Journal
NEW PHYTOLOGIST
Volume 233, Issue 1, Pages 555-568Publisher
WILEY
DOI: 10.1111/nph.17793
Keywords
ancestral recombination graph; background selection; genomic variation; linked selection; Quercus; recombination rate; selective sweeps
Categories
Funding
- Guangdong Natural Science Funds for Distinguished Young Scholar [2018B030306040]
- National Natural Science Foundation of China [NSFC 31971673, 31901325]
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Natural selection plays a key role in shaping genetic diversity within and between species, with selective sweeps and background selection influencing genomic variation. Results from studying oak species genomes show the impact of different types of selection models and the importance of linked selection in shaping genetic diversity.
Natural selection shapes genome-wide patterns of diversity within species and divergence between species. However, quantifying the efficacy of selection and elucidating the relative importance of different types of selection in shaping genomic variation remain challenging. We sequenced whole genomes of 101 individuals of three closely related oak species to track the divergence history, and to dissect the impacts of selective sweeps and background selection on patterns of genomic variation. We estimated that the three species diverged around the late Neogene and experienced a bottleneck during the Pleistocene. We detected genomic regions with elevated relative differentiation ('F-ST-islands'). Population genetic inferences from the site frequency spectrum and ancestral recombination graph indicated that F-ST-islands were formed by selective sweeps. We 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. Our 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.
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