Genome and transcriptome variation in Aquilegia viridiflora underlies the adaptive evolution to the environment in the early stage of speciation

The elucidation of adaptive evolution mechanisms in the early stage of speciation is important for understanding the origin and evolution of species. Aquilegia viridiflora is in the early stage of speciation, has a wide distribution range, and shows obvious phenotypic variation among its different populations. In this study, to analyze the adaptive evolution mechanism of phenotypic differences in the early stages of speciation, we analyzed the phenotypes, genomes, and transcriptomes of different populations of A. viridiflora. Our results indicated that A. viridiflora originated in northwestern China, and the uplift of the northeastern Qinghai--Tibet Plateau in the late Miocene may have caused its differentiation. Aqcoe5G459400 was a key gene in the early stage of A. viridiflora speciation. Its expression was reduced in environments with large temperature differences between day and night, causing A. viridiflora to develop larger flowers and enhancing its attractiveness to pollinators. Our research revealed the genetic basis of the adaptive evolution of the phenotype in the early stage of speciation and provides new evidence of the pattern of speciation via adaptative radiation in columbine.