Genomic divergence of Stellera chamaejasme through local selection across the Qinghai–Tibet plateau and northern China

Abstract

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.

Drivers of genomic landscapes of differentiation acrossPopulusdivergence gradient

“…Theory and empirical studies support the idea that these islands can form around loci underlying local adaptation and/or reproductive isolation (e.g. Tavares, et al 2018;McCulloch, et al 2020;Hu, et al 2022). Thus, delineating differentiation islands has recently become a major topic of research in the field of speciation and adaptation genomics (Burri 2017b;Martin and Jiggins 2017;Ravinet, et al 2018;Tavares, et al 2018;Stankowski, et al 2019).…”

Genomic divergence between two sister Ostrya species through linked selection and recombination

“…There were also obvious differences in the adaptations of O. japonica and O. chinensis to local environmental conditions. Although both the PSGs and CNDGs showed a significant overlapping with the identified islands, the overlap number was small suggesting the selection of non‐island regions may important during their divergence (Hu et al, 2022 ). The functions of PSGs and CNDGs were mainly related to plant development, responses to stimuli, and reproduction (Tables S8 and S11 ), which, being fundamental processes in a plant's life‐cycle, may have been responsible for the reproductive isolation of the two species.…”

Genomic divergence between two sister Medicago species triggered by the quaternary climatic oscillations on the Qinghai–Tibet plateau and northern China

“…Under the latter scenario, genomic islands derived from divergent selection with gene flow tend to be clustered together. Although numerous studies have revealed that divergent sorting of ancient polymorphism is the major mode in generating genomic islands (e.g., Han et al, 2017;Hu et al, 2022;Ke et al, 2022;Ma et al, 2018), the contribution of gene flow in generating the genomic islands could not be excluded here because of the continuous gene flow and both heterogeneous and clustered distribution of islands observed between the two species. In addition, we found decreased levels of genetic diversity, Tajima's D and recombination rates across genomic islands, and a strong association between islands of divergence and these selection signals (Table S5).…”