Genomic divergence between two sister Medicago species triggered by the Quaternary climatic oscillations in the Qinghai-Tibet Plateau and northern China.

Abstract

Speciation is a central topic in evolutionary biology. However, it remains poorly understood of how genomic divergence originated and accumulatedin the face of gene flow during ecological adaptation. Closely related species that have adapted to distinct environments but inhabit some overlapping ranges provide an ideal system to evaluate this issue.Here, we combine population genomics and species distribution models (SDMs) to examine genomic divergences between two sister species, Medicago ruthenicaand M. archiducis-nicolai, that occur in northern China and the northeast Qinghai-Tibet Plateau (QTP), respectively, with overlapping distribution in the border of the two regions.Medicago ruthenicaand M. archiducis-nicolai are well-delimited based on population genomic data, although hybrids exist in sympatric sampling locations. Coalescent simulations and SDMs suggest that the two species diverged from each other in the Quaternary but have been in continuous contact with gene flow occurring between the two species ever since. We also discovered positive selection signatures associated with genes both outside and within genomic islands in both species that are likely involved in adaptations to arid and high-altitude environments. Our findings provide insights into how natural selection and climatic changes in the Quaternary initiated and maintained interspecific divergence of the two sister species.