Locations of the 652 horse mtDNAs sampled for this study or previously published. Numbers before brackets represent local sample sizes, and numbers in brackets represent geographically well-documented samples whose breeds agree with their traced maternal origin. The pie charts depict the occurrence of the “pony” mtDNA type C1 in horses with documented ancestry.

Geographical distribution of the samples of cluster D1 with documented ancestry. The D1 Breed composition, including samples without documented ancestry, is as follows (% of samples of breed): 5 Arabs (5%), 1 Belgian (100%), 1 Arabian-Barb cross (14%), 7 Andalusians (50%), 7 Barbs (54%), 1 Norwegian Fjord (9%), 1 Friesian (50%), 1 Holsteiner (10%), 1 Icelandic (13%), 2 Caspians (29%), 5 Lusitanos (56%), 24 Mustangs (31%), 2 Rhineland heavy drafts (8%), 3 Rottalers (33%), 2 Shires (20%), 2 Trakehners (40%), 3 Lipizzans (23%), 2 Yunnans (100%), 1 Shetland (20%), 1 historical sample (13%), and 12 EC (according to ref. 3).

Phylogenetic network of 652 horse mtDNA sequences. The bold lines indicate a postulated most parsimonious tree. Circles are proportional to the number of horses they represent. Links represent mutations at the mtDNA nps indicated alongside. The node A6 is the root of the network according to equid outgroups. Each sample name is composed as follows: the first letter indicates the first author (B = Bowling; D = Dhar, GenBank; I = Ishida; J–Jansen, this study; K = Kavar or Kim; L = Lister; O = Oh, GenBank; V = Vilà), the second and third letter indicates the breed (AB = Arabian–Barb cross, AL = Andalusian, AN = ancient sample according to ref. 2, AR = Arabian, BA = Barb, BE = Belgian, CH = Cheju, DU = Dülmener, EC = according to ref. 2, EX = Exmoor, FE = Fell, FJ = Fjord, FR = Friesian, HO = Holsteiner, IS = Icelandic, JAP = Japanese, KA = Caspian, KO = Konik, KP = Kazakh, LI = Lipizzan, LU = Lusitano, MO = Mongolian domestic, MU = Mustang, NN = no breed given, NO = Noriker, OL = Oldenburger, PL = Pleistocene Alaskan, PR = Przewalski's, QH = Quarter, RD = Rhineland heavy draft, RO = Rottaler, SC = Scottish Highland, SE = Senner, SH = Shire, SO = Sorraia, SP = Shetland, SU = Suffolk punch, TR = Trakehner, TS = Tsushima, VB = Thoroughbred, WB = Warmblood, WP = Welsh, YU = Yunnan), and the final number is taken from the original study. For circles encompassing several horses, only one sample name is given.