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Globally Relaxed Selection and Local Adaptation in Boechera stricta.

Publication ,  Journal Article
Liang, Y-Y; Chen, X-Y; Zhou, B-F; Mitchell-Olds, T; Wang, B
Published in: Genome biology and evolution
April 2022

The strength of selection varies among populations and across the genome, but the determinants of efficacy of selection remain unclear. In this study, we used whole-genome sequencing data from 467 Boechera stricta accessions to quantify the strength of selection and characterize the pattern of local adaptation. We found low genetic diversity on 0-fold degenerate sites and conserved non-coding sites, indicating functional constraints on these regions. The estimated distribution of fitness effects and the proportion of fixed substitutions suggest relaxed negative and positive selection in B. stricta. Among the four population groups, the NOR and WES groups have smaller effective population size (Ne), higher proportions of effectively neutral sites, and lower rates of adaptive evolution compared with UTA and COL groups, reflecting the effect of Ne on the efficacy of natural selection. We also found weaker selection on GC-biased sites compared with GC-conservative (unbiased) sites, suggested that GC-biased gene conversion has affected the strength of selection in B. stricta. We found mixed evidence for the role of the recombination rate on the efficacy of selection. The positive and negative selection was stronger in high-recombination regions compared with low-recombination regions in COL but not in other groups. By scanning the genome, we found different subsets of selected genes suggesting differential adaptation among B. stricta groups. These results show that differences in effective population size, nucleotide composition, and recombination rate are important determinants of the efficacy of selection. This study enriches our understanding of the roles of natural selection and local adaptation in shaping genomic variation.

Duke Scholars

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Published In

Genome biology and evolution

DOI

EISSN

1759-6653

ISSN

1759-6653

Publication Date

April 2022

Volume

14

Issue

4

Start / End Page

evac043

Related Subject Headings

  • Selection, Genetic
  • Genomics
  • Genome
  • Gene Conversion
  • Evolution, Molecular
  • Developmental Biology
  • Brassicaceae
  • 3105 Genetics
  • 3104 Evolutionary biology
  • 3101 Biochemistry and cell biology
 

Citation

APA
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ICMJE
MLA
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Liang, Y.-Y., Chen, X.-Y., Zhou, B.-F., Mitchell-Olds, T., & Wang, B. (2022). Globally Relaxed Selection and Local Adaptation in Boechera stricta. Genome Biology and Evolution, 14(4), evac043. https://doi.org/10.1093/gbe/evac043
Liang, Yi-Ye, Xue-Yan Chen, Biao-Feng Zhou, Thomas Mitchell-Olds, and Baosheng Wang. “Globally Relaxed Selection and Local Adaptation in Boechera stricta.Genome Biology and Evolution 14, no. 4 (April 2022): evac043. https://doi.org/10.1093/gbe/evac043.
Liang Y-Y, Chen X-Y, Zhou B-F, Mitchell-Olds T, Wang B. Globally Relaxed Selection and Local Adaptation in Boechera stricta. Genome biology and evolution. 2022 Apr;14(4):evac043.
Liang, Yi-Ye, et al. “Globally Relaxed Selection and Local Adaptation in Boechera stricta.Genome Biology and Evolution, vol. 14, no. 4, Apr. 2022, p. evac043. Epmc, doi:10.1093/gbe/evac043.
Liang Y-Y, Chen X-Y, Zhou B-F, Mitchell-Olds T, Wang B. Globally Relaxed Selection and Local Adaptation in Boechera stricta. Genome biology and evolution. 2022 Apr;14(4):evac043.
Journal cover image

Published In

Genome biology and evolution

DOI

EISSN

1759-6653

ISSN

1759-6653

Publication Date

April 2022

Volume

14

Issue

4

Start / End Page

evac043

Related Subject Headings

  • Selection, Genetic
  • Genomics
  • Genome
  • Gene Conversion
  • Evolution, Molecular
  • Developmental Biology
  • Brassicaceae
  • 3105 Genetics
  • 3104 Evolutionary biology
  • 3101 Biochemistry and cell biology