G C A T T A C G G C A T genes Article Traces of Late Bronze and Early Iron Age Mongolian Horse Mitochondrial Lineages in Modern Populations Mariya A. Kusliy 1,* , Nadezhda V. Vorobieva 1, Alexey A. Tishkin 2, Alexey I. Makunin 1 , Anna S. Druzhkova 1, Vladimir A. Trifonov 1 , Tumur-O. Iderkhangai 3 and Alexander S. Graphodatsky 1 1 Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, 630090 Novosibirsk, Russia;
[email protected] (N.V.V.);
[email protected] (A.I.M.);
[email protected] (A.S.D.);
[email protected] (V.A.T.);
[email protected] (A.S.G.) 2 Department of Archaeology, Ethnography and Museology, Altai State University, 656049 Barnaul, Russia;
[email protected] 3 Department of Archaeology, Ulaanbaatar State University, Ulaanbaatar 13343, Mongolia;
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[email protected] 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 infor- mation 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 meth- ods. Phylogenetic analysis involving ancient, historical, and modern mitogenomes of horses from Citation: Kusliy, M.A.; Vorobieva, Mongolia and other regions showed the presence of three mitochondrial haplogroups in the ancient N.V.; Tishkin, A.A.; Makunin, A.I.; Mongolian horse populations studied here and similar haplotype composition of ancient and modern Druzhkova, A.S.; Trifonov, V.A.; horse populations of Mongolia.