**3. Results**

#### *3.1. Estimation of Consensus Genotypes for Museum Samples*

The concentrations of dsDNA extracted from the museum specimens exceeded the set threshold of 1 ng/μL and varied from 2.88 to 38.40 ng/μL in different samples (Supplementary Materials, Table S1). Out of the 24 museum specimens, 18 samples were successfully genotyped for all 11 loci. For four samples, the consensus genotypes were obtained for 10 loci, including two samples of the Kyrgyz breed (H176, H181) and one sample each of the Kalmyk (H210) and Kazakh (H355) breeds. Two samples of Kyrgyz breed (H180 and H181) were genotyped for 9 loci (Supplementary Materials, Table S2a). No amplification failure was observed in the BM2113 locus. Among the other 10 loci, the ratio of positive PCRs varied from 99.23% in BM1824 to 72.31% in BM1818, corresponding to an amplification failure of 0.77% and 27.69%, respectively. The quality of genotyping differed between microsatellite loci and varied from QI = 0.96 in TGLA53 and TGLA122 to QI = 1.00 in

BM2113 and BM1824. We identified the allelic dropout (ADO) in 2.35% of the estimated heterozygous genotypes with variations from 0.92% in TGLA227 to 5.80% in the SPS115 locus. Three loci (BM2113, BM1824, and ETH10) were free of ADO. We found false alleles (FAs) in six genotyped loci, whereby the FA rate varied from 0.78% in ETH10 to 2.13% in BM1818. Five loci (BM2113, INRA23, TGLA126, ETH225, and BM1824) were free of FAs. The error rate varied from 0.78% in ETH10 to 4.76% in TGLA122—an average of 2.32%. No genotyping errors were observed in the BM2113 and BM1824 loci. The probability values of correct genotyping (*p*) for each locus met the set threshold (*p* < 0.001) (Supplementary Materials, Table S3). Therefore, all studied loci that passed quality control were selected for further analysis.

Out of 145 modern specimens, the genotypes for all 11 loci were estimated for 136 samples, while for 8 and 1 samples the microsatellite genotypes were obtained for 10 and 9 loci, respectively (Supplementary Materials, Table S2b).
