LAUSR

Understanding how populations diverge and new species arise is a central question in evolutionary biology. “Allopatric” divergence through geographical isolation is considered to be the commonest mechanism generating species biodiversity in mountain ecosystems. However, the underlying genomic dynamics, especially genomic islands of elevated divergence and genes that are highly diverged as a result of lineage‐specific selection, remain poorly understood. Stellera chamaejasme has a wide geographical range across the Qinghai–Tibet Plateau and northern China, making it a good model with which to explore genomic divergence during speciation in mountain ecosystems. We assembled a high‐quality, chromosome‐level genome for this species and resequenced the genomes of 24 populations across its major distribution. Our population genomic analyses recovered four distinct genetic lineages corresponding to geographical distributions with contrasting environments. However, we revealed continuous gene flow during the historical divergences of these four lineages. Interlineage hybrids and plastome introgressions were frequently found in regions of contact, which further increased gene flow between two contacting lineages in the recent past. The elevated divergences were highly heterogeneous across the genome and selection of ancestral polymorphisims and divergence hitchhiking contributed greatly to the formation of genomic islands. The highly diverged and lineage‐specific positively selected genes within and outside genomic islands were annotated to be mainly involved in local adaptation. Our results suggest that genomic divergence in S. chamaejasme is likely to have been triggered and maintained by local selection together with geographical isolation.