Data from: Historical connectivity, contemporary isolation, and local adaptation in a widespread but discontinuously distributed species, Rhododendron oldhamii, endemic to Taiwan

Elucidation of the evolutionary processes that constrain or facilitate
adaptive divergence is a central goal in evolutionary biology, especially
in non-model organisms. We tested whether changes in dynamics of gene flow
(historical vs contemporary) caused population isolation and examined
local adaptation in response to environmental selective forces in
fragmented Rhododendron oldhamii populations. Variation in 26 expressed
sequence tag-simple sequence repeat loci from 18 populations in Taiwan was
investigated by examining patterns of genetic diversity, inbreeding,
geographic structure, recent bottlenecks, and historical and contemporary
gene flow. Selection associated with environmental variables was also
examined. Bayesian clustering analysis revealed four regional population
groups of north, central, south and southeast with significant genetic
differentiation. Historical bottlenecks beginning 9168–13,092 years ago
and ending 1584–3504 years ago were revealed by estimates using
approximate Bayesian computation for all four regional samples analyzed.
Recent migration within and across geographic regions was limited.
However, major dispersal sources were found within geographic regions.
Altitudinal clines of allelic frequencies of environmentally associated
positively selected outliers were found, indicating adaptive divergence.
Our results point to a transition from historical population connectivity
toward contemporary population isolation and divergence on a regional
scale. Spatial and temporal dispersal differences may have resulted in
regional population divergence and local adaptation associated with
environmental variables, which may have played roles as selective forces
at a regional scale.