New progress on linked selection shapes the landscape of genomic variation

How evolutionary forces shape patterns of genetic diversity within species and divergence between species is a fundamental question in evolutionary biology. The neutral theory of molecular evolution states that most polymorphisms within species are generally neutral and under mutation-drift equilibrium, and divergence between species is due to the accumulation of neutral substitutions rather than adaptation. Recent studies in population genomics have revealed widespread signatures of selection in many species, indicating that genomic landscapes are predominantly influenced by natural selection. Although the importance of selection in shaping genomic variation is clearly established, quantifying the efficacy of selection and elucidating the relative contribution of different selection models remain challenging.

Yi-Ye Liang (PhD student) and Professor Baosheng Wang from SCBG investigated how linked selection shaping genomic variation in oak species. By sequencing whole genomes of 101 individuals of three closely related oak species, they estimated that theses species diverged around the late Neogene and experienced a bottleneck during the Pleistocene. Based on population genetic inferences from the site frequency spectrum and ancestral recombination graph, they revealed that genomic regions with elevated differentiation were formed by selective sweeps. They also found extensive positive selection; the fixation of adaptive mutations and reduction neutral diversity around substitutions generated a signature of selective sweeps. Prevalent negative selection and background selection have reduced genetic diversity in both genic and intergenic regions and contributed substantially to the baseline variation in genetic diversity. These results demonstrate the importance of linked selection in shaping genomic variation, and illustrate how the extent and strength of different selection models vary across the genome.

This stuyd was supported by the Guangdong Natural Science Funds for Distinguished Young Scholar and the NSFC to Baosheng Wang. The research article was published online in New Phytologist, titled “Linked selection shapes the landscape of genomic variation in three oak species”, for details see https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.17793

Fig.1 Genome-wide differentiation among the three oak species.