Molecular identification and phylogenetic analysis of marmots in the Xinjiang's Altai Mountains, a newly discovered plague focus of China.

The Altai Mountains in Xinjiang have been recognized as a new plague focus in China since 2023. Although previous morphological studies suggested that marmots in this region belong to Marmota baibacina, this classification remained unconfirmed at the molecular level. In this study, 37 marmot samples were collected: including 10 M. baibacina from the northern Tianshan Mountains, 9 M. baibacina from the southern Tianshan Mountains, and 18 unverified individuals from the Altai Mountains. The COI, Cytb, and D-loop gene fragments were sequenced and subjected to phylogenetic analysis. Homology comparisons revealed greater than 95% sequence identity across all samples, with all matches corresponding to marmot populations. Genetic distances between groups (1%-7%) exceeded those within groups (0%-2%). F st values among populations ranged from 0.55780 to 0.98449, indicating significant differentiation, particularly between the southern Tianshan population and the other two groups. In contrast, genetic divergence between the Altai and northern Tianshan populations was minimal. Maximum likelihood trees based on COI and Cytb sequences strongly supported a close phylogenetic relationship between the northern Tianshan and Altai marmots, which clustered together, while the southern Tianshan population formed a separate clade. The D-loop region provided lower phylogenetic resolution. Based on these results, we confirm that the marmots in the Altai Mountains belong to M. baibacina and classify this plague focus as a M. baibacina-Spermophilus undulatus focus, given that S. undulatus is also a documented reservoir host in the area. These findings provide a molecular basis for targeted plague surveillance and control. The close genetic affinity between the northern Tianshan and Altai populations further suggests they may represent the same subspecies.