How populations diverge into different lineages is a central issue in
evolutionary biology. Despite the increasing evidence indicating that
such divergences do not need geographic isolation, numerous phenotypic
differentiations show a distributional correspondence. In addition, gene
flow has been widely detected during and through such diverging
processes. We used one widely distributed Aquilegia viridiflora complex
as a model system to examine genomic differentiation and corresponding
phenotypic variations along geographic gradients. Our phenotypic
analyses of 90 individuals from 20 populations from northwest to
northeast China identified two phenotypic groups along the geographic
cline. All examined traits are distinct between them although a few
intermediate individuals occur in their contacting regions. We further
sequenced the genomes of the representative individuals of each
population. However, we recovered four distinct genetic lineages based
on both nuclear genomes and plastomes that were different from
phenotypic differentiation. In particular, we recovered numerous genetic
hybrids in the contact regions of four lineages. Gene flow is widespread
and continuous between four lineages but much higher between contacting
lineages than geographically isolated lineages. In addition, many genes
with fast lineage-specific mutations were identified to be involved in
local adaptation. Our results suggest that both geographic isolation and
local selection exerted by the environment may together create
geographic distributions of phenotypic variations as well as the
underlying genomic divergences in numerous lineages.