60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2

60,000 years of interactions between Central and Eastern Africa documented by major African mitochondrial haplogroup L2 Marina Silva, Farida Alshamali, Paula Silva, Carla Carrilho, Flávio Mandlate, Maria Jesus Trovoada, Viktor Černý, Luísa Pereira, Pedro Soares Supplementary Fig. 1. Comparison between ML and Bayesian age estimates. Correlation between ML and Bayesian branch lengths, in nucleotides (a). Variations in the ratio between ML and Bayesian node age estimates compared to the ML age of the branches, in years (b). Supplementary Fig. 2. BSPs indicating the median of the Ne associated to haplogroup L2 through time. BSP based on all L2 complete sequences from sub-Saharan Africa (a), with a maximum time (~78 ka) corresponding to the mean posterior estimate of the genealogy rootheight. BSPs for different African regions: Western/Central Africa (b), Eastern Africa/Near East/Arabia Peninsula (c) and Southern Africa (d). Supplementary Fig. 3. Graphs of population increments for Western/Central Africa (WA/CA), Eastern Africa/Near East/ Arabian Peninsula (EA/Arabia) and Southern Africa Supplementary Fig. 4. MDS plot based on Sltkin’s linearized FST, excluding L2a and L0a sequences. Colour code: WA – Western Africa, CA – Central Africa, EA – Eastern Africa, SA – Southern Africa. Supplementary Fig. 5. Haplogroup composition of sub-Saharan African regions (WA – Western Africa, CA – Central Africa, EA – Eastern Africa, SA – Southern Africa), compared to Sudan, Luhya (LWK), Kunda, Shona and Nyaneka. The map was obtained from the website www.outline-world-map.com. Excel file: Supplementary Table 1. Phylogenetic tree of mtDNA haplogroup L2. Most parsimonious phylogeny of mtDNA haplogroup L2, based on a total of 801 L2 complete mitogenomes. Polymorphic positions annotated along the branches (mutations in relation to an ancestral state): uppercase for transitions and lowercase for transversions, back mutations indicated with an exclamation mark (double back mutations indicated with two exclamation marks), insertions and deletions indicated by a dot and the letter "d", respectively (shaded in grey; not considered for age estimations). New branch labels in red and shaded in yellow, braches with major alterations in comparison to PhyloTree Build 16 in rose. More detailed information on the samples and/or references on Supplementary Table 3. Supplementary Table 2. Phylogenetic tree of mtDNA haplogroup L0a. Most parsimonious phylogeny of mtDNA haplogroup L0a, based on a total of 303 L0a complete mitogenomes. Polymorphic positions annotated along the branches (mutations in relation to an ancestral state): uppercase for transitions and lowercase for transversions, back mutations indicated with an exclamation mark (double back mutations indicated with two exclamation marks), insertions and deletions indicated by a dot and the letter "d", respectively (shaded in grey; not considered for age estimations). More detailed information on the samples and /or references on Supplementary Table 4. Sample Haplogroup Region Country / Ethnic group Additional information Reference ETH31 L2a1+143 EA Ethiopia - Present study EU092671 L2a1+143+16189 NA Morocco Jew 1 HG03121 L2a1+143+16189 CA Nigeria Esan 2 JQ044837 L2a1+143+16189 WA Burkina Faso - 3 SUD43 L2a1+143+16189 EA Sudan - Present study SUD12 L2a1+143+16189 EA Sudan - Present study ETH5 L2a1+143+16189 EA Ethiopia - Present study SOM76 L2a1+143+16189 EA Somalia - Present study EU092679 L2a1+143+16189+16192 AP / NE Israel Palestinian 1 EU092782 L2a1+143+16189+16192 AP / NE Oman - 1 EU092793 L2a1+143+16189+16192 AP / NE Yemen - 1 JQ702430 L2a1+143+16189+16192 AM USA - 1 EU092806 L2a1+143+16189+16192 NA Morocco - 1 Howell434 L2a1+143+16189+16192 AM USA - 4 EU092659 L2a1+143+16189+16192 AP / NE Israel Druze 1 FJ460527 L2a1+143+16189+16192 NA Tunisia - 5 EU092674 L2a1+143+16189+16192 EA Ethiopia Jew 1 HG03342 L2a1+143+16189+16192 CA Nigeria Esan 2 ETH23 L2a1+143+16189+16192 EA Ethiopia - Present study EU092823 L2a1+143+16189+16192 NA Libya - 1 EU092658 L2a1+143+16189+16192 AP / NE Israel Bedouin 1 EU597491 L2a1+143+16189+16192 AP / NE Israel Bedouin 6 FJ460520 L2a1+143+16189+16309 NA Tunisia - 5 JQ044822 L2a1+143+16189+16309 WA Burkina Faso - 3 JQ044839 L2a1+143+16189+16309 WA Burkina Faso - 3 HG03485 L2a1+143+16189+16309 WA Sierra Leone Mende 2 JQ045062 L2a1+16189 WA Burkina Faso - 3 HG03028 L2a1+16189 WA Gambia - 2 Howell195 L2a1a AM USA - 4 Howell382 L2a1a AM USA - 4 Howell577 L2a1a AM USA - 4 EU092916 L2a1a EA Kenya - 4 DQ304926 L2a1a AM USA - 7 JQ044922 L2a1a WA Burkina Faso - 3 DQ304927 L2a1a AM USA - 7 HG03114 L2a1a CA Nigeria Esan 2 DQ304928 L2a1a AM USA - 7 HG02588 L2a1a WA Gambia - 2 DQ304924 L2a1a AM USA - 7 Supplementary Table 3. List of 801 complete L2 sequences used for phylogenetic reconstruction and phylogeography analysis. Codes for regions: AM – America, CA – Central Africa, EA – Eastern Africa, NA – Northern Africa, NE/AP – Near East/Arabian Peninsula, SA – Southern Africa, WA – Western Africa, EUR – Europe. Abbreviations: G. Bissau – Guinea-Bissau, S. Africa – South Africa, STP – São Tomé and Príncipe, S. Arabia – Saudi Arabia, USA – United States of America. Additional information on ethnicity or geographical location indicated whenever provided by the authors. Branches labelled in this study are underlined. DQ304932 L2a1a AM USA - 7 HG02501 L2a1a AM Barbados African Caribbean 2 JQ044942 L2a1a WA Burkina Faso - 3 JQ044885 L2a1a WA Burkina Faso - 3 JQ044961 L2a1a WA Burkina Faso - 3 SUD56 L2a1a EA Sudan - Present study HG02852 L2a1a WA Gambia - 2 HG02860 L2a1a WA Gambia - 2 JQ044927 L2a1a WA Burkina Faso - 3 JQ044983 L2a1a WA Burkina Faso - 3 JQ044992 L2a1a WA Burkina Faso - 3 JQ705087 L2a1a - unknown - 8 JQ044911 L2a1a WA Burkina Faso - 3 JQ044818 L2a1a WA Burkina Faso - 3 HG03563 L2a1a WA Sierra Leone Mende 2 KJ185692 L2a1a SA Zambia Mbunda 9 KJ185688 L2a1a SA Zambia Mbunda 9 MOZ326 L2a1a SA Mozambique - Present study MOZ33 L2a1a SA Mozambique - Present study SOM68 L2a1a EA Somalia - Present study Howell162 L2a1a1 AM USA - 4 Howell156 L2a1a1 AM USA - 4 Howell571 L2a1a1 AM USA - 4 DQ304925 L2a1a1 AM USA - 7 DQ304933 L2a1a1 AM USA - 7 JQ706014 L2a1a1 - unknown - 8 JQ045001 L2a1a1 WA Burkina Faso - 3 JQ044977 L2a1a1 WA Burkina Faso - 3 JQ045005 L2a1a1 WA Burkina Faso - 3 JQ045020 L2a1a1 WA Burkina Faso - 3 JQ045066 L2a1a1 WA Burkina Faso - 3 JQ045074 L2a1a1 WA Burkina Faso - 3 KJ185589 L2a1a1 SA Zambia Lozi 9 KJ185982 L2a1a1 SA Zambia Lunda 9 KJ185827 L2a1a1 SA Angola Ovimbundu 9 HG03460 L2a1a1 WA Sierra Leone Mende 2 HG03578 L2a1a1 WA Sierra Leone Mende 2 HG02922 L2a1a1 CA Nigeria Esan 2 HG03410 L2a1a1 WA Sierra Leone Mende 2 HG03548 L2a1a1 WA Sierra Leone Mende 2 HQ425645 L2a1a2 AM USA - Family Tree HG01363 L2a1a2 AM Colombia Medellín 2 JQ044987 L2a1a2 WA Burkina Faso - 3 HG03123 L2a1a2 CA Nigeria Esan 2 KC622072 L2a1a2 SA Botswana Kalanga 10 JQ044997 L2a1a2 WA Burkina Faso - 3 Supplementary Table 3. (continued) KJ185728 L2a1f SA Zambia Nkoya 9 KJ185899 L2a1f SA Zambia Kwangwa 9 NA19023 L2a1f EA Kenya Luhya 2 KJ185429 L2a1f SA Zambia Luchazi 9 KJ185897 L2a1f SA Zambia Kwangwa 9 KJ185893 L2a1f SA Zambia Kwangwa 9 KJ185680 L2a1f SA Zambia Mbunda 9 JX303832 L2a1f SA Zambia Subiya 13 DQ304954 L2a1f AM USA - 7 JQ705150 L2a1f - unknown - 8 DQ304953 L2a1f AM USA - 7 DQ304956 L2a1f AM USA - 7 DQ304952 L2a1f AM USA - 7 JQ704668 L2a1f - unknown - 8 DQ304966 L2a1f AM USA - 7 JQ703960 L2a1f - unknown - 8 JQ044859 L2a1f WA Burkina Faso - 3 Howell567 L2a1f AM USA - 4 HG03159 L2a1f CA Nigeria Esan 2 JQ045006 L2a1f WA Burkina Faso - 3 HG03514 L2a1f CA Nigeria Esan 2 JQ045061 L2a1f WA Burkina Faso - 3 HG02979 L2a1f CA Nigeria Esan 2 HG02885 L2a1f WA Gambia - 2 HG03199 L2a1f CA Nigeria Esan 2 AY195776 L2a1f SA S. Africa - 19 KC622076 L2a1f SA Botswana Tswana 10 KJ185681 L2a1f SA Zambia Mbunda 9 KJ185683 L2a1f SA Zambia Mbunda 9 KJ185985 L2a1f SA Zambia Mambwe 9 Howell233 L2a1f AM USA - 4 Howell565 L2a1f AM USA - 4 DQ304959 L2a1f AM USA - 7 DQ304962 L2a1f AM USA - 7 DQ304965 L2a1f AM USA - 7 JQ045090 L2a1f WA Yoruba Yoruba 3 DQ304960 L2a1f1 AM USA - 7 DQ304963 L2a1f1 AM USA - 7 DQ304964 L2a1f1 AM USA - 7 EU092961 L2a1f1 AM USA - 1 HG03575 L2a1f1 WA Sierra Leone Mende 2 JQ701814 L2a1f1 AM USA - 8 DQ304961 L2a1f1 AM USA - 7 DQ304955 L2a1f1 AM USA - 7 KJ185685 L2a1f1 SA Zambia Mbunda 9 HG02557 L2a1f1 AM Barbados African Caribbean 2 Supplementary Table 3. (continued) HG03135 L2a1f1 CA Nigeria Esan 2 KJ186002 L2a1f1 SA Zambia Tumbuka 9 KJ185933 L2a1f1 SA Zambia Makoma 9 DQ304967 L2a1f1 AM USA - 7 HG02476 L2a1f1 AM Barbados African Caribbean 2 HG03297 L2a1f1 CA Nigeria Esan 2 DQ304937 L2a1f1 AM USA - 7 HG03163 L2a1f1 CA Nigeria Esan 2 Howell208 L2a1f1 AM USA - 4 JX303780 L2a1f1 SA Zambia Tonga 13 DQ304958 L2a1f1a AM USA - 7 DQ304934 L2a1f1a AM USA - 7 JQ045097 L2a1f2 WA Yoruba Yoruba 3 JQ045039 L2a1f2 WA Burkina Faso - 3 DQ304957 L2a1f2 AM USA - 7 HG02481 L2a1f2 AM Barbados African Caribbean 2 EU597561 L2a1f3 EA Kenya - 6 JX303805 L2a1f3 SA Zambia Kwamashi 13 KJ185583 L2a1f3 SA Zambia Lozi 9 KJ185596 L2a1f3 SA Zambia Lozi 9 KJ185582 L2a1f3 SA Zambia Lozi 9 KC622118 L2a1f3 SA Botswana Kgalagadi 10 KJ185895 L2a1f3 SA Zambia Kwangwa 9 JQ044861 L2a1f3 WA Burkina Faso - 3 JX303752 L2a1g SA Zambia Tonga 13 JX303906 L2a1g SA Zambia Subiya 13 KJ185894 L2a1g SA Zambia Kwangwa 9 KJ185693 L2a1g SA Zambia Mbunda 9 JX303798 L2a1g SA Zambia Totela 13 EU092676 L2a1h AP / NE Israel Palestinian 1 EU092914 L2a1h EA Kenya - 1 KJ186003 L2a1h SA Zambia Tumbuka 9 MOZ301 L2a1h SA Mozambique - Present study JQ044905 L2a1i WA Burkina Faso - 3 JQ045077 L2a1i WA Burkina Faso - 3 Howell388 L2a1i AM USA - 4 HG03432 L2a1i WA Sierra Leone Mende 2 HG03461 L2a1i WA Sierra Leone Mende 2 EU092719 L2a1i WA G. Bissau FulaForro Behar, 2008 HG03064 L2a1i WA Sierra Leone Mende 2 JQ044958 L2a1i WA Burkina Faso - 3 JQ045080 L2a1i WA Burkina Faso - 3 JQ045102 L2a1i WA Yoruba Yoruba 3 JQ044881 L2a1i1 WA Burkina Faso - 3 Howell193 L2a1i1 AM USA - 4 HG02554 L2a1i1 AM Barbados African Caribbean 2 Supplementary Table 3. (continued) AF346976 L2a1i1 - unknown Effik 12 NA18878 L2a1i1 CA Nigeria Yoruba 2 JX303857 L2a1i1 SA Zambia Fwe 13 KC622169 L2a1i1 SA Namibia Mbukushu 10 KJ185597 L2a1i1 SA Zambia Lozi 9 KJ185598 L2a1i1 SA Zambia Lozi 9 JX303909 L2a1i1 SA Zambia Subiya 13 KJ185690 L2a1i1 SA Zambia Mbunda 9 JX303853 L2a1i1 SA Zambia Fwe 13 KJ185900 L2a1i1 SA Zambia Kwangwa 9 SOM64 L2a1j EA Somalia - Present study EU092756 L2a1j AP / NE Jordan - 1 EU092816 L2a1j NA Morocco Arab 1 EU200760 L2a1k EUR Czech Rep - 17 EU200763 L2a1k EUR Slovenia - 17 JQ045047 L2a1l WA Burkina Faso - 3 JQ044956 L2a1l1 WA Burkina Faso - 3 JQ044919 L2a1l1 WA Burkina Faso - 3 JQ044955 L2a1l1 WA Burkina Faso - 3 HG01286 L2a1l1 AM Puerto Rico - 2 HG03428 L2a1l1 WA Sierra Leone Mende 2 HG03457 L2a1l1 WA Sierra Leone Mende 2 HG03382 L2a1l1 WA Sierra Leone Mende 2 HG03097 L2a1l1 WA Sierra Leone Mende 2 HG02568 L2a1l1 WA Gambia - 2 HG03401 L2a1l1 WA Sierra Leone Mende 2 HG03085 L2a1l1 WA Sierra Leone Mende 2 HG03547 L2a1l1 WA Sierra Leone Mende 2 JQ044817 L2a1l1a WA Burkina Faso - 3 EU092812 L2a1l1a NA Morocco Arab 1 FJ769771 L2a1l1a AM Bahamas - Family Tree JQ044966 L2a1l1a WA Burkina Faso - 3 JQ044897 L2a1l1a WA Burkina Faso - 3 DQ304939 L2a1l1a AM USA - 7 JQ044932 L2a1l1a WA Burkina Faso - 3 EU092807 L2a1l1a NA Morocco - 1 EU092721 L2a1l2 WA G. Bissau Mandinga 1 HG02716 L2a1l2 WA Gambia - 2 HG02620 L2a1l2 WA Gambia - 2 HG02629 L2a1l2 WA Gambia - 2 JQ044978 L2a1l2 WA Burkina Faso - 3 JQ044994 L2a1l2 WA Burkina Faso - 3 JQ705185 L2a1l2a EUR Russia Jew 8 JQ705049 L2a1l2a EUR Poland Jew 8 Howell401 L2a1l2a AM USA - 4 Howell564 L2a1l2a AM USA - 4 Supplementary Table 3. (continued) EU092687 L2a1l2a AP / NE Israel Ashkenazi 1 EU547188 L2a1l2a EUR Poland Jew Family Tree JN204423 L2a1l2a EUR Poland Jew Family Tree JX266264 L2a1l2a EUR Poland Podhale 20 JQ705589 L2a1l2a1 EUR Romania - 8 EU564850 L2a1l2a2 - unknown - Family Tree JQ702015 L2a1l2a3 EUR Poland Jew 8 JQ702904 L2a1l2a4 - unknown - 8 JX266265 L2a1l2a5 EUR Poland Kashubia 20 JQ044804 L2a1m WA Burkina Faso - 3 JQ045040 L2a1m WA Burkina Faso - 3 JQ044916 L2a1m WA Burkina Faso - 3 DQ304940 L2a1m1 AM USA - 7 Howell563 L2a1m1 AM USA - 4 JQ701914 L2a1m1 EUR Ireland - 8 DQ304938 L2a1m1 AM USA - 7 JQ044908 L2a1m1 WA Burkina Faso - 3 JQ703065 L2a1n - unknown - 8 JQ044944 L2a1n WA Burkina Faso - 3 DQ304941 L2a1n AM USA - 7 JQ045000 L2a1o WA Burkina Faso - 3 EU092739 L2a1o AP / NE Syria - 1 JX303870 L2a1q SA Zambia Fwe 13 KC622159 L2a1q SA Namibia Kwanyama 10 NA19381 L2a1q EA Kenya Luhya 2 SOM49 L2a1r EA Somalia - Present study SOM17 L2a1r EA Somalia - Present study SOM59 L2a1r EA Somalia - Present study SOM96 L2a1r EA Somalia - Present study SOM81 L2a1r EA Somalia - Present study EU092896 L2a2a CA Chad Sara 1 SUD102 L2a2a EA Sudan - Present study HM771205 L2a2a1 CA Pygmy - 14 SUD75 L2a2a1 EA Sudan - Present study EU092902 L2a2a1 CA Chad Sara 1 EU092882 L2a2a1 CA Chad Sara 1 HM771191 L2a2b CA Pygmy - 14 HM771207 L2a2b CA Pygmy - 14 KJ185986 L2a2b SA Zambia Mambwe 9 EU597525 L2a2b1 CA Mbuti Pygmy - 6 HM771193 L2a2b1 CA Pygmy - 14 AY195788 L2a2b1 SA S. Africa San 19 HM771192 L2a2b1 CA Pygmy - 14 EU597549 L2a2b1 CA Mbuti Pygmy - 6 HM771194 L2a2b1 CA Pygmy - 14 HM771208 L2a2b1 CA Pygmy - 14 Supplementary Table 3. (continued) HM771195 L2a2b1 CA Pygmy - 14 HM771206 L2a3 CA Pygmy - 14 HM771197 L2a4a CA Pygmy - 14 HM771213 L2a4a CA Pygmy - 14 HM771210 L2a4a CA Pygmy - 14 HM771209 L2a4a CA Pygmy - 14 HM771214 L2a4a CA Pygmy - 14 HM771211 L2a4a CA Pygmy - 14 HM771196 L2a4a CA Pygmy - 14 HM771212 L2a4a CA Pygmy - 14 HM771215 L2a4a CA Pygmy - 14 KJ185525 L2a5 SA Angola Kuvale 9 NA19045 L2a5a EA Kenya Luhya 2 HQ384199 L2a5a EUR Spain - 21 HM596745 L2a5a1a1 AM Bermuda - Family Tree JX303829 L2a5a1a1 SA Zambia Kwamashi 13 KJ185684 L2a5a1a1 SA Zambia Mbunda 9 KJ185687 L2a5a1a1 SA Zambia Mbunda 9 KJ185682 L2a5a1a1 SA Zambia Mbunda 9 KJ185952 L2a5a1a1 SA Zambia Nyengo 9 KJ185734 L2a5a1a1 SA Zambia Nkoya 9 KJ185953 L2a5a1a2 SA Zambia Nyengo 9 KJ185592 L2a5a1a2 SA Zambia Lozi 9 KJ185954 L2a5a1a2 SA Zambia Nyengo 9 KJ185942 L2a5a1a2 SA Zambia Mwenyi 9 KJ185932 L2a5a1a2 SA Zambia Makoma 9 KJ185730 L2a5a1a2 SA Zambia Nkoya 9 KJ185729 L2a5a1a2 SA Zambia Nkoya 9 KJ185427 L2a5a1b SA Zambia Luchazi 9 KJ185830 L2a5a1b SA Angola Ovimbundu 9 KJ185441 L2a5a1b SA Zambia Luvale 9 KJ185593 L2a5a1b SA Zambia Lozi 9 KJ185594 L2a5a1b SA Zambia Lozi 9 KJ185823 L2a5a1b SA Angola Ovimbundu 9 JN214443 L2b EUR Spain Galicia 11 EU092734 L2b WA G. Bissau Mandinga 1 HG02645 L2b WA Gambia - 2 JQ045008 L2b WA Burkina Faso - 3 EU092747 L2b1 AP / NE S. Arabia - 1 EU092766 L2b1 NA Egypt - 1 HG02982 L2b1a WA Gambia - 2 JQ044854 L2b1a WA Burkina Faso - 3 HG03291 L2b1a CA Nigeria Esan 2 Tor66(#26) L2b1a AM Dominica - 16 HG01403 L2b1a AM Puerto Rico - 2 DQ304981 L2b1a AM USA - 7 Supplementary Table 3. (continued) HG02760 L2b1a WA Gambia - 2 Howell175 L2b1a AM USA - 4 HG03472 L2b1a WA Sierra Leone Mende 2 EU092664 L2b1a2 AP / NE Israel Bedouin 1 EU092722 L2b1a2 WA G. Bissau Manjaco 1 DQ304985 L2b1a2 AM USA - 7 HG02887 L2b1a2 WA Gambia - 2 HG03046 L2b1a2 WA Gambia - 2 JQ045013 L2b1a2 WA Burkina Faso - 3 JQ044890 L2b1a2 WA Burkina Faso - 3 JQ045037 L2b1a2 WA Burkina Faso - 3 DQ304978 L2b1a3 AM USA - 7 DQ304979 L2b1a3 AM USA - 7 DQ304980 L2b1a3 AM USA - 7 DQ304982 L2b1a3 AM USA - 7 DQ304983 L2b1a3 AM USA - 7 DQ304984 L2b1a3 AM USA - 7 HG03515 L2b1a3 CA Nigeria Esan 2 AY195766 L2b1a3 SA S. Africa - 19 EU092854 L2b1a3 SA S. Africa San 1 KJ185460 L2b1a3 SA Zambia Tokaleya 9 KJ185857 L2b1a3 SA Zambia Ovimbundu 9 FJ460535 L2b1a3 NA Tunisia - 5 KJ185956 L2b1a3 SA Zambia Nyengo 9 KJ185832 L2b1a3 SA Angola Ovimbundu 9 KJ185489 L2b1a3 SA Angola Ganguela 9 KJ185772 L2b1a3 SA Angola Nyaneka 9 KJ185443 L2b1a3 SA Zambia Luvale 9 KJ185600 L2b1a3 SA Zambia Lozi 9 JQ701833 L2b1a3 EUR unknown African European 8 JQ702694 L2b1a3 - unknown - 8 JX303882 L2b1a3 SA Zambia Shanjo 13 KJ185869 L2b1a3 SA Zambia Kwamulonga 9 KJ185599 L2b1a3 SA Zambia Lozi 9 NA19024 L2b1a3 EA Kenya Luhya 2 Howell568 L2b1a4 AM USA - 4 JN214453 L2b1a4 EUR Italy Liguria 11 JN214454 L2b1a4 EUR Italy Liguria 11 JQ044800 L2b1b WA Burkina Faso - 3 HG02952 L2b1b CA Nigeria Esan 2 Howell574 L2b1b AM USA - 4 FJ228403 L2b1b WA Senegal - Family Tree HM771226 L2b1b CA Pygmy - 14 KJ185444 L2b1b SA Zambia Luvale 9 JQ044910 L2b2 WA Burkina Faso - 3 EU092692 L2b2 SA Mozambique Ronga 1 Supplementary Table 3. (continued) KJ185974 L2b2 SA Zambia Kaonde 9 SUD87 L2b2 EA Sudan - Present study JQ044797 L2b2 WA Burkina Faso - 3 JQ045043 L2b2 WA Burkina Faso - 3 JQ044846 L2b2a WA Burkina Faso - 3 STP84 L2b2a WA STP - Present study JX303841 L2b2a SA Zambia Kwamashi 13 KJ185694 L2b2a SA Zambia Mbunda 9 JX303807 L2b2a SA Zambia Kwamashi 13 KJ185833 L2b2a SA Angola Ovimbundu 9 KJ185831 L2b2a SA Angola Ovimbundu 9 EU092661 L2b3 EA Ethiopia - 1 FJ460526 L2b3 NA Tunisia - 5 HG02804 L2b3 WA Gambia - 2 HG02595 L2b3 WA Gambia - 2 HG02837 L2b3 WA Gambia - 2 HG02555 L2b3 AM Barbados African Caribbean 2 JQ702123 L2b3a AM Hawaii - 8 Howell222 L2b3a AM USA - 4 JQ702626 L2b3a - unknown - 8 Howell385 L2b3a AM USA - 4 JQ044882 L2c WA Burkina Faso - 3 STP43 L2c WA STP - Present study JQ701954 L2c - unknown - 8 HG03484 L2c WA Sierra Leone Mende 2 EU092723 L2c WA G. Bissau Fula 1 JQ705120 L2c - unknown - 8 HG03376 L2c WA Sierra Leone Mende 2 HG03451 L2c WA Sierra Leone Mende 2 HG03473 L2c WA Sierra Leone Mende 2 HG02703 L2c WA Gambia - 2 JQ702169 L2c - unknown - 8 JQ044878 L2c WA Burkina Faso - 3 JQ044941 L2c WA Burkina Faso - 3 HG03049 L2c WA Gambia - 2 KJ185773 L2c SA Angola Nyaneka 9 HG03433 L2c WA Sierra Leone Mende 2 HG03455 L2c WA Sierra Leone Mende 2 HG03476 L2c WA Sierra Leone Mende 2 HG03091 L2c WA Sierra Leone Mende 2 HG03225 L2c WA Sierra Leone Mende 2 HG02814 L2c WA Gambia - 2 HG02882 L2c WA Gambia - 2 HG02888 L2c WA Gambia - 2 HG02624 L2c WA Gambia - 2 HG02642 L2c WA Gambia - 2 Supplementary Table 3. (continued) JQ044989 L2c1 WA Burkina Faso - 3 JQ044858 L2c1 WA Burkina Faso - 3 JQ045002 L2c1 WA Burkina Faso - 3 HG02759 L2c1 WA Gambia - 2 HG02505 L2c1 AM Barbados African Caribbean 2 EU092813 L2c1a NA Morocco - 1 JN214433 L2c1a EUR Spain Andalusia 11 HG03048 L2c1a WA Gambia - 2 JQ045106 L2c1a WA Mandenka Mandenka 3 JQ045105 L2c1a WA Mandenka Mandenka 3 JQ045068 L2c1a WA Burkina Faso - 3 JQ045022 L2c1a WA Burkina Faso - 3 JQ044887 L2c1a WA Burkina Faso - 3 JQ044901 L2c1a WA Burkina Faso - 3 AF381981 L2c1a NA Mauritania - 22 EU092754 L2c2 AP / NE Lebanon - 1 EU092697 L2c2 SA Mozambique Mozambique 1 JQ045042 L2c2 WA Burkina Faso - 3 Tor67(#08) L2c2 AM Dominica - 16 DQ304986 L2c2 AM USA - 7 Howell573 L2c2 AM USA - 4 HG03069 L2c2 WA Sierra Leone Mende 2 HG03388 L2c2 WA Sierra Leone Mende 2 DQ304989 L2c2 AM USA - 7 JQ044920 L2c2 WA Burkina Faso - 3 JQ045010 L2c2 WA Burkina Faso - 3 HG02836 L2c2 WA Gambia - 2 DQ304988 L2c2a AM USA - 7 EU092955 L2c2a AM USA - 1 EU092957 L2c2a AM USA - 1 JQ704740 L2c2a1 - unknown - 8 HG03157 L2c2a1 CA Nigeria Esan 2 DQ304987 L2c2a1 AM USA - 7 KJ185994 L2c2a1 SA Zambia Ndundulu 9 KJ185603 L2c2a1 SA Zambia Lozi 9 KJ185877 L2c2a1 SA Zambia Kwandi 9 KJ185601 L2c2a1 SA Zambia Lozi 9 KJ185605 L2c2a1 SA Zambia Lozi 9 KJ185539 L2c2a1 SA Zambia Kololo 9 KJ185983 L2c2a1 SA Zambia Lunda 9 JX303792 L2c2a1 SA Zambia Totela 13 KJ185604 L2c2a1 SA Zambia Lozi 9 JX303863 L2c2a1 SA Zambia Fwe 13 JX303750 L2c2a1 SA Zambia Totela 13 HG03354 L2c2b1 CA Nigeria Esan 2 JQ704094 L2c2b1a - unknown - 8 Supplementary Table 3. (continued) NA18517 L2c2b1a CA Nigeria Yoruba 2 EU092710 L2c2b1b EUR Netherlands Dutch 1 KJ185834 L2c2b1b SA Angola Ovimbundu 9 KC622075 L2c2b1b SA Botswana Kalanga 10 KJ185775 L2c2b1b SA Angola Nyaneka 9 KJ185526 L2c2b1b SA Angola Kuvale 9 KJ185774 L2c2b1b SA Angola Nyaneka 9 KJ185602 L2c2b1b SA Angola Lozi 9 JQ044853 L2c2b2 WA Burkina Faso - 3 JQ044917 L2c3 WA Burkina Faso - 3 HG03074 L2c3 WA Sierra Leone Mende 2 JQ044810 L2c3 WA Burkina Faso - 3 JQ044971 L2c3 WA Burkina Faso - 3 JQ705626 L2c3 - unknown - 8 Howell575 L2c3 AM USA - 4 Howell572 L2c3 AM USA - 4 AF346995 L2c3a - unknown Mandenka 12 JQ045104 L2c3a WA Mandenka Mandenka 3 JQ045109 L2c3a WA Mandenka Mandenka 3 JQ702115 L2c4 - unknown - 8 HG02757 L2c4 WA Gambia - 2 HG02878 L2c4 WA Gambia - 2 HG02756 L2c4 WA Gambia - 2 JQ044914 L2c4 WA Burkina Faso - 3 JQ044921 L2c4 WA Burkina Faso - 3 HG02715 L2c5 WA Gambia - 2 AY195785 L2c5 SA S. Africa S. Africa 19 HG02643 L2c5 WA Gambia - 2 HG02896 L2c5 WA Gambia - 2 HG02462 L2c5 WA Gambia - 2 HG02667 L2c5 WA Gambia - 2 JQ045030 L2c6 WA Burkina Faso - 3 HG03072 L2c6 WA Sierra Leone Mende 2 HG02879 L2c6 WA Gambia - 2 STP48 L2c6 WA STP - Present study EU597570 L2d AM unknown Latin America 6 SUD86 L2d EA Sudan - Present study HG02536 L2d AM Barbados African Caribbean 2 HG02881 L2d WA Gambia - 2 EU092817 L2d NA Algeria Arab 1 HG02799 L2d WA Gambia - 2 HG02545 L2d1 AM Barbados African Caribbean 2 HG03437 L2d1 WA Sierra Leone Mende 2 HG03279 L2d1 CA Nigeria Esan 2 JQ045050 L2d1a WA Burkina Faso - 3 HG02970 L2d1a CA Nigeria Esan 2 Supplementary Table 3. (continued) KJ185421 L2d1a SA Zambia Chokwe 9 JQ044948 L2d1a WA Burkina Faso - 3 JQ045044 L2d1a WA Burkina Faso - 3 EU092794 L2d1a AP / NE Yemen - 1 JQ045060 L2d1a WA Burkina Faso - 3 Howell160 L2d1a AM USA - 4 DQ341062 L2d1a EA Ethiopia - 23 JQ044929 L2d1a WA Burkina Faso - 3 JQ045011 L2d1a WA Burkina Faso - 3 JX303748 L2d1a SA Zambia Totela 13 FJ460523 L2e1a NA Tunisia - 5 HG03367 L2e1a CA Nigeria Esan 2 HG03130 L2e1a1 CA Nigeria Esan 2 KJ185902 L2e1a1a SA Zambia Kwangwa 9 KJ185607 L2e1a1a SA Zambia Lozi 9 KJ185695 L2e1a1a SA Zambia Mbunda 9 KJ185608 L2e1a1a SA Zambia Lozi 9 KJ185606 L2e1a1a SA Zambia Lozi 9 SUD103 L2e1b EA Sudan - Present study JQ044816 L2e1b WA Burkina Faso - 3 Howell153 L2e1b AM USA - 4 STP12 L2e1b WA STP - Present study Tor64(#28) L2e2 AM Dominica - 16 HG03209 L2e2 WA Sierra Leone Mende 2 HG03240 L2e3 WA Gambia - 2 EU092724 L2e3 WA G. Bissau Mandinga 1 References 1. Behar, D. M. et al. The Dawn of Human Matrilineal Diversity. The American Journal of Human Genetics 82, 1130–1140 (2008). 2. Abecasis, G. R. et al. An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56–65 (2012). 3. Barbieri, C. et al. Contrasting maternal and paternal histories in the linguistic context of Burkina Faso. Molecular Biology and Evolution 29, 1213–1223 (2012). 4. Howell, N., Elson, J. L., Turnbull, D. M. & Herrnstadt, C. African Haplogroup L mtDNA sequences show violations of clock-lfike evolution. Molecular Biology and Evolution 21, 1843–1854 (2004). 5. Costa, M. D. et al. Data from complete mtDNA sequencing of Tunisian centenarians: testing haplogroup association and the “golden mean” to longevity. Mechanisms of Ageing and Development 130, 222–226 (2009). 6. Hartmann, A. et al. Validation of microarray-based resequencing of 93 worldwide mitochondrial genomes. Human Mutation 30, 115–122 (2009). Annex 2. (continued) Supplementary Table 3. (continued) JQ705109 L0a2a2a - unknown - 7 JX303763 L0a2a2a SA Zambia Totela 2 JX303772 L0a2a2a SA Zambia Totela 2 JX303778 L0a2a2a SA Zambia Totela 2 JX303786 L0a2a2a SA Zambia Tonga 2 JX303826 L0a2a2a SA Zambia Kwamashi 2 JX303904 L0a2a2a SA Zambia Totela 2 KC622056 L0a2a2a SA Botswana Tswana 14 KC622064 L0a2a2a SA Botswana Tswana 14 KC622187 L0a2a2a SA Namibia Kwanyama 14 KF672819 L0a2a2a SA Mozambique - 3 KF672824 L0a2a2a WA STP - 3 KF672825 L0a2a2a EA Somalia - 3 KF672832 L0a2a2a SA Mozambique - 3 KF672835 L0a2a2a EA Somalia - 3 KJ185394 L0a2a2a SA Zambia Aushi 4 KJ185458 L0a2a2a SA Zambia Tokaleya 4 KJ185477 L0a2a2a SA Angola Ganguela 4 KJ185478 L0a2a2a SA Angola Ganguela 4 KJ185479 L0a2a2a SA Angola Ganguela 4 KJ185544 L0a2a2a SA Zambia Lozi 4 KJ185556 L0a2a2a SA Zambia Lozi 4 KJ185657 L0a2a2a SA Zambia Mbunda 4 KJ185658 L0a2a2a SA Zambia Mbunda 4 KJ185721 L0a2a2a SA Zambia Nkoya 4 KJ185749 L0a2a2a SA Angola Nyaneka 4 KJ185802 L0a2a2a SA Angola Ovimbundu 4 KJ185804 L0a2a2a SA Angola Ovimbundu 4 KJ185862 L0a2a2a SA Zambia Tswana 4 KJ185970 L0a2a2a SA Zambia Chewa 4 NA19312 L0a2a2a EA Kenya Luhya 1 NA19328 L0a2a2a EA Kenya Luhya 1 NA19402 L0a2a2a EA Kenya Luhya 1 NA19904 L0a2a2a AM USA - 1 JX303831 L0a2a2a1 SA Zambia Kwamashi 2 JX303835 L0a2a2a1 SA Zambia Kwamashi 2 KJ185541 L0a2a2a1 SA Zambia Lozi 4 KJ185550 L0a2a2a1 SA Zambia Lozi 4 KJ185553 L0a2a2a1 SA Zambia Lozi 4 KJ185655 L0a2a2a1 SA Zambia Mbunda 4 KJ185719 L0a2a2a1 SA Zambia Nkoya 4 KJ185803 L0a2a2a1 SA Angola Ovimbundu 4 KJ185946 L0a2a2a1 SA Zambia Nyengo 4 KJ185947 L0a2a2a1 SA Zambia Nyengo 4 NA19713 L0a2a2a1 AM USA - 1 NA19985 L0a2a2a1 AM USA - 1 AF346998 L0a2b CA Congo Mbuti Pygmy 8 AF346999 L0a2b CA Congo Mbuti Pygmy 8 AM711903 L0a2b CA Congo Pygmy 19 Supplementary Table 4. (continued) EU597537 L0a2b CA Congo Pygmy 20 HM771189 L0a2b CA Congo Pygmy 16 HM771190 L0a2b CA Congo Pygmy 16 HM771199 L0a2b CA Congo Pygmy 16 HM771202 L0a2b CA Congo Pygmy 16 HM771188 L0a2b1 CA Congo Pygmy 16 HM771200 L0a2b1 CA Congo Pygmy 16 HM771201 L0a2b1 CA Congo Pygmy 16 EF556174 L0a2c EA Ethiopia Jew 21 KF672813 L0a2c EA Somalia - 3 EU092913 L0a2d EA Kenya - 5 KJ185399 L0a2d SA Zambia Bemba 4 KJ185463 L0a2d SA Zambia Tonga 4 EU092900 L0a3 CA Chad Sara 5 KF672796 L0a3 CA Cameroon Bulahay 3 EU092906 L0a4 EA Kenya - 5 References 1. Abecasis, G. R. et al. An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56–65 (2012). 2. Barbieri, C., Butthof, A., Bostoen, K. & Pakendorf, B. Genetic perspectives on the origin of clicks in Bantu languages from southwestern Zambia. European Journal of Human Genetics 21, 430– 436 (2013). 3. Rito, T. et al. The first modern human dispersals across Africa. PloS one 8, e80031 (2013). 4. Barbieri, C. et al. 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Behar, D. M. et al. Counting the founders: the matrilineal genetic ancestry of the Jewish Diaspora. PloS one 3, e2062 (2008). Region Country Capital GPS Coordinates (WGS 84) References WA BF Ouagadougou 12°21′26″ N 1°32′07″ W 1–3 CV Praia 14°55’15" N 23° 30’30" W 4 Gambia Banjul 13°27′11″ N 16°34′39″ W 5 Ghana Accra 5°33′00″ N 0°12′00″ W 6 Mali Bamako 12°39′00″ N 8°00′00″ W 1,3,7,8 STP São Tomé 0°20′10″ N 6°40′53″ E 9,10 Senegal Dakar 14°41′34″ N 17°26′48″ W 2,11,12 S.Leone Freetown 8°29′4″ N 13°14′04″ W 5,13 CA Cameroon Yaoundé 3°52′00’‘ N 11°31′00’‘ E 3,6,14 Chad N’Djamena 12°06′47″ N 15°02′57″ E 3,11 Congo Brazzaville 4°16′04″ S 15°17′31″ E 11 Eq. Guinea Malabo 3°45′00’‘ N 8°46′59″ E 9 Niger Niamey 13°31′17″ N 02°06′19″ E 1,3,11 Nigeria Abuja 9°04′00″ N 7°29′00″ E 3,5,6,11 W. Sahara El Aaiún 27°09′13″ N 13°12′12″ W 12,15 EA Ethiopia Addis Ababa 9°01′48″ N 38°44′24″ E 16–19 Kenya Nairobi 1°17′31’‘ S 36°49′19’’ E 5,11,20,21 Rwanda Kigali 1°56′38″ S 30°03′34″ E 22 Somalia Mogadishu 02°02′ N 45°21′ E 11,19 Sudan Khartoum 15°32′47’‘ N 32°32′00’’ E 19,23 Tanzania Dodoma 06° 10’23" S 35° 44’31" E 24 Angola Luanda 8°50′18″ S 13°14′04″ E 25–27 Botswana Gaborone 24°39′29″ S 25°54′44″ E 28 Cabinda Cabinda 5°33′36″ S 12°11′24″ E 29 SA Madagascar Antananarivo 18°54′51’‘ S 47°31′51’‘ E 30 Mozambique Maputo 25°57′55″ S 32°35′21″ E 31,32 Namibia Windhoek 22°34′12″ S 17°05′01″ E 28 South Africa Pretoria 25°44′46″ S 28°11′17″ E 33,34 Zambia Lusaka 15°24′29″ S 28°17′10″ E 35,36 Zimbabwe Harare 17°51′50″ S 31°01′47″ E 22 NA Algeria Algiers 36º45′08″ N 3°02′31″ E 15 Egypt Cairo 30°03′29″ N 31°13′44″ E 37,38 Libya Tripoli 32°54′08″ N 13°11′09″ E 39 Mauritania Nouakchott 18°06′01″ N 15°56′59″ W 8,12 Morocco Rabat 34°00′47″ N 6°49′57″ W 12,37,40 Tunisia Tunis 36°49′08″ N 10°09′56″ E 15,41–44 Supplementary Table 5. GPS coordinates in WGS-84 (World Geodetic System, 1984) of capital cities used as reference points to construct L2 frequency distribution and references for the 12880 HVS-I sequences used to assess L2 frequency. Codes for regions: CA – Central Africa, EA – Eastern Africa, NA – Northern Africa, SA – Southern Africa, WA – Western Africa. Abbreviations: BF – Burkina Faso, CV – Cape Verde, Eq. Guinea – Equatorial Guinea, STP – São Tomé and Príncipe, S. Leone – Sierra Leone, W. Sahara – Western Sahara. References 1. Pereira, L. et al. Linking the sub-Saharan and West Eurasian gene pools: maternal and paternal heritage of the Tuareg nomads from the African Sahel. European Journal of Human Genetics 18, 915–923 (2010). 2. Barbieri, C. et al. Contrasting maternal and paternal histories in the linguistic context of Burkina Faso. Molecular Biology and Evolution 29, 1213–1223 (2012). 3. Černý, V. et al. Genetic Structure of Pastoral and Farmer Populations in the African Sahel. 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American Journal of Physical Anthropology 139, 253–260 (2009). ~ Region Country Population Code N Language group Additional information Reference EA Ethiopia Daasanach Daa 49 Cushitic Agropastoralist 1 Dawro-Konta Daw 137 Omotic Agropastoralist 2 Nyangatom Nya 112 Nilotic Agropastoralist 1 General population Eth 77 - - 3 Kenya El Molo Elm 52 Cushitic Fishing 2 Luo Luo 49 Nilotic Agropastoralist, fishing 2 Luhya LWK 120 Bantu Agriculturalist 4 Maasai Maa 81 Nilotic Seminomadic pastoralist 2 Turkana Turk 37 Nilotic Seminomadic pastoralist 5 Rwanda Hutu Hutu 42 Bantu - 6 Somalia General population Som 177 - - 3,5 Sudan General population Sud 178 - - 3,7 Tanzania Burunge Buru 38 Cushitic Agriculturalist 8 Datog Dat 31 Nilotic Pastoralist, Agriculturalist 8 WA Burkina Faso Various groups BF 291 - - 9 Cape Verde General population CV 295 - - 10 Gambia Western Division GWD 113 - - 4 Mali Bambara Mali 158 Mande - 11,12 Malinke Mande - Senegal Mandenka Man 131 Mande - 5,9 Wolof Wol 61 Wolof - 13,14 Sierra Leone Mende MSL 85 Mel - 4 CA Eq. Guinea Bioko Bio 45 Bantu - 15 Cameroon Ngumba Ngu 88 Bantu - 16 Gabon Akele Ake 48 Bantu - 16 Ateke Ate 54 Bantu - Benga Beng 50 Bantu - Duma Duma 47 Bantu - Eshira Eshi 40 Bantu - Eviya Evi 38 Bantu - Fang Fang 66 Bantu - Galoa Gal 51 Bantu - Kota Kota 56 Bantu - Makina Mak 45 Bantu - Mitsogo Mits 64 Bantu - Supplementary Table 6. Information on the populations used to assess pairwise genetic distances and to compute the MDS plots. References for the 4880 HVS-I sequences used. Codes for regions: CA – Central Africa, EA – Eastern Africa, SA – Southern Africa, WA – Western Africa. Abbreviations: Eq. Guinea – Equatorial Guinea, STP – São Tomé and Príncipe. Nzebi Nze 63 Bantu - Punu Punu 52 Bantu - Shake Sha 51 Bantu - Nigeria Esan ESN 99 Edoid - 4 Yoruba Yor 193 Yoruboid - 4,5,9 STP General population STP 54 - - 15 SA Angola Mbundu Ang 466 Bantu - 17 West-Savanna Bantu - 18 Cabinda (Fiote) Cab 109 Bantu - 19 Kuvale Kuv 55 Bantu Seminomadic pastoralists 20 Nyaneka Nyane 59 Bantu Agriculturalist 20 Mozambique General population Moz 187 - - 21,22 Zambia Bisa Bisa 42 Bantu - 23 Fwe Fwe 33 Bantu Agropastoralist 24 Kunda Kunda 36 Bantu - 23 Kwamashi Kwam 35 Bantu Agriculturalist 20 Kwangwa Kwang 35 Bantu - 20 Lozi Lozi 110 Bantu Agriculturalist 20 Mbunda Mbun 64 Bantu Agriculturalist 20 Nkoya Nkoy 32 Bantu Agriculturalist 20 Tonga Ton 37 Bantu Agriculturalist 24 Zimbabwe Shona Sho 62 Bantu - 6 References 1. Poloni, E. S. et al. Genetic evidence for complexity in ethnic differentiation and history in East Africa. Annals of Human Genetics 73, 582–600 (2009). 2. 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