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Gene expression drives the evolution of dominance

Christian D. Huber, Arun Durvasula, Angela M. Hancock and 1 more

Nature Communications · 2018

doi:10.1101/182865

Abstract

Dominance is a fundamental concept in molecular genetics and has implications for understanding patterns of genetic variation, evolution, and complex traits. However, despite its importance, the degree of dominance in natural populations is poorly quantified. Here, we leverage multiple mating systems in natural populations of Arabidopsis to co-estimate the distribution of fitness effects and dominance coefficients of new amino acid changing mutations. We find that more deleterious mutations are more likely to be recessive than less deleterious mutations. Further, this pattern holds across gene categories, but varies with the connectivity and expression patterns of genes. Our work argues that dominance arises as a consequence of the functional importance of genes and their optimal expression levels.

References 47

  1. 1.

    Henn BM, Botigué LR, Bustamante CD, Clark AG, Gravel S. Estimating the mutation load in human genomes. Nat. Rev. Genet. 2015;16:333-343.

    Not in our library10.1038/nrg3931

  2. 2.

    Simons YB, Sella G. The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives. Curr. Opin. Genet. Dev. 2016;41:150-158.

    Not in our library10.1016/j.gde.2016.09.006

  3. 3.

    Teshima KM, Przeworski M. Directional positive selection on an allele of arbitrary dominance. Genetics. 2006;172:713-718.

    Not in our library10.1534/genetics.105.044065

  4. 4.

    Sanjak JS, Long AD, Thornton KR. A Model of compound heterozygous, loss-of-function alleles is broadly consistent with observations from complex-disease GWAS datasets. PLoS Genet. 2017;13:e1006573.

    Not in our library10.1371/journal.pgen.1006573

  5. 5.

    Fisher RA. The possible modification of the response of the wild type to recurrent mutations. Am. Nat. 1928;62:115-126.

    Not in our library10.1086/280193

  6. 6.

    Wright S. Fisher’s theory of dominance. Am. Nat. 1929;63:274-279.

    Not in our library10.1086/280260

  7. 7.

    Kacser H, Burns JA. The molecular basis of dominance. Genetics. 1981;97:639-666.

    Not in our library10.1093/genetics/97.3-4.639

  8. 8.

    Haldane JBS. A note on Fisher’s theory of the origin of dominance, and on a correlation between dominance and linkage. Am. Nat. 1930;64:87-90.

    Not in our library10.1086/280299

  9. 9.

    Hurst LD, Randerson JP. Dosage, deletions and dominance: simple models of the evolution of gene expression. J. Theor. Biol. 2000;205:641-647.

    Not in our library10.1006/jtbi.2000.2095

  10. 10.

    Charlesworth B. Evidence against Fisher’s theory of dominance. Nature. 1979;278:848-849.

    Not in our library10.1038/278848a0

  11. 11.

    Mukai T, Chigusa SI, Mettler LE, Crow JF. Mutation rate and dominance of genes affecting viability in Drosophila melanogaster. Genetics. 1972;72:335-355.

    Not in our library10.1093/genetics/72.2.335

  12. 12.

    Simmons MJ, Crow JF. Mutations affecting fitness in Drosophila populations. Annu. Rev. Genet. 1977;11:49-78.

    Not in our library10.1146/annurev.ge.11.120177.000405

  13. 13.

    Phadnis N, Fry JD. Widespread correlations between dominance and homozygous effects of mutations: implications for theories of dominance. Genetics. 2005;171:385-392.

    Not in our library10.1534/genetics.104.039016

  14. 14.

    Williamson S, Fledel-Alon A, Bustamante CD. Population genetics of polymorphism and divergence for diploid selection models with arbitrary dominance. Genetics. 2004;168:463-475.

    Not in our library10.1534/genetics.103.024745

  15. 15.

    Balick DJ, Do R, Cassa CA, Reich D, Sunyaev SR. Dominance of deleterious alleles controls the response to a population bottleneck. PLoS Genet. 2015;11:e1005436.

    Not in our library10.1371/journal.pgen.1005436

  16. 16.

    Novikova PY, et al. Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism. Nat. Genet. 2016;48:1077-1082.

    Not in our library10.1038/ng.3617

  17. 17.

    Durvasula A, et al. African genomes illuminate the early history and transition to selfing in Arabidopsis thaliana. Proc. Natl Acad. Sci. 2017;114:5213-5218.

    Not in our library10.1073/pnas.1616736114

  18. 18.

    Williamson SH, et al. Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proc. Natl Acad. Sci. USA. 2005;102:7882-7887.

    Not in our library10.1073/pnas.0502300102

  19. 19.
  20. 20.

    Agrawal AF, Whitlock MC. Inferences about the distribution of dominance drawn from yeast gene knockout data. Genetics. 2011;187:553-566.

    Not in our library10.1534/genetics.110.124560

  21. 21.

    Manna F, Martin G, Lenormand T. Fitness landscapes: an alternative theory for the dominance of mutation. Genetics. 2011;189:923-937.

    Not in our library10.1534/genetics.111.132944

  22. 22.

    Frumkin I, et al. Gene architectures that minimize cost of gene expression. Mol. Cell. 2017;65:142-153.

    Not in our library10.1016/j.molcel.2016.11.007

  23. 23.

    Gao F, Luo H, Zhang CT, Zhang R. Gene essentiality analysis based on DEG 10, an updated database of essential genes. Methods Mol. Biol. 2015;1279:219-233.

    Not in our library10.1007/978-1-4939-2398-4_14

  24. 24.

    Bedford T, Hartl DL. Optimization of gene expression by natural selection. Proc. Natl Acad. Sci. USA. 2009;106:1133-1138.

    Not in our library10.1073/pnas.0812009106

  25. 25.

    Orr HA. A test of Fisher’s theory of dominance. Proc. Natl Acad. Sci. 1991;88:11413-11415.

    Not in our library10.1073/pnas.88.24.11413

  26. 26.

    Lamesch P, et al. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res. 2012;40:D1202-D1210.

    Not in our library10.1093/nar/gkr1090

  27. 27.

    Hu TT, et al. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat. Genet. 2011;43:476-481.

    Not in our library10.1038/ng.807

  28. 28.

    Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. Preprint at ArXiv13033997 Q-Bio (2013).

    Not in our library

  29. 29.

    DePristo MA, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 2011;43:491-498.

    Not in our library10.1038/ng.806

  30. 30.

    Cingolani P, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 2012;6:80-92.

    Not in our library10.4161/fly.19695

  31. 31.
  32. 32.

    Zheng X, et al. A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics. 2012;28:3326-3328.

    Not in our library10.1093/bioinformatics/bts606

  33. 33.

    Szklarczyk D, et al. The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible. Nucleic Acids Res. 2017;45:D362-D368.

    Not in our library10.1093/nar/gkw937

  34. 34.

    Kawakatsu T, et al. Epigenomic diversity in a global collection of Arabidopsis thaliana accessions. Cell. 2016;166:492-505.

    Not in our library10.1016/j.cell.2016.06.044

  35. 35.

    Shaw FH, Geyer CJ, Shaw RG. A comprehensive model of mutations affecting fitness and inferences for Arabidopsis thaliana. Evolution. 2002;56:453-463.

    Not in our library10.1111/j.0014-3820.2002.tb01358.x

  36. 36.

    Huber CD, Kim BY, Marsden CD, Lohmueller KE. Determining the factors driving selective effects of new nonsynonymous mutations. Proc. Natl Acad. Sci. 2017;114:4465-4470.

    Not in our library10.1073/pnas.1619508114

  37. 37.

    Gossmann TI, Keightley PD, Eyre-Walker A. The effect of variation in the effective population size on the rate of adaptive molecular evolution in eukaryotes. Genome Biol. Evol. 2012;4:658-667.

    Not in our library10.1093/gbe/evs027

  38. 38.

    Kim BY, Huber CD, Lohmueller KE. Inference of the distribution of selection coefficients for new nonsynonymous mutations using large samples. Genetics. 2017;206:345-361.

    Not in our library10.1534/genetics.116.197145

  39. 39.

    Press, W. H., Teukolsky, S. A., Vetterling, W. T. & Flannery, B. P. Numerical Recipes 3rd Edn: The Art of Scientific Computing (Cambridge University Press, New York, 2007).

    Not in our library

  40. 40.

    Ossowski S, et al. The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science. 2010;327:92-94.

    Not in our library10.1126/science.1180677

All 47 references

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