Drivers of intraspecific differentiation of the alpine cold tolerant herb Notopterygium oviforme: the roles of isolation by distance and ecological factors

Determining the driver mechanisms of phenotypic and genetic divergence of
species have long been the central topic in evolutionary biology. However,
the relative roles of isolation by distance (IBD) and environment factors
in contributing to species divergence is largely undetermined in perennial
herbs in East Asia. In this study, we collected population genetic samples
of a cold-tolerant perennial herb Notopterygium oviforme in central China.
We integrated the population transcriptomes, whole chloroplast genomes,
genotyping-by-sequencing, microsatellite markers and ecological
environment factors to determine the relative contributions of geography,
climatic and soil factors on genetic, chemical and phenotypic trait
divergence. The clearly genetic distinction was identified between the
west Qinling (WQ) and east Qinling Mountains (EQ) geographical groups
within N. oviforme. Interestingly, the two groups have existed the
obviously niche conservatism, which might have caused the similarity of
most leaf functional traits. Multiple matrix regression with randomization
analysis showed that the spatial pattern of intraspecific divergence
mainly resulted from effect of IBD, not isolation by environment.
Meanwhile, transcriptomic expression divergence and some ecological
factors have played the key roles in differentiation of intraspecific
lineage. Approximate Bayesian Computation showed that both lineages have
experienced the historically population expansion, and the recent range
contraction. Molecular dating suggested that the intraspecific divergence
was closely associated with the dramatically uplifts of the Qinling
Mountains in East Asia. These results demonstrated that the geography,
geological and environmental factors together shaped the cryptic
intraspecific diversification and population dynamics shifts of perennial
cold tolerant herb.