The genome information files of Stellera chamaejasme

AbstractUnderstanding how populations diverge and new species arise is a central questionin evolutionary biology. “Allopatric” divergence through geographical isolation is con?sidered to be the commonest mechanism generating species biodiversity in mountainecosystems. However, the underlying genomic dynamics, especially genomic islandsof elevated divergence and genes that are highly diverged as a result of lineage?specific selection, remain poorly understood. <i>Stellera chamaejasme</i> has a wide geo?graphical range across the Qinghai–Tibet Plateau and northern China, making it agood model with which to explore genomic divergence during speciation in mountainecosystems. We assembled a high-quality, chromosome-level genome for this speciesand resequenced the genomes of 24 populations across its major distribution. Ourpopulation genomic analyses recovered four distinct genetic lineages correspond?ing to geographical distributions with contrasting environments. However, we re?vealed continuous gene flow during the historical divergences of these four lineages.Interlineage hybrids and plastome introgressions were frequently found in regions ofcontact, which further increased gene flow between two contacting lineages in therecent past. The elevated divergences were highly heterogeneous across the genomeand selection of ancestral polymorphisims and divergence hitchhiking contributedgreatly to the formation of genomic islands. The highly diverged and lineage-specificpositively selected genes within and outside genomic islands were annotated to bemainly involved in local adaptation. Our results suggest that genomic divergence in<i>S. chamaejasme</i> is likely to have been triggered and maintained by local selection to?gether with geographical isolation.