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

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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Figure 1: Illustration demonstrating fNM potential compensation and possible adaptation in a protein-coding gene.
Figure 2: Prevalence assessment of potential compensation for fNMs in amniotes.
Figure 3: Analysis of shared non-compensated fRNMs between all possible tree branches.

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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.

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Correspondence to Dan Mishmar.

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Supplementary information

Supplementary Information

Supplementary Figures 1–5; supplementary Tables 1–4 (PDF 1434 kb)

Supplementary Dataset 1

Nodal mutations identified in mtDNA tRNAs genes, mtDNA rRNAs genes and nodal mutations identified in mtDNA protein coding genes. (XLSX 3372 kb)

Supplementary Dataset 2

Nodal mutations identified in nDNA-encoded protein genes. (XLSX 16633 kb)

Supplementary Dataset 3

MATLAB scripts generated for the analysis presented in this Article. (ZIP 3831 kb)

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Levin, L., Mishmar, D. The genomic landscape of evolutionary convergence in mammals, birds and reptiles. Nat Ecol Evol 1, 0041 (2017). https://doi.org/10.1038/s41559-016-0041

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