Species are the constituent units of ecosystems, and even species that have severe conflicts with humans play irreplaceable and important roles in maintaining ecosystem stability. Spermophilus dauricus has long been considered a harmful animal because of its ability to damage grasslands and agriculture, as well as its status as a primary host of Yersinia pestis . Consequently, it has been subject to eradication areas in human activity areas, which may lead to a reduction in its genetic diversity. Genetic diversity is the core foundation for maintaining species continuity, yet this is precisely the aspect lacking in research on S. dauricus . In this study, we performed mitochondrial genome sequencing of 73 individuals sampled across an extensive geographic region of S. dauricus and conducted population genetic and species distribution model analyses. The results revealed that S. dauricus is primarily distributed in three fragmented yet connected regions: the Northeast China Plain distribution area, the Hulunbuir Plateau distribution area, and the Bashang Plateau distribution area. Populations across these three present regions exhibit genetic differences but do not display subspecific relationships. The populations in the Hulunbuir Plateau and Bashang Plateau likely originated from the population in the Northeast Plain. Furthermore, all three populations of S. dauricus have experienced a continuous population decline in the past few thousand years, which we hypothesize may be related to the development of human rice cultivation and nomadism over the past few thousand years. This study highlights the role of human production activities in the decline of the effective population of rodents.

The Daurian ground squirrel (Spermophilus dauricus) is an important animal model that is frequently used by researchers studying the physiological ecology of hibernation in China. There has been considerable controversy regarding the classification of its subspecies, and there is a lack of relevant comparisons of morphometric data. To clarify this issue, this study aims to systematically compare five external morphological traits and 20 cranial traits of S. dauricus collected from 10 locations within China to assess the phenotypic differentiation of S. dauricus within China. Through morphological cluster analysis (MCA), discriminant function analysis (DFA), and principal component analysis (PCA), the samples from 10 locations (FK, n = 5; JZ, n = 11; DQ, n = 7; KP, n = 6; HEB, n = 4; EE, n = 10; CF, n = 3; ZB, n = 6; CD, n = 8; WL, n = 7) can be divided into three geographical populations: the Northeast population (NE); the Inner Mongolia population (IM); and the Hebei population (HB). There is significant morphological variation in four external traits and 19 cranial traits among populations within the species. Specifically, the NE population presented greater body length, tail length, and cranial dimensions. The IM population has the shortest tail, whereas the HB population has the smallest overall body size—its tail length, however, falls between those of the NE and IM populations. These morphological differences may be related to differences in habitat. This study revealed a significant correlation between environmental factors and the morphological traits of S. dauricus. Redundancy analysis (RDA) further revealed that the mean annual temperature (MAT) and mean annual precipitation (MAP) significantly affected the morphological traits of S. dauricus. This study challenges the current subspecies classification, clarifies the geographical morphological variation pattern of S. dauricus, reveals the influence of the environment on the differentiation of its morphological traits, and provides new morphological evidence for resolving the controversy over its subspecies classification.