Known as the’third polar region’,the Qinghai-Tibet Plateau represents one of the harshest highland environments in the world and yet a number of organisms thrive there.Previous studies of birds,animals and humans have focused on well-differentiated populations in later stages ofphenotypic divergence.The adaptive processes during the initial phase of highland adaptation remain poorly understood.We studied a human commensal,the Eurasian Tree Sparrow,which has followed human agriculture to the Qinghai-Tibet Plateau.Despite strong phenotypic differentiation at multiple levels,in particular in muscle-related phenotypes,highland and lowland populations show shallow genomic divergence and the colonization event occurred within the past few thousand years.In a one-month acclimation experiment investigating phenotypic plasticity,we exposed adult lowland tree sparrows to a hypoxic environment and did not observe muscle changes.Through population genetic analyses,we identified a signature ofpolygenic adaptation,whereby shifts in allele frequencies are spread across multiple loci,many of which are associated with muscle-related processes.Our results reveal a case of positive selection in which polygenic adaptation appears to drive rapid phenotypic evolution,shedding light on early stages of adaptive evolution to a novel environment.