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Reply to: Existing methods are effective at measuring natural selection on gene expression

The Original Article was published on 07 November 2022

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References

  1. Fraser, H. B. Existing methods are effective at measuring natural selection on gene expression. Nat. Ecol. Evol. https://doi.org/10.1038/s41559-022-01889-7 (2022).

  2. Price, P. D. et al. Detecting signatures of selection on gene expression. Nat. Ecol. Evol. 6, 1035–1045 (2022).

    Article  PubMed  Google Scholar 

  3. Lüpold, S., Linz, G. M., Rivers, J. W., Westneat, D. F. & Birkhead, T. R. Sperm competition selects beyond relative testes size in birds. Evolution 63, 391–402 (2009).

    Article  PubMed  Google Scholar 

  4. Montgomery, S. H. & Merrill, R. M. Divergence in brain composition during the early stages of ecological specialization in Heliconius butterflies. J. Evol. Biol. 30, 571–582 (2017).

    Article  CAS  PubMed  Google Scholar 

  5. Firman, R. C. et al. Evolutionary change in testes tissue composition among experimental populations of house mice. Evolution 69, 848–855 (2015).

    Article  PubMed  Google Scholar 

  6. Kaskan, P. M. et al. Peripheral variability and central constancy in mammalian visual system evolution. Proc. Biol. Sci. 272, 91–100 (2005).

    PubMed  PubMed Central  Google Scholar 

  7. Mank, J. E. & Rideout, E. J. Developmental mechanisms of sex differences: from cells to organisms. Development 148, dev199750 (2021).

    Article  CAS  PubMed  Google Scholar 

  8. Khan, Z. et al. Primate transcript and protein expression levels evolve under compensatory selection pressures. Science 342, 1100–1104 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Gokhman, D. et al. Human–chimpanzee fused cells reveal cis-regulatory divergence underlying skeletal evolution. Nat. Genet. 53, 467–476 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Agoglia, R. M. et al. Primate cell fusion disentangles gene regulatory divergence in neurodevelopment. Nature 592, 421–427 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Orr, H. A. Testing natural selection vs. genetic drift in phenotypic evolution using quantitative trait locus data. Genetics 149, 2099–2104 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Fraser, H. B., Moses, A. M. & Schadt, E. E. Evidence for widespread adaptive evolution of gene expression in budding yeast. Proc. Natl Acad. Sci. USA 107, 2977–2982 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Fraser, H. B. Genome‐wide approaches to the study of adaptive gene expression evolution: systematic studies of evolutionary adaptations involving gene expression will allow many fundamental questions in evolutionary biology to be addressed. Bioessays 33, 469–477 (2011).

    Article  CAS  PubMed  Google Scholar 

  14. Tirosh, I., Reikhav, S., Levy, A. A. & Barkai, N. A yeast hybrid provides insight into the evolution of gene expression regulation. Science 324, 659–662 (2009).

    Article  CAS  PubMed  Google Scholar 

  15. Singh-Babak, S. D., Babak, T., Fraser, H. B. & Johnson, A. D. Lineage-specific selection and the evolution of virulence in the Candida clade. Proc. Natl Acad. Sci. USA 118, e2016818118 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Naranjo, S. et al. Dissecting the genetic basis of a complex cis-regulatory adaptation. PLoS Genet. 11, e1005751 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  17. Fraser, H. B. et al. Systematic detection of polygenic cis-regulatory evolution. PLoS Genet. 7, e1002023 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Fraser, H. B. et al. Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity. Genome Res. 22, 1930–1939 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Correspondence to Peter D. Price or Alison E. Wright.

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Price, P.D., Palmer Droguett, D.H., Taylor, J.A. et al. Reply to: Existing methods are effective at measuring natural selection on gene expression. Nat Ecol Evol 6, 1838–1839 (2022). https://doi.org/10.1038/s41559-022-01916-7

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