Abstract
The Mongolian horse is one of the most ancient and relatively unmanaged horse breeds. The population history of the Mongolian horse remains poorly understood due to a lack of information on ancient and modern DNA. Here, we report nearly complete mitochondrial genome data obtained from five ancient Mongolian horse samples of the Khereksur and Deer Stone culture (late 2nd to 1st third of the 1st millennium BC) and one ancient horse specimen from the Xiongnu culture (1st century BC to 1st century AD) using target enrichment and high-throughput sequencing methods. Phylogenetic analysis involving ancient, historical, and modern mitogenomes of horses from Mongolia and other regions showed the presence of three mitochondrial haplogroups in the ancient Mongolian horse populations studied here and similar haplotype composition of ancient and modern horse populations of Mongolia. Our results revealed genetic continuity between the Mongolian horse populations of the Khereksur and Deer Stone culture and those of the Xiongnu culture owing to the presence of related mitotypes. Besides, we report close phylogenetic relationships between haplotypes of the Khereksur and Deer Stone horses and the horses of indigenous breeds of the Middle East (Caspian and Iranian), China (Naqu, Yunnan, and Jinjiang), and Italy (Giara) as well as genetic similarity between the Xiongnu Mongolian horses and those of the most ancient breeds of the Middle East (Arabian) and Central Asia (Akhal-Teke). Despite all the migrations of the Mongolian peoples over the past 3000 years, mitochondrial haplogroup composition of Mongolian horse populations remains almost unchanged.
Highlights
The Mongolian horse breed is referred to as a “landrace breed” because these horses are free-ranging and to a lesser extent have experienced selective pressures applied by breeders [1]
The assumption that the ancient Mongolian horse population might have been ancestral to many modern horse breeds [3] is supported by the highest levels of within-breed diversity according to genome-wide autosomal, microsatellite, protein, and mitochondrial polymorphism data [1,3,7,8]
The main characteristics of ancient DNA molecules are cytosine deamination resulting in an increased C → T substitution rate and an increased complementary G → A substitution rate towards 500 and 300 read termini, respectively, as well as DNA degradation to small fragments, generally below 100 bp [37]
Summary
The Mongolian horse breed is referred to as a “landrace breed” because these horses are free-ranging and to a lesser extent have experienced selective pressures applied by breeders [1]. The assumption that the ancient Mongolian horse population might have been ancestral to many modern horse breeds [3] is supported by the highest levels of within-breed diversity according to genome-wide autosomal, microsatellite, protein, and mitochondrial polymorphism data [1,3,7,8]. A few ancient horse populations of Mongolia have been investigated at the mitochondrial level [4,12,13]. These studies have determined hypervariable region mitotypes of three ancient horses found in burials of the
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