Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia

1 Online Resource 1 Quantifying the legacy of the Chinese Neolithic on the maternal genetic heritage of Taiwan and Island Southeast Asia Andreia Brandão1,2,3,4, Khen Khong Eng5,6, Teresa Rito1,7,8, Bruno Cavadas1,2, David Bulbeck9, Francesca Gandini3, Maria Pala3, Maru Mormina5,10, Bob Hudson11, Joyce White12, Tsang-Ming Ko13, Mokhtar Saidin6, Zainuddin Zafarina14,15, Stephen Oppenheimer16, Martin B Richards3,5,+, Luísa Pereira1,2,17,+, Pedro Soares1,2,5,18,+ 1IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal 2i3S (Instituto de Investigação e Inovação em Saúde, Universidade do Porto), 4200 Porto, Portugal. 3Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, United Kingdom 4ICBAS (Instituto Ciências Biomédicas Abel Salazar), Universidade do Porto, Rua de Jorge Viterbo Ferreira n.º 228, 4050-313 Porto, Portugal. 5Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, United Kingdom 6Centre for Global Archaeological Research, Universiti Sains Malaysia, 11800 USM Penang, Malaysia 7Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal 8ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal 9Department of Archaeology and Natural History, College of Asia and the Pacific, The Australian National University, Acton ACT 2601, Canberra, Australia 10Department of Applied Social Studies, University of Winchester, Sparkford Road, Winchester SO22 4NR, United Kingdom 11Archaeology Department, University of Sydney, New South Wales 2006, Australia 12Dept. of Anthropology, University of Pennsylvania Museum, 3260 South St. Philadelphia, United States of America. 13Department of Obstetrics and Gynecology, National Taiwan University, Roosevelt Rd., Taipei 10617, Taiwan 14Malaysian Institute of Pharmaceuticals and Nutraceuticals Malaysia, National Institutes of Biotechnology Malaysia, Penang, Malaysia 2 15Human Identification Unit, School of Health Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia. 16Institute of Human Sciences, School of Anthropology, University of Oxford, The Pauling Centre, 58a Banbury Road, Oxford OX2 6QS, United Kingdom 17Faculty of Medicine, University of Porto, Al. Prof. Hernâni Monteiro, 4200 - 319 Porto, Portugal 18CBMA (Centre of Molecular and Environmental Biology), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal +These authors contributed equally to this work Correspondence should be addressed to: Professor Martin B. Richards; Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, United Kingdom email: [email protected] Telephone number: +44 1484 471676 3 Figure S1. Map showing the geographic distribution and the sample sizes for the dataset used in the Surfer analyses. 4 Figure S2. Frequency distribution maps for mtDNA haplogroups examined in this study, based on HVS-I data. Maps created using Surfer. 5 Figure S3. Bayesian skyline plots for mtDNA haplogroups examined in this study, assuming a generation time of 25 years. The black lines represent the posterior median of the effective population size through time, and the grey regions represent the 95% confidence interval. 6 Figure S4. Phylogeographic patterns in ISEA. (a) ML ages of key mtDNA clades in ISEA and their ancestral nodes. (b) Number of mutations between key mtDNA clades in ISEA and their ancestral nodes. b a 7 Figure S5. Bayesian skyline plots for ISEA, with the whole-mtDNA data set available, assuming a generation of 25 years. The black line represents the posterior effective population size through time, and the grey regions represents the 95% confidence interval. 8 Table S1. List of the 114 whole-mtDNA genomes sequenced and characterized in this study and corresponding geographic region. Sample ID Location Haplogroup BAN13 Indonesia, South Kalimantan B4b1a2 BJ135 Malaysia, Perak, Banjar Malay B4b1a2 KA34 Taiwan, Ami B4b1a2 KB103 Micronesia, Kiribati B4b1a2 KB67 Taiwan, Bunun B4b1a2 KB71 Taiwan, Bunun B4b1a2 KT55 Taiwan, Tsou B4b1a2 NAU2 Micronesia, Nauru B4b1a2 DOX2185 Vietnam, Tay Nung B4b1a2a DOX3064 Vietnam, Tay Nung B4b1a2a DOX4368 Vietnam, Kinh B4c1b DOX4329 Vietnam, Kinh B4c1b2 AMB02 Indonesia, Ambon B4c1b2a2 BG094 Malaysia, Johor, Bugis Malay B4c1b2a2 BJ133 Malaysia, Perak, Banjar Malay B4c1b2a2 BRU40 Brunei B4c1b2a2 BW62 Malaysia, Jawa Malay B4c1b2a2 KK94 Malaysia, Sabah B4c1b2a2 KY32 Taiwan, Yami B4c1b2a2 MB34 Malaysia, Kelantan Malay B4c1b2a2 MI28 Malaysia, Negeri Sembilan, Minangkabau Malay B4c1b2a2 MI30 Malaysia, Negeri Sembilan, Minangkabau Malay B4c1b2a2 MI50 Malaysia, Negeri Sembilan, Minangkabau Malay B4c1b2a2 MI61 Malaysia, Negeri Sembilan, Minangkabau Malay B4c1b2a2 RP02 Malaysia, Kelantan Malay B4c1b2a2 RW179 Malaysia, Perak, Rawa Malay B4c1b2a2 DOX3048 Vietnam, Tay Nung B4c1b2c RW161 Malaysia, Rawa Malay B5b1c JW83 Malaysia, Jawa Malay B5b1c 8A Malaysia, Batek Malay B5b1c KP01 Taiwan, Paiwan D5 WA4 Myanmar (Burma), Pakokku, Burmese D5a2a1+!16172 DKK4149 Vietnam, Kinh D5b DOX2196 Vietnam, Tay Nung D5b DOX6681 Vietnam, Tay Nung D5b KP28 Taiwan, Paiwan D5b KP67 Taiwan, Paiwan D5b PAI05 Taiwan, Paiwan D5b 9 AMI01 Taiwan, Ami D5b1c1 KA53 Taiwan, Ami D5b1c1 MND24 Indonesia, Manado D5b1c1 DKX4098 Vietnam, Kinh D5c+16311 MB39 Malaysia, Kelantan Mala F1a4a DHX4312 Vietnam, Kinh F3a VNM293 Vietnam F3a MB33 Malaysia, Kelantan Mala F3a+207 BRU36 Brunei F3a1 DOX701 Vietnam, Tay Nung F3a1 DOX708 Vietnam, Tay Nung F3a1 KDH05 Vietnam, Tay Nung F3a1 LAO5-03 Laos, Hmong F3a1 LAO5-05 Laos, Hmong F3a1 LAO5-11 Laos, Hmong F3a1 ALO162 Indonesia, Alor F3b1 BAN02 Indonesia, South Kalimantan F3b1 BRU58 Brunei F3b1 FIL56 Philippines, Surigaonon F3b1 KK43 Malaysia, Sabah F3b1 KP42 Taiwan, Paiwan F3b1 KP50 Taiwan, Paiwan F3b1 KP57 Taiwan, Paiwan F3b1 KP70 Taiwan, Paiwan F3b1 MC01 Malaysia, Kelantan Malay F3b1 PAI02 Taiwan, Paiwan F3b1 PAI17 Taiwan, Paiwan F3b1 PRY127 Indonesia, Palangkaraya F3b1 C72 China N9a1 DOX2193 Vietnam, Tay Nung N9a10 DOX2221 Vietnam, Tay Nung N9a10 LAO1-08 Laos, Hmong N9a10 AMI16 Taiwan, Ami N9a10a KA40 Taiwan, Ami N9a10a KT11 Taiwan, Tsou N9a10a C84 China N9a1'3 PAI10 Taiwan, Paiwan N9a3 DKK4276 Vietnam, Kinh N9a6 DKK4471 Vietnam, Kinh N9a6 DOX2000 Vietnam, Tay Nung N9a6 DOX4107 Vietnam, Stieng N9a6 MI41 Malaysia, Negeri Sembilan, Minangkabau Malay N9a6 RP32 Malaysia, Kelantan Malay N9a6 136B Malaysia, Temuan N9a6a 16 GQ119011 Indonesia (Tabbada et al. 2010) GQ119009, GQ119014, GQ119015 Taiwan (Tabbada et al. 2010) N9 AP012369, AP012372, AP012373, AP012384, AP012421, AP012393, AP012395, AP012396, AP012397, AP012398, AP012399, AP012401, AP012402, AP012403, AP012404, AP012408, AP012410, AP012411, AP012412, AP012413 Malaysia (Jinam et al. 2012) HG00479, HG00500, HG00592, JN857052, HG00406, HG00620, HG00556, HG00577, HG00584, NA18740, HG00531, HG00422, NA18747, NA18748 China (The 1000 Genomes Project Consortium 2012) HG02521, HG01855, HG02040, HG02032 Vietnam (The 1000 Genomes Project Consortium 2012) AP010744 Japan (Bilal et al. 2008) JN857042, JN857023, JN857038, JN857053, JN857057, JN857027, Russia (Derenko et al. 2012) HM589048 China Family Tree DNA HM596703 Indonesia, Sumatra (Gunnarsdóttir et al. 2011b) FJ748719 Tibet (Ji et al. 2012) KF540662, KF540722, KF540679, KF540684, KF540744 Taiwan (Ko et al. 2014) DQ834255, DQ834258 Vietnam Phan et al. (unpublished) AP008261, AP008726, AP008608, AP008714 Japan (Tanaka et al. 2004) HM776708 Russia (Sukernik et al. 2012) R9b HG02382, HG02410, HG01796, HG00663, NA18779, NA18781 China (The 1000 Genomes Project Consortium 2012) HG01874, HG02017, HG02087, HG02035, HG02061, HG02020 Vietnam (The 1000 Genomes Project Consortium 2012) GU733737 Philippines, Mamanwa; negrito group (Gunnarsdóttir et al. 2011a) DQ981471, DQ981469, DQ981470, DQ981474, DQ981475, Vietnam (Hill et al. 2006) DQ981473 Thailand (Hill et al. 2006) DQ981472 Malaysia, Orang sli (Hill et al. 2006) DQ981465 Indonesia, Java (Hill et al. 2006) DQ981466 Indonesia, Sumatra, Palembang (Hill et al. 2006) DQ981467 Indonesia, Sumatra, Padang (Hill et al. 2006) DQ981468 Indonesia, Sulawesi, Manado (Hill et al. 2006) KF540682, KF540702, KF540748, KF541026, KF541027 Taiwan (Ko et al. 2014) AY255152 China (Kong et al. 2003) 17 AY963579 Malaysia, Semelai (Macaulay et al. 2005) FJ147308 Russia (Sukernik et al. 2012) GU810062 Thailand Pradutkanchana et al. (unpublished) EF114273, EF114274, EF114275 China (Wang et al. 2007) JQ411477 China Zhang et al. (unpublished) R9c HG00534, HG00445, HG00407 China (The 1000 Genomes Project Consortium 2012) KC994001, KC994055, KC994057, KC994066, KC994068, KC994078, KC994160 Philippines (Delfin et al. 2014) JN857032 North Asia, Mongolia (Derenko et al. 2012) GU733759 Philippines, Manobo (Gunnarsdóttir et al. 2011a) KF540813, KF540625, KF540804, KF540806, KF540831, KF540842, KF540867, KF540898, KF540911, KF541010, KF541011, KF541013, KF541021, KF541022, KF541033, KF541039, KF541043, KF541045, KF541049, KF541050 Taiwan (Ko et al. 2014) JF739535, JF739539 Philippines, Palawan Island (Scholes et al. 2011) JX289135 Myanmar (Burma) (Summerer et al. 2014) GQ119007 Taiwan (Tabbada et al. 2010) GQ119010 Indonesia (Tabbada et al. 2010) Y HG02026 Vietnam (The 1000 Genomes Project Consortium 2012) KC994149, KC993979, KC993980, KC993982, KC993988, KC993992, KC994003, KC994035, KC994040, KC994060, KC994067, KC994129, KC994130, KC994131, KC994134, KC994137 Philippines (Delfin et al. 2014) EF153813, EF153825, EF153812, EF153798 Russia (Derenko et al. 2007) KF148108, KF148113, KF148129, KF148143, KF148335, KF148337, KF148339, KF148340, KF148341, KF148342, KF148343, KF148344, KF148345, KF148346, KF148347, KF148348, KF148349, KF148352, KF148353, KF148354, KF148359, KF148361, KF148362, KF148363, KF148365, KF148368, KF148370, KF148371, KF148372, KF148373, KF148486, KF148507, KF148508, KF148513, KF148525 Russia (Duggan et al. 2013) GU733733 Philippines, Mamanwa; (Gunnarsdóttir et 18 negrito group al. 2011a) GU733823 Philippines, Surigaonon (Gunnarsdóttir et al. 2011a) GU733768, GU733787, GU733798 Philippines, Manobo (Gunnarsdóttir et al. 2011a) HM596648, HM596672, HM596675 Indonesia, Sumatra (Gunnarsdóttir et al. 2011b) EU007848, EU007853, EU007854, EU007855, EU007892 North Asia, Mongolia (Ingman and Gyllensten 2007) AP009439 Japan (Kazuno et al. 2005) KF540727, KF540560, KF540577, KF540941 Taiwan (Ko et al. 2014) DQ272121 China (Kong et al. 2006) GU123044 Russia (Malyarchuk et al. 2010) AY195792 Asia (Mishmar et al. 2003) AY255138 Asia (Kong et al. 2003) GQ119016, GQ119013, GQ119019, GQ119032 Taiwan (Tabbada et al. 2010) AP008723, AP008764 Japan (Tanaka et al. 2004) NA18134 China (The 1000 Genomes Project Consortium 2012) NA18974 Japan (The 1000 Genomes Project Consortium 2012) 19 Table S3. Age estimates using rho (ρ) and ML for haplogroups B4b1, B4c1, B5b, D5, F1a4, F3, N9a, R9b, R9c and Y2, and its major subclades. Ages and 95% confidence intervals (CI) in thousands of years. Nodes N PAML Rho Total Synonymous Age CI Age CI Age CI B4 226 46,500 [33,900–59,600] 39,500 [27,000–52,500] 45,100 [23,000–67,600] B4b 130 28,400 [18,500–38,700] 25,500 [14,000–37,700] 32,600 [9,500–55,600] B4b1 129 25,100 [17,000–33,600] 22,600 [12,600–33,200] 32,600 [9,400–55,900] B4b1+150 2 11,000 [1,500–20,900] 10,600 [3,200–18,400] 15,800 [300–31,200] B4b1a 119 19,900 [10,700–29,400] 17,000 [9,700–24,700] 17,800 [5,400–30,300] B4b1a+207 117 17,700 [10,200–25,500] 14,200 [9,100–19,500] 17,700 [5,100–30,400] B4b1a1 16 4,400 [2,300–6,700] 4,600 [2,100–7,000] 4,900 [1,900–8,000] B4b1a1a 6 2,600 [600–4,600] 2,600 [500–4,700] 1,300 [0–3,900] B4b1a2 89 9,300 [6,800–11,800] 8,700 [6,400–11,000] 9,100 [5,300–12,900] B4b1a2+1313 4 1,200 [0–3,600] 900 [0–2,600] 0 [0–0] B4b1a2+14783 5 600 [0–1,900] 500 [0–1,500] 0 [0–0] B4b1a2+16365 16 3,600 [0–9,000] 3,700 [500–7,100] 8,900 [0–18,200] B4b1a2+16465 3 3,400 [0–9,200] 2,600 [0–6,400] 2,600 [0–7,800] B4b1a2+178 2 1,600 [0–10,800] 1,300 [0–3,800] 0 [0–0] B4b1a2+204 2 4,800 [0–8,700] 7,900 [1,500–14,500] 0 [0–0] B4b1a2+207 4 4,600 [0–10,300] 5,200 [400–10,200] 9,900 [0–22,700] B4b1a2+709 9 4,100 [0–14,700] 3,700 [300–7,200] 7,900 [0–17,100] B4b1a2a 9 7,900 [5,100–10,500] 12,400 [5,400–19,800] 14,00 [0–29,200] B4b1a2a+150 2 5,400 [0–11,300] 5,200 [100–10,500] 4,000 [0–11,700] B4b1a2a+15301 7 7,200 [4,100–10,300] 11,000 [4,000–18,300] 9,000 [0–20,700] B4b1a2b 11 3,700 [0–7,600] 5,200 [1,300–9,300] 5,700 [0–13,400] B4b1a2b+8659 5 1,900 [0–4,500] 5,200 [600–9,900] 3,200 [0–9,300] B4b1a2c 6 1,500 [0–5,700] 1,700 [0–5,100] 5,300 [0–15,600] B4b1a2c+11809 4 500 [0–4,100] 0 [0–0] 0 [0–0] B4b1a2d 4 600 [0–1,700] 600 [0–1,900] 2,000 [0–5,800] B4b1a3 12 9,500 [2,800–16,400] 11,100 [3,200–19,400] 11,200 [0–24,700] B4b1a3a 10 3,200 [400–5,900] 3,400 [1,000–5,700] 4,000 [0–8,600] B4b1a3a+4026 2 1,200 [0–3,400] 1,300 [0–3,800] 0 [0–0] B4b1a3a+827 2 800 [0–2,300] 1,300 [0–3,800] 4,000 [0–11,700] B4b1b'c 8 21,700 [13,400–30,300] 17,900 [8,900–27,400] 22,700 [2,900–42,600] 20 B4b1c 2 17,100 [9,300–25,300] 14,200 [5,800–22,900] 15,800 [0–32,000] B4b1c+8343 2 12,300 [4,300–20,700] 9,200 [2,300–16,400] 3,900 [0–11,700] B4b1c1 5 5,600 [2,200–9,100] 4,200 [1,300–7,100] 4,700 [0–10,100] B4b'd'e'j 131 37,100 [25,400–49,300] 34,300 [18,900–50,700] 48,000 [16,500–79,600] B4c 95 36,800 [23,500–50,800] 32,000 [18,300–46,500] 22,400 [8,800–36,100] B4c1 94 32,000 [18,300–46,600] 29,200 [16,700–42,300] 22,500 [8,700–36,200] B4c1a 17 12,400 [4,300–21,000] 9,800 [5,300–14,400] 10,200 [5,200–15,200] B4c1a1 11 9,200 [5,400–13,200] 9,400 [5,700–13,100] 12,200 [5,200–19,200] B4c1a1a 3 8,200 [4,500–12,000] 13,400 [6,000–21,000] 10,500 [0–23,100] B4c1a1a1 2 7,400 [3,800–11,200] 16,200 [6,800–25,100] 3,900 [0–11,700] B4c1a1b 2 7,400 [3,100–11,900] 9,200 [2,300–16,400] 15,800 [300–31,200] B4c1a1c 2 2,400 [0–6,400] 2,600 [0–6,200] 3,900 [0–11,700] B4c1a2 5 6,200 [2,000–10,700] 4,200 [1,200–7,100] 7,900 [1,000–14,800] B4c1a'b 90 29,000 [15,000–43,600] 26,300 [14,700–38,500] 22,600 [8,300–36,900] B4c1b 73 24,600 [16,600–32,800] 20,800 [10,800–31,400] 23,700 [6,400–40,900] B4c1b1 3 5,200 [700–9,800] 6,700 [600–13,700] 10,500 [0–25,100] B4c1b1a 2 900 [0–2,700] 1,300 [0–3,800] 0 [0–0] B4c1b2 69 20,700 [13,700–27,800] 17,600 [8,700–27,000] 23,900 [5,600–42,100] B4c1b2+195 5 17,400 [7,300–27,900] 13,400 [5,900–21,200] 17,300 [2,500–32,200] B4c1b2a 56 14,500 [6,400–23,000] 11,200 [3,800–19,000] 15,500 [0–31,400] B4c1b2a+15301 54 10,800 [800–21,300] 8,400 [2,900–14,200] 7,900 [2,100–13,700] B4c1b2a2 53 8,000 [5,600–10,500] 5,800 [3,500–8,100] 7,700 [1,900–13,600] B4c1b2a2+3221 4 2,200 [0–9,500] 2,600 [0–6,700] 0 [0–0] B4c1b2a2+3666 2 3,600 [0–7,600] 2,600 [0–6,200] 0 [0–0] B4c1b2a2+4226 3 5,500 [1,700–9,500] 5,200 [0–10,800] 13,100 [0–28,600] B4c1b2a2+4937 19 300 [0–700] 200 [0–600] 800 [0–1,900] B4c1b2a2+6383 2 1,700 [0–4,900] 2,600 [0–6,200] 3,900 [0–11,700] B4c1b2a2+7598 4 1,600 [0–4,400] 1,300 [0–3,100] 0 [0–0] B4c1b2c 8 15,000 [9,200–21,000] 15,800 [9,600–22,300] 15,800 [6,300–25,200] B4c1b2c+10493 3 2,600 [0–6,300] 5,200 [400–10,200] 7,900 [0–19,400] B4c1b2c+16129 3 14,100 [8,300–20,100] 20,000 [10,300–30,100] 18,400 [4,800–32,000] B4c1c 4 14,500 [5,500–23,900] 9,900 [3,200–17,000] 3,900 [0–9,400] B4c1c1 3 8,600 [2,500–15,000] 7,900 [2,700–13,300] 5,300 [0–12,500] B5 90 44,700 [33,300–56,500] 65,600 [43,200–89,300] 66,800 [34,300–99,200] B5b 89 29,800 [20,700–39,300] 34,300 [24,300–44,700] 43,500 [24,500–62,500] B5b+204 62 28,700 [19,600–38,200] 29,800 [18,900–41,100] 48,800 [23,400–74,200] B5b1 54 23,900 [13,900–34,300] 27,000 [15,800–38,800] 44,700 [19,200–70,300] B5b1+204 2 18,400 [5,200–32,500] 10,600 [3,200–18,400] 15,800 [300–31,200] B5b1a 15 19,000 [8,500–29,800] 20,500 [9,300–32,400] 12,600 [0–25,800] 21 B5b1a1 3 7,400 [1,500–13,600] 7,000 [2,100–12,000] 5,300 [0–12,500] B5b1a2 12 4,900 [1,900–8,000] 4,600 [2,200–6,900] 6,600 [1,200–12,000] B5b1a2a 3 2,200 [0–8,300] 2,600 [0–6,400] 5,300 [0–15,600] B5b1a2a+6929 2 879 [0–7,500] 1,300 [0–3,800] 0 [0–0] B5b1c 34 6,700 [4,000–9,400] 8,600 [3,500–13,800] 15,000 [1000–29,300] B5b1c+1275 2 1,300 [0–3,900] 1,300 [0–3,800] 0 [0–0] B5b1c+234 2 1,100 [0–4,300] 0 [0–0] 0 [0–0] B5b1c1 20 4,100 [1,000–7,300] 5,200 [1,200–9,400] 7,500 [0–17,800] B5b1c1+103 7 2,600 [0–6,300] 3,300 [500–6,200] 4,500 [0–9,900] B5b1c1a 13 2,000 [300–3,800] 2,200 [600–3,800] 1,200 [0–3,600] B5b1c1a+16497 2 816 [0–2,400] 1,300 [0–3,800] 0 [0–0] B5b1c1a+9455 2 816 [0–2,300] 1,300 [0–3,800] 0 [0–0] B5b2 27 21,900 [15,200–28,900] 22,900 [14,000–32,100] 15,500 [8,400–22,600] B5b2a 22 19,700 [12,900–26,900] 19,700 [10,800–28,700] 11,500 [4,800–18,100] B5b2a+5964 2 15,400 [7,000–24,200] 12,000 [4,000–20,300] 19,700 [2,400–37,000] B5b2a1 19 17,000 [10,000–24,400] 14,600 [8,300–21,100] 9,500 [2,300–16,800] B5b2a1a 8 4,800 [1,500–8,100] 4,300 [1,700–6,700] 3,900 [100–7,800] B5b2a1a+195 2 1,500 [0–4,500] 1,300 [0–3,800] 3,900 [0–11,700] B5b2a1b 10 9,600 [4,900–14,500] 8,700 [4,300–13,200] 4,700 [900–8,500] B5b2a1b1 5 8,400 [3,800–13,200] 9,000 [2,800–15,400] 1,600 [0–4,700] B5b2a1b1+8894 4 2,700 [0–7,100] 2,600 [0–6,700] 0 [0–0] B5b2c 3 11,300 [5,500–17,300] 13,400 [6,000–21,000] 21,000 [4,700–37,300] B5b2c+9299 2 7,700 [1,900–13,700] 7,900 [1,500–14,500] 19,700 [2,400–37,000] B5b3 4 13,200 [4,400–22,400] 13,400 [6,600–20,400] 3,900 [0–9,400] B5b3b 3 11,400 [2,400–21,000] 7,900 [2,700–13,600] 2,600 [0–7,800] F 116 49,400 [39,600–59,500] 60,000 [40,800–80,100] 49,100 [24,000–74,300] F1 28 27,200 [16,300–38,700] 28,000 [13,100–43,800] 27,600 [2,900–52,400] F1a 27 20,400 [11,100–30,200] 21,900 [9,000–35,600] 19,900 [0–40,300] F1a4 26 16,300 [7,000–26,000] 18,600 [6,500–31,300] 11,500 [0–26,100] F1a4a 25 11,700 [3,000–21,000] 10,600 [2,600–19,000] 11,700 [0–26,800] F1a4a1 23 4,300 [1,800–6,800] 5,200 [1,500–9,000] 3,900 [800–7,100] F1a4a1a 15 3,300 [1,300–5,300] 3,500 [1,500–5,500] 3,700 [1,000–6,400] F1a4a1a+152 4 700 [0–2,000] 600 [0–1,900] 0 [0–0] F3 88 31,700 [21,500–42,300] 37,900 [22,900–53,700] 35,400 [12,400–58,400] F3a 20 26,600 [16,500–37,200] 31,500 [18,700–45,000] 26,400 [6,000–46,800] F3a+195 4 11,800 [0–31,800] 13,400 [5,000–22,200] 0 [0–0] F3a1 16 16,600 [9,000–24,500] 15,600 [9,300–22,200] 13,300 [1,280–25,300] F3a1+16093 3 11,600 [3,000–20,500] 11,500 [3,500–20,000] 13,100 [0–26,800] F3a1+16093+5913 2 1,300 [0–9,600] 1,300 [0–3,900] 0 [0–0] 22 F3a1+204 3 2,000 [0–5,700] 1,800 [0–4,100] 0 [0–0] F3a1+9854 10 16,600 [8,500–25,000] 15,000 [7,700–22,700] 7,100 [0–16,700] F3a1+9854+4824 7 2,400 [100–4,900] 1,800 [0–3,400] 1,300 [0–3,900] F3a1+9854+7151 3 8,600 [2,800–14,700] 10,700 [3,600–17,900] 2,600 [0–7,800] F3b 68 25,200 [15,400–35,400] 28,900 [13,600–45,100] 27,800 [13,500–52,200] F3b+2392 3 5,700 [0–14,300] 3,500 [0–7,700] 2,600 [0–7,800] F3b1 65 12,400 [5,200–20,000] 12,000 [4,700–19,700] 12,100 [0–25,100] F3b1a'c 52 8,200 [1,700–14,900] 7,000 [2,200–11,900] 3,500 [1,100–5,900] F3b1a 15 4,600 [1,700–7,500] 4,600 [2,100–6,900] 3,700 [1,000–6,400] F3b1b 11 6,900 [3,300–10,400] 5,000 [1,600–8,500] 7,300 [0–16,200] N9 254 50,600 [37,100–64,600] 38,452 [27,700–49,600] 36,100 [20,700–51,400] N9a 127 20,000 [14,500–25,500] 17,500 [13,000–22,100] 18,400 [10,900–25,900] N9a1 14 6,500 [3,800–9,200] 6,400 [4,000–8,800] 6,200 [2,200–10,200] N9a1+12007 2 3,800 [700–6,700] 2,600 [0–6,200] 7,900 [0–18,800] N9a10 18 16,600 [11,000–22,400] 14,600 [8,800–20,600] 14,900 [4,600–25,200] N9a10+16189 3 5,000 [0–10,600] 3,500 [100–6,900] 2,700 [0–7,800] N9a10+16311 3 8,400 [1,600–15,600] 6,100 [1,600–10,800] 5,300 [0–12,500] N9a10+9055 2 12,100 [5,200–19,300] 13,400 [5,000–22,200] 3,900 [0–11,700] N9a10a 9 10,000 [4,700–15,400] 9,100 [4,100–14,200] 14,000 [1,600–26,400] N9a10a1 6 6,300 [200–12,500] 5,200 [1,200–9,300] 6,600 [0–14,300] N9a10a+9821 2 8,300 [3,300–13,400] 10,600 [3,200–18,400] 11,800 [0–25,200] N9a1'3 25 15,700 [8,800–22,800] 15,200 [8,400–22,200] 19,200 [6,400–32,300] N9a1a 2 4,900 [1,600–8,200] 6,600 [800–12,500] 0 [0–0] N9a2 18 9,600 [3,700–15,700] 9,300 [4,200–14,400] 7,900 [1,900–13,800] N9a2'4'5 32 17,200 [10,200–24,600] 13,600 [8,200–19,200] 16,300 [5,700–26,800] N9a2'4'5+195 4 2,300 [0–6,00] 2,600 [0–5,700] 0 [0–0] N9a2a 13 6,500 [0–10,000] 6,600 [3,400–9,700] 5,600 [0–11,500] N9a2a1 3 3,000 [0–6,600] 3,500 [100–6,900] 2,600 [0–7,800] N9a2a2 4 2,300 [0–4,800] 2,000 [0–4,200] 2,000 [0–5,800] N9a2a3 2 3,700 [73–7,400] 5,200 [100–10,500] 0 [0–0] N9a2c 3 2,600 [0–7,800] 2,600 [0–5,600] 2,600 [0–7,800] N9a3 10 8,800 [4,700–13,000] 7,900 [4,500–11,400] 11,800 [4,400–19,200] N9a3+195 2 3,600 [0–9,500] 2,600 [0–6,200] 3,900 [0–11,700] N9a3+4913 2 1,600 [0–4,600] 1,300 [0–3,800] 0 [0–0] N9a4 9 5,300 [500–10,200] 4,000 [500–7,700] 9,600 [0–20,100] N9a4a 5 1,500 [0–3,500] 1,600 [0–3,300] 1,600 [0–4,700] N9a4b+9156 3 3,200 [0–7,900] 1,700 [0–4,200] 2,600 [0–7,800] N9a6 45 14,800 [9,900–19,800] 12,700 [7,100–18,400] 9,600 [2,900–16,400] N9a6+15080 2 10,200 [1,200–19,800] 7,900 [1,500–14,500] 11,800 [0–25,200] 23 N9a6+16292 3 13,600 [8,200–19,200] 21,000 [11,400–30,900] 21,000 [6,500–35,600] N9a6+3849 3 10,600 [4,000–17,400] 8,800 [2,800–15,000] 7,900 [0–16,800] N9a6a 20 8,700 [2,400–14,600] 7,200 [2,700–11,800] 8,700 [0–17,700] N9a6a1 8 2,500 [300–4,800] 2,600 [200–4,500] 3,000 [0–6,300] N9a6a4 2 3,900 [0–9,400] 3,900 [0–8,400] 3,900 [0–11,700] N9a6b 15 200 [0–600] 200 [0–500] 0 [0–0] N9a8 3 14,600 [8,300–21,200] 14,300 [7,100–21,700] 15,800 [3,200–28,400] N9a9 3 13,000 [5,300–21,000] 9,700 [3,900–15,700] 10,500 [200–20,800] N9b 29 17,300 [11,700–23,000] 11,700 [7,500–16,100] 10,600 [4,500–16,700] N9b1 10 13,900 [8,000–20,000] 12,300 [7,500–17,100] 10,200 [3,900–16,600] N9b1a 2 12,500 [6,600–18,600] 19,000 [8,800–29,800] 15,800 [300–31,200] N9b1b 2 3,100 [0–8,700] 2,600 [0–6,200] 7,900 [0–18,800] N9b1c 5 9,000 [3,000–15,200] 8,400 [3,800–13,200] 7,900 [0–16,100] N9b1c1+15061 2 7,300 [2,500–12,300] 14,800 [5,900–24,100] 11,800 [0–25,200] N9b2 4 15,900 [10,000–21,900] 19,700 [11,400–28,400] 17,700 [6,200–29,300] N9b2+16309 4 14,200 [8,200–20,500] 17,100 [8,800–25,800] 15,800 [3,200–28,400] R9 134 51,000 [41,200–61,000] 53,300 [40,400–66,600] 54,100 [33,700–74,600] R9b 45 38,700 [23,900–54,300] 32,800 [20,400–45,900] 31,400 [13,600–49,200] R9b1 41 22,600 [12,600–33,200] 23,800 [15,000–33,000] 19,800 [8,700–30,900] R9b1a 32 18,600 [10,800–26,700] 20,700 [13,200–28,500] 23,900 [9,700–38,100] R9b1a1 18 11,700 [6,000–17,300] 13,400 [6,600–20,300] 9,600 [3,800–15,500] R9b1a1a 17 9,300 [4,800–13,900] 10,800 [6,200–15,500] 9,300 [3,200–15,300] R9b1a1a+16192 8 7,800 [1,000–14,900] 11,300 [4,400–18,500] 8,900 [0–18,500] R9b1a1a+16234 3 7,000 [2,600–11,500] 7,000 [1,500–12,600] 13,100 [0–26,800] R9b1a1a+7633 3 4,500 [0–15,100] 4,300 [0–9,600] 0 [0–0] R9b1a2 8 15,900 [8,100–24,000] 15,200 [8,300–22,200] 10,800 [1,600–20,100] R9b1a2b 5 12,200 [200–25,000] 10,000 [3,700–16,700] 12,600 [0–25,700] R9b1a2a 3 9,400 [3,300–15,600] 10,600 [4,000–17,400] 7,900 [0–19,400] R9b1a2a+11077 2 6,000 [0–12,200] 6,600 [800–12,500] 0 [0–0] R9b1a3 6 10,200 [1,000–19,900] 12,400 [3,700–21,600] 18,400 [1,300–35,500] R9b1a3+152 5 7,100 [2,100–12,300] 9,000 [1,800–16,400] 22,100 [1,600–42,500] R9b1b 8 6,700 [800–12,900] 6,500 [2,200–11,100] 3,900 [0–10,100] R9b2 4 5,700 [1,300–10,200] 5,200 [1,600–9,000] 5,900 [0–12,600] R9c1 45 28,500 [17,200–40,300] 25,200 [13,200–37,900] 33,100 [9,600–56,600] R9c1+12618 10 17,700 [7,500–28,500] 13,900 [6,900–21,200] 8,700 [0–17,500] R9c1+150 2 11,900 [1,500–22,900] 10,600 [3,200–18,400] 11,800 [0–25,200] R9c1a 33 5,900 [3,700–8,300] 5,100 [2,600–7,800] 6,900 [400–13,500] R9c1a+11197 10 2,000 [300–3,600] 1,600 [100–3,100] 3,000 [0–7,000] R9c1a+12123 2 4,00 [800–7,600] 5,200 [100–10,500] 0 [0–0] 24 R9c1a+1462 5 3,00 [0–7,900] 3,600 [0–8,200] 4,700 [0–14,000] Y 98 28,00 [16,100–40,500] 24,200 [14,000–34,900] 31,200 [11,600–50,900] Y1 48 15,500 [8,000–23,300] 10,700 [3,800–17,900] 13,800 [0–27,900] Y1a 42 4,400 [2,100–6,700] 5,000 [2,500–7,400] 5,100 [1,300–8,800] Y1a+12397 3 2,300 [0–7,000] 2,600 [0–6,400] 0 [0–0] Y1a+12732 3 2,900 [700–5,200] 4,000 [1,100–6,800] 2,600 [0–6,300] Y1a+16266 12 900 [0–2,200] 1,000 [0–2,500] 0 [0–0] Y1a+16292 8 3,700 [700–6,700] 6,200 [800–11,800] 14,800 [0–29,900] Y1b 4 10,200 [3,200–17,600] 7,200 [1,600–13,100] 7,900 [0–17,300] Y1b1 3 3,800 [0–15,100] 1,700 [0–5,100] 5,300 [0–15,600] Y2 50 9,600 [5,000–14,400] 9,200 [3,100–15,600] 8,800 [0–20,100] Y2+5435 2 5,000 [0–10,400] 5,200 [100–10,500] 7,900 [0–18,800] Y2a 43 6,100 [3,200–9,100] 6,700 [2,000–11,500] 8,400 [0–21,400] Y2a1 36 4,100 [2,300–5,900] 4,500 [2,400–6,600] 1,500 [400–2,700] Y2a1+146 4 3,000 [0–6,200] 4,600 [0–9,300] 0 [0–0] Y2a1+228 5 3,300 [1,400–5,200] 4,700 [1,600–7,900] 4,700 [0–10,100] Y2a1a 7 2,300 [200–4,400] 3,000 [0–6,900] 1,100 [0–3,300] Y2a1+4767 3 900 [0–5,800] 0 [0–0] 0 [0–0] Y2b 3 3,400 [0–9,400] 1,700 [0–4,100] 2,600 [0–7,800] D 176 41,700 [29,500–54,300] 49,900 [31,900–68,900] 43,300 [18,100–68,600] D5 174 33,300 [24,600–42,200] 34,500 [23,000–46,500] 35,600 [15,500–55,800] D5a 95 21,000 [13,900–28,500] 20,300 [9,700–31,500] 12,000 [3,600–20,500] D5a2 88 16,900 [9,100–25,100] 14,900 [6,700–23,500] 11,900 [2,900–21,000] D5a2+16172 2 14,500 [4,100–25,400] 17,600 [7,800–27,900] 19,700 [2,400–37,000] D5a2a 83 14,900 [3,300–27,200] 12,100 [5,300–19,200] 11,500 [1,900–21,100] D5a2a+16092 82 13,600 [8,700–18,800] 9,500 [5,100–13,900] 11,600 [1,900–21,300] D5a2a1 32 12,800 [8,100–17,600] 14,900 [9,500–20,400] 14,800 [8,100–21,500] D5a2a1+16092 6 10,800 [6,000–15,700] 11,100 [6,600–15,600] 11,800 [4,100–19,600] D5a2a1+16172 24 12,000 [8,600–15,700] 13,100 [8,800–17,600] 15,400 [6,800–24,100] D5a2a1a 10 9,000 [3,600–14,800] 8,400 [4,100–12,900] 12,600 [2,800–22,400] D5a2a1a1 3 6,600 [1,100–12,400] 6,100 [400–12,000] 5,300 [0–12,500] D5a2a1a2 5 4,100 [300–8,100] 6,300 [1,700–11,000] 12,600 [1,900–23,300] D5a2a1b 5 9,500 [3,700–15,500] 11,700 [6,000–17,500] 6,300 [100–12,500] D5a2a1b+T16092C 2 9,500 [3,100–16,100] 9,700 [3,900–15,700] 7,900 [0–16,800] D5a2a2 49 1,200 [400–2,000] 1,800 [700–2,900] 1,700 [0–4,100] D5a2a2+13584 2 800 [0–1,800] 2,600 [0–6,200] 0 [0–0] D5a2a2+4880 7 600 [0–2,000] 2,600 [0–6,300] 0 [0–0] D5a3 6 16,900 [9,800–24,200] 15,700 [6,500–25,400] 15,800 [300–31,200] D5a3a 5 13,400 [6,200–20,900] 13,400 [4,200–23,000] 17,300 [0–35,600] 25 D5a3a1a 4 3,700 [0–8,600] 3,900 [300–7,600] 2,000 [0–5,800] D5a3a1a+146 2 1,300 [0–11,800] 1,300 [0–3,800] 0 [0–0] D5a'b 162 30,600 [22,100–39,400] 30,500 [19,800–41,700] 28,800 [13,600–44,000] D5b 67 19,300 [13,100–25,500] 17,800 [10,800–25,000] 25,700 [9,700–41,600] D5b+263 4 8,600 [100–17,400] 12,000 [5,200–19,000] 3,900 [0–9,400] D5b+263+9992 3 8,600 [3,200–14,100] 11,500 [4,700–18,600] 5,300 [0–12,000] D5b1 23 17,100 [11,700–22,600] 22,600 [12,600–33,200] 26,800 [9,800–43,700] D5b1a1 2 13,200 [5,800–20,900] 10,600 [3,200–18,400] 7,900 [0–18,800] D5b1b 3 12,000 [5,700–18,600] 9,700 [3,900–15,700] 13,200 [1,600–24,700] D5b1c 16 15,500 [9,900–21,200] 23,200 [10,100–37,000] 29,100 [5,200–52,900] D5b1c1 15 9,100 [4,000–14,400] 12,300 [4,300–20,600] 21,000 [900–41,100] D5b1c1+15724 14 6,600 [1,700–11,700] 10,000 [3,400–16,900] 14,500 [0–29,600] D5b1c1a 11 6,000 [0–13,800] 7,400 [1,200–13,900] 8,600 [0–19,500] D5b1d 2 9,400 [3,300–15,800] 9,200 [2,300–16,500] 19,700 [2,400–37,000] D5b3 40 10,900 [5,600–16,400] 9,900 [2,400–17,700] 17,700 [0–37,100] D5b3+7241 35 3,600 [1,100–6,100] 4,600 [500–8,800] 2,900 [0–6,300] D5c 12 24,000 [16,000–32,200] 29,000 [16,700–41,900] 15,800 [3,200–28,400] D5c+16311 3 22,500 [15,200–29,900] 26,800 [16,600–37,400] 28,900 [11,800–46,000] D5c1+16190 9 13,600 [6,300–21,200] 14,300 [5,400–23,700] 3,500 [100–6,900] Table S4. Entrance age estimates of the mtDNA lineages in this study in ISEA or Taiwan. mtDNA lineages Region Age estimate (years) 95% confidence interval N9a6a ISEA 8,600 2,200 – 15,200 Y2a ISEA 5,300 2,800 – 7,900 B4b1a2 ISEA 5,300 3,200 – 7,400 Taiwan 6,700 4,300 – 9,200 B4c1b2a2 ISEA 7,600 4,900 – 10,400 Taiwan 1,000 300 – 1,800 B5b1c ISEA (Philippines) 8,900 6,500 – 11,300 R9b1a1a ISEA 7,900 2,100 – 13,900 R9c1a ISEA 5,900 3,300 – 8,600 Taiwan 4,800 1,100 – 8,700 F1a4a1 ISEA 3,400 1,200 – 5,600 F3b1 Taiwan 5,800 700 – 11,100 D5b1c1a ISEA 4,600 0 – 9,300 32 clearly different ancestries. F3a is mostly present in MSEA, such as Vietnam, Laos, Malaysia and southern China, suggesting that this clade has a MSEA ancestry. The daughter clade, F3a1, dates to ~16 ka (16.6 [9.0; 24.5] ka) and, similarly to its ancestral clade, displays a MSEA origin centred on Vietnam and Laos. The sister clade F3b is divided into two subclades. One, F3b2, is rare and was detected only in South China, while F3b1, dating to ~12 ka (12.4 [5.2; 20.0] ka), is by far the more common subclade of F3b and is largely restricted to Austronesian-speaking populations in ISEA and Taiwan. Within F3b1, F3b1b is restricted to ISEA while F3b1a is found in ISEA and Taiwan, strongly suggesting an origin in ISEA and a migration into Taiwan. A founder age into Taiwan (5.8 [0.7; 11.1] ka) (Table S4), is concordant with the hypothesis that this clade accompanied postglacial dispersed from ISEA towards Taiwan, again most probably as a result of sea-level rises. Overall, indeed, the age and distribution of haplogroup F3 shows many similarities with haplogroup E (Soares et al. 2008). It likewise emerged in ancient Sundaland over 30 ka, but probably further to the west, within what is now MSEA. Two subclades within haplogroup F3b1 show traces of expansion in the last 8 ka in ISEA, with one reaching Taiwan. The BSP for mtDNA haplogroup F3 shows two population expansion periods, the first between ~5–10 ka and the second within the last 4 ka (Table 2). Given the phylogeographic and phylogenetic patterns of F3 overall, it seems likely that this clade dispersed more than once within the Sunda region over the last ~16 ka. Haplogroup D5 The mtDNA haplogroup D5 dates to just over ~30 ka (33.3 [24.6; 42.2] ka), and is widely distributed throughout East and Southeast Asia. There are two basal branches, D5a‟b and D5c. The latter further separates into D5c1 and D5c2, both with a probable North/Northeast Asian origin. D5a‟b separates into two major subclades: D5a, which is widely dispersed throughout East and Northeast Asia, and D5b, which is extremely frequent in Taiwan and less frequent in Southeast Asia. This clade splits into two subclades, D5b1 and D5b3 (a newly defined branch). D5b3 dates to ~11 ka (10.9 [5.6; 16.4] ka) (Table 1) and is largely restricted to Chinese and Taiwanese populations, and virtually absent in ISEA. Given the existence of several Taiwanese branches dating to less than 4 ka, it seems likely that D5b3 moved between 10 ka and 3 ka, suggesting that it could have arrived in Taiwan with the Neolithic rice-farmers from South China. However, it did not follow the Austronesian movement OOT, resembling in thsi respect the patterns of mtDNA haplogroups N9a10a and M7b1d3. Within D5b1, subclade D5b1c1, dating to ~9 ka (9.1 [4.0; 14.4] ka) is the only D5 subclade to disperse to insular Southeast Asia. This subclade includes a cluster with ancestry in Taiwan, D5b1c1a, dating ~6 ka (6.0 [0; 13.8] ka), restricted to Austronesian-speaking populations. Although the tree might seem to imply a deeper ancestry in ISEA than in Taiwan, this is caused by a single HVS-I variant, 16092, that is mildly fast and could represent homoplasy. A founder age into ISEA is ~4.6 [0; 9.3] ka, again suggesting a Neolithic OOT marker clade. The population increase between ~13 ka till ~3.5 ka, with a peak at ~7.7 ka (Table 2), mostly shows a signal of early population expansion within South China. In contrast to other clades described above, the Austronesian component in the BSP is somewhat low which does not make 33 any hypothetical OOT expansion important in the overall BSP against postglacial expansions in continental Asia. Although it is a probable OOT marker its presence in ISEA is low, at comparable levels to another OOT candidate, M7b3 (Soares et al. 2015). 34 References Bandelt H-J, Achilli A, Kong Q-P, Salas A, Lutz-Bonengel S, Sun C, Zhang Y-P, Torroni A, Yao Y-G (2005) Low “penetrance” of phylogenetic knowledge in mitochondrial disease studies. Biochem Biophys Res Commun 333:122-130. 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