Abstract
<title>Abstract</title> <p> High-altitude environments, characterized by low partial oxygen pressure, low temperatures, and elevated UV radiation, impose selective pressures that can shape physiological and molecular adaptation in small mammals. One pathway involves positive selection on mitochondrial genes encoding proteins of the oxidative phosphorylation (OXPHOS) system, which are linked to cellular respiration, energy metabolism, and hypoxia tolerance. In this study, we tested whether adaptation to elevational zones in nine endemic Ethiopian <italic>Lophuromys</italic> rat species is reflected in mitogenomic selection patterns. Complete mitochondrial genomes were analyzed to assess the type and intensity of selection on 12 mitochondrial protein-coding genes. Our results revealed that purifying selection was the dominant evolutionary force, maintaining the structural and functional integrity of mitochondrial proteins. Signals of positive selection were rare, lineage-specific, and showed a tendency to accumulate in species living at high altitude and in high-elevation-associated mitochondrial lineages. Radical amino acid substitutions affecting key physicochemical properties were unevenly distributed, but several occurred in high-elevation-associated mitochondrial backgrounds. Introgressed mitochondrial DNA variants lacked consistent signatures of positive selection or shared radical amino acid substitutions in OXPHOS genes, suggesting that their spread is unlikely to represent classic adaptive introgression and may instead reflect demographic processes, genetic drift, and possible replacement of eroded mitogenomes. These findings indicate that the radiation of <italic>Lophuromys</italic> across the Ethiopian Highlands occurred with limited lineage-specific positive selection on mitochondrial protein-coding genes. Instead, adaptation to hypoxic and thermally challenging environments likely involved a combination of localized mitochondrial changes and alternative physiological or regulatory mechanisms, while purifying selection preserved mitochondrial function. </p>