Diverse mitogenomic variations contribute to population differentiation in Eurasian Tree Sparrows (Passer montanus)

Mitochondrial genomes play a crucial role in species adaptation to diverse evolutionary pressures. While positive selection in mitochondrial genes has sometimes been linked to extreme environmental adaptations, large-scale studies of mitogenomic evolution across diverse habitats remain limited. As one of the world’s most widely distributed birds, the Eurasian tree sparrow (<i>Passer montanus</i>) occupies variable habitats, making it an ideal model for studying environmental adaptations. Here, we examined the mitogenomic adaptations in tree sparrow populations across China. Our analyses revealed significant mitochondrial divergence in geographically isolated populations, particularly in southern Xizang on the Qinghai-Xizang Plateau, and the continental islands of Hainan and Taiwan. In southern Xizang, population-specific non-synonymous substitutions in COX2 and COX3 may enhance protein stability, reflecting potential responses to hypoxia and cold. In contrast, putative adaptive mutations in ATP6 (Hainan) and ND5 (Taiwan) may reduce the stability of their respective proteins. Additionally, population-specific changes in certain tRNAs in the Hainan population may increase their structural flexibility, potentially contributing to island-specific adaptation. These findings highlight the role of mitochondrial genomes in responding to ecological variation and geographic barriers, underscoring the prospective functional consequences of mitogenomic evolution.