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

Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 75237 Uppsala, Sweden.
Nature (Impact Factor: 42.35). 01/2013; 495(7441). DOI: 10.1038/nature11837
Source: PubMed

ABSTRACT The domestication of dogs was an important episode in the development of human civilization. The precise timing and location of this event is debated 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 domestication. 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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Available from: Matthew T Webster, Feb 13, 2015
    • "copy number detection. Local realignment around documented and novel insertion-deletion events was performed using published indel data (Axelsson et al. 2013), and base quality recalibration using dbSNP and positions from the Illumina Canine HD chip data as training sets with GATK 3.2-2 (DePristo et al. 2011). Putative SNVs were identified in each sample and genotyped across all 188 samples simultaneously using GATK HaplotypeCaller in GVCF mode (Van der Auwera et al. 2013). "
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    Genome Research 07/2015; DOI:10.1101/gr.190314.115 · 13.85 Impact Factor
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    • "Cold Spring Harbor Laboratory Press on August 19, 2015 -Published by Downloaded from the amylase genes have been suggested to be a result of adaptation to a starch-rich diet in human populations (Perry et al. 2007) and dogs (Axelsson et al. 2013). However, the genes analyzed in these studies (i.e., the salivary gene Amy1 and the pancreatic gene Amy2b) are not part of the duplications in our study, and we are currently investigating alternative interpretations for the pattern observed in this region (M Linnenbrink and D Tautz, in prep.). "
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    Genome Research 07/2015; DOI:10.1101/gr.187187.114 · 13.85 Impact Factor
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    • "Over the past few years, comparative genomics has been widely employed as a tool to understand the genetic bases of many fundamental evolutionary questions, including adaptation (Axelsson, et al. 2013; Jones, et al. 2012; Yi, et al. 2010; Zhao, et al. 2013), speciation (Ellegren, et al. 2012; Poelstra, et al. 2014; Soria-Carrasco, et al. 2014), and genetic variation (Guo, et al. 2012). When the genome sequencing data is not available, transcriptome sequencing is an effective and accessible approach to initiate comparative genomic analyses on non-model organisms, because they contain large number of protein-coding genes likely enriched for targets of natural selection. "
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