Letter | Published:

The genomic signature of dog domestication reveals adaptation to a starch-rich diet

Nature volume 495, pages 360364 (21 March 2013) | Download Citation

Abstract

The domestication of dogs was an important episode in the development of human civilization. The precise timing and location of this event is debated1,2,3,4,5 and little is known about the genetic changes that accompanied the transformation of ancient wolves into domestic dogs. Here we conduct whole-genome resequencing of dogs and wolves to identify 3.8 million genetic variants used to identify 36 genomic regions that probably represent targets for selection during dog domestication. Nineteen of these regions contain genes important in brain function, eight of which belong to nervous system development pathways and potentially underlie behavioural changes central to dog domestication6. Ten genes with key roles in starch digestion and fat metabolism also show signals of selection. We identify candidate mutations in key genes and provide functional support for an increased starch digestion in dogs relative to wolves. Our results indicate that novel adaptations allowing the early ancestors of modern dogs to thrive on a diet rich in starch, relative to the carnivorous diet of wolves, constituted a crucial step in the early domestication of dogs.

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Sequence Read Archive

Data deposits

Sequence reads are available under the accession number SRA061854 (NCBI Sequence Read Archive).

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Acknowledgements

We thank Järvzoo, Nordens ark and the Canine Biobank at Uppsala University and the Swedish University of Agricultural Sciences for providing samples, Uppsala Genomics Platform at SciLifeLab Uppsala for generating the resequencing data, the UPPNEX platform for assisting with computational infrastructure for data analysis and the Broad Institute Genomics Platform for validation genotyping. The project was funded by the SSF, the Swedish Research Council, the Swedish Research Council Formas, Uppsala University and a EURYI to K.L.-T. funded by the ESF supporting also E.A.; K.M. was funded by the Higher Education Commission, Pakistan.

Author information

Affiliations

  1. Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75237 Uppsala, Sweden

    • Erik Axelsson
    • , Abhirami Ratnakumar
    • , Maja-Louise Arendt
    • , Khurram Maqbool
    • , Matthew T. Webster
    •  & Kerstin Lindblad-Toh
  2. Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02139, USA

    • Michele Perloski
    •  & Kerstin Lindblad-Toh
  3. Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences, 73091 Riddarhyttan, Sweden

    • Olof Liberg
  4. Department of Forestry and Wildlife Management, Faculty of Applied Ecology and Agricultural Sciences, Hedmark University College, Campus Evenstad, NO-2418 Elverum, Norway

    • Jon M. Arnemo
  5. Department of Wildlife, Fish and Environmental Studies, Faculty of Forest Sciences, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden

    • Jon M. Arnemo
  6. Science for Life Laboratory, Department of Clinical Sciences, Swedish University of Agricultural Sciences, 75651 Uppsala, Sweden

    • Åke Hedhammar

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Contributions

K.L.-T. and Å.H. designed the study. K.L.-T. and E.A. oversaw the study. M.-L.A. coordinated and performed the majority of the sample collecting and O.L. and J.M.A. provided samples of critical importance. E.A. performed the SNP detection and selection analyses; A.R. identified candidate causative mutations and analysed haplotypes in CDRs; K.M. detected CNVs bioinformatically; M.T.W. performed phylogenetic analysis and analysed the Canine HD-array data; A.R. performed the maltase activity assay; M.-L.A. validated CNVs and quantified mRNA expression of candidate genes; M.P. performed validation SNP genotyping; E.A., A.R., M.-L.A. and K.L-T. interpreted the data; E.A. and K.L.-T. wrote the paper with input from the other authors.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Erik Axelsson or Kerstin Lindblad-Toh.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    This file contains Supplementary Discussions sections 1-9, Supplementary references, Supplementary Figures 1-24 and Supplementary Tables 1-25.

Zip files

  1. 1.

    Supplementary Data 1

    This zipped file lists the position of short indels in the canine genome.

  2. 2.

    Supplementary Data 2

    This zipped file lists the position of CNVs in the canine genome.

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DOI

https://doi.org/10.1038/nature11837

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