Supplementary Figure S2. Principal Component Analysis (PCA) Plot Generated Using PAST

Supplementary Figure S1. Phylogenetic Tree with frequency distribution of

E haplogroups in Eritreans (this study) and populations from Africa, Middle

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,

COP, BEJ, GAA, MES, ARA; (Ethiopian populations) AMH, EJEW, ORO;

SEN, MAR, MBE, YEM, SAR, OMA, SOM, EGY, TUR, SHW, ALG, TUN,

MAL, BFAS, BSA, KSA, (Italian populations) INC, IC1, IC2, IAP, ISI, ISR,

SBAS. N=total number of samples analyzed; E=total number of chromosomes positive for E haplogroup. Y chromosomes from Eritrea (this study) and

Sudan23 genotyped for E-M78 sub-haplogroups were retracted back to the E-

M78 level during all the analyses.

Supplementary Figure S2. Principal Component Analysis (PCA) plot generated using PAST program by employing FST values from Arlequin 3.11.

Components 1 and 2 represent 61% and 22% of the variations, respectively.

Populations’ descriptions are given in supplementary Table S1.

1 Tables

Table 1. Summary of AMOVA analysis. The grouping of populations in their

linguistic and geographical location was done as discussed in the text.

% 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)

Supplementary Table S1. Linguistic affiliation and life style of populations

involved in the analysis. Abbreviations used throughout the analysis are given

in brackets.

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