**2. Materials and Methods**

#### *2.1. Sample Collection*

The museum (historical) skulls of Kalmyk (KALM\_H, *n* = 10), Kyrgyz (KRGZ\_H, *n* = 11), and Kazakh (KZKH\_H, *n* = 3) cattle dated to the first quarter of the 20th century were derived from the craniological collection of the Museum of Livestock named after E.F. Liskun (Moscow Agricultural Academy named after K.A. Timiryazev) (Figure 1).

**Figure 1.** Museum skulls of cattle breeds used for the the study dated by the first quarter of 20th century: (**a**)—Kalmyk, (**b**)—Kyrgyz, (**c**)—Kazakh.

The modern samples of Kalmyk (KALM\_M, *n* = 28), Kyrgyz (KRGZ\_M, *n* = 20), and Kazakh white-headed (KZWH\_M, *n* = 30) cattle were derived from the Bioresource collection "Bank of genetic materials of domestic and wild animals and birds" of the L.K. Ernst Federal Research Center for Animal Husbandry. Tissue samples (ear skin) from modern animals were collected by trained personnel under strict veterinary rules in accordance

with the guidelines for conducting laboratory research (tests) in the implementation of the veterinary control (supervision) approved by the Council Decision Eurasian Economic Commission No. 80 (10 November 2017). The 1–2 mm2 pieces of ear skin were used for DNA extraction using Nexttec columns (Nexttec Biotechnology GmbH, Leverkusen, Germany), according to the manufacturer's instructions.

Additionally, we included modern samples of Mongolian cattle (MONG\_M, *n* = 41) as a kinship breed with a similar genetic origin, which probably contributed to the development of Kalmyk cattle. Additionally, we included in the dataset samples of modern representatives of the Hereford breed (HRFD\_M, *n* = 26) because of their great contribution to the development of the modern gene pool of Kazakh white-headed cattle.
