Supporting Information

Zhao et al. 10.1073/pnas.0907844106 SI Text

1. Andrews RM, et al. (1999) Reanalysis and revision of the Cambridge reference sequence 5. Sun C, et al. (2006) The dazzling array of basal branches in the mtDNA macrohaplo- for human mitochondrial DNA. Nat Genet 23:147. group M from India as inferred from complete genomes. Mol Biol Evol 23:683–690. 2. Kong Q-P, et al. (2003) Phylogeny of East Asian mitochondrial DNA lineages inferred 6. Olivieri A, et al. (2006) The mtDNA legacy of the Levantine early Upper Palaeolithic in from complete sequences. Am J Hum Genet 73:671–676. Africa. Science 314:1767–1770. 3. Palanichamy MG, et al. (2004) Phylogeny of mitochondrial DNA macrohaplogroup N in 7. Bandelt H-J, Macaulay V, Richards M (2000) Median networks: Speedy construction and India, based on complete sequencing: Implications for the peopling of South Asia. Am J greedy reduction, one simulation, and two case studies from human mtDNA. Mol Hum Genet 75:966–978. Phylogenet Evol 16:8–28. 4. Kong Q-P, et al. (2006) Updating the East Asian mtDNA phylogeny: A prerequisite for 8. Soares P, et al. (2009) Correcting for purifying selection: An improved human mito- the identification of pathogenic mutations. Hum Mol Genet 15:2076–2086. chondrial molecular clock. Am J Hum Genet 84:740–759.

Zhao et al. www.pnas.org/cgi/content/short/0907844106 1of7 N9a1 Y F1a1a F2a F2b F4a B4a B4b1 B5a2 B5b2 R11 J1b1 T1a T2 R2 U2 U4 U7 K H Tibetan- specific

16189 16108 16134 16362 16187 16463 Northern 16248 F1b 16309 16129 16234 16189 16092 16274 16093 16234 16111 F1a1 16284 16111 16186 182 16266 B4c1 146 16136 16129 16299 16261 16163 16296 16162 F1c 16311 499 16261 195 16399 16249 16222 152 16519 F1a 16362 B5a 16111 16232A 16291 16203 16311 B5b 16172 16318T 16311 16207 16311 16051 16356 Common 16172 10454 152 16145 16071 152 16224 -7025a A10 146 189 N9a 16231 152 R9b 16266A 16243 16069 152 11299 F1a’c 185 @16223 210 204 295 16355 16126 242 16189 16362 16293C 14178 16129 16189 B4 F1 16145 A 240 16261 -12406o 16390 16140 195 16257A 10609 16217 16519 F 8584 16294 150 HV B 10310 16319 249d 16290 8281-8289d 16126 14766 663/+663e R9 73 235 12372 152 16304 1811 13928C 16189 4216 R 5417 16223 N 12705

M7b1 C5a Z M8a M11 M12 G1a1 G1a2 G3a1 D4a3 D4g2a D4i D4j D4n D4o1 D4o2 D5a2a D5b M9a M9c M13b M16 M4b1 M1

16148 @16327 16051 16189 16093 16189 16192 16164 16261 146 16263 16249 16319 16232 16172 16519 16295 16066 16362 16092 94 16274 16093 16158 16357 16215 16316 M13a 16129 16093 16209 456 152 16086 195 150 16274 16311 16519 16260 152 16294 1169616355A 150 143 D4b1 298 16316 16256 16311 C5 16185 16325 16290 16311 16269 G2a1 16T 200 D5a2 16257 16519 152 150 16184 D4a 16519 16129 16381 16168 16295 16319 M10a 16519 16311 326 16290 16189 513 16260 16288 +14465s 16381 16519 16249 318 16234 16227 15721 M7b M7c 16266 16362 13651 16189 215 16172 16319 15629 C 16129 16270 12007 16129 146 12030 16290 15520 G2a 152 16093 511 6680 +10644k G3 195 15510 16297 D5 152 6446 16327 204 6680 195 146 +13262a 16234 150 4164 16278 D4 16189 16274 150 M10 -10397a 150 3010/-3008l M9’b 16188 249d G M7b’c 16145 M8 6253 3394/+3391e 6023 16311 4833/+4831f -5176a 153 152 +9820g 12549 4883 6455 16298 199 4715 16362 M

489 L3

Fig. S1. Classification tree of the identified mtDNA lineages in our Tibetan samples. This tree was constructed based on published phylogenetic trees (2–6), as summarized in Table S3. The lineages found in Tibetans were classified tentatively into 3 groups: Tibetan-specific, Northern (i.e., northern Altaic populations, Tibeto-Burman populations, and Hans), and Common (based on population data listed in Table S2). The characteristic mutations [recorded according to the revised Cambridge reference sequence (1)] considered and typed in the present study are indicated on the branches with an arbitrary order. The A/C length polymorphism in regions 303–315 and 16182–16188 was disregarded for tree reconstruction. Suffixes ‘‘A,’’ ‘‘C,’’ and ‘‘T’’ refer to transversions; ‘‘d‘‘ denotes deletion; and recurrent mutations are underlined. The restriction enzymes are designated by the following codes: a, AluI; e, HaeIII; f, HhaI; g, HinfI; k, RsaI; l, TaqI; o, HincII; and s, AccI. ’’Ϫ‘‘ and ’’ϩ‘‘ denote the absence and presence of the restriction site, respectively.

Zhao et al. www.pnas.org/cgi/content/short/0907844106 2of7 Tibetan Kazak Han Buryat Mg Sala 2TW M9a2 : HN Tujia Hui 17.51 [10.48, 24.54] kya Yugur 16178 16248 Yi 3N SC Bai Dongxiang SD Mg Bonan Q Tu 2R N 16086 G 16309 16356 SX SX 16265T 16176 16355 16051 16114G 16319 16124 16154 N 16086 16092A 16274 G LN XJ 16294 2SX 16293 LN SD 16294 16094 16185 16209 YN 3 16256 16148 Q JS 3Q XJ Q 16111 16092 GS S YN 7.90 [4.73, 11. 06] kya 2 HN YN 16145 @16362 16291 SX 2 2ZJ @16362 16154 R 20R 21N SD SDLN XJ 16184 16111A 16354 NM 4G 16289 16265C 16076 16357 S 4QH 16129 Y 16093 16093 16189 R 3Y 3R * IM 16111G 16194 Q 2N 2R G R 16212 16266 16264Y 16093 16166 16300 16335 R R 16093Y 2R 16231 16094 Y Y Y @16223 IM N N 16194C N M9a (N = 143): 17.03 [12.58, 21.48] kya * 16223-16234-16316-16362-73-153-263

Fig. S2. Median network of haplogroup M9a. This network was constructed manually according to Bandelt et al. (7). The data used here were collected from the literature (Table S2) and the present study (Tables S3 and S5). The sequence information used for network construction was confined to segment 16047–16497. Suffixes ‘‘A,’’ ‘‘C,’’ ‘‘G,’’ and ‘‘T’’ refer to transversions; ‘‘Y’’ specifies heteroplasmic status C/T at the site; recurrent mutations are underlined; and ‘‘@’’ denotes a reverse mutation. Time estimation was carried out based on segment 16051–16400 as described previously (8). Codes ‘‘N,’’ ‘‘R,’’ ‘‘Q,’’ ‘‘Y,’’ ‘‘S,’’ and ‘‘G’’ refer to sampling locations (Nakchu, Shigatse, Qinghai, Yunnan, Sichuan, and Gansu, respectively) of different regional Tibetan populations. The asterisk denotes the ancestral node of the haplogroup defined by motif 16223-16234-16316-16362-73-153-263.

Zhao et al. www.pnas.org/cgi/content/short/0907844106 3of7 R 2Q Tibetan Q 16103 Yi 16325 16320 16188 Mosuo R Mg Bai 16317 16360 3N Y Pumi G 16288 R 8R 5 16256 Hani S 16287 5 2Q 16265C Mg Y 16093 * Q Sala 16086 2R R 16311 She 2Y S 16168 Va 16243 3 2R 2 16183

R M9c (N=60): N 16051 9.73 [6.62, 12.84] kya

G

2Q * 16158-16223-16234-16362-73-150-152-153-263

Fig. S3. Median network of haplogroup M9c. The asterisk denotes the ancestral node of the haplogroup defined by motif 16158-16223-16234-16362-73- 150-152-153-263. For more information, see Fig. S2.

Zhao et al. www.pnas.org/cgi/content/short/0907844106 4of7 6.67 [4.00, 9.34] kya 5.56 [2.45, 8.67] kya 3R N 3Y

Y 16104 @16188 16129 16103 @16381 N XJ 16310 @16168 16400 16172 2N 3 16362 Q G Y 16189 R 7N Y 16093 3R 7Y 3R @16257 G 16148 M13b Tibetan M13a Mg 16311 16311 16381 16257 Pumi 16189 16168 Bai 4 Naxi * M13 (N=53) Dongxiang Yugur * 16145-16188-16223-73-152-263 Kor Japan

Fig. S4. Median network of haplogroup M13. The asterisk denotes the ancestral node of the haplogroup defined by motif 16145-16188-16223-73-152-263. For more information, see Fig. S2.

Zhao et al. www.pnas.org/cgi/content/short/0907844106 5of7 Q Tibetan 2R 16390 Pumi @16274 3Q 2R Naxi N Q Hani Y 16153 16399 16148 16234G 16356 Bonan 16157 R 3Y 2Q G 16225 16355 N Y * 16176 16368 G3a1 (N=25): 17.34 [10.81, 23.88] kya 2

* 16215-16223-16274-16T-73-143-150-263

Fig. S5. Median network of haplogroup G3a1. The asterisk denotes the ancestral node of the haplogroup defined by motif 16215-16223-16274-16T-73-143- 150-263. For more information, see Fig. S2.

Zhao et al. www.pnas.org/cgi/content/short/0907844106 6of7 2.57 [1.28, 3.85] kya Tibetan R Han R Mg LN 16243 16172 Pumi 16126 16263 Yi SH Mosuo 9R 5N HN Naxi Y 3 2Q Yugur 5.27 [2.78, 7.75] kya R Dongxiang XJ 16093 Sala 16066 16359 R 16362 16318T 3Y 16287 G 2Q R 16311 R 4 16234 XJ 2N YN 2 2 CQ 16300 16140 2 *G N 16189 16213 16357 16129 16352 Q 16092 A10 (N=60): 17.79 [8.75, 26.83] kya AH TW

* 16223-16290-16293C-16319-73-152-235-263

Fig. S6. Median network of haplogroup A10. The asterisk denotes the ancestral node of the haplogroup defined by motif 16223-16290-16293C-16319-73- 152-235-263. For more information, see Fig. S2.

Other Supporting Information Files

Table S1 Table S2 Table S3 Table S4 Table S5

Zhao et al. www.pnas.org/cgi/content/short/0907844106 7of7