<p>Supplementary Figure S1. Phylogenetic Tree with frequency distribution of </p><p>E haplogroups in Eritreans (this study) and populations from Africa, Middle </p><p>East and Europe obtained from previous published works. Abbreviations for population names are as given in supplementary Table S1. (Eritrean populations) AFA, BIL, HID, KUN, NAR, SAH, TGR, TIG; (Sudanese populations) DIN, SHI, NUE, BOR, NUB, MAS, FUR, NUBN, FUL, HAS, </p><p>COP, BEJ, GAA, MES, ARA; (Ethiopian populations) AMH, EJEW, ORO; </p><p>SEN, MAR, MBE, YEM, SAR, OMA, SOM, EGY, TUR, SHW, ALG, TUN, </p><p>MAL, BFAS, BSA, KSA, (Italian populations) INC, IC1, IC2, IAP, ISI, ISR, </p><p>SBAS. N=total number of samples analyzed; E=total number of chromosomes positive for E haplogroup. Y chromosomes from Eritrea (this study) and </p><p>Sudan23 genotyped for E-M78 sub-haplogroups were retracted back to the E-</p><p>M78 level during all the analyses. </p><p>Supplementary Figure S2. Principal Component Analysis (PCA) plot generated using PAST program by employing FST values from Arlequin 3.11. </p><p>Components 1 and 2 represent 61% and 22% of the variations, respectively. </p><p>Populations’ descriptions are given in supplementary Table S1.</p><p>1 Tables</p><p>Table 1. Summary of AMOVA analysis. The grouping of populations in their </p><p> linguistic and geographical location was done as discussed in the text.</p><p>% Fixation indices (p Source of variations category Groups Geography 18.73variation FSC:0.35259value) values) (0.00000) linguistic 25.89 FSC: 0.26488 (0.00000) Populations within Geography 28.66 FST :0.47383 (0.00000) groups Linguistic 19.63 FST: 0.45523 (0.00000) Geography 52.62 FCT: 0.18728 (0.00000) Among populations linguistic 54.48 FCT: 0.25873 (0.00000)</p><p>Supplementary Table S1. Linguistic affiliation and life style of populations </p><p> involved in the analysis. Abbreviations used throughout the analysis are given </p><p> in brackets. </p><p> present or past Linguistic affiliatione Populations history Family Level Afar (AFA) Nomadic Pastoralists Afro-asiatic Cushitic Bilen (BIL) Pastoralists Afro-asiatic Cushitic Hidarb Nomadic Pastoralists Afro-asiatic Cushitic (HID) 2 Kunama Pastoralists Nilo-saharan eastern Sudanic Nara (NAR) (KUN) Nomadic Pastoralists Nilo-saharan eastern Sudanic Rashaida Pastoralists Afro-asiatic Semitic Saho (SAH) Pastoralists Afro-asiatic Cushitic Tigre Agro-pastoralists Afro-asiatic Semitic Tigrigna (TGR) Agriculturalists Afro-asiatic Semitic Dinka (TIG) Pastoralists Nilo-saharan Eastern Sudanic Shilluk (DIN) Agro-Pastoralists Nilo-saharan Eastern Sudanic Nuer (NUE) (SHI) Pastoralsists Nilo-saharan Eastern Sudanic Borgu Agriculturalists Nilo-saharan Maban Nuba Nilo- Eastern (BOR) Agro-Pastoralists Masalit (NUB) Agro-pastoralists saharan+kordofoniaNilo-saharan Sudanic+kordofoniaMaban Fur (FUR) (MAS) Agriculturalists Nilo-saharan Fur Nubians Agriculturalists Nilo-saharan Eastern Sudanic Fulani (BUBN) Nomadic Pastoralists Niger-Congo Atlantic Hausa (FUL) Agriculturalists Afro-asiatic Chadic Copts (HAS) Agriculturalists Afro-asiatic Egyptian Beja (BEJ) (COP) Pastoralists Afro-asiatic Cushitic Gaalien Agriculturalists Afro-asiatic Semitic Meseria (GAA) Nomadic Pastoralists Afro-asiatic Semitic Arakien (MES) Agriculturalists Afro-asiatic Semitic Amhara (ARA) Agro-pastoralists Afro-asiatic Semitic Ethiopia (AMH) Agro-pastoralists Afro-asiatic Semitic Oromo Jews Pastoralists Afro-asiatic Omotic Senegal (ORO) Pastoralists Niger-Kordofian Atlantic Morocco (SEN) Pastoralists Afro-asiatic semitic Morocco Arabs Nomadic-pastoralists Afro-asiatic Berber Yemen Berbers Agro-pastoralists Afro-asiatic Semitic Saudi (YEM) Pastoralists Afro-asiatic Semitic Oman Arabia Agro-pastoralists Afro-asiatic Semitic Somalia (OMA) Pastoralists Afro-asiatic Cushitic (SOM) 3 Egypt Agro-pastoralists Afro-asiatic Semitic Turkey (Arabs) Agro-pastoralists Ughuz Ural-Altaic Saharawi (TUR) Pastoralists Afro-asiatic Semitic Algeria (SHW) Pastoralist Afro-asiatic Semitic Tunisia (ALG) Agro-pastoralists Afro-asiatic Semitic Mali (MAL) (TUN) Pastoralists Niger-Congo Mande Burkina Pastoralists Niger-Congo Sudanic Bantu Faso Agriculturalists Niger-Congo Bantu Khoisan (South Hunther-gatherers Khoisan Khoisan Italia North (South Agro-Pastoralists Indo-European Italic Italia Center Agro-Pastoralists Indo-European Italic Italia Central1 Agro-Pastoralists Indo-European Italic Italian Central2 Agro-Pastoralists Indo-European Italic Italian Appelia Agro-Pastoralists Indo-European Italic Italian Sicily (ISI) Agro-Pastoralists Indo-European Italic Spanish Sardinia Agro-Pastoralists Basque Basque Basquee classification according to www.ethnologue.com</p><p>4</p>