Data from: Genetic diversity and evolutionary history of four closely related Aquilegia species revealed by ten nuclear gene fragments

Recently the genus Aquilegia is emerging as the new model system for plant development, ecology and evolution studies. Previous researches demonstrated that pollinator shift might drive the diversification of North American Aquilegia species and natural selection on the length of spur might play a crucial role. In this genus, A. ecalcarata is the only taxon which has lost spur and nectar on the petal. Previous phylogenetic result indicated that A. ecalcarata, A. yabeana, A. oxysepala var. kansuensis and A. rockii comprised a monophyletic group. However, the genetic diversity pattern of them remains unknown. Besides, little is known about the evolutionary relationship among the four species on population level. Here we carried out a population genetics study with 21 representative populations based on 10 single-copy nuclear gene fragments and found out: 1) A. yabeana conserved the highest genetic diversity (both πsil and θsil) while A. oxysepala var. kansuensis had the lowest level; 2) A. ecalcarata splitted into two groups with one population clustered with A. rockii and the rest five populations clustered with A. oxysepala var. kansuensis; 3) allele frequency spectrum showed an excess of low frequency alleles in all four species, implying that they may undergo the mutation-drift equilibrium. Our findings provide the first investigation of genetic diversity and evolutionary relationship in A. yabeana, A. oxysepala var. kansuensis, A. rockii, A. ecalcarata, and lay foundation for future evolutionary studies like speciation mediated by pollinators.