Article

The genomic landscape of evolutionary convergence in mammals, birds and reptiles

  • Nature Ecology & Evolution volume 1, Article number: 0041 (2017)
  • doi:10.1038/s41559-016-0041
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Abstract

Many lineage-defining (nodal) mutations possess high functionality. However, differentiating adaptive nodal mutations from those that are functionally compensated remains challenging. To address this challenge, we identified functional nodal mutations (fNMs) in ~3,400 nuclear DNA (nDNA) and 4 mitochondrial DNA (mtDNA) protein structures from 91 and 1,003 species, respectively, representing the entire mammalian, bird and reptile phylogeny. A screen for candidate compensatory mutations among co-occurring amino acid changes in close structural proximity revealed that such compensated fNMs encompass 37% and 27% of the mtDNA and nDNA datasets, respectively. Analysis of the remaining (non-compensated) mutations, which are enriched for adaptive mutations, showed that birds and mammals share most such recurrent fNMs (N = 51). Among the latter, we discovered mutations in thermoregulation-related genes. These represent the best candidates to explain the molecular basis of convergent body thermoregulation in birds and mammals. Our analysis reveals the landscape of possible mutational compensation and convergence in amniote phylogeny.

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Acknowledgements

We thank R. Zarivach for critical discussions and the Negev Foundation for a Scholarship of Excellence awarded to L.L. This study was funded by research grants from the Israeli Science Foundation (610/12), Binational Science Foundation and a US Army Life Science division grant 67993LS awarded to D.M.

Author information

Affiliations

  1. Department of Life Sciences, Building 40, Room 009, Ben Gurion University of the Negev, Beer-Sheva, Israel 8410501

    • Liron Levin
    •  & Dan Mishmar

Authors

  1. Search for Liron Levin in:

  2. Search for Dan Mishmar in:

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Dan Mishmar.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    Supplementary Figures 1–5; supplementary Tables 1–4

Excel files

  1. 1.

    Supplementary Dataset 1

    Nodal mutations identified in mtDNA tRNAs genes, mtDNA rRNAs genes and nodal mutations identified in mtDNA protein coding genes.

  2. 2.

    Supplementary Dataset 2

    Nodal mutations identified in nDNA-encoded protein genes.

Zip files

  1. 1.

    Supplementary Dataset 3

    MATLAB scripts generated for the analysis presented in this Article.