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Broad-scale variation in human genetic diversity levels is predicted by purifying selection on coding and non-coding

David A Murphy1,2, Eyal Elyashiv1,3, Guy Amster1,4

  • 1Department of Biological Sciences, Columbia University, New York, United States.

Elife
|October 5, 2022
PubMed
Summary

Background selection, not selective sweeps, is the primary driver of human genetic diversity. This process, involving purifying selection against harmful mutations, significantly impacts genetic variation across autosomes.

Keywords:
Background selectionSelective sweepsdemographic historyevolutionary biologygeneticsgenomicshumanneutral diversitypositive selectionpurifying selection

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Area of Science:

  • Population genetics
  • Evolutionary biology
  • Human genomics

Background:

  • Genetic variation is shaped by natural selection acting on linked DNA sites.
  • The relative importance of selective sweeps (beneficial mutations) versus background selection (deleterious mutations) in humans is debated.

Purpose of the Study:

  • To determine the dominant mode of linked selection shaping human genetic diversity.
  • To quantify the contributions of background selection and selective sweeps to neutral genetic variation in humans.

Main Methods:

  • Analysis of autosomal polymorphism data from the 1000 Genomes Project.
  • Statistical modeling to jointly assess the effects of background selection and selective sweeps.
  • Controlling for genomic mutation rate variation.

Main Results:

  • Background selection alone explains approximately 60% of the variance in human genetic diversity at megabase scales.
  • Incorporating selective sweeps did not improve the model's fit; they appear to have minimal impact on linked neutral diversity.
  • Phylogenetic conservation accurately predicts regions under purifying selection, with most deleterious mutations occurring in non-exonic regions.

Conclusions:

  • Background selection is the predominant form of linked selection influencing human genetic diversity.
  • Purifying selection against deleterious mutations has a substantial and widespread effect on human autosomes.