A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals

Additional file 1 A genetic chronology for the Indian Subcontinent points to heavily sexbiased dispersals Marina Silva1+, Marisa Oliveira2,3+, Daniel Vieira4,5, Andreia Brandão2,3, Teresa Rito2,6,7, Joana B. Pereira2,3, Ross M. Fraser8,9, Bob Hudson10, Francesca Gandini1, Ceiridwen Edwards1, Maria Pala1, John Koch11, James F. Wilson8,12, Luísa Pereira2,3, Martin B. Richards1*, Pedro Soares3,5* 1 Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, United Kingdom 2 i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), R. Alfredo Allen 208, 4200135 Porto, Portugal. 3 IPATIMUP (Instituto de Patologia e Imunologia Molecular da Universidade do Porto), Rua Júlio Amaral de Carvalho 45, 4200-135 Porto, Portugal 4 Department of Informatics, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal 5 CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal 6 Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal 7 ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal 8 Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, Scotland, UK 9 Synpromics Ltd, Nine Edinburgh Bioquarter, Edinburgh EH16 4UX, UK 10 Archaeology Department, University of Sydney, New South Wales NSW 2006, Australia 11 University of Wales Centre for Advanced Welsh and Celtic Studies, National Library of Wales, Aberystwyth, SY23 3HH, Wales, UK 12 MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, Scotland, UK +,* Both authors contributed equally to this work Corresponding authors: Martin B. Richards: m.b.richard[email protected]; Pedro Soares: [email protected]minho.pt Fig. S1. BSP for haplogroup M in different regions of the subcontinent: (a) West, (b) South, (c) Central and (d) East South Asia. 2 12 14 16 18 20 22 24 26 28 30 32 ka N1a1b1 34 36 38 40 42 I1 4446 48 5052 54 4 6 8 10 N1a2 W3a1 W3a1+1709 W3a1+143 W3a1b W+194 W4a W4 W6 X2 R0a+709 R0a R0a2+11152 V2a HV HV+146! HV+73! HV+9716 HV+16311! HV2a2 HV14 HV12 HV13 H7b H13 H13a1a H13a2a H13a2a+8952 H13a2a+153 H15a1a H29 R1a1 J1b1 J1b1a1 J1b1b1+16222 J1b1b+8494 J1b3 J1b3b J1b3b+16235! J1d T1a1 T1a1 T1a1+4917 T1a1b1 T1a1+146 T2 T2 T2a1a T2b T2b2 T2d1b T2d1a T2e2 T2+195 U1 U1a1 U1a1a2a U1a3+10253 U1a3a pre-U1c K K1a1b2a K2a5 K2a5+2831+189 56 58 60 6264 LGM Caucasus / Anatolia Iran Arabian Peninsula South Asia (exclusively) South Asia (non exclusively) R2a R2a+7142 R2a+8143 HV2 H2b Europe PLEISTOCENE HOLOCENE U7 U7+14131 U7a U7a2 U7a+12373 U7a3a+6150 pre-U7a3b U7b+153 U7b+16309! Neolithic Fig. S2. Putative origin and age ranges (95% confidence interval) for non-autochthonous mtDNA lineages found in South Asia. The colours represent the most likely source for each lineage; branches exclusively with South Asian complete sequences coloured in green, whereas branches that also harbour sequences from other regions in white and with green contour. Ages according to ML estimates. Fig.S3. ADMIXTURE analysis for all K values. Information on the populations included in Table S3. Africa Europe Anatolia + Caucasus Arabia + Near East South Asia East Asia Central Asia k=2 k=3 k=4 k=5 k=6 k=7 k=8 k=9 k=10 Fig.S4. sNMF analysis of modern populations for all K values. Information on the populations included in Table S3. Fig.S5. Cross-validation errors for different values of K for ADMIXTURE: (a) considering only modern populations and (b) including the Yamnaya in the analysis. a. b. Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference Sample Haplogroup Origin (Population) Region Reference FJ770945 M India South Asia (Fornarino et al. 2009) JF742212 M Nepal: Kathmandu South Asia - Central (Wang et al. 2012) FJ383814 M Orissa South Asia - East (Chandrasekar et al. 2009) JX289110 M Myanmar Southeast Asia (Summerer et al. 2014) AY922300 M Uttar Pradesh South Asia - Central (Sun et al. 2006) HG04210 M STU South Asia - South (Abecasis et al. 2012) HG04076 M ITU South Asia - South (Abecasis et al. 2012) JX289097 M Myanmar Southeast Asia (Summerer et al. 2014) JX289130 M Myanmar Southeast Asia (Summerer et al. 2014) HG03594 M BEB South Asia - East (Abecasis et al. 2012) JX289131 M Myanmar Southeast Asia (Summerer et al. 2014) HG03611 M BEB South Asia - East (Abecasis et al. 2012) HG04033 M STU South Asia - South (Abecasis et al. 2012) HG03643 M STU South Asia - South (Abecasis et al. 2012) HG03668 M PJL South Asia - West (Abecasis et al. 2012) DQ246828 M Bihar South Asia - East (Rajkumar et al. 2005) FJ770941 M Andhra Pradesh South Asia - South (Fornarino et al. 2009) JX289123 M Myanmar Southeast Asia (Summerer et al. 2014) JX289119 M13'46'61 Myanmar Southeast Asia (Summerer et al. 2014) FJ383772 M13'46'61 Nepal South Asia - Central (Chandrasekar et al. 2009) FJ383770 M13'46'61 Nepal South Asia - Central (Chandrasekar et al. 2009) FJ383773 M13'46'61 Nepal South Asia - Central (Chandrasekar et al. 2009) FJ383771 M13'46'61 Nepal South Asia - Central (Chandrasekar et al. 2009) HM030546 M13'46'61 China East Asia (Kong et al. 2011) KK178 M13'46'61 Borneo: Kota Kinabalu Southeast Asia This study VNM396 M13'46'61 Vietnam Southeast Asia This study JX289113 M13'46'61 Myanmar Southeast Asia (Summerer et al. 2014) FJ383769 M13'46'61 Arunachal Pradesh South Asia - East (Chandrasekar et al. 2009) FJ383775 M13'46'61 Arunachal Pradesh South Asia - East (Chandrasekar et al. 2009) FJ383776 M13'46'61 Arunachal Pradesh South Asia - East (Chandrasekar et al. 2009) FJ383777 M13'46'61 Arunachal Pradesh South Asia - East (Chandrasekar et al. 2009) FJ383774 M13'46'61 Arunachal Pradesh South Asia - East (Chandrasekar et al. 2009) FJ770957 M13'46'61 Nepal South Asia - Central (Fornarino et al. 2009) AY963577 M13'46'61 Semang (Jahai) Southeast Asia (Macaulay et al. 2005) HG03743 M2 STU South Asia - South (Abecasis et al. 2012) EU443499 M2 Malpaharia South Asia - East (Kumar et al. 2008) FJ383284 M2 Jharkhand South Asia - East (Chandrasekar et al. 2009) AY922303 M2 Andhra Pradesh South Asia - South (Sun et al. 2006) AY922306 M2 Andhra Pradesh South Asia - South (Sun et al. 2006) FJ383292 M2 Maharashtra South Asia - South (Chandrasekar et al. 2009) HG03857 M2 STU South Asia - South (Abecasis et al. 2012) Table S1. List of complete mtDNA sequences belonging to South Asian autochthonous haplogroups. Population codes: BEB – Bengali from Bangladesh; GIH – Gujarati Indian from Houston, Texas; ITU – Indian Telugu from the UK; PJL – Punjabi from Lahore, Pakistan; STU – Sri Lankan Tamil from the UK. Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference HG03978 M2 ITU South Asia - South (Abecasis et al. 2012) HG04042 M2 STU South Asia - South (Abecasis et al. 2012) HG03866 M2 ITU South Asia - South (Abecasis et al. 2012) HG03951 M2 STU South Asia - South (Abecasis et al. 2012) FJ383254 M2 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383253 M2 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383251 M2 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383252 M2 Rajasthan South Asia - West (Chandrasekar et al. 2009) EU443454 M2 Dungri Bhil South Asia - West (Kumar et al. 2008) EU443457 M2 Dungri Bhil South Asia - West (Kumar et al. 2008) EU443455 M2 Dungri Bhil South Asia - West (Kumar et al. 2008) EU443456 M2 Dungri Bhil South Asia - West (Kumar et al. 2008) FJ383246 M2 Maharashtra South Asia - South (Chandrasekar et al. 2009) EU443443 M2 Maharashtra South Asia - South (Kumar et al. 2008) EU443444 M2 Maharashtra South Asia - South (Kumar et al. 2008) EU443445 M2 Maharashtra South Asia - South (Kumar et al. 2008) GU480007 M2 Madhya Pradesh South Asia - Central (Sharma et al. 2012) GU480005 M2 Madhya Pradesh South Asia - Central (Sharma et al. 2012) EU443506 M2 Jharkhand South Asia - East (Kumar et al. 2008) HG03585 M2 BEB South Asia - East (Abecasis et al. 2012) EU443502 M2 Maharashtra South Asia - South (Kumar et al. 2008) EU443490 M2 Gujarat South Asia - West (Kumar et al. 2008) EU443489 M2 Gujarat South Asia - West (Kumar et al. 2008) EU443468 M2 Maharashtra South Asia - South (Kumar et al. 2008) FJ383272 M2 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383274 M2 Maharashtra South Asia - South (Chandrasekar et al. 2009) EU443471 M2 Maharashtra South Asia - South (Kumar et al. 2008) EU443500 M2 Maharashtra South Asia - South (Kumar et al. 2008) EU443501 M2 Maharashtra South Asia - South (Kumar et al. 2008) EU443470 M2 Maharashtra South Asia - South (Kumar et al. 2008) EU443467 M2 Maharashtra South Asia - South (Kumar et al. 2008) EU443469 M2 Maharashtra South Asia - South (Kumar et al. 2008) FJ383273 M2 Maharashtra South Asia - South (Chandrasekar et al. 2009) EU443503 M2 Maharashtra South Asia - South (Kumar et al. 2008) EU443492 M2 Chhattisgarh South Asia - Central (Kumar et al. 2008) EU443493 M2 Chhattisgarh South Asia - Central (Kumar et al. 2008) EU443495 M2 Chhattisgarh South Asia - Central (Kumar et al. 2008) EU443494 M2 Chhattisgarh South Asia - Central (Kumar et al. 2008) NA21103 M2 GIH South Asia - West (Abecasis et al. 2012) EU443478 M2 Chhattisgarh South Asia - Central (Kumar et al. 2008) EU443477 M2 Chhattisgarh South Asia - Central (Kumar et al. 2008) FJ383280 M2 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference EU443479 M2 Chhattisgarh South Asia - Central (Kumar et al. 2008) FJ383276 M2 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383277 M2 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383281 M2 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383282 M2 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383279 M2 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383275 M2 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383278 M2 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383283 M2 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) EU443476 M2 Chhattisgarh South Asia - Central (Kumar et al. 2008) EU443480 M2 Chhattisgarh South Asia - Central (Kumar et al. 2008) FJ383287 M2 Madhya Pradesh South Asia - Central (Chandrasekar et al. 2009) FJ383288 M2 Madhya Pradesh South Asia - Central (Chandrasekar et al. 2009) HG04211 M2 ITU South Asia - South (Abecasis et al. 2012) EU597516 M2 Pakistan: Sindhi South Asia - West (Hartmann et al. 2009) HG02691 M2 PJL South Asia - West (Abecasis et al. 2012) HG03913 M2 BEB South Asia - East (Abecasis et al. 2012) HG02654 M2 PJL South Asia - West (Abecasis et al. 2012) HG02655 M2 PJL South Asia - West (Abecasis et al. 2012) FJ383247 M2 Maharashtra South Asia - South (Chandrasekar et al. 2009) EU443460 M2 Andhra Pradesh South Asia - South (Kumar et al. 2008) FJ383244 M2 Maharashtra South Asia - South (Chandrasekar et al. 2009) EU443472 M2 Maharashtra South Asia - South (Kumar et al. 2008) EU443488 M2 Gujarat South Asia - West (Kumar et al. 2008) EU443508 M2 Madhya Pradesh South Asia - Central (Kumar et al. 2008) FJ383240 M2 Maharashtra South Asia - South (Chandrasekar et al. 2009) EU443473 M2 Maharashtra South Asia - South (Kumar et al. 2008) FJ383243 M2 Maharashtra South Asia - South (Chandrasekar et al. 2009) EU443507 M2 Madhya Pradesh South Asia - Central (Kumar et al. 2008) FJ383286 M2 Madhya Pradesh South Asia - Central (Chandrasekar et al. 2009) EU443509 M2 Madhya Pradesh South Asia - Central (Kumar et al. 2008) EU443510 M2 Madhya Pradesh South Asia - Central (Kumar et al. 2008) FJ383290 M2 Madhya Pradesh South Asia - Central (Chandrasekar et al. 2009) FJ383285 M2 Madhya Pradesh South Asia - Central (Chandrasekar et al. 2009) FJ383289 M2 Madhya Pradesh South Asia - Central (Chandrasekar et al. 2009) EU443505 M2 Jharkhand South Asia - East (Kumar et al. 2008) FJ383291 M2 Bihar South Asia - East (Chandrasekar et al. 2009) EU443450 M2 Karnataka South Asia - South (Kumar et al. 2008) FJ383255 M2 Karnataka South Asia - South (Chandrasekar et al. 2009) EU443464 M2 Karnataka South Asia - South (Kumar et al. 2008) EU443462 M2 Karnataka South Asia - South (Kumar et al. 2008) EU443513 M2 Orissa South Asia - East (Kumar et al. 2008) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference EU443511 M2 Orissa South Asia - East (Kumar et al. 2008) EU443514 M2 Orissa South Asia - East (Kumar et al. 2008) EU443446 M2 Maharashtra South Asia - South (Kumar et al. 2008) EU443447 M2 Maharashtra South Asia - South (Kumar et al. 2008) EU443448 M2 Maharashtra South Asia - South (Kumar et al. 2008) EU443491 M2 Gujarat South Asia - West (Kumar et al. 2008) EU443487 M2 Gujarat South Asia - West (Kumar et al. 2008) FJ383239 M2 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383242 M2 Maharashtra South Asia - South (Chandrasekar et al. 2009) EU443475 M2 Maharashtra South Asia - South (Kumar et al. 2008) FJ383238 M2 Maharashtra South Asia - South (Chandrasekar et al. 2009) EU443474 M2 Maharashtra South Asia - South (Kumar et al. 2008) FJ383245 M2 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383241 M2 Maharashtra South Asia - South (Chandrasekar et al. 2009) EU443486 M2 Chhattisgarh South Asia - Central (Kumar et al. 2008) EU443484 M2 Chhattisgarh South Asia - Central (Kumar et al. 2008) EU443512 M2 Orissa South Asia - East (Kumar et al. 2008) AY922305 M2 Andhra Pradesh South Asia - South (Sun et al. 2006) NA21104 M2 GIH South Asia - West (Abecasis et al. 2012) EU443452 M2 Karnataka South Asia - South (Kumar et al. 2008) EU443453 M2 Karnataka South Asia - South (Kumar et al. 2008) EU443451 M2 Karnataka South Asia - South (Kumar et al. 2008) EU443449 M2 Betta Kuruba South Asia - South (Kumar et al. 2008) FJ383265 M2 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383258 M2 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383263 M2 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383262 M2 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383261 M2 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383260 M2 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383259 M2 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383257 M2 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383266 M2 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383269 M2 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383270 M2 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383264 M2 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383256 M2 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383268 M2 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383271 M2 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383267 M2 Karnataka South Asia - South (Chandrasekar et al. 2009) HG03684 M2 STU South Asia - South (Abecasis et al. 2012) EU443466 M2 Karnataka South Asia - South (Kumar et al. 2008) EU443463 M2 Karnataka South Asia - South (Kumar et al. 2008) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference EU443465 M2 Karnataka South Asia - South (Kumar et al. 2008) HG04173 M2 BEB South Asia - East (Abecasis et al. 2012) EU443458 M2 Andhra Pradesh South Asia - South Rao (direct submission) EU443459 M2 Andhra Pradesh South Asia - South (Kumar et al. 2008) EU443461 M2 Andhra Pradesh South Asia - South (Kumar et al. 2008) AY922308 M2 Andhra Pradesh South Asia - South Sun (direct submission) EU443485 M2 Chhattisgarh South Asia - Central (Kumar et al. 2008) EU443481 M2 Chhattisgarh South Asia - Central (Kumar et al. 2008) FJ383249 M2 Madhya Pradesh South Asia - Central (Chandrasekar et al. 2009) FJ383250 M2 Madhya Pradesh South Asia - Central (Chandrasekar et al. 2009) HG03007 M2 BEB South Asia - East (Abecasis et al. 2012) HG03950 M2 STU South Asia - South (Abecasis et al. 2012) FJ383248 M2 Maharashtra South Asia - South (Chandrasekar et al. 2009) EU443483 M2 Chhattisgarh South Asia - Central (Kumar et al. 2008) EU443482 M2 Chhattisgarh South Asia - Central (Kumar et al. 2008) EU443504 M2 Jharkhand South Asia - East (Kumar et al. 2008) NA20905 M2 GIH South Asia - West (Abecasis et al. 2012) HM156675 M2 Andhra Pradesh South Asia - South (Govindaraj et al. 2011) HM156678 M2 Andhra Pradesh South Asia - South (Govindaraj et al. 2011) EU443496 M2 Jharkhand South Asia - East (Kumar et al. 2008) EU443497 M2 Jharkhand South Asia - East (Kumar et al. 2008) EU443498 M2 Jharkhand South Asia - East (Kumar et al. 2008) NA20885 M2 GIH South Asia - West (Abecasis et al. 2012) NA20882 M2 GIH South Asia - West (Abecasis et al. 2012) NA20900 M2 GIH South Asia - West (Abecasis et al. 2012) KC911426 M2 Iran: Persian Southwest Asia (Derenko et al. 2013) DQ408676 M3 Kerala South Asia - South (Thangaraj et al. 2006) KC887464 M3 Cambodia Southeast Asia (Zhang et al. 2013) KC887465 M3 Cambodia Southeast Asia (Zhang et al. 2013) KC887463 M3 Cambodia Southeast Asia (Zhang et al. 2013) KC505095 M3 Cambodia Southeast Asia (Zhang et al. 2013) KC887466 M3 Cambodia Southeast Asia (Zhang et al. 2013) KC887467 M3 Cambodia Southeast Asia (Zhang et al. 2013) KC887468 M3 Cambodia Southeast Asia (Zhang et al. 2013) KC887469 M3 Cambodia Southeast Asia (Zhang et al. 2013) KC887471 M3 Cambodia Southeast Asia (Zhang et al. 2013) KC887474 M3 Cambodia Southeast Asia (Zhang et al. 2013) KC887470 M3 Cambodia Southeast Asia (Zhang et al. 2013) KF056281 M3 Sherpa South Asia - Central (Kang et al. 2013) KF056282 M3 Sherpa South Asia - Central (Kang et al. 2013) KF056283 M3 Sherpa South Asia - Central (Kang et al. 2013) HG03781 M3 ITU South Asia - South (Abecasis et al. 2012) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference FJ770946 M3 India South Asia (Fornarino et al. 2009) JF742206 M3 Nepal: Kathmandu South Asia - Central (Wang et al. 2012) DQ246826 M3 Maharashtra South Asia - South (Rajkumar et al. 2005) F6 M3 Myanmar Southeast Asia This study HG03910 M3 BEB South Asia - East (Abecasis et al. 2012) HG04161 M3 BEB South Asia - East (Abecasis et al. 2012) HG04019 M3 ITU South Asia - South (Abecasis et al. 2012) HG03974 M3 ITU South Asia - South (Abecasis et al. 2012) HG03976 M3 ITU South Asia - South (Abecasis et al. 2012) FJ383522 M3 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383513 M3 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383523 M3 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383524 M3 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383525 M3 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383526 M3 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383527 M3 Rajasthan South Asia - West (Chandrasekar et al. 2009) KJ446720 M3 Pakistan: Sindhi South Asia - West HGDP - Zheng et al. (unpublished) HG03616 M3 BEB South Asia - East (Abecasis et al. 2012) KJ446721 M3 Pakistan: Sindhi South Asia - West HGDP - Zheng et al. (unpublished) HG04155 M3 BEB South Asia - East (Abecasis et al. 2012) AY922263 M3 Uttar Pradesh South Asia - Central (Sun et al. 2006) HM852820 M3 Iran Southwest Asia (Schönberg et al. 2011) JF742216 M3 Nepal: Kathmandu South Asia - Central (Wang et al. 2012) HG03940 M3 BEB South Asia - East (Abecasis et al. 2012) HG03824 M3 BEB South Asia - East (Abecasis et al. 2012) HG04183 M3 BEB South Asia - East (Abecasis et al. 2012) HG04186 M3 BEB South Asia - East (Abecasis et al. 2012) FJ383538 M3 Gujarat South Asia - West (Chandrasekar et al. 2009) FJ383536 M3 Gujarat South Asia - West (Chandrasekar et al. 2009) FJ383539 M3 Gujarat South Asia - West (Chandrasekar et al. 2009) FJ383537 M3 Gujarat South Asia - West (Chandrasekar et al. 2009) FJ383540 M3 Gujarat South Asia - West (Chandrasekar et al. 2009) HG02793 M3 PJL South Asia - West (Abecasis et al. 2012) KJ446716 M3 Pakistan: Makrani South Asia - West HGDP - Zheng et al. (unpublished) KJ446717 M3 Pakistan: Makrani South Asia - West HGDP - Zheng et al. (unpublished) KJ446713 M3 Pakistan: Hazara South Asia - West HGDP - Zheng et al. (unpublished) KJ446714 M3 Pakistan: Hazara South Asia - West HGDP - Zheng et al. (unpublished) KC911530 M3 Iran: Persian Southwest Asia (Derenko et al. 2013) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference KJ446719 M3 Pakistan: Brahui South Asia - West HGDP - Zheng et al. (unpublished) KJ446718 M3 Pakistan: Brahui South Asia - West HGDP - Zheng et al. (unpublished) HG03686 M3 STU South Asia - South (Abecasis et al. 2012) JQ702447 M3 unknown unknown (Behar et al. 2012) JQ704107 M3 unknown unknown (Behar et al. 2012) HG03925 M3 BEB South Asia - East (Abecasis et al. 2012) HG03907 M3 BEB South Asia - East (Abecasis et al. 2012) JF742210 M3 Nepal: Kathmandu South Asia - Central (Wang et al. 2012) HM156695 M3 Andhra Pradesh: Mahabubnagar South Asia - South (Govindaraj et al. 2011) FJ383514 M3 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383515 M3 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383516 M3 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383517 M3 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383520 M3 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383521 M3 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383535 M3 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383519 M3 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383534 M3 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383518 M3 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) AY922266 M3 Andhra Pradesh South Asia - South (Sun et al. 2006) KJ446722 M3 Pakistan: Burusho South Asia - West HGDP - Zheng et al. (unpublished) HG03229 M3 PJL South Asia - West (Abecasis et al. 2012) HG03636 M3 PJL South Asia - West (Abecasis et al. 2012) NA21092 M3 GIH South Asia - West (Abecasis et al. 2012) HG01583 M3 PJL South Asia - West (Abecasis et al. 2012) HG02684 M3 PJL South Asia - West (Abecasis et al. 2012) KJ446723 M3 Pakistan: Pathan South Asia - West HGDP - Zheng et al. (unpublished) KJ446724 M3 Pakistan: Sindhi South Asia - West HGDP - Zheng et al. (unpublished) KJ446725 M3 Pakistan: Balochi South Asia - West HGDP - Zheng et al. (unpublished) KJ446726 M3 Pakistan: Balochi South Asia - West HGDP - Zheng et al. (unpublished) HG03717 M3 ITU South Asia - South (Abecasis et al. 2012) HG03772 M3 ITU South Asia - South (Abecasis et al. 2012) HG03773 M3 ITU South Asia - South (Abecasis et al. 2012) HG04017 M3 ITU South Asia - South (Abecasis et al. 2012) HG04054 M3 ITU South Asia - South (Abecasis et al. 2012) HG04096 M3 ITU South Asia - South (Abecasis et al. 2012) FJ383531 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383533 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference FJ383530 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383528 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383532 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) HG03968 M3 ITU South Asia - South (Abecasis et al. 2012) FJ383529 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) GU810074 M3 Thailand Southeast Asia Pradutkanchana et al. (unpublished) HG03875 M3 ITU South Asia - South (Abecasis et al. 2012) FJ383541 M3 Maharashtra South Asia - South (Chandrasekar et al. 2009) KJ446715 M3 Pakistan: Brahui South Asia - West HGDP - Zheng et al. (unpublished) HG04164 M3 BEB South Asia - East (Abecasis et al. 2012) FJ383542 M3 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) HG03745 M3 STU South Asia - South (Abecasis et al. 2012) FJ770942 M3 Andhra Pradesh South Asia - South (Fornarino et al. 2009) HG04140 M3 BEB South Asia - East (Abecasis et al. 2012) HG03012 M3 BEB South Asia - East (Abecasis et al. 2012) FJ770965 M3 Nepal South Asia - Central (Fornarino et al. 2009) FJ383459 M3 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383472 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383474 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383471 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383462 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383476 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383464 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383473 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383475 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383467 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383468 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383469 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383477 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383478 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383479 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383480 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383481 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383466 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383483 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383484 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383485 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383461 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383465 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383470 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383460 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference FJ383463 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383482 M3 Karnataka South Asia - South (Chandrasekar et al. 2009) HG03948 M4’67 STU South Asia - South (Abecasis et al. 2012) HG03673 M4’67 STU South Asia - South (Abecasis et al. 2012) NA20894 M4’67 GIH South Asia - West (Abecasis et al. 2012) HG02688 M4’67 PJL South Asia - West (Abecasis et al. 2012) FJ383293 M4’67 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383296 M4’67 Maharashtra South Asia - South (Chandrasekar et al. 2009) HG02658 M4’67 PJL South Asia - West (Abecasis et al. 2012) HG03687 M4’67 STU South Asia - South (Abecasis et al. 2012) KJ446709 M4’67 Pakistan: Makrani South Asia - West HGDP - Zheng et al. (unpublished) KJ446710 M4’67 Pakistan: Makrani South Asia - West HGDP - Zheng et al. (unpublished) KJ446711 M4’67 Pakistan: Hazara South Asia - West HGDP - Zheng et al. (unpublished) KJ446712 M4’67 Pakistan: Hazara South Asia - West HGDP - Zheng et al. (unpublished) KC911394 M4’67 Iran: Persian Southwest Asia (Derenko et al. 2013) HG03720 M4’67 ITU South Asia - South (Abecasis et al. 2012) HG03792 M4’67 ITU South Asia - South (Abecasis et al. 2012) NA20853 M4’67 GIH South Asia - West (Abecasis et al. 2012) HG03746 M4’67 STU South Asia - South (Abecasis et al. 2012) AY922278 M4’67 Andhra Pradesh South Asia - South (Sun et al. 2006) KC911313 M4’67 Iran: Qashqai Southwest Asia (Derenko et al. 2013) DQ408679 M4’67 Gujarat South Asia - West (Thangaraj et al. 2006) KJ446708 M4’67 Pakistan: Pathan South Asia - West HGDP - Zheng et al. (unpublished) HG03805 M4’67 BEB South Asia - East (Abecasis et al. 2012) AY922291 M4’67 Andhra Pradesh South Asia - South (Sun et al. 2006) AY922297 M4’67 Andhra Pradesh South Asia - South (Sun et al. 2006) HG03808 M4’67 BEB South Asia - East (Abecasis et al. 2012) HG04176 M4’67 BEB South Asia - East (Abecasis et al. 2012) HG04229 M4’67 STU South Asia - South (Abecasis et al. 2012) HG02792 M4’67 PJL South Asia - West (Abecasis et al. 2012) HM036536 M4’67 Great Himalayas: Ladakh tribe South Asia - Central Sharma et al. (unpublished) KJ446732 M4’67 Pakistan: Sindhi South Asia - West HGDP - Zheng et al. (unpublished) HM036576 M4’67 Great Himalayas: Ladakh tribe South Asia - Central Sharma et al. (unpublished) KJ446731 M4’67 Pakistan: Balochi South Asia - West HGDP - Zheng et al. (unpublished) GQ337623 M4’67 India South Asia (Palanichamy et al. 2014) JX289111 M4’67 Myanmar Southeast Asia (Summerer et al. 2014) GQ337562 M4’67 India South Asia (Palanichamy et al. 2014) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference AY922261 M4’67 Uttar Pradesh South Asia - Central (Sun et al. 2006) FJ383297 M4’67 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383298 M4’67 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383299 M4’67 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383295 M4’67 Maharashtra South Asia - South (Chandrasekar et al. 2009) KJ446730 M4’67 Pakistan: Balochi South Asia - West HGDP - Zheng et al. (unpublished) HG02699 M4’67 PJL South Asia - West (Abecasis et al. 2012) HG04177 M4’67 BEB South Asia - East (Abecasis et al. 2012) HG03718 M4’67 ITU South Asia - South (Abecasis et al. 2012) HG04063 M4’67 ITU South Asia - South (Abecasis et al. 2012) FJ383300 M4’67 Arunachal Pradesh South Asia - East (Chandrasekar et al. 2009) FJ383294 M4’67 Arunachal Pradesh South Asia - East (Chandrasekar et al. 2009) HG03672 M4’67 STU South Asia - South (Abecasis et al. 2012) JX289108 M4’67 Myanmar Southeast Asia (Summerer et al. 2014) FJ383337 M4’67 Bihar South Asia - East (Chandrasekar et al. 2009) FJ383335 M4’67 Orissa South Asia - East (Chandrasekar et al. 2009) JQ705662 M4’67 United Kingdom Europe (Behar et al. 2012) KC911475 M4’67 Iran: Persian Southwest Asia (Derenko et al. 2013) KJ446728 M4’67 Pakistan: Sindhi South Asia - West HGDP - Zheng et al. (unpublished) HG03016 M4’67 PJL South Asia - West (Abecasis et al. 2012) HG03663 M4’67 PJL South Asia - West (Abecasis et al. 2012) HG03867 M4’67 ITU South Asia - South (Abecasis et al. 2012) HG04080 M4’67 ITU South Asia - South (Abecasis et al. 2012) HG04146 M4’67 BEB South Asia - East (Abecasis et al. 2012) HG03765 M4’67 PJL South Asia - West (Abecasis et al. 2012) HG04001 M4’67 ITU South Asia - South (Abecasis et al. 2012) FJ383336 M4’67 Madhya Pradesh South Asia - Central (Chandrasekar et al. 2009) DQ408674 M4’67 Bihar South Asia - East (Thangaraj et al. 2006) DQ246825 M4’67 Bihar South Asia - East (Rajkumar et al. 2005) JQ446407 M4’67 India South Asia Khan et al. (unpublished) HM156679 M4’67 Andhra Pradesh: Mahabubnagar South Asia - South (Govindaraj et al. 2011) JF742214 M4’67 Nepal South Asia - Central (Wang et al. 2012) KJ446729 M4’67 China: Uygur East Asia HGDP - Zheng et al. (unpublished) KF055880 M4’67 Spain: Romani Europe (Gómez-Carballa et al. 2013) AY922270 M4’67 Uttar Pradesh South Asia - Central (Sun et al. 2006) HG04060 M4’67 ITU South Asia - South (Abecasis et al. 2012) HG03730 M4’67 ITU South Asia - South (Abecasis et al. 2012) HG03646 M4’67 STU South Asia - South (Abecasis et al. 2012) JX289116 M4’67 Myanmar Southeast Asia (Summerer et al. 2014) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference NA21127 M5 GIH South Asia - West (Abecasis et al. 2012) KJ446695 M5 Pakistan: Brahui South Asia - West HGDP - Zheng et al. (unpublished) KJ446696 M5 Pakistan: Brahui South Asia - West HGDP - Zheng et al. (unpublished) KJ446697 M5 Pakistan: Brahui South Asia - West HGDP - Zheng et al. (unpublished) KJ446698 M5 Pakistan: Balochi South Asia - West HGDP - Zheng et al. (unpublished) KJ446699 M5 Pakistan: Makrani South Asia - West HGDP - Zheng et al. (unpublished) KJ446700 M5 Pakistan: Makrani South Asia - West HGDP - Zheng et al. (unpublished) KJ446701 M5 Pakistan: Brahui South Asia - West HGDP - Zheng et al. (unpublished) HM852834 M5 Iran Southwest Asia (Schönberg et al. 2011) EU597563 M5 Pakistan: Brahui South Asia - West (Hartmann et al. 2009) KC911312 M5 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911579 M5 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911321 M5 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911351 M5 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911557 M5 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911596 M5 Iran: Persian Southwest Asia (Derenko et al. 2013) HM156691 M5 Andhra Pradesh South Asia - South (Govindaraj et al. 2011) FJ383570 M5 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383572 M5 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383573 M5 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383559 M5 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383562 M5 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383567 M5 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383561 M5 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383565 M5 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383563 M5 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383560 M5 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383580 M5 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383581 M5 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383586 M5 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383583 M5 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383554 M5 Madhya Pradesh South Asia - Central (Chandrasekar et al. 2009) FJ383590 M5 Gujarat South Asia - West (Chandrasekar et al. 2009) NA21125 M5 GIH South Asia - West (Abecasis et al. 2012) FJ383571 M5 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383569 M5 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383566 M5 Rajasthan South Asia - West (Chandrasekar et al. 2009) EF556195 M5 Kerala: Cochin South Asia - South (Behar et al. 2008) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference KJ446691 M5 Pakistan: Pathan South Asia - West HGDP - Zheng et al. (unpublished) DQ408675 M5 Orissa South Asia - East (Thangaraj et al. 2006) FJ383594 M5 Maharashtra South Asia - South (Chandrasekar et al. 2009) HG03589 M5 BEB South Asia - East (Abecasis et al. 2012) DQ246814 M5 Karnataka South Asia - South (Rajkumar et al. 2005) HG03006 M5 BEB South Asia - East (Abecasis et al. 2012) HG02681 M5 PJL South Asia - West (Abecasis et al. 2012) HG03708 M5 PJL South Asia - West (Abecasis et al. 2012) HG03944 M5 STU South Asia - South (Abecasis et al. 2012) HG03885 M5 STU South Asia - South (Abecasis et al. 2012) HM852843 M5 Iran Southwest Asia (Schönberg et al. 2011) HG04006 M5 STU South Asia - South (Abecasis et al. 2012) KJ446692 M5 Pakistan: Pathan South Asia - West HGDP - Zheng et al. (unpublished) NA21122 M5 GIH South Asia - West (Abecasis et al. 2012) NA21114 M5 GIH South Asia - West (Abecasis et al. 2012) NA20911 M5 GIH South Asia - West (Abecasis et al. 2012) NA21128 M5 GIH South Asia - West (Abecasis et al. 2012) FJ383557 M5 Madhya Pradesh South Asia - Central (Chandrasekar et al. 2009) FJ770955 M5 Nepal South Asia - Central (Fornarino et al. 2009) KC577360 M5 Mauritius Africa (Fregel et al. 2014) FJ383589 M5 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383543 M5 Orissa South Asia - East (Chandrasekar et al. 2009) FJ383596 M5 Arunachal Pradesh South Asia - East (Chandrasekar et al. 2009) FJ383595 M5 Arunachal Pradesh South Asia - East (Chandrasekar et al. 2009) FJ383592 M5 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383588 M5 Jharkhand South Asia - East (Chandrasekar et al. 2009) HG04094 M5 ITU South Asia - South (Abecasis et al. 2012) FJ383550 M5 Orissa South Asia - East (Chandrasekar et al. 2009) FJ383545 M5 Orissa South Asia - East (Chandrasekar et al. 2009) FJ383576 M5 Bihar South Asia - East (Chandrasekar et al. 2009) HM036533 M5 Great Himalayas: Ladakh tribe South Asia - Central Sharma et al. (unpublished) HM036571 M5 Great Himalayas: Ladakh tribe South Asia - Central Sharma et al. (unpublished) JF742201 M5 Nepal: Kathmandu South Asia - Central (Wang et al. 2012) JF742202 M5 Nepal: Kathmandu South Asia - Central (Wang et al. 2012) KF056269 M5 Sherpa South Asia - Central (Kang et al. 2013) FJ383575 M5 Bihar South Asia - East (Chandrasekar et al. 2009) FJ383551 M5 Jharkhand South Asia - East (Chandrasekar et al. 2009) AY922292 M5 Andhra Pradesh South Asia - South (Sun et al. 2006) AY922281 M5 Uttar Pradesh South Asia - Central (Sun et al. 2006) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference AY922282 M5 Uttar Pradesh South Asia - Central (Sun et al. 2006) HG03971 M5 ITU South Asia - South (Abecasis et al. 2012) NA21143 M5 GIH South Asia - West (Abecasis et al. 2012) FJ383546 M5 Orissa South Asia - East (Chandrasekar et al. 2009) FJ383558 M5 Madhya Pradesh South Asia - Central (Chandrasekar et al. 2009) FJ770953 M5 Nepal South Asia - Central (Fornarino et al. 2009) KF056270 M5 Sherpa South Asia - Central (Kang et al. 2013) DQ246832 M5 West Bengal South Asia - East (Rajkumar et al. 2005) FJ383301 M6 Maharashtra South Asia - South (Chandrasekar et al. 2009) DQ408677 M6 Kerala South Asia - South (Thangaraj et al. 2006) HG02727 M6 PJL South Asia - West (Abecasis et al. 2012) HG04219 M6 ITU South Asia - South (Abecasis et al. 2012) HG02725 M6 PJL South Asia - West (Abecasis et al. 2012) HG02789 M6 PJL South Asia - West (Abecasis et al. 2012) HG02493 M6 PJL South Asia - West (Abecasis et al. 2012) HG02778 M6 PJL South Asia - West (Abecasis et al. 2012) HG03019 M6 PJL South Asia - West (Abecasis et al. 2012) HG03018 M6 PJL South Asia - West (Abecasis et al. 2012) HG03022 M6 PJL South Asia - West (Abecasis et al. 2012) JQ703707 M6 India South Asia (Behar et al. 2012) AY922307 M6 Andhra Pradesh South Asia - South (Sun et al. 2006) HG03774 M6 ITU South Asia - South (Abecasis et al. 2012) HG03713 M6 ITU South Asia - South (Abecasis et al. 2012) HG03722 M6 ITU South Asia - South (Abecasis et al. 2012) HG03756 M6 STU South Asia - South (Abecasis et al. 2012) HG03709 M6 PJL South Asia - West (Abecasis et al. 2012) HG04198 M6 ITU South Asia - South (Abecasis et al. 2012) AY922296 M6 Andhra Pradesh South Asia - South (Sun et al. 2006) FJ383308 M6 Bihar South Asia - East (Chandrasekar et al. 2009) FJ383307 M6 Bihar South Asia - East (Chandrasekar et al. 2009) FJ383306 M6 Bihar South Asia - East (Chandrasekar et al. 2009) FJ383309 M6 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383304 M6 Orissa South Asia - East (Chandrasekar et al. 2009) FJ383302 M6 Orissa South Asia - East (Chandrasekar et al. 2009) FJ383303 M6 Orissa South Asia - East (Chandrasekar et al. 2009) HG03977 M6 ITU South Asia - South (Abecasis et al. 2012) HG04206 M6 ITU South Asia - South (Abecasis et al. 2012) HG03986 M6 STU South Asia - South (Abecasis et al. 2012) HG03705 M6 PJL South Asia - West (Abecasis et al. 2012) HG03928 M6 BEB South Asia - East (Abecasis et al. 2012) AY950300 M31 Andaman South Asia - East (Thangaraj et al. 2005) AY950298 M31 Andaman South Asia - East (Thangaraj et al. 2005) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference AY950297 M31 Andaman South Asia - East (Thangaraj et al. 2005) DQ149515 M31 Jarawa South Asia - East (Barik et al. 2008) DQ149516 M31 Jarawa South Asia - East (Barik et al. 2008) DQ149519 M31 Jarawa South Asia - East (Barik et al. 2008) DQ149511 M31 Jarawa South Asia - East (Barik et al. 2008) DQ149520 M31 Jarawa South Asia - East (Barik et al. 2008) AY950293 M31 Andaman South Asia - East (Thangaraj et al. 2005) AY950294 M31 Andaman South Asia - East (Thangaraj et al. 2005) DQ408673 M31 Andaman South Asia - East (Thangaraj et al. 2006) HQ438683 M31 Bangladesh South Asia - East (Wang et al. 2011) HQ438684 M31 Myanmar Southeast Asia (Wang et al. 2011) HQ438687 M31 East India South Asia - East (Wang et al. 2011) HQ438689 M31 East India South Asia - East (Wang et al. 2011) HQ438688 M31 West Bengal South Asia - East (Wang et al. 2011) EU075305 M31 Jharkhand South Asia - East (Barik et al. 2008) EU075306 M31 Jharkhand South Asia - East (Barik et al. 2008) EF060263 M31 Orissa South Asia - East (Barik et al. 2008) EF060264 M31 Orissa South Asia - East (Barik et al. 2008) EF060262 M31 Orissa South Asia - East (Barik et al. 2008) EF060266 M31 Orissa South Asia - East (Barik et al. 2008) EF060265 M31 Orissa South Asia - East (Barik et al. 2008) HQ438685 M31 Northeast India South Asia - East (Wang et al. 2011) WB8 M31 Myanmar Southeast Asia This study WD1 M31 Myanmar Southeast Asia This study HQ438686 M31 West Bengal South Asia - East (Wang et al. 2011) FJ770962 M31 Nepal South Asia - Central (Fornarino et al. 2009) Redd_Bh23 M31 Meghalaya South Asia - East Reddy et al. (2007) DQ149513 M32'56 Jarawa South Asia - East (Barik et al. 2008) DQ149514 M32'56 Jarawa South Asia - East (Barik et al. 2008) DQ149517 M32'56 Jarawa South Asia - East (Barik et al. 2008) DQ149512 M32'56 Jarawa South Asia - East (Barik et al. 2008) DQ149518 M32'56 Jarawa South Asia - East (Barik et al. 2008) AY950291 M32'56 Jarawa South Asia - East (Thangaraj et al. 2005) AY950292 M32'56 Jarawa South Asia - East (Thangaraj et al. 2005) AY950295 M32'56 Jarawa South Asia - East (Thangaraj et al. 2005) AY950296 M32'56 Andaman South Asia - East (Thangaraj et al. 2005) AY950299 M32'56 Andaman South Asia - East (Thangaraj et al. 2005) FJ383487 M32'56 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383486 M32'56 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ770951 M33 India South Asia (Fornarino et al. 2009) FJ383348 M33 Jharkhand South Asia - East (Chandrasekar et al. 2009) FJ383349 M33 Jharkhand South Asia - East (Chandrasekar et al. 2009) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference FJ383350 M33 Jharkhand South Asia - East (Chandrasekar et al. 2009) FJ383346 M33 Jharkhand South Asia - East (Chandrasekar et al. 2009) FJ383347 M33 Jharkhand South Asia - East (Chandrasekar et al. 2009) HG03634 M33 PJL South Asia - West (Abecasis et al. 2012) HG03922 M33 BEB South Asia - East (Abecasis et al. 2012) FJ770963 M33 Nepal South Asia - Central (Fornarino et al. 2009) JF742205 M33 Nepal: Kathmandu South Asia - Central (Wang et al. 2012) FJ383344 M33 Sikkim South Asia - East (Chandrasekar et al. 2009) FJ383340 M33 Sikkim South Asia - East (Chandrasekar et al. 2009) FJ383341 M33 Sikkim South Asia - East (Chandrasekar et al. 2009) FJ383339 M33 Sikkim South Asia - East (Chandrasekar et al. 2009) FJ383342 M33 Sikkim South Asia - East (Chandrasekar et al. 2009) FJ383343 M33 Sikkim South Asia - East (Chandrasekar et al. 2009) FJ383345 M33 Sikkim South Asia - East (Chandrasekar et al. 2009) DQ408680 M33 Gujarat South Asia - West (Thangaraj et al. 2006) FJ383358 M33 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383353 M33 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383354 M33 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383356 M33 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383355 M33 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383352 M33 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383357 M33 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383361 M33 Maharashtra South Asia - South (Chandrasekar et al. 2009) HG03642 M33 STU South Asia - South (Abecasis et al. 2012) JQ702439 M33 Qatar Southwest Asia (Behar et al. 2012) AY922276 M33 Uttar Pradesh South Asia - Central (Sun et al. 2006) FJ383338 M33 Madhya Pradesh South Asia - Central (Chandrasekar et al. 2009) FJ383360 M33 Madhya Pradesh South Asia - Central (Chandrasekar et al. 2009) HG03989 M33 STU South Asia - South (Abecasis et al. 2012) JN540042 M33 Iraq: Marsh Arab Southwest Asia (Al-Zahery et al. 2011) JX289104 M33 Myanmar Southeast Asia (Summerer et al. 2014) FJ383359 M33 Assam South Asia - East (Chandrasekar et al. 2009) FJ770950 M33 India South Asia (Fornarino et al. 2009) HG02660 M33 PJL South Asia - West (Abecasis et al. 2012) FJ770960 M33 Nepal South Asia - Central (Fornarino et al. 2009) HG04202 M33 ITU South Asia - South (Abecasis et al. 2012) Redd_Ga11 M33 Meghalaya South Asia - East Reddy et al. (2007) JF742198 M33 Nepal: Kathmandu South Asia - Central (Wang et al. 2012) AY922298 M33 West Bengal South Asia - East (Sun et al. 2006) FJ383351 M33 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) HG04171 M33 BEB South Asia - East (Abecasis et al. 2012) FJ383362 M33 Arunachal Pradesh South Asia - East (Chandrasekar et al. 2009) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference Redd_Pn14 M33 Arunachal Pradesh South Asia - East Reddy et al. (2007) FJ770968 M33 Nepal South Asia - Central (Fornarino et al. 2009) KC252506 M33 Taiwan East Asia (Loo et al. 2014) JQ702003 M33 unknown unknown (Behar et al. 2012) KC252508 M33 Taiwan East Asia (Loo et al. 2014) AY922274 M34'57 Uttar Pradesh South Asia - Central (Sun et al. 2006) FJ383681 M34'57 Madhya Pradesh South Asia - Central (Chandrasekar et al. 2009) HG03884 M34'57 STU South Asia - South (Abecasis et al. 2012) FJ383682 M34'57 Orissa South Asia - East (Chandrasekar et al. 2009) FJ383680 M34'57 Bihar South Asia - East (Chandrasekar et al. 2009) HG04153 M34'57 BEB South Asia - East (Abecasis et al. 2012) DQ408672 M34'57 Karnataka South Asia - South (Thangaraj et al. 2006) AY922304 M34'57 Uttar Pradesh South Asia - Central (Sun et al. 2006) JX289117 M34'57 Myanmar Southeast Asia (Summerer et al. 2014) FJ383764 M34'57 Madhya Pradesh South Asia - Central (Chandrasekar et al. 2009) KJ446727 M34'57 Pakistan: Sindhi South Asia - West HGDP - Zheng et al. (unpublished) FJ383763 M34'57 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383762 M34'57 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383760 M34'57 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383761 M34'57 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383757 M34'57 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383759 M34'57 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383758 M34'57 Rajasthan South Asia - West (Chandrasekar et al. 2009) FJ383380 M35 Madhya Pradesh South Asia - Central (Chandrasekar et al. 2009) HG04185 M35 BEB South Asia - East (Abecasis et al. 2012) FJ770952 M35 India South Asia (Fornarino et al. 2009) FJ383391 M35 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383384 M35 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383387 M35 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383388 M35 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383385 M35 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383389 M35 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383386 M35 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383390 M35 Karnataka South Asia - South (Chandrasekar et al. 2009) AY289074 M35 Mullukurunan South Asia - South (Ingman and Gyllensten 2003) HG03800 M35 BEB South Asia - East (Abecasis et al. 2012) HG03731 M35 ITU South Asia - South (Abecasis et al. 2012) HG03869 M35 ITU South Asia - South (Abecasis et al. 2012) HG03697 M35 STU South Asia - South (Abecasis et al. 2012) HG03882 M35 ITU South Asia - South (Abecasis et al. 2012) HG04062 M35 ITU South Asia - South (Abecasis et al. 2012) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference HM156693 M35 Andhra Pradesh South Asia - South (Govindaraj et al. 2011) FJ383365 M35 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383364 M35 Maharashtra South Asia - South (Chandrasekar et al. 2009) AY922264 M35 Andhra Pradesh South Asia - South (Sun et al. 2006) FJ383368 M35 Rajasthan South Asia - West (Chandrasekar et al. 2009) AY922279 M35 Andhra Pradesh South Asia - South (Sun et al. 2006) FJ383363 M35 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383372 M35 Maharashtra South Asia - South (Chandrasekar et al. 2009) AY922272 M35 Andhra Pradesh South Asia - South (Sun et al. 2006) HG03856 M35 STU South Asia - South (Abecasis et al. 2012) HG04059 M35 ITU South Asia - South (Abecasis et al. 2012) NA21116 M35 GIH South Asia - West (Abecasis et al. 2012) HG03832 M35 BEB South Asia - East (Abecasis et al. 2012) FJ383393 M35 Assam South Asia - East (Chandrasekar et al. 2009) FJ383369 M35 Assam South Asia - East (Chandrasekar et al. 2009) FJ383370 M35 Assam South Asia - East (Chandrasekar et al. 2009) FJ383371 M35 Assam South Asia - East (Chandrasekar et al. 2009) NA20869 M35 GIH South Asia - West (Abecasis et al. 2012) NA20876 M35 GIH South Asia - West (Abecasis et al. 2012) JF742208 M35 Nepal South Asia - Central (Wang et al. 2012) HG03615 M35 BEB South Asia - East (Abecasis et al. 2012) FJ383377 M35 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383374 M35 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383375 M35 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383378 M35 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383379 M35 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383376 M35 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) HM156677 M35 Andhra Pradesh South Asia - South (Govindaraj et al. 2011) HG04070 M35 ITU South Asia - South (Abecasis et al. 2012) HG04020 M35 ITU South Asia - South (Abecasis et al. 2012) HM036544 M35 Great Himalayas: Ladakh tribe South Asia - Central Sharma et al. (unpublished) HM036535 M35 Great Himalayas: Ladakh tribe South Asia - Central Sharma et al. (unpublished) HM036559 M35 Great Himalayas: Ladakh tribe South Asia - Central Sharma et al. (unpublished) HM036575 M35 Great Himalayas: Ladakh tribe South Asia - Central Sharma et al. (unpublished) FJ770966 M35 Nepal South Asia - Central (Fornarino et al. 2009) FJ383392 M35 Arunachal Pradesh South Asia - East (Chandrasekar et al. 2009) GU810066 M35 Thailand Southeast Asia Pradutkanchana et al. (unpublished) JF742209 M35 Nepal South Asia - Central (Wang et al. 2012) FJ383381 M35 Gujarat South Asia - West (Chandrasekar et al. 2009) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference FJ383373 M35 Bihar South Asia - East (Chandrasekar et al. 2009) JF742215 M35 Nepal South Asia - Central (Wang et al. 2012) FJ383383 M35 Gujarat South Asia - West (Chandrasekar et al. 2009) FJ383382 M35 Gujarat South Asia - West (Chandrasekar et al. 2009) FJ383366 M35 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383367 M35 Maharashtra South Asia - South (Chandrasekar et al. 2009) GU480006 M35 Madhya Pradesh South Asia - Central (Sharma et al. 2012) HG04216 M35 ITU South Asia - South (Abecasis et al. 2012) HG02601 M35 PJL South Asia - West (Abecasis et al. 2012) HG03917 M35 BEB South Asia - East (Abecasis et al. 2012) FJ770956 M35 Nepal South Asia - Central (Fornarino et al. 2009) AY922288 M39 Uttar Pradesh South Asia - Central (Sun et al. 2006) AY922269 M39 Andhra Pradesh South Asia - South (Sun et al. 2006) AY922293 M39 Andhra Pradesh South Asia - South (Sun et al. 2006) HG04209 M39 ITU South Asia - South (Abecasis et al. 2012) FJ383714 M39 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383710 M39 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383715 M39 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383705 M39 Bihar South Asia - East (Chandrasekar et al. 2009) FJ383712 M39 Jharkhand South Asia - East (Chandrasekar et al. 2009) FJ383706 M39 Bihar South Asia - East (Chandrasekar et al. 2009) FJ383702 M39 Orissa South Asia - East (Chandrasekar et al. 2009) FJ383708 M39 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383713 M39 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383707 M39 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383709 M39 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383703 M39 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383711 M39 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) AY922262 M39 Andhra Pradesh South Asia - South (Sun et al. 2006) HG03870 M39 ITU South Asia - South (Abecasis et al. 2012) HG03838 M39 STU South Asia - South (Abecasis et al. 2012) AY922275 M39 Andhra Pradesh South Asia - South (Sun et al. 2006) NA20897 M39 GIH South Asia - West (Abecasis et al. 2012) HG02597 M39 PJL South Asia - West (Abecasis et al. 2012) NA20888 M39 GIH South Asia - West (Abecasis et al. 2012) NA20906 M39 GIH South Asia - West (Abecasis et al. 2012) NA20908 M39 GIH South Asia - West (Abecasis et al. 2012) FJ383704 M39 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383701 M39 Maharashtra South Asia - South (Chandrasekar et al. 2009) FJ383699 M39 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383697 M39 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383696 M39 Karnataka South Asia - South (Chandrasekar et al. 2009) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference FJ383698 M39 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383700 M39 Karnataka South Asia - South (Chandrasekar et al. 2009) HG03787 M39 ITU South Asia - South (Abecasis et al. 2012) HG03963 M39 ITU South Asia - South (Abecasis et al. 2012) AY922287 M40 Andhra Pradesh South Asia - South (Sun et al. 2006) NA20864 M40 GIH South Asia - West (Abecasis et al. 2012) HG03896 M40 STU South Asia - South (Abecasis et al. 2012) HG04075 M40 STU South Asia - South (Abecasis et al. 2012) HG04015 M40 ITU South Asia - South (Abecasis et al. 2012) AY922284 M40 Andhra Pradesh South Asia - South (Sun et al. 2006) FJ383807 M40 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383786 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383784 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383785 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383796 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383797 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383802 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383789 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383805 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383793 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383804 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383782 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383783 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383780 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383806 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383779 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383794 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383798 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383790 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383803 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383778 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383781 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383787 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383788 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383800 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383791 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383792 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383808 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383811 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383809 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383795 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383799 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference FJ383801 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383810 M40 Karnataka South Asia - South (Chandrasekar et al. 2009) FJ383409 M40 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383406 M40 Jharkhand South Asia - East (Chandrasekar et al. 2009) NA20874 M40 GIH South Asia - West (Abecasis et al. 2012) FJ383425 M40 Bihar South Asia - East (Chandrasekar et al. 2009) FJ383413 M40 Madhya Pradesh South Asia - Central (Chandrasekar et al. 2009) FJ383423 M40 Madhya Pradesh South Asia - Central (Chandrasekar et al. 2009) FJ383421 M40 Bihar South Asia - East (Chandrasekar et al. 2009) FJ383426 M40 Bihar South Asia - East (Chandrasekar et al. 2009) FJ383427 M40 Bihar South Asia - East (Chandrasekar et al. 2009) FJ383422 M40 Bihar South Asia - East (Chandrasekar et al. 2009) FJ383424 M40 Bihar South Asia - East (Chandrasekar et al. 2009) HG04180 M40 BEB South Asia - East (Abecasis et al. 2012) FJ383419 M40 Orissa South Asia - East (Chandrasekar et al. 2009) FJ383420 M40 Orissa South Asia - East (Chandrasekar et al. 2009) FJ383417 M40 Orissa South Asia - East (Chandrasekar et al. 2009) FJ383414 M40 Orissa South Asia - East (Chandrasekar et al. 2009) FJ383412 M40 Arunachal Pradesh South Asia - East (Chandrasekar et al. 2009) FJ383410 M40 Arunachal Pradesh South Asia - East (Chandrasekar et al. 2009) FJ383411 M40 Arunachal Pradesh South Asia - East (Chandrasekar et al. 2009) FJ383407 M40 Madhya Pradesh South Asia - Central (Chandrasekar et al. 2009) FJ383408 M40 Madhya Pradesh South Asia - Central (Chandrasekar et al. 2009) HG03771 M40 ITU South Asia - South (Abecasis et al. 2012) FJ383418 M40 Orissa South Asia - East (Chandrasekar et al. 2009) FJ383416 M40 Orissa South Asia - East (Chandrasekar et al. 2009) FJ383415 M40 Orissa South Asia - East (Chandrasekar et al. 2009) AY922295 M40 Andhra Pradesh South Asia - South (Sun et al. 2006) AY922271 M40 Andhra Pradesh South Asia - South (Sun et al. 2006) AY922294 M40 Andhra Pradesh South Asia - South (Sun et al. 2006) AY922280 M41 Andhra Pradesh South Asia - South (Sun et al. 2006) FJ383718 M41 Jharkhand South Asia - East (Chandrasekar et al. 2009) FJ383717 M41 Jharkhand South Asia - East (Chandrasekar et al. 2009) FJ383716 M41 Jharkhand South Asia - East (Chandrasekar et al. 2009) FJ383719 M41 Jharkhand South Asia - East (Chandrasekar et al. 2009) HG03593 M41 BEB South Asia - East (Abecasis et al. 2012) DQ513521 M41 Andhra Pradesh South Asia - South (Thangaraj et al. 2006) FJ383722 M41 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383721 M41 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) FJ383720 M41 Chhattisgarh South Asia - Central (Chandrasekar et al. 2009) GU480001 M41 Madhya Pradesh South Asia - Central (Sharma et al. 2012) DQ513522 M41 Andhra Pradesh South Asia - South (Thangaraj et al. 2006) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference HG03947 R7 STU South Asia - South (Abecasis et al. 2012) HG04029 R7 STU South Asia - South (Abecasis et al. 2012) HG03851 R7 STU South Asia - South (Abecasis et al. 2012) KK27 R7 Borneo, East Malaysia: Kota Kinabalu Southeast Asia This study FJ467953 R8 Andhra Pradesh South Asia - South (Thangaraj et al. 2009) JF742196 R8 Nepal: Kathmandu South Asia - Central (Wang et al. 2012) JF742200 R8 Nepal: Kathmandu South Asia - Central (Wang et al. 2012) FJ467943 R8 Jharkhand South Asia - East (Thangaraj et al. 2009) KC911621 R8 Iran: Qashqai Southwest Asia (Derenko et al. 2013) FJ467978 R8 Madhya Pradesh South Asia - Central (Thangaraj et al. 2009) AY714012 R8 Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) FJ467951 R8 Orissa South Asia - East (Thangaraj et al. 2009) FJ467979 R8 Andhra Pradesh South Asia - South (Thangaraj et al. 2009) FJ467949 R8 Andhra Pradesh South Asia - South (Thangaraj et al. 2009) FJ467944 R8 Madhya Pradesh South Asia - Central (Thangaraj et al. 2009) FJ467955 R8 Andhra Pradesh South Asia - South (Thangaraj et al. 2009) FJ467966 R8 Madhya Pradesh South Asia - Central (Thangaraj et al. 2009) GU480002 R8 Madhya Pradesh South Asia - Central (Sharma et al. 2012) FJ467942 R8 Gujarat South Asia - West (Thangaraj et al. 2009) FJ467956 R8 Uttar Pradesh South Asia - Central (Thangaraj et al. 2009) FJ467947 R8 Orissa South Asia - East (Thangaraj et al. 2009) FJ467964 R8 Chhattisgarh South Asia - Central (Thangaraj et al. 2009) FJ467965 R8 Chhattisgarh South Asia - Central (Thangaraj et al. 2009) FJ004808 R8 Maharashtra South Asia - South (Chaubey et al. 2008) FJ467952 R8 Jharkhand South Asia - East (Thangaraj et al. 2009) FJ004818 R8 Andhra Pradesh South Asia - South (Chaubey et al. 2008) FJ004820 R8 Andhra Pradesh South Asia - South (Chaubey et al. 2008) FJ467993 R8 Gujarat South Asia - West (Thangaraj et al. 2009) FJ467976 R8 Orissa South Asia - East (Thangaraj et al. 2009) FJ467983 R8 Orissa South Asia - East (Thangaraj et al. 2009) FJ467971 R8 Orissa South Asia - East (Thangaraj et al. 2009) FJ467982 R8 Andhra Pradesh South Asia - South (Thangaraj et al. 2009) FJ467975 R8 Orissa South Asia - East (Thangaraj et al. 2009) FJ467974 R8 Orissa South Asia - East (Thangaraj et al. 2009) FJ004838 R8 Andhra Pradesh South Asia - South (Chaubey et al. 2008) AY714011 R8 Meghalaya South Asia - East (Palanichamy et al. 2004) FJ467984 R8 Madhya Pradesh South Asia - Central (Thangaraj et al. 2009) FJ467972 R8 Orissa South Asia - East (Thangaraj et al. 2009) FJ467973 R8 Orissa South Asia - East (Thangaraj et al. 2009) FJ467968 R8 Orissa South Asia - East (Thangaraj et al. 2009) FJ467969 R8 Orissa South Asia - East (Thangaraj et al. 2009) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference FJ467970 R8 Orissa South Asia - East (Thangaraj et al. 2009) FJ467950 R8 Andhra Pradesh South Asia - South (Thangaraj et al. 2009) NA21144 R8 GIH South Asia - West (Abecasis et al. 2012) FJ467945 R8 Andhra Pradesh South Asia - South (Thangaraj et al. 2009) FJ004836 R8 Andhra Pradesh South Asia - South (Chaubey et al. 2008) FJ467980 R8 Andhra Pradesh South Asia - South (Thangaraj et al. 2009) FJ467986 R8 Andhra Pradesh South Asia - South (Thangaraj et al. 2009) FJ467985 R8 Andhra Pradesh South Asia - South (Thangaraj et al. 2009) FJ467946 R8 Andhra Pradesh South Asia - South (Thangaraj et al. 2009) FJ467967 R8 Andhra Pradesh South Asia - South (Thangaraj et al. 2009) FJ467981 R8 Andhra Pradesh South Asia - South (Thangaraj et al. 2009) FJ467941 R8 Andhra Pradesh South Asia - South (Thangaraj et al. 2009) FJ467961 R8 Gujarat South Asia - West (Thangaraj et al. 2009) FJ467962 R8 Gujarat South Asia - West (Thangaraj et al. 2009) FJ467963 R8 Gujarat South Asia - West (Thangaraj et al. 2009) FJ467960 R8 Gujarat South Asia - West (Thangaraj et al. 2009) FJ467958 R8 Gujarat South Asia - West (Thangaraj et al. 2009) FJ467959 R8 Gujarat South Asia - West (Thangaraj et al. 2009) FJ467957 R8 Gujarat South Asia - West (Thangaraj et al. 2009) FJ467948 R8 Tamil Nadu South Asia - South (Thangaraj et al. 2009) HG03864 R8 ITU South Asia - South (Abecasis et al. 2012) FJ467977 R8 Jharkhand South Asia - East (Thangaraj et al. 2009) AY714009 R8 Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) FJ467954 R8 Andhra Pradesh South Asia - South (Thangaraj et al. 2009) FJ467940 R8 Andhra Pradesh South Asia - South (Thangaraj et al. 2009) HM156676 R8 Andhra Pradesh South Asia - South (Govindaraj et al. 2011) HG03736 R8 STU South Asia - South (Abecasis et al. 2012) FJ467989 R8 Orissa South Asia - East (Thangaraj et al. 2009) FJ467991 R8 Orissa South Asia - East (Thangaraj et al. 2009) FJ467992 R8 Orissa South Asia - East (Thangaraj et al. 2009) FJ467990 R8 Orissa South Asia - East (Thangaraj et al. 2009) FJ467987 R8 Orissa South Asia - East (Thangaraj et al. 2009) FJ467988 R8 Orissa South Asia - East (Thangaraj et al. 2009) AY714006 R30 Andhra Pradesh South Asia - South (Palanichamy et al. 2004) HG03887 R30 STU South Asia - South (Abecasis et al. 2012) HG04061 R30 ITU South Asia - South (Abecasis et al. 2012) AY714001 R30 Andhra Pradesh South Asia - South (Palanichamy et al. 2004) FJ770961 R30 Nepal South Asia - Central (Fornarino et al. 2009) PAD90 R30 Indonesia: Padang Southeast Asia This study FJ004824 R30 Sri Lanka South Asia - South (Chaubey et al. 2008) HG03645 R30 STU South Asia - South (Abecasis et al. 2012) HG03949 R30 STU South Asia - South (Abecasis et al. 2012) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference HG03872 R30 ITU South Asia - South (Abecasis et al. 2012) KC911324 R30 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911618 R30 Iran: Persian Southwest Asia (Derenko et al. 2013) HG04018 R30 ITU South Asia - South (Abecasis et al. 2012) GU170818 R30 Tamil Nadu South Asia - South (Rani et al. 2010) NA21110 R30 GIH South Asia - West (Abecasis et al. 2012) HG03937 R30 BEB South Asia - East (Abecasis et al. 2012) HG03911 R30 BEB South Asia - East (Abecasis et al. 2012) AY714032 R30 Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) HG01593 R30 PJL South Asia - West (Abecasis et al. 2012) AY714047 R30 Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) FJ004827 R30 Punjab South Asia - West (Chaubey et al. 2008) AY714050 R30 Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) HG02697 R30 PJL South Asia - West (Abecasis et al. 2012) KF038316 R30 Gujarat: Surat South Asia - West Wilson (direct submission) HG03714 R30 ITU South Asia - South (Abecasis et al. 2012) HG03679 R30 STU South Asia - South (Abecasis et al. 2012) HG03680 R30 STU South Asia - South (Abecasis et al. 2012) NA21102 R30 GIH South Asia - West (Abecasis et al. 2012) NA21105 R30 GIH South Asia - West (Abecasis et al. 2012) NA20902 R30 GIH South Asia - West (Abecasis et al. 2012) HG03788 R30 ITU South Asia - South (Abecasis et al. 2012) HG03874 R30 ITU South Asia - South (Abecasis et al. 2012) NA20856 R30 GIH South Asia - West (Abecasis et al. 2012) NA21115 R30 GIH South Asia - West (Abecasis et al. 2012) FJ004807 R30 Maharashtra South Asia - South (Chaubey et al. 2008) GU170815 R30 Tamil Nadu South Asia - South (Rani et al. 2010) AY714021 R31 Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) FJ004826 R31 Rajasthan South Asia - West (Chaubey et al. 2008) FJ004825 R31 Rajasthan South Asia - West (Chaubey et al. 2008) NA21137 R31 GIH South Asia - West (Abecasis et al. 2012) NA20861 R31 GIH South Asia - West (Abecasis et al. 2012) NA21089 R31 GIH South Asia - West (Abecasis et al. 2012) JQ705959 R31 unknown unknown (Behar et al. 2012) AY714046 R31 Andhra Pradesh South Asia - South (Palanichamy et al. 2004) AY714048 R31 Andhra Pradesh South Asia - South (Palanichamy et al. 2004) HG03755 R31 STU South Asia - South (Abecasis et al. 2012) HG03738 R31 STU South Asia - South (Abecasis et al. 2012) HG03750 R31 STU South Asia - South (Abecasis et al. 2012) HG03854 R31 STU South Asia - South (Abecasis et al. 2012) AY713992 U2 Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) HG03742 U2 ITU South Asia - South (Abecasis et al. 2012) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference HG03985 U2 STU South Asia - South (Abecasis et al. 2012) HG04002 U2 ITU South Asia - South (Abecasis et al. 2012) AY713990 U2 Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) AY882379 U2 Pakistan South Asia - West (Achilli et al. 2005) HG03829 U2 BEB South Asia - East (Abecasis et al. 2012) NA20866 U2 GIH South Asia - West (Abecasis et al. 2012) JX488759 U2 Eastern Indian South Asia - East Family Tree HG03653 U2 PJL South Asia - West (Abecasis et al. 2012) NA20875 U2 GIH South Asia - West (Abecasis et al. 2012) NA20904 U2 GIH South Asia - West (Abecasis et al. 2012) HG03960 U2 ITU South Asia - South (Abecasis et al. 2012) AY714020 U2 Meghalaya South Asia - East (Palanichamy et al. 2004) HG03861 U2 ITU South Asia - South (Abecasis et al. 2012) WA8 U2 Myanmar Southeast Asia This study HG04106 U2 STU South Asia - South (Abecasis et al. 2012) HG03695 U2 STU South Asia - South (Abecasis et al. 2012) HG03754 U2 STU South Asia - South (Abecasis et al. 2012) HG04107 U2 STU South Asia - South (Abecasis et al. 2012) NA21119 U2 GIH South Asia - West (Abecasis et al. 2012) HG03767 U2 PJL South Asia - West (Abecasis et al. 2012) AY714025 U2 Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) HG03694 U2 STU South Asia - South (Abecasis et al. 2012) HG03823 U2 BEB South Asia - East (Abecasis et al. 2012) HG03826 U2 BEB South Asia - East (Abecasis et al. 2012) HG04038 U2 STU South Asia - South (Abecasis et al. 2012) HG04212 U2 ITU South Asia - South (Abecasis et al. 2012) NA21095 U2 GIH South Asia - West (Abecasis et al. 2012) HM156680 U2 Andhra Pradesh: Mahabubnagar South Asia - South (Govindaraj et al. 2011) HM156685 U2 Andhra Pradesh: Mahabubnagar South Asia - South (Govindaraj et al. 2011) HQ153103 U2 Sri Lanka South Asia - South Illeperuma & Bamshad (unpublished) AY714027 U2 Andhra Pradesh South Asia - South (Palanichamy et al. 2004) HG04200 U2 ITU South Asia - South (Abecasis et al. 2012) NA20887 U2 GIH South Asia - West (Abecasis et al. 2012) AY882380 U2 Pakistan South Asia - West (Achilli et al. 2005) HG03703 U2 PJL South Asia - West (Abecasis et al. 2012) HG04222 U2 ITU South Asia - South (Abecasis et al. 2012) HG02603 U2 PJL South Asia - West (Abecasis et al. 2012) HG03603 U2 BEB South Asia - East (Abecasis et al. 2012) HG03908 U2 BEB South Asia - East (Abecasis et al. 2012) HG03802 U2 BEB South Asia - East (Abecasis et al. 2012) HG04158 U2 BEB South Asia - East (Abecasis et al. 2012) Table S1. (continued) Sample Haplogroup Origin (Population) Region Reference HG04214 U2 ITU South Asia - South (Abecasis et al. 2012) AY714010 U2 West Bengal South Asia - East (Palanichamy et al. 2004) KC911315 U2 Iran: Persian Southwest Asia (Derenko et al. 2013) AY882381 U2 Pakistan South Asia - West (Achilli et al. 2005) HG03619 U2 PJL South Asia - West (Abecasis et al. 2012) NA21111 U2 GIH South Asia - West (Abecasis et al. 2012) AY714005 U2 Andhra Pradesh South Asia - South (Palanichamy et al. 2004) HG03817 U2 BEB South Asia - East (Abecasis et al. 2012) HG03691 U2 STU South Asia - South (Abecasis et al. 2012) HG04099 U2 STU South Asia - South (Abecasis et al. 2012) HM036565 U2 Great Himalayas: Ladakh tribe South Asia - Central Sharma et al. (unpublished) HM036556 U2 Great Himalayas: Ladakh tribe South Asia - Central Sharma et al. (unpublished) KC911602 U2 Iran: Persian Southwest Asia (Derenko et al. 2013) JQ706041 U2 Iran Southwest Asia (Behar et al. 2012) KC911489 U2 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911405 U2 Iran: Bakhtiari Southwest Asia (Derenko et al. 2013) KC911513 U2 Iran: Qashqai Southwest Asia (Derenko et al. 2013) KC911479 U2 Iran: Persian Southwest Asia (Derenko et al. 2013) AY714040 U2 Andhra Pradesh: Thogataveera South Asia - South (Palanichamy et al. 2004) KC911567 U2 Azerbaijan: Azeri Southwest Asia (Derenko et al. 2013) HM156683 U2 Andhra Pradesh: Mahabubnagar South Asia - South (Govindaraj et al. 2011) HM156688 U2 Andhra Pradesh: Mahabubnagar South Asia - South (Govindaraj et al. 2011) References: Abecasis GR, Auton A, Brooks LD, et al (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491:56–65. Achilli A, Rengo C, Battaglia V, et al (2005) Saami and Berbers--an unexpected mitochondrial DNA link. Am J Hum Genet 76:883–6. 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(continued) Sample Haplogroup Origin (Population) Region Reference Sample Haplogroup Origin (Population) Region Reference EU597524 H1 Czech Republic Europe (Hartmann et al. 2009) EU747355 H1 Germany Europe Family Tree JQ702008 H1 Germany Europe (Behar et al. 2012) JQ702174 H1 unknown unknown (Behar et al. 2012) JQ702182 H1 unknown unknown (Behar et al. 2012) JQ704245 H1 Ireland Europe (Behar et al. 2012) JQ704536 H1 unknown unknown (Behar et al. 2012) JX885690 H1 England Europe Family Tree AY713977 H1 India: Andhra Pradesh South Asia - South (Palanichamy et al. 2004) AY738961 H2 Iraq Southwest Asia (Achilli et al. 2004) HQ659667 H2 Germany Europe Family Tree JQ702621 H2 unknown unknown (Behar et al. 2012) JQ704274 H2 unknown unknown (Behar et al. 2012) JQ704530 H2 unknown unknown (Behar et al. 2012) NA07051 H2 CEU Europe (Sudmant et al. 2015) NA20585 H2 TSI Europe (Sudmant et al. 2015) NA20802 H2 TSI Europe (Sudmant et al. 2015) EU597574 H2 Pakistan: Brahui South Asia - West (Hartmann et al. 2009) HG01586 H2 PJL South Asia - West (Sudmant et al. 2015) HG04039 H2 STU South Asia - South (Sudmant et al. 2015) KJ446362 H2 Pakistan: Pathan South Asia - West HGDP - Zheng, et al. (unpublished) KP763834 H2 India South Asia (Palanichamy et al. 2015) NA20872 H2 GIH South Asia - West (Sudmant et al. 2015) KJ856744 H2 Altai Central Asia/Siberia (Derenko et al. 2014) KJ856726 H2 Altai Central Asia/Siberia (Derenko et al. 2014) KJ856720 H2 Khamnigan Central Asia/Siberia (Derenko et al. 2014) KF161829 H2 Denmark Europe (Li et al. 2014) KJ446360 H2 Russia Europe HGDP - Zheng, et al. (unpublished) KC990675 H2 Possibly India South Asia Ramanan et al. (unpublished) JQ705227 H2 unknown unknown (Behar et al. 2012) JQ702943 H2 Greece Europe (Behar et al. 2012) EU600329 H6 Druze Southwest Asia (Shlush et al. 2008) FJ348203 H6 Hutterite Europe HGDP - Zheng, et al. (unpublished) JQ702285 H6 unknown unknown (Behar et al. 2012) NA20850 H6 GIH South Asia - West (Sudmant et al. 2015) HM852826 H7 Iran Southwest Asia (Schönberg et al. 2011) JQ702601 H7 Germany Europe (Behar et al. 2012) JQ702990 H7 unknown unknown (Behar et al. 2012) JQ704890 H7 unknown unknown (Behar et al. 2012) KC911403 H7 Iran: Persian Southwest Asia (Derenko et al. 2013) Table S2. List of non-autochthonous complete modern mtDNA sequences used in our analyses. Population codes: BEB – Bengali from Bangladesh; GIH – Gujarati Indian from Houston, Texas; ITU – Indian Telugu from the UK; PJL – Punjabi from Lahore, Pakistan; STU – Sri Lankan Tamil from the UK; TSI – Tuscans from Italy; KHV – Kinh from Ho Chi Minh City, Vietnam; CDX – Chinese Dai from Xishuangbanna, China; CEU – Utah Residents (CEPH) with Northern and Western Ancestry. Table S2. (continued) Sample Haplogroup Origin (Population) Region Reference NA20870 H7 GIH South Asia - West (Sudmant et al. 2015) AY713978 H9 India: Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) AY738969 H9 Italy Europe (Achilli et al. 2004) JQ705022 H9 Germany Europe (Behar et al. 2012) AY339409 H13 Finland Europe (Finnilä et al. 2001) AY495107 H13 Europe Europe (Coble et al. 2004) AY495149 H13 Europe Europe (Coble et al. 2004) EF556150 H13 Israel: Jew Southwest Asia (Behar et al. 2008a) EU597515 H13 Palestine Southwest Asia (Hartmann et al. 2009) AY713980 H13 India: Andhra Pradesh South Asia - South (Palanichamy et al. 2004) AY713982 H13 India: Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) JQ702112 H13 England Europe (Behar et al. 2012) JQ703858 H13 Ireland Europe (Behar et al. 2012) KC911327 H13 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911369 H13 Iran: Qashqai Southwest Asia (Derenko et al. 2013) KC911443 H13 Iran: Indian Southwest Asia (Derenko et al. 2013) KC911454 H13 Russia: Saratov Region Europe (Derenko et al. 2013) HG01589 H13 PJL South Asia - West (Sudmant et al. 2015) HG02651 H13 PJL South Asia - West (Sudmant et al. 2015) HG03692 H13 STU South Asia - South (Sudmant et al. 2015) HG03844 H13 STU South Asia - South (Sudmant et al. 2015) HG03849 H13 STU South Asia - South (Sudmant et al. 2015) HG03995 H13 STU South Asia - South (Sudmant et al. 2015) KJ446338 H13 Pakistan: Balochi South Asia - West HGDP - Zheng, et al. (unpublished) KJ446339 H13 Pakistan: Balochi South Asia - West HGDP - Zheng, et al. (unpublished) KJ446340 H13 Pakistan: Brahui South Asia - West HGDP - Zheng, et al. (unpublished) KJ446341 H13 Pakistan: Balochi South Asia - West HGDP - Zheng, et al. (unpublished) AY713995 H15 India: Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) AY495146 H15 Europe Europe (Coble et al. 2004) HM852832 H15 Iran Southwest Asia (Schönberg et al. 2011) JQ704364 H15 unknown unknown (Behar et al. 2012) KC911289 H15 Iran: Azeri Southwest Asia (Derenko et al. 2013) KC911292 H15 Iran: Persian Southwest Asia (Derenko et al. 2013) EU600335 H29 Druze Southwest Asia (Shlush et al. 2008) EU600343 H29 Druze Southwest Asia (Shlush et al. 2008) JQ704540 H29 Italy Europe (Behar et al. 2012) KC911535 H29 Iran: Azeri Southwest Asia (Derenko et al. 2013) NA20896 H29 GIH South Asia - West (Sudmant et al. 2015) NA21098 H29 GIH South Asia - West (Sudmant et al. 2015) AY713981 HV India: Andhra Pradesh South Asia - South (Palanichamy et al. 2004) EF222251 HV Poland Europe (Malyarchuk et al. 2008b) Table S2. (continued) Sample Haplogroup Origin (Population) Region Reference EU545435 HV Russia Europe (Malyarchuk et al. 2008b) HM852792 HV Azeri Southwest Asia (Schönberg et al. 2011) HM852816 HV Iran Southwest Asia (Schönberg et al. 2011) HQ287727 HV Armenia Southwest Asia Family Tree HQ436102 HV Armenia Southwest Asia Family Tree JF313325 HV Sweden Europe Family Tree KC765916 HV Bulgaria Europe Family Tree KC911391 HV Iran: Persian Southwest Asia (Derenko et al. 2013) KC911408 HV Iran: Persian Southwest Asia (Derenko et al. 2013) KC911439 HV Iran: Persian Southwest Asia (Derenko et al. 2013) KC911472 HV Iran: Persian Southwest Asia (Derenko et al. 2013) HG02491 HV PJL South Asia - West (Sudmant et al. 2015) HG02661 HV PJL South Asia - West (Sudmant et al. 2015) HG03235 HV PJL South Asia - West (Sudmant et al. 2015) HM776579 HV India: Tamil Nadu South Asia - South Family Tree DQ523620 HV0 Sardinia Europe (Fraumene et al. 2006) JQ705544 HV0 unknown unknown (Behar et al. 2012) AY713986 HV2 India: Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) HM852806 HV2 Azeri Southwest Asia (Schönberg et al. 2011) KC911372 HV2 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911452 HV2 Iran: Qashqai Southwest Asia (Derenko et al. 2013) NA20867 HV2 GIH South Asia - West (Sudmant et al. 2015) AY713976 HV12 India: Andhra Pradesh South Asia - South (Palanichamy et al. 2004) AY713987 HV12 India: Andhra Pradesh South Asia - South (Palanichamy et al. 2004) HM852785 HV12 Armenia Southwest Asia (Schönberg et al. 2011) KC911301 HV12 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911424 HV12 Iran: Qashqai Southwest Asia (Derenko et al. 2013) KC911482 HV12 Iran: Mazandarani Southwest Asia (Derenko et al. 2013) HG03009 HV12 BEB South Asia - East (Sudmant et al. 2015) NA21112 HV12 GIH South Asia - West (Sudmant et al. 2015) HM852828 HV13 Iran Southwest Asia (Schönberg et al. 2011) JF700125 HV13 Armenia Southwest Asia Family Tree KC911298 HV13 Iran: Persian Southwest Asia (Derenko et al. 2013) HG02652 HV13 PJL South Asia - West (Sudmant et al. 2015) AY713988 HV14 India: Andhra Pradesh South Asia - South (Palanichamy et al. 2004) KC911456 HV14 Iran: Persian Southwest Asia (Derenko et al. 2013) NA18743 HV14 Han Chinese East Asia (Sudmant et al. 2015) HG03873 HV14 ITU South Asia - South (Sudmant et al. 2015) HG03890 HV14 STU South Asia - South (Sudmant et al. 2015) HG03895 HV14 STU South Asia - South (Sudmant et al. 2015) HG03900 HV14 STU South Asia - South (Sudmant et al. 2015) HG03998 HV14 STU South Asia - South (Sudmant et al. 2015) HG03999 HV14 STU South Asia - South (Sudmant et al. 2015) HG04003 HV14 STU South Asia - South (Sudmant et al. 2015) Table S2. (continued) Sample Haplogroup Origin (Population) Region Reference AY495301 T2 Europe Europe (Coble et al. 2004) AY495304 T2 Europe Europe (Coble et al. 2004) HG04025 T2 ITU South Asia - South (Sudmant et al. 2015) EF060363 T2 Italy Europe (La Morgia et al. 2008) FJ238094 T2 Armenia Southwest Asia Family Tree FJ656215 T2 Russia Europe HGDP - Zheng, et al. (unpublished) GU565218 T2 unknown unknown Family Tree HM852766 T2 Armenia Southwest Asia (Schönberg et al. 2011) HM852781 T2 Armenia Southwest Asia (Schönberg et al. 2011) HM852899 T2 Georgia Southwest Asia (Schönberg et al. 2011) JQ702108 T2 Germany Europe (Behar et al. 2012) JQ702594 T2 Scotland Europe (Behar et al. 2012) JQ703754 T2 Scotland Europe (Behar et al. 2012) JQ705133 T2 Ireland Europe (Behar et al. 2012) KC911414 T2 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911414 T2 Iran: Persian Southwest Asia (Derenko et al. 2013) KJ445844 T2 Palestine Southwest Asia HGDP - Zheng, et al. (unpublished) KJ445845 T2 Israel: Bedouin Southwest Asia HGDP - Zheng, et al. (unpublished) KJ445849 T2 Palestine Southwest Asia HGDP - Zheng, et al. (unpublished) KJ445856 T2 Palestine Southwest Asia HGDP - Zheng, et al. (unpublished) KJ445862 T2 Russia: Adygei, Caucasus Southwest Asia HGDP - Zheng, et al. (unpublished) KJ445863 T2 Russia: Adygei, Caucasus Southwest Asia HGDP - Zheng, et al. (unpublished) KJ445851 T2 Pakistan: Sindhi South Asia - West HGDP - Zheng, et al. (unpublished) KJ445855 T2 Pakistan: Burusho South Asia - West HGDP - Zheng, et al. (unpublished) KJ445860 T2 Pakistan: Kalash South Asia - West HGDP - Zheng, et al. (unpublished) KJ445861 T2 Pakistan: Brahui South Asia - West HGDP - Zheng, et al. (unpublished) NA20901 T2 GIH South Asia - West (Sudmant et al. 2015) AY289073 U1 India: Koraga South Asia - South (Ingman and Gyllensten 2003) AY714038 U1 India: Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) AY714042 U1 India: Andhra Pradesh South Asia - South (Palanichamy et al. 2004) EF556194 U1 Cochin Jew South Asia (Behar et al. 2008a) HG03780 U1 ITU South Asia - South (Sudmant et al. 2015) HG03862 U1 ITU South Asia - South (Sudmant et al. 2015) HG03886 U1 STU South Asia - South (Sudmant et al. 2015) HG04098 U1 ITU South Asia - South (Sudmant et al. 2015) HM156682 U1 India South Asia (Govindaraj et al. 2011) Table S2. (continued) Sample Haplogroup Origin (Population) Region Reference AY882396 U1 Adygei Southwest Asia (Achilli et al. 2004) EF556161 U1 Iran: Jew Southwest Asia (Behar et al. 2008a) EF661008 U1 Italy Europe (Gasparre et al. 2007) FJ748753 U1 Tibet East Asia (Ji et al. 2012) GU218692 U1 Greece Europe Family Tree HM852789 U1 Azeri Southwest Asia (Schönberg et al. 2011) HM852790 U1 Azeri Southwest Asia (Schönberg et al. 2011) HM852847 U1 Turk Southwest Asia (Schönberg et al. 2011) KC477757 U1 Iraq - Kurd Southwest Asia Family Tree KC911306 U1 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911344 U1 Iran: Armenian Southwest Asia (Derenko et al. 2013) KC911457 U1 Iran: Azeri Southwest Asia (Derenko et al. 2013) KC911527 U1 Iran: Qashqai Southwest Asia (Derenko et al. 2013) KJ445918 U1 Russia: Adygei, Caucasus Southwest Asia HGDP - Zheng, et al. (unpublished) KJ445919 U1 Israel: Druze Southwest Asia HGDP - Zheng, et al. (unpublished) KJ445921 U1 Palestine Southwest Asia HGDP - Zheng, et al. (unpublished) KJ445920 U1 Pakistan: Hazara South Asia - West HGDP - Zheng, et al. (unpublished) NA21097 U1 GIH South Asia - West (Sudmant et al. 2015) AY714026 U2 India: Andhra Pradesh South Asia - South (Palanichamy et al. 2004) AY714040 U2 India: Andhra Pradesh South Asia - South (Palanichamy et al. 2004) AY714049 U2 India: Andhra Pradesh South Asia - South (Palanichamy et al. 2004) HG03960 U2 ITU South Asia - South (Sudmant et al. 2015) HM156683 U2 India South Asia (Govindaraj et al. 2011) HM156688 U2 India South Asia (Govindaraj et al. 2011) AF381995 U2 Jordan Southwest Asia (Maca-Meyer et al. 2001) EF528162 U2 unknown unknown Family Tree EF661006 U2 Italy Europe (Gasparre et al. 2007) FJ493504 U2 Russia Europe (Sukernik et al. 2012) FJ828532 U2 unknown unknown Family Tree JQ701890 U2 unknown unknown (Behar et al. 2012) JQ701947 U2 unknown unknown (Behar et al. 2012) JQ702004 U2 unknown unknown (Behar et al. 2012) JQ702106 U2 unknown unknown (Behar et al. 2012) JQ702663 U2 unknown unknown (Behar et al. 2012) JQ705559 U2 unknown unknown (Behar et al. 2012) JQ705711 U2 England Europe (Behar et al. 2012) JQ705900 U2 England Europe (Behar et al. 2012) KC911479 U2 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911513 U2 Iran: Qashqai Southwest Asia (Derenko et al. 2013) NA20904 U2 GIH South Asia - West (Sudmant et al. 2015) AY714023 U3 India: Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) Table S2. (continued) Sample Haplogroup Origin (Population) Region Reference HM852797 U3 Azeri Southwest Asia (Schönberg et al. 2011) HM852819 U3 Iran Southwest Asia (Schönberg et al. 2011) HM852891 U3 Georgia Southwest Asia (Schönberg et al. 2011) JQ704130 U3 Hungary Europe (Behar et al. 2012) KC911459 U3 Iran: Qashqai Southwest Asia (Derenko et al. 2013) KC911334 U4 Iran: Qashqai Southwest Asia (Derenko et al. 2013) HG03897 U5 STU South Asia - South (Sudmant et al. 2015) HG04159 U5 BEB South Asia - East (Sudmant et al. 2015) JF906114 U5 India South Asia Family Tree DQ156210 U5 Spain Europe (Montiel-Sosa et al. 2006) EU597527 U5 Palestine Southwest Asia (Hartmann et al. 2009) GU296543 U5 Poland Europe (Malyarchuk et al. 2010b) GU296570 U5 Czech Republic Europe (Malyarchuk et al. 2010b) GU296581 U5 Belarus Europe (Malyarchuk et al. 2010b) GU296583 U5 Belarus Europe (Malyarchuk et al. 2010b) HM852782 U5 Armenia Southwest Asia (Schönberg et al. 2011) JQ582984 U5 England Europe Family Tree JQ702310 U5 unknown unknown (Behar et al. 2012) JQ702913 U5 unknown unknown (Behar et al. 2012) JQ704112 U5 Scotland Europe (Behar et al. 2012) JQ705429 U5 England Europe (Behar et al. 2012) KC569552 U5 USA Europe Family Tree KC911325 U5 Iran: Qashqai Southwest Asia (Derenko et al. 2013) KC911503 U5 Iran: Qashqai Southwest Asia (Derenko et al. 2013) KC911532 U5 Iran: Qashqai Southwest Asia (Derenko et al. 2013) NA20854 U5 GIH South Asia - West (Sudmant et al. 2015) AY714004 U7 India: Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) AY714013 U7 India: Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) AY714014 U7 India: Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) AY882391 U7 Pakistan South Asia - West (Achilli et al. 2004) GU213243 U7 India: Uttar Pradesh South Asia - Central (Palanichamy et al. 2015) GU213244 U7 India: Tamil Nadu South Asia - South (Palanichamy et al. 2015) GU213245 U7 Bangladesh South Asia - East (Palanichamy et al. 2015) GU213246 U7 Bangladesh South Asia - East (Palanichamy et al. 2015) GU213247 U7 India: Uttar Pradesh South Asia - Central (Palanichamy et al. 2015) GU213248 U7 India: Uttar Pradesh South Asia - Central (Palanichamy et al. 2015) GU213249 U7 India: Tamil Nadu South Asia - South (Palanichamy et al. 2015) GU213250 U7 India: Tamil Nadu South Asia - South (Palanichamy et al. 2015) GU213251 U7 India: West Bengal South Asia - East (Palanichamy et al. 2015) GU213252 U7 India: West Bengal South Asia - East (Palanichamy et al. 2015) GU213253 U7 India: Tamil Nadu South Asia - South (Palanichamy et al. 2015) GU213254 U7 India: Tamil Nadu South Asia - South (Palanichamy et al. 2015) GU480003 U7 India: Madhya Pradesh South Asia - Central (Sharma et al. 2012) HG02494 U7 PJL South Asia - West (Sudmant et al. 2015) Table S2. (continued) Sample Haplogroup Origin (Population) Region Reference HG02648 U7 PJL South Asia - West (Sudmant et al. 2015) HG02694 U7 PJL South Asia - West (Sudmant et al. 2015) HG02724 U7 PJL South Asia - West (Sudmant et al. 2015) HG02731 U7 PJL South Asia - West (Sudmant et al. 2015) HG02775 U7 PJL South Asia - West (Sudmant et al. 2015) HG03681 U7 STU South Asia - South (Sudmant et al. 2015) HG03696 U7 STU South Asia - South (Sudmant et al. 2015) HG03711 U7 STU South Asia - South (Sudmant et al. 2015) HG04056 U7 ITU South Asia - South (Sudmant et al. 2015) HG04134 U7 BEB South Asia - East (Sudmant et al. 2015) AF382011 U7 Spain Europe (Maca-Meyer et al. 2001) AY339547 U7 Finland Europe (Finnilä et al. 2001) AY339548 U7 Finland Europe (Finnilä et al. 2001) KJ445973 U7 Pakistan: Brahui South Asia - West HGDP - Zheng, et al. (unpublished) KJ445974 U7 Pakistan: Brahui South Asia - West HGDP - Zheng, et al. (unpublished) EF556179 U7 Iran: Jew Southwest Asia (Behar et al. 2008a) EU445683 U7 Italy: Isle of Elba Europe (Brisighelli et al. 2009) EU445684 U7 Italy: Isle of Elba Europe (Brisighelli et al. 2009) EU445685 U7 Italy: Isle of Elba Europe (Brisighelli et al. 2009) EU445686 U7 Italy: Isle of Elba Europe (Brisighelli et al. 2009) EU445687 U7 Italy: Isle of Elba Europe (Brisighelli et al. 2009) EU445688 U7 Italy: Isle of Elba Europe (Brisighelli et al. 2009) EU445689 U7 Italy: Isle of Elba Europe (Brisighelli et al. 2009) EU445690 U7 Italy: Isle of Elba Europe (Brisighelli et al. 2009) EU445691 U7 Italy: Isle of Elba Europe (Brisighelli et al. 2009), 2009 EU597503 U7 Israel: Bedouin Southwest Asia (Hartmann et al. 2009) FJ858878 U7 Russia: North-West Siberia East Asia (Sukernik et al. 2012) GQ176284 U7 Finland Europe Family Tree GU213236 U7 Russia Europe (Palanichamy et al. 2015) GU213237 U7 Kalmyk Europe (Palanichamy et al. 2015) GU213238 U7 Russia Europe (Palanichamy et al. 2015) GU213239 U7 Iran: Persian Southwest Asia (Palanichamy et al. 2015) GU213240 U7 Bargut East Asia (Palanichamy et al. 2015) GU213241 U7 Slovakia Europe (Palanichamy et al. 2015) GU213242 U7 Russia Europe (Palanichamy et al. 2015) KJ445975 U7 Pakistan: Burusho South Asia - West HGDP - Zheng, et al. (unpublished) KJ445976 U7 Pakistan: Pathan South Asia - West HGDP - Zheng, et al. (unpublished) KJ445977 U7 Pakistan: Hazara South Asia - West HGDP - Zheng, et al. (unpublished) KJ445979 U7 Pakistan: Brahui South Asia - West HGDP - Zheng, et al. (unpublished) Table S2. (continued) Sample Haplogroup Origin (Population) Region Reference KJ445980 U7 Pakistan: Burusho South Asia - West HGDP - Zheng, et al. (unpublished) GU213255 U7 unknown unknown (Palanichamy et al. 2015) GU213256 U7 unknown unknown (Palanichamy et al. 2015) GU213257 U7 unknown unknown (Palanichamy et al. 2015) GU213258 U7 unknown unknown (Palanichamy et al. 2015) GU213259 U7 unknown unknown (Palanichamy et al. 2015) GU327373 U7 unknown unknown Zhang, et al. (unpublished) HM852777 U7 Armenia Southwest Asia (Schönberg et al. 2011) HM852788 U7 Azeri Southwest Asia (Schönberg et al. 2011) HM852791 U7 Azeri Southwest Asia (Schönberg et al. 2011) HM852801 U7 Azeri Southwest Asia (Schönberg et al. 2011) HM852823 U7 Iran Southwest Asia (Schönberg et al. 2011) HM852853 U7 Turk Southwest Asia (Schönberg et al. 2011) JQ701923 U7 unknown unknown (Behar et al. 2012) JQ703913 U7 unknown unknown (Behar et al. 2012) JQ703978 U7 Poland: Ashkenazi Jew Europe (Behar et al. 2012) JQ704100 U7 unknown unknown (Behar et al. 2012) JQ705198 U7 unknown unknown (Behar et al. 2012) JQ705966 U7 Iraq: Kirkuk, Mizrachi Southwest Asia (Behar et al. 2012) KC911278 U7 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911287 U7 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911288 U7 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911299 U7 Iran: Qashqai Southwest Asia (Derenko et al. 2013) KC911347 U7 Iran: Lur Southwest Asia (Derenko et al. 2013) KC911392 U7 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911402 U7 Iran: Lur Southwest Asia (Derenko et al. 2013) KC911415 U7 Iran: Qashqai Southwest Asia (Derenko et al. 2013) KC911448 U7 Iran: Qashqai Southwest Asia (Derenko et al. 2013) KC911455 U7 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911470 U7 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911508 U7 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911509 U7 Iran: Kurd Southwest Asia (Derenko et al. 2013) KC911526 U7 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911553 U7 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911563 U7 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911615 U7 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911620 U7 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911622 U7 Iran: Persian Southwest Asia (Derenko et al. 2013) KJ445972 U7 Israel: Bedouin Southwest Asia HGDP - Zheng, et al. (unpublished) NA18130 U7 Han Chinese East Asia (Sudmant et al. 2015) KP763839 U7 India: Uttar Pradesh South Asia (Palanichamy et al. 2015) NA20862 U7 GIH South Asia - West (Sudmant et al. 2015) Table S2. (continued) Sample Haplogroup Origin (Population) Region Reference NA20889 U7 GIH South Asia - West (Sudmant et al. 2015) NA21107 U7 GIH South Asia - West (Sudmant et al. 2015) NA21113 U7 GIH South Asia - West (Sudmant et al. 2015) NA21130 U7 GIH South Asia - West (Sudmant et al. 2015) HM852759 U8 Armenia Southwest Asia (Schönberg et al. 2011) JQ702759 U8 unknown unknown (Behar et al. 2012) AY882390 U9 Pakistan South Asia - West (Achilli et al. 2004) EU597540 U9 Pakistan: Pathan South Asia - West (Hartmann et al. 2009) FJ770944 U9 India: Andhra Pradesh South Asia (Fornarino et al. 2009) HG03777 U9 ITU South Asia - South (Sudmant et al. 2015) HG03916 U9 BEB South Asia - East (Sudmant et al. 2015) HG04118 U9 ITU South Asia - South (Sudmant et al. 2015) KJ445948 U9 Pakistan: Makrani South Asia - West HGDP - Zheng, et al. (unpublished) KP763838 U9 India South Asia (Palanichamy et al. 2015) KP763849 U9 India South Asia (Palanichamy et al. 2015) AY882389 U9 Ethiopia Africa (Achilli et al. 2004) GU990521 U9 USA America Family Tree NA21108 U9 GIH South Asia - West (Sudmant et al. 2015) AY713979 V India: Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) AY195750 V unknown unknown (Mishmar et al. 2003) AY495307 V Europe Europe (Coble et al. 2004) AY495309 V Europe Europe (Coble et al. 2004) AY495311 V Europe Europe (Coble et al. 2004) AY495315 V Europe Europe (Coble et al. 2004) AY495320 V Europe Europe (Coble et al. 2004) AY495322 V Europe Europe (Coble et al. 2004) AY495326 V Europe Europe (Coble et al. 2004) JN630803 V Spain: Jew Europe Family Tree KC911406 V Iran: Persian Southwest Asia (Derenko et al. 2013) JQ705658 V2 England Europe (Behar et al. 2012) JQ245778 W Yemen Southwest Asia (Fernandes et al. 2012) KC911341 W Iran: Persian Southwest Asia (Derenko et al. 2013) AY714039 W1 India: Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) HG03228 W1 PJL South Asia - West (Sudmant et al. 2015) EU257638 W1 unknown unknown Family Tree EU558696 W1 England Europe Family Tree FJ472633 W1 unknown unknown Family Tree GU123002 W1 Russia Europe (Malyarchuk et al. 2010a) JQ245768 W1 Turkey Southwest Asia (Fernandes et al. 2012) JQ702050 W1 unknown unknown (Behar et al. 2012) JQ702450 W1 unknown unknown (Behar et al. 2012) JQ706021 W1 United Kingdom Europe (Behar et al. 2012) JQ898579 W1 Ashkenazi Jew Europe Family Tree Table S2. (continued) Sample Haplogroup Origin (Population) Region Reference KC911433 W1 Iran: Persian Southwest Asia (Derenko et al. 2013) KC911537 W1 Iran: Qashqai Southwest Asia (Derenko et al. 2013) AY714043 W3 India: Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) GU002155 W3 India: Punjab South Asia Family Tree HG03778 W3 ITU South Asia - South (Sudmant et al. 2015) HG03785 W3 ITU South Asia - South (Sudmant et al. 2015) HG03786 W3 ITU South Asia - South (Sudmant et al. 2015) HG03815 W3 BEB South Asia - East (Sudmant et al. 2015) HG04026 W3 ITU South Asia - South (Sudmant et al. 2015) HG04156 W3 BEB South Asia - East (Sudmant et al. 2015) KJ445931 W3 Pakistan: Pathan South Asia - West HGDP - Zheng, et al. (unpublished) KJ445932 W3 Pakistan: Pathan South Asia - West HGDP - Zheng, et al. (unpublished) KJ445933 W3 Pakistan: Sindhi South Asia - West HGDP - Zheng, et al. (unpublished) KJ445934 W3 Pakistan: Pathan South Asia - West HGDP - Zheng, et al. (unpublished) JQ245741 W3 Azerbaijan Southwest Asia (Fernandes et al. 2012) JQ245760 W3 Turkey: Kurd Southwest Asia (Fernandes et al. 2012) JQ702421 W3 unknown unknown (Behar et al. 2012) JQ705313 W3 Austria Europe (Behar et al. 2012) AY714018 W4 India: Uttar Pradesh South Asia - Central (Palanichamy et al. 2004) NA20858 W4 GIH South Asia - West (Sudmant et al. 2015) GU045487 W4 Ulter Scots Europe Family Tree JQ245758 W4 Turkey: Kurd Southwest Asia (Fernandes et al. 2012) HG02734 W6 PJL South Asia - West (Sudmant et al. 2015) HG04239 W6 ITU South Asia - South (Sudmant et al. 2015) NA20851 W6 GIH South Asia - West (Sudmant et al. 2015) JF902025 W6 England Europe Family Tree JQ245723 W6 Russia: North Ossetia Southwest Asia (Fernandes et al. 2012) JQ245736 W6 Russia: North Ossetia Southwest Asia (Fernandes et al. 2012) JQ245769 W6 Turkey Southwest Asia (Fernandes et al. 2012) JQ705793 W6 England Europe (Behar et al. 2012) KC911604 W6 Iran: Persian Southwest Asia (Derenko et al. 2013) HG02733 X PJL South Asia - West (Sudmant et al. 2015) NA20886 X GIH South Asia - West (Sudmant et al. 2015) NA20898 X GIH South Asia - West (Sudmant et al. 2015) EU600318 X Druze Southwest Asia (Shlush et al. 2008) HM852799 X Azeri Southwest Asia (Schönberg et al. 2011) JQ245765 X Turkey Southwest Asia (Fernandes et al. 2012) KC911291 X Iran: Qashqai Southwest Asia (Derenko et al. 2013) Table S2. (continued) Sample Haplogroup Origin (Population) Region Reference References: Achilli A, Rengo C, Magri C, et al (2004) The molecular dissection of mtDNA haplogroup H confirms that the Franco-Cantabrian glacial refuge was a major source for the European gene pool. Am J Hum Genet 75:910– 918. Al-Abri A, Podgorná E, Rose JI, et al (2012) Pleistocene-Holocene boundary in Southern Arabia from the perspective of human mtDNA variation. Am J Phys Anthropol 149:291–8. Behar DM, Metspalu E, Kivisild T, et al (2008a) Counting the founders: the matrilineal genetic ancestry of the Jewish Diaspora. PLoS One 3:e2062. Behar DM, Metspalu E, Kivisild T, et al (2006) The matrilineal ancestry of Ashkenazi Jewry: portrait of a recent founder event. Am J Hum Genet 78:487–97. Behar DM, van Oven M, Rosset S, et al (2012) A “Copernican” reassessment of the human mitochondrial DNA tree from its root. Am J Hum Genet 90:675–84. 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Derenko M, Malyarchuk B, Bahmanimehr A, et al (2013) Complete Mitochondrial DNA Diversity in Iranians. PLoS One 8:e80673. Derenko M, Malyarchuk B, Denisova G, et al (2014) Western Eurasian ancestry in modern Siberians based on mitogenomic data. BMC Evol Biol 14:217. Detjen AK, Tinschert S, Kaufmann D, et al (2007) Analysis of mitochondrial DNA in discordant monozygotic twins with neurofibromatosis type 1. Twin Res Hum Genet 10:486–95. Fernandes V, Alshamali F, Alves M, et al (2012) The Arabian cradle: mitochondrial relicts of the first steps along the southern route out of Africa. Am J Hum Genet 90:347–55. Finnilä S, Lehtonen MS, Majamaa K (2001) Phylogenetic network for European mtDNA. Am J Hum Genet 68:1475–84. Fornarino S, Pala M, Battaglia V, et al (2009) Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation. BMC Evol Biol 9:154. 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