 spa-14 tur-21 tur-5

hun-5

eng-O63 bav-39

gre-4 bas-14

MXL-NA19664

I1

bhu-1892

pal-5366

TSI-NA20527

eng-hgT

bhu-1157

nor-16 CEU-NA12155 TSI-NA20796 bhu-0956 gre-15 bav-26 hun-39 hun-43 tur-17 hun-38 den-30 hun-35 hun-28 bav-52 ser-19 ser-27 hun-25 saa-1 ork-565 ork-579 ork-583 ork-010 ork-036m nor-26 nor-23 eng-hgR1a bhu-0984 gre-10 bav-31 gre-80 TSI-NA20785 hun-33 spa-26u tur-11 bhu-1953 hun-34 spa-40 eng-O15 ser-7 hun-3 bav-56 den-36 fri-1317 den-189 fri-1788 den-104 den-34 eng-F2 nor-27 den-192 bav-27 eng-H38 d e n - 8 2-83 ork-564 fri-1313 den-SN den-186 ork-004 CEU-NA12872 hun-46 den-190 bav-8 fri-1324 bav-29 ork-008 hun-40 eng-O44 TSI-NA20586 fri-1329 CEU-NA07048 eng-O45 fri-1718 ork-022m ire-0116 CEU-NA07357 fri-1516 ser-5 CEU-NA12144 TSI-NA20792 spa-47 hun-2 TSI-NA20783 ire-0078 spa-25 spa-37 ork-585 bas-2 CEU-NA11831 eng-W17 den-150 bav-19 ork-577 spa-54u bav-54 spa-41 spa-63 CEU-NA12043 CEU-NA10851 eng-H18 bas-12 ork-552 eng-G9 ork-584 eng-O93 spa -2 TSI-NA20581 CEU-NA12814 nor-28 eng-F6 TSI-NA20810 ire-112 ork-007 eng-W20 CEU-NA12812 ire-0120 spa-60 ire-0109 ire-0107 ork-571 ire-132 TSI-NA20759 CEU-NA11994 eng-F58 eng-O23 bas-3 bas-9 spa-22 bas-8 spa-31 bas-13 bas-1 bas-5 den-191 nor-3 nor-25 nor-9 TSI-NA20798 TSI-NA20803 TSI-NA20806 TSI-NA20538 ire-74 bas-18 eng-W11 nor-24 ire-0136 ire-0059 CEU-NA12154 ire-55 nor-29 ire-0100 eng-W13 ire-0068 ire-0052 ire-0053 bav-41 ork-575 bas-7 TSI-NA20752 spa-53 bas-11 CEU-NA12716 CEU-NA12707 hun-26 nor-8 bas-6 CEU-NA12874 ork-567 bav-32 bas-15 spa-60u bas-4 bas-10

Figure S1: Maximum-parsimony tree showing sample names. The phylogeny is the same as that shown in Figure 3, but includes sample names.

I2

CHB-NA18632 CHB-NA18561 CHB-NA18603 CHB-NA18637 bhu-1560 CHB-NA18636 CHB-NA18605 bhu-1609 CHB-NA18633 CHB-NA18611 CHB-NA18621 CHB-NA18635 CHB-NA18572 CHB-NA18562 CHB-NA18609 CHB-NA18623 CHB-NA18622 bhu-1554 CHB-NA18624 CHB-NA18558 CHB-NA18608 bhu-1142 bhu-1586 gre-192 tur-15 bhu-1582 saa-18 saa-7 nor-13 saa-6 saa-13 saa-2 gre-37 saa-17 saa-3 saa-8 saa-12 saa-16 saa-15 eng-hgQ-2 bhu-1564 bhu-1813 eng-hgQ-1

ork-026m

J

ire-0114

ser-3

gre-12

G

gre-87 bav-40 nor-17 bav-12 bav-30 CEU-NA12003 den-157 den-50-51

ire-94 ire-0095 gre-86 ser-6 gre-82 gre-5 gre-1 ser-20 gre-84m ser-16 ser-21 fri-1311 ser-28 hun-9 hun-1 CEU-NA11992 ork-525 nor-15 fri-1312 fri-1725 nor-20 fri-1319 nor-14 ser-1 ser-12 eng-O109 bav-53 hun-27 ser-4 den-158 ser-30 ser-23 saa-9 saa-10 saa-5 saa-14 CEU-NA11829 nor-2 nor-21 den-152 hun-37 den-183 CEU-NA12750 den-207 nor-7 den-113 fri-1325 ire-0130 fri-1048 fri-1938 fri-1309 fri-1722 bav-57 fri-1937 fri-1087 den-176 CEU-NA06994 ork-573 saa-11 saa-20 saa-19 tur-9 tur-19 nep-0387 tur-18 bhu-1611

TSI-NA20758

C H

L T O N

Q R1a

R1b