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Table S1. Material used, and various population groupings used in the analyses. Groupings 1-3 Popgene (groupings according to geographical distribution see map (Fig. 1); Grouping 4-6: Modeclus 4 clusters K=18, 3 clusters K=22, 2 clusters K=27 (respectively). * Accepted population grouping. n 2 4 6 1 * 5

o Sample # Origin Longitude East Latitude North Altitude as 3 g g g g g i t n n g n n n a i i i i i n recorded in m l p p i p p p u u u p u u u

above sea level p o o u o o o o r r r r r o P r G G G G G G

95 Former Yugoslavia 1 1 1 1 96 Iran - Azerbaijan West 45 44 36 44 2 2 2 2 4 2 2 112 Iran - Azerbaijan West 46 52 32 33 2 2 2 2 4 2 2 90 Iran – Ilam area 46 27 33 37 3 2 4 2 4 2 2 113 Iran – Ilam 46 27 33 37 3 2 4 2 4 2 2 98 Iran – Kermanshahan area 46 25 34 20 4 2 3 2 4 2 2 1 Lebanon – Baalbek area 36 10 34 2 1050 5 3 2 3 4 2 2 4 Lebanon – Baalbek 36 13 33 57 1240 5 3 2 3 4 2 2 86 Lebanon – Baalbek 36 5 34 12 1810 5 3 2 3 4 2 2 92 Lebanon – Baalbek 36 2 34 9 1470 5 3 2 3 4 2 2 105 Lebanon – Baalbek 36 8 34 7 1050 5 3 2 3 4 2 2 5 Syria – Aleppo area 37 0 34 25 580 6 4 1 4 4 2 2 13 Syria – Aleppo 34 57 34 30 540 6 4 1 4 4 2 2 24 Syria – Aleppo 37 1 34 28 6 4 1 4 3 3 1 25 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 26 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 27 Syria – Aleppo 37 1 34 28 6 4 1 4 3 1 2 28 Syria – Aleppo 37 1 34 28 6 4 1 4 3 3 1 29 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 30 Syria – Aleppo 37 1 34 28 1200 6 4 1 4 3 1 2 31 Syria – Aleppo 37 1 34 28 1200 6 4 1 4 1 3 1 32 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 33 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 34 Syria – Aleppo 37 1 34 28 1200 6 4 1 4 3 1 2 35 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 36 Syria – Aleppo 37 1 34 28 6 4 1 4 3 1 2 37 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 Baum and Bailey page 2 of 6 pages

38 Syria – Aleppo 37 1 34 28 6 4 1 4 1 3 1 39 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 40 Syria – Aleppo 37 1 34 28 1200 6 4 1 4 3 3 1 41 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 42 Syria – Aleppo 37 1 34 28 1200 6 4 1 4 1 3 1 43 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 44 Syria – Aleppo 37 1 34 28 6 4 1 4 1 3 1 45 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 46 Syria – Aleppo 37 1 34 28 6 4 1 4 3 1 2 48 Syria – Aleppo 37 1 34 28 6 4 1 4 3 1 2 49 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 50 Syria – Aleppo 37 1 34 28 6 4 1 4 1 3 1 51 Syria – Aleppo 37 1 34 28 6 4 1 4 2 2 1 52 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 53 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 54 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 55 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 56 Syria – Aleppo 37 1 34 28 1200 6 4 1 4 3 1 2 57 Syria – Aleppo 37 1 34 28 1200 6 4 1 4 2 1 1 58 Syria – Aleppo 37 1 34 28 1200 6 4 1 4 1 3 1 59 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 60 Syria – Aleppo 37 1 34 28 6 4 1 4 3 1 2 61 Syria – Aleppo 37 1 34 28 1200 6 4 1 4 1 2 2 62 Syria – Aleppo 37 1 34 28 1200 6 4 1 4 3 1 2 63 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 64 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 65 Syria – Aleppo 37 1 34 28 6 4 1 4 3 3 1 66 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 68 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 69 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 70 Syria – Aleppo 37 1 34 28 6 4 1 4 1 3 1 71 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 72 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 73 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 74 Syria – Aleppo 37 1 34 28 1200 6 4 1 4 2 1 1 75 Syria – Aleppo 37 1 34 28 6 4 1 4 1 3 1 76 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 Baum and Bailey page 3 of 6 pages

77 Syria – Aleppo 37 1 34 28 6 4 1 4 1 3 1 78 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 79 Syria – Aleppo 37 1 34 28 6 4 1 4 3 1 2 80 Syria – Aleppo 37 1 34 28 6 4 1 4 3 3 1 81 Syria – Aleppo 37 1 34 28 6 4 1 4 3 1 2 82 Syria – Aleppo 37 1 34 28 6 4 1 4 3 1 2 83 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 84 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 85 Syria – Aleppo 37 1 34 28 6 4 1 4 1 1 2 88 Syria – Aleppo 37 1 34 28 6 4 1 4 1 1 2 91 Syria – Aleppo 34 57 34 30 6 4 1 4 4 2 2 94 Syria – Aleppo 37 32 34 37 6 4 1 4 1 2 2 101 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 102 Syria – Aleppo 37 40 34 34 545 6 4 1 4 1 2 2 115 Syria – Aleppo 38 24 34 47 555 6 4 1 4 1 2 2 153 Syria – Aleppo 37 1 34 28 6 4 1 4 3 1 2 154 Syria – Aleppo 37 1 34 28 6 4 1 4 3 1 2 155 Syria – Aleppo 37 1 34 28 6 4 1 4 3 1 2 156 Syria – Aleppo 37 1 34 28 6 4 1 4 3 1 2 157 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 158 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 159 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 160 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 161 Syria – Aleppo 37 1 34 28 6 4 1 4 3 3 1 162 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 163 Syria – Aleppo 37 1 34 28 6 4 1 4 1 3 2 164 Syria – Aleppo 37 1 34 28 6 4 1 4 1 3 2 165 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 166 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 167 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 168 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 169 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 2 170 Syria – Aleppo 37 1 34 28 6 4 1 4 2 2 2 171 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 172 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 173 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 174 Syria – Aleppo 37 1 34 28 700 6 4 1 4 2 3 1 Baum and Bailey page 4 of 6 pages

175 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 176 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 177 Syria – Aleppo 37 1 34 28 6 4 1 4 3 1 2 178 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 179 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 180 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 181 Syria – Aleppo 37 1 34 28 6 4 1 4 3 1 2 182 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 183 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 184 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 185 Syria – Aleppo 37 1 34 28 6 4 1 4 3 1 2 186 Syria – Aleppo 37 1 34 28 6 4 1 4 2 3 1 187 Syria – Aleppo 37 1 34 28 6 4 1 4 1 2 2 189 Syria – Aleppo 6 4 1 4 1 2 2 190 Syria – Aleppo 6 4 1 4 2 3 1 97 Syria I(raq) - Al-Hassaka area 42 9 37 12 500 7 5 3 2 11 Syria – Damascus area 34 2 33 38 1175 8 3 1 3 1 2 2 18 Syria – Damascus 34 7 33 48 1420 8 3 1 3 1 2 2 114 Syria – Damascus 34 10 33 42 8 3 1 3 3 3 1 8 Syria – Sweida area 34 53 32 41 1350 9 3 2 3 4 2 2 10 Syria – Sweida 34 44 32 48 1550 9 3 2 3 4 2 2 12 Syria – Sweida 34 47 32 43 1740 9 3 2 3 4 2 2 21 Syria – Sweida 34 53 32 41 1350 9 3 2 3 4 2 2 23 Syria – Sweida 34 49 32 38 1480 9 3 2 3 4 2 2 87 Syria – Sweida 34 50 32 41 1400 9 3 2 3 4 2 2 93 Syria – Sweida 34 49 32 38 1480 9 3 2 3 4 2 2 104 Syria – Sweida 34 47 32 40 1550 9 3 2 3 4 2 2 108 Syria – Sweida 34 41 32 55 1300 9 3 2 3 4 2 2 109 Syria – Sweida 34 42 32 29 1447 9 3 2 3 4 2 2 110 Syria – Sweida 34 47 32 45 1500 9 3 2 3 4 2 2 22 Turkey - 10 6 2 5 4 2 2 99 Turkey - 10 6 2 5 4 2 2 103 Turkey - 10 6 2 5 4 2 2 111 Turkey - 10 6 2 5 2 3 2 6 Turkey – Corum area 34 5 40 42 1590 11 6 1 5 1 3 1 14 Turkey – Corum 34 5 40 42 1590 11 6 1 5 1 2 2 15 Turkey – Corum 34 5 40 42 1590 11 6 1 5 4 2 2 Baum and Bailey page 5 of 6 pages

89 Turkey – Corum 34 5 40 42 1590 11 6 1 5 1 2 2 2 Turkey – Gaziantep area 37 28 34 55 455 12 4 1 4 1 2 2 3 Turkey – Gaziantep 37 13 34 42 445 12 4 1 4 3 2 2 7 Turkey – Gaziantep 37 31 37 14 490 12 4 1 4 4 2 2 9 Turkey – Gaziantep 34 55 34 54 950 12 4 1 4 4 2 2 16 Turkey – Gaziantep 37 32 37 14 430 12 4 1 4 1 2 2 17 Turkey – Gaziantep 37 10 34 55 870 12 4 1 4 1 2 2 19 Turkey – Gaziantep 37 31 34 52 435 12 4 1 4 1 2 1 20 Turkey – Gaziantep 34 57 34 52 700 12 4 1 4 1 2 2 100 Turkey – Gaziantep 37 28 34 45 530 12 4 1 4 4 2 2 106 Turkey – Gaziantep 37 31 34 51 440 12 4 1 4 1 3 1 107 Turkey – Gaziantep 37 17 34 44 700 12 4 1 4 3 3 1 116 Turkey – Gaziantep 37 30 34 58 700 12 4 1 4 1 2 2 117 Turkey – Gaziantep 37 30 34 58 700 12 4 1 4 1 2 2 118 Turkey – Gaziantep 37 30 34 58 700 12 4 1 4 1 2 2 119 Turkey – Gaziantep 37 30 34 58 700 12 4 1 4 1 2 2 120 Turkey – Gaziantep 37 30 34 58 700 12 4 1 4 3 3 1 121 Turkey – Gaziantep 37 30 34 58 700 12 4 1 4 1 2 2 122 Turkey – Gaziantep 37 30 34 58 700 12 4 1 4 1 2 2 123 Turkey – Gaziantep 37 30 34 58 700 12 4 1 4 1 2 2 124 Turkey – Gaziantep 37 30 34 58 700 12 4 1 4 1 2 2 125 Turkey – Gaziantep 37 7 37 43 550 12 4 1 4 1 2 2 141 Turkey – Gaziantep 30 34 59 700 12 4 1 4 1 2 2 191 Turkey – Gaziantep 37 30 34 58 700 12 4 1 4 1 2 2 192 Turkey – Gaziantep 37 30 34 58 700 12 4 1 4 1 2 2 193 Turkey – Gaziantep 37 30 34 58 700 12 4 1 4 1 2 2 194 Turkey – Gaziantep 37 30 34 58 12 4 1 4 1 2 2 195 Turkey – Gaziantep 37 30 34 58 700 12 4 1 4 1 2 2 196 Turkey – Gaziantep 37 30 34 58 700 12 4 1 4 1 2 2 197 Turkey – Gaziantep 37 30 34 58 700 12 4 1 4 1 2 2 198 Turkey – Gaziantep 37 30 34 58 700 12 4 1 4 1 2 2 199 Turkey – Gaziantep 37 30 34 58 700 12 4 1 4 1 2 2 200 Turkey – Gaziantep 37 30 34 58 700 12 4 1 4 1 2 2 201 Turkey – Gaziantep 37 30 34 58 700 12 4 1 4 1 2 2 202 Turkey – Gaziantep 37 30 34 58 700 12 4 1 4 1 2 2 126 Turkey - Sanli Urfa area 37 57 37 12 415 13 7 2 4 4 2 2 128 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 4 2 2 Baum and Bailey page 6 of 6 pages

129 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 4 2 2 130 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 4 2 2 131 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 4 2 2 132 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 4 2 2 133 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 4 2 2 134 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 4 2 2 135 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 4 2 2 136 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 4 2 2 137 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 4 2 2 138 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 4 2 2 139 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 4 2 2 140 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 4 2 2 142 Turkey - Sanli Urfa 33 37 40 1100 13 7 2 4 4 2 2 143 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 4 2 2 144 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 4 2 2 145 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 4 2 2 146 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 4 2 2 147 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 1 2 2 148 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 4 2 2 149 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 4 2 2 150 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 1 2 2 151 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 4 2 2 152 Turkey - Sanli Urfa 38 12 37 13 420 13 7 2 4 1 2 2