Table S1. 151 horse isolates (68 breeds) used in this study.
No. ID / Group / Breed / Country / Accession no.1. AkT01 / 6 / Akhal-Teke / Central Asia / JN398450
2. AkT02 / 6 / Akhal-Teke / Central Asia / JN398449
3. AkT03 / 6 / Akhal-Teke / Central Asia / JN398453
4. AkT04 / 6 / Akhal-Teke / Central Asia / JN398452
5. AkT05 / 6 / Akhal-Teke / Central Asia / JN398435
6. AkT06 / 2 / Akhal-Teke / Central Asia / JN398404
7. AkT07 / 2 / Akhal-Teke / Central Asia / JN398410
8. AkT08 / 4 / Akhal-Teke / Central Asia / JN398424
9. AkT09 / 4 / Akhal-Teke / Central Asia / JN398422
10. AkT10 / 1 / Akhal-Teke / Central Asia / JN398385
11. AkT11 / 1 / Akhal-Teke / Central Asia / JN398393
12. AkT12 / 1 / Akhal-Teke / Central Asia / HQ439441
13. AkT13 / 6 / Akhal-Teke / Central Asia / HQ439442
14. Alt01 / 2 / Altai / Central Asia / HQ439443
15. Alt02 / 6 / Altai / Central Asia / HQ439444
16. AmP01 / 4 / American Paint / North America / JN398421
17. And01 / 4 / Andalusian / South Europe / JN398430
18. And02 / 6 / Andalusian / South Europe / JN398443
19. App01 / 4 / Appaloosa / North America / HQ439446
20. Arb01 / 6 / Arabian / Middle East / JN398448
21. Arb02 / 1 / Arabian / Middle East / JN398392
22. Arb03 / 2 / Arabian / Middle East / JN398406
23. Arb04 / 4 / Arabian / Middle East / JN398434
24. Arb05 / 1 / Arabian / Middle East / JN398380
25. Arb06 / 2 / Arabian / Middle East / JN398412
26. Arb07 / 6 / Arabian / Middle East / HQ439447
27. Arb08 / 6 / Arabian / Middle East / HQ439448
28. Arb09 / 1 / Arabian / Middle East / HQ439449
29. Ard01 / 6 / Ardennais / West Europe / HQ439450
30. BaC01 / 4 / Bashkir Curly / North America / HQ439451
31. BaC02 / 4 / Bashkir Curly / North America / HQ439452
32. Bar01 / 4 / Barb / North Africa / HQ439453
33. BeD01 / 3 / Belgian Draft / Central Europe / JN398420
34. BlF01 / 1 / Black Forest / Central Europe / HQ439487
35. Cam01 / 2 / Camargue / West Europe / HQ439454
36. ChP01 / 1 / Chincoteague Pony / North America / JN398377
37. Cly01 / 6 / Clydesdale / North Europe / JN398439
38. Cly02 / 6 / Clydesdale / West Europe / HQ439455
39. CsP01 / 1 / Caspian Pony / Middle East / JN398378
40. CsP02 / 4 / Caspian Pony / Middle East / JN398428
41. CsP03 / 6 / Caspian Pony / Middle East / JN398447
42. CsP04 / 2 / Caspian Pony / Middle East / JN398416
43. CsP05 / 6 / Caspian Pony / Middle East / JN398436
44. Deq01 / 6 / Deqin / Central Asia / EF597514
45. EnS01 / 6 / English Shire / North Europe / JN398440
46. ExP01 / 6 / Exmoor Pony / North Europe / JN398442
47. Fre01 / 6 / Friesian / Central Europe / JN398438
48. Gia01 / 2 / Giara (Sardinia) / South Europe / JN398411
49. Gia02 / 2 / Giara (Sardinia) / South Europe / JN398407
50. GRP01 / 4 / German Riding Pony / Central Europe / HQ439461
51. GSH01 / 4 / German Sport Horse / Central Europe / HQ439456
52. Haf01 / 6 / Haflinger / Central Europe / HQ439464
53. Han01 / 6 / Hanoverian / Central Europe / HQ439457
54. Hol01 / 1 / Holstein / Central Europe / HQ439458
55. HuC01 / 4 / Hungarian Coldblood / Central Europe / HQ439494
56. IcH01 / 1 / Icelandic Horse / North Europe / JN398400
57. IcH02 / 1 / Icelandic Horse / North Europe / JN398399
58. IcH03 / 6 / Icelandic Horse / North Europe / HQ439465
59. IcH04 / 6 / Icelandic Horse / North Europe / HQ439466
60. Irn01 / 4 / Unspecified Iranian / Middle East / JN398423
61. Irn02 / 3 / Unspecified Iranian / Middle East / JN398419
62. Irn03 / 6 / Unspecified Iranian / Middle East / JN398446
63. Irn04 / 5 / Unspecified Iranian / Middle East / JN398457
64. Irn05 / 2 / Unspecified Iranian / Middle East / JN398405
65. Irn06 / 6 / Unspecified Iranian / Middle East / JN398444
66. Irn07 / 6 / Unspecified Iranian / Middle East / JN398451
67. Irn08 / 6 / Unspecified Iranian / Middle East / JN398455
68. Irn09 / 1 / Unspecified Iranian / Middle East / JN398395
69. Irn10 / 2 / Unspecified Iranian / Middle East / JN398415
70. Irn11 / 2 / Unspecified Iranian / Middle East / JN398414
71. Irn12 / 6 / Unspecified Iranian / Middle East / JN398445
72. Irn13 / 4 / Unspecified Iranian / Middle East / JN398433
73. Irn14 / 1 / Unspecified Iranian / Middle East / JN398383
74. Ita01 / 1 / Unspecified Italian / South Europe / JN398390
75. Ita02 / 2 / Unspecified Italian / South Europe / JN398409
76. Ita03 / 4 / Unspecified Italian / South Europe / JN398425
77. *Jeju01 / 6 / Jeju / Korea (Jeju) / KF038159
78. *Jeju02 / 6 / Jeju / Korea (Jeju) / KF038160
79. *Jeju03 / 2 / Jeju / Korea (Jeju) / KF038161
80. *Jeju04 / 1 / Jeju / Korea (Jeju) / KF038162
81. *Jeju05 / 3 / Jeju / Korea (Jeju) / KF038163
82. *Jeju06 / 1 / Jeju / Korea (Jeju) / KF038164
83. Kab01 / 2 / Kabardin / East Europe / HQ439468
84. KiH01 / 1 / KinskyHorse / Central Europe / HQ439469
85. KiH02 / 4 / Kinsky Horse / Central Europe / HQ439470
86. Kla01 / 6 / Kladruber / Central Europe / HQ439445
87. Kla02 / 1 / Kladruber / Central Europe / HQ439471
88. Kla03 / 2 / Kladruber / Central Europe / HQ439472
89. Kon01 / 4 / Konik / Central Europe / HQ439473
90. Kus01 / 2 / Kustanai / Central Asia / HQ439476
91. Kuz01 / 1 / Kuznet / East Europe / HQ439474
92. Kuz02 / 1 / Kuznet / East Europe / HQ439475
93. Lew01 / 6 / Lewitzer / Central Europe / HQ439477
94. Lie01 / 4 / Liebenthaler / Central Europe / HQ439478
95. Lie02 / 2 / Liebenthaler / Central Europe / HQ439479
96. Lus01 / 1 / Lusitano / Portugal / X79547
97. *Mon01 / 4 / Mongolian / Mongol / KF038165
98. *Mon02 / 4 / Mongolian / Mongol / KF038166
99. Mrm01 / 6 / Maremmano / South Europe / JN398437
100. Mrm02 / 6 / Maremmano / South Europe / JN398454
101. Mrm03 / 4 / Maremmano / South Europe / JN398427
102. Mrm04 / 4 / Maremmano / South Europe / JN398432
103. Mrm05 / 2 / Maremmano / South Europe / JN398401
104. Mrm06 / 2 / Maremmano / South Europe / JN398413
105. Mrm07 / 1 / Maremmano / South Europe / JN398382
106. Mrm08 / 1 / Maremmano / South Europe / JN398388
107. Mrm09 / 5 / Maremmano / South Europe / JN398456
108. Mrm10 / 4 / Maremmano / South Europe / JN398426
109. Mrm11 / 1 / Maremmano / South Europe / JN398381
110. Mrm12 / 1 / Maremmano / South Europe / JN398379
111. Mrm13 / 1 / Maremmano / South Europe / JN398397
112. Mrm14 / 1 / Maremmano / South Europe / JN398387
113. Mrm15 / 3 / Maremmano / South Europe / JN398418
114. Naq01 / 2 / Naqu / Central Asia / EF597513
115. NoF01 / 1 / Norwegian Fjord / North Europe / JN398398
116. NoF02 / 2 / Norwegian Fjord / North Europe / HQ439463
117. Nor01 / 2 / Noriker / Central Europe / HQ439480
118. Old01 / 4 / Oldenburg / North Europe / JN398429
119. Old02 / 4 / Oldenburg / Central Europe / HQ439459
120. OrT01 / 2 / Orlov Trotter / East Europe / HQ439481
121. PaH01 / 4 / Painted Horse / North America / HQ439482
122. Per01 / 4 / Percheron / West Europe / HQ439483
123. Prz01 / 2 / Przewalskii / Central Asia / JN398402
124. Prz02 / 2 / Przewalskii / East Asia / HQ439484
125. RHD01 / 1 / Rhineland Heavy Draft / Central Europe / HQ439491
126. RHD02 / 6 / Rhineland Heavy Draft / West Europe / HQ439485
127. RRH01 / 1 / Russian Riding Horse / East Europe / HQ439486
128. Sad01 / 6 / Saddlebred / North America / JN398441
129. ShA01 / 1 / Shagya Arab / Central Europe / HQ439488
130. She01 / 1 / Shetland / West Europe / HQ439489
131. Shi01 / 2 / Shire / West Europe / HQ439490
132. Sil01 / 4 / Silesian / Central Europe / JN398431
133. SpH01 / 4 / Spotted Horse / Central Europe / HQ439492
134. SuP01 / 1 / Suffolk Punch / North Europe / JN398396
135. Syr01 / 1 / Unspecified Syrian / Middle East / JN398394
136. Syr02 / 1 / Unspecified Syrian / Middle East / JN398384
137. Syr03 / 2 / Unspecified Syrian / Middle East / JN398408
138. Syr04 / 1 / Unspecified Syrian / Middle East / JN398391
139. Syr05 / 1 / Unspecified Syrian / Middle East / JN398389
140. Thor01 / 1 / Thoroughbred / West Europe / HQ439462
141. Tra01 / 2 / Trakhener / North Europe / JN398417
142. Tra02 / 4 / Trakehner / Central Europe / HQ439493
143. VHD01 / 6 / Vladimir Heavy Draught / East Europe / HQ439500
144. Via01 / 6 / Viatka / East Europe / HQ439495
145. WeC01 / 2 / Welsh Cob / West Europe / HQ439496
146. WeP01 / 2 / Welsh Pony / West Europe / HQ439497
147. WeP02 / 4 / Welsh Pony / West Europe / HQ439498
148. WeP03 / 2 / Welsh Pony / West Europe / HQ439499
149. Wes01 / 1 / Westphalian / Central Europe / JN398386
150. Wes02 / 1 / Westphalian / Central Europe / HQ439460
151. Yak01 / 6 / Yakut / East Asia / HQ439467
152. Donkey / Equus asinus (outgroup) / North Europe / X97337
Note: New sequences marked with asterisk.