Genomic analysis of ancient wild animal remains is of not only great significance for the conservation and utilization of genetic resources of wild animal species but also crucial for helping us understand the diet compositions and hunting activities of ancient human beings as well as their social-economic development patterns. Ancient DNA technology has been widely employed in archaeological research. Among its numerous strengths, its potential to decipher the genetic information carried by biological samples at the molecular level has been widely acknowledged, and many researchers have utilized ancient DNA analysis to distinguish between domestic and wild animals. Moreover, when combined with historical and archaeological evidence, it offers us robust scientific and technological support, enabling us to comprehensively understand ancient human societies, including their origins and evolutionary processes.

In this study, the ancient DNA of nine animal samples, which were excavated from the Changning, Mogou, Quanhucun, and Dashigou sites in Northwest China and morphologically identified as either “sheep” or “goats”, was investigated using ancient DNA technology. Ancient DNA extraction, library construction, and high-throughput sequencing were carried out, and the mitochondrial genome sequences of the nine samples were successfully obtained. Alignment analysis was performed between the genomic sequences of these samples and the 146 mitochondrial genomic sequences of Cervidae and Bovidae (used as reference data). The results of the alignment analysis indicated that these nine samples were identified as belonging to four different wild animal species within the families of Cervidae and Bovidae: the Siberian roe deer (Capreolus pygargus) of the genus Capreolus within the subfamily Odocoileinae; the Przewalski’s gazelle (Procapra przewalskii) and Tibetan gazelle (Procapra picticaudata) of the genus Procapra within the subfamily Antilopinae; and the Sumatran serow (Capricornis sumatraensis) of the genus Capricornis within the subfamily Caprinae.

Two phylogenetic analyses were conducted on the mitochondrial genome data extracted from the Odocoileinae, Caprinae, and Antilopinae subfamilies. Bayesian phylogenetic trees and Maximum Likelihood phylogenetic trees were constructed. It was demonstrated that each of the nine samples clustered with the corresponding species identified by the alignment analysis, which was consistent with the results of the principal component analysis on the same data set, where the nine samples were assigned to the corresponding species identified in the alignment analysis. Genetic distance calculations between individuals based on ancient and modern samples revealed that each of the nine samples was genetically closest to the specific species identified.

All of the above results emphasize that ancient DNA technology can overcome the limitations of morphological methods in the species identification of ancient animals. Considering other wild animal bone remains excavated from the four sites, it can be concluded that the ancient people in prehistoric Northwest China used wild animals as a supplement to domestic animal resources for food, sacrificial offerings, and bone tool manufacture. This study is of great significance as it provides new evidence at the molecular level and corroborates the findings of previous archaeological research on animals in prehistoric times.