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: 41.46). 01/2013; 495(7441). DOI: 10.1038/nature11837
Source: PubMed


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
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    • "Several clear examples of the beneficial nature of CNVs exist. For instance, amplification of the CCL3L1 gene lowers risk of HIV progression (Gonzalez et al. 2005), and amylase copy number correlates with dietary starch levels in both humans (Perry et al. 2007) and domesticated dogs (Axelsson et al. 2013). However, there is accumulating evidence that CNV may be generally deleterious and subject to purifying selection. "
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    ABSTRACT: If copy number variants (CNVs) are predominantly deleterious, we would expect them to be more efficiently purged from populations with a large effective population size (Ne) than from populations with a small Ne. Malaria parasites (Plasmodium falciparum) provide an excellent organism to examine this prediction, because this protozoan shows a broad spectrum of population structures within a single species, with large, stable, outbred populations in Africa, small unstable inbred populations in South America and with intermediate population characteristics in South East Asia. We characterized 122 single-clone parasites, without prior laboratory culture, from malaria-infected patients in 7 countries in Africa, SE Asia and S. America using a high density SNP/CNV microarray. We scored 134 high-confidence CNVs across the parasite exome, including 33 deletions and 102 amplifications, which ranged in size from <500bp to 59kb, as well as 10,107 flanking, biallelic SNPs. Overall, CNVs were rare, small and skewed towards low frequency variants, consistent with the deleterious model. Relative to African and SE Asian populations, CNVs were significantly more common in S. America, showed significantly less skew in allele frequencies, and were significantly larger. On this background of low frequency CNV, we also identified several high-frequency CNVs under putative positive selection using an FST outlier analysis. These included known adaptive CNVs containing rh2b and pfmdr1, and several other CNVs (e.g. DNA helicase, and 3 conserved proteins) that require further investigation. Our data are consistent with a significant impact of genetic structure on CNV burden in an important human pathogen.
    Full-text · Article · Nov 2015 · Molecular Biology and Evolution
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    • "Those subsidies have increased substantially since the appearance of Neolithic societies, as agriculture and, particularly, livestock and domesticated farm animals provided additional food to other commensal species (Chamberlain et al. 2005; Agudo et al. 2010). A prime example comes from the appearance of dogs domesticated from wild wolves, related to the exploitation of waste dumps near increasingly common human settlements (Axelsson et al. 2013). However, the most dramatic humanbased changes in ecosystems (such as habitat transformation and its consequences) arrived with the industrial revolution, with the appearance of technology and the successful battle against infectious diseases , triggering a human population explosion across the planet. "

    Full-text · Dataset · Nov 2015
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    • "Water was available ad libitum. Wolves were fed two or three times a week, dogs on a daily basis, wolves mainly with carcasses of rabbits and deer, dogs mainly with dry food, owing to the different specific dietary requirements of wolves and dogs (Axelsson et al., 2013). From puppyhood on, all animals were regularly trained and participated in different behavioural tests. "
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    ABSTRACT: Exploration is important for animals to be able to gather information about features of their environment that may directly or indirectly influence survival and reproduction. Closely related to exploration is neophobia, which may reduce exposure to danger, but also constrain explorative behaviour. Here we investigated the effects of social relationships on neophobia and exploration in wolves, Canis lupus, and dogs, Canis familiaris. Eleven pack-living wolves reared by human foster parents and 13 identically raised and kept dogs were tested in a novel object test under three different conditions: (1) alone, (2) paired with a pack mate and (3) together with the entire pack. Dogs were less neophobic than wolves and interacted faster with the novel objects. However, the dogs showed overall less interest in the novel objects than wolves, which investigated the objects for longer than the dogs. Both wolves and dogs manipulated objects for longer when paired or in the pack than when alone. While kinship facilitated the investigation of novel objects in the pair condition in both wolves and dogs, rank distance had opposite effects. Our results suggest that the presence of conspecifics supported the exploration of novel objects in both wolves and dogs, particularly within kin and that this may be interpreted as risk sharing. The reduced latency to approach objects and less time spent exploring objects in dogs compared to wolves may be interpreted as an effect of domestication.
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