Mitochondrial DNA and the origins of the domestic horse

Abstract

The place and date of the domestication of the horse has long been a matter for debate among archaeologists. To determine whether horses were domesticated from one or several ancestral horse populations, we sequenced the mitochondrial D-loop for 318 horses from 25 oriental and European breeds, including American mustangs. Adding these sequences to previously published data, the total comes to 652, the largest currently available database. From these sequences, a phylogenetic network was constructed that showed that most of the 93 different mitochondrial (mt)DNA types grouped into 17 distinct phylogenetic clusters. Several of the clusters correspond to breeds and/or geographic areas, notably cluster A2, which is specific to Przewalski's horses, cluster C1, which is distinctive for northern European ponies, and cluster D1, which is well represented in Iberian and northwest African breeds. A consideration of the horse mtDNA mutation rate together with the archaeological timeframe for domestication requires at least 77 successfully breeding mares recruited from the wild. The extensive genetic diversity of these 77 ancestral mares leads us to conclude that several distinct horse populations were involved in the domestication of the horse.

Fig 1.

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.

Fig 2.

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. , AR = Arabian, BA = Barb, BE = Belgian, CH = Cheju, DU = Dülmener, EC = according to ref. , 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.

Fig 3.

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).