Quantifying adaptive evolution and the effects of natural selection across the Norway spruce genome

• Published in: Molecular ecology 2023-10, Vol.32 (19), p.5288-5304
• Main Authors: Wang, Xi, Ingvarsson, Pär K.
• Format: Article
• Language: English
• Subjects: Balancing; balancing selection; Biochemistry and Molecular Biology; Biokemi och molekylärbiologi; Biological activity; Evolution & development; Evolutionary Biology; Evolutionsbiologi; Genetics; Genetik; Genomes; Genomics; Natural selection; negative selection; Picea abies; Pine trees; Population statistics; positive selection; Recombination; Statistical analysis; Trees; whole-genome re-sequencing
• ISSN: 0962-1083; 1365-294X; 1365-294X
• DOI: 10.1111/mec.17106

Detecting natural selection is one of the major goals of evolutionary genomics. Here, we sequenced the whole genome of 25 Picea abies individuals and quantified the amount of selection across the genome. Using an estimate of the distribution of fitness effects, we showed that both negative selection and the rate of positively selected substitutions are very limited in coding regions. We found a positive correlation between the rate of adaptive substitutions and recombination rate and a negative correlation between the rate of adaptive substitutions and gene density, suggesting a widespread influence from Hill–Robertson interference on the efficiency of protein adaptation in P. abies . Finally, the distinct population statistics between genomic regions under either positive or balancing selection with that under neutral regions indicated the impact of natural selection on the genomic architecture of Norway spruce. Further gene ontology enrichment analysis for genes located in regions identified as undergoing either positive or long‐term balancing selection also highlighted the specific molecular functions and biological processes that appear to be targets of selection in Norway spruce.