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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    • "Free-ranging dogs are an indispensable part of the human ecology in India, and they are highly dependent on humans, who chiefly live on a carbohydrate-rich diet (Mohan et al. 2009), for their survival. They live mostly on a carbohydrate-rich omnivorous diet similar to humans (NRC 2006), a fact that has very recently been attributed to the evolutionary adaptations of dogs during their process of transition from wolves (Axelsson et al. 2013). As scavengers, they feed mostly at garbage dumps and dustbins, and are responsible for removing a lot of the human waste in the urban areas, which also leads to dogs being associated with a lack of hygiene. "
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    ABSTRACT: Animals that scavenge in and around human settlements need to utilise a broad range of resources, and thus generalist scavengers are likely to be better adapted to human-dominated habitats. In India, free-ranging dogs (Canis lupus familiaris) live in close proximity with humans in diverse habitats, from forest fringes to metropolises, and are heavily dependent on humans for their food. It has been argued that the ability to digest carbohydrates was one of the driving forces for dog domestication. Though dogs are better adapted to digest carbohydrates than other canids, pet dogs show a clear preference for animal proteins. Our observations on streets of urban and semi-urban localities show that the free-ranging dogs are scavengers which primarily receive carbohydrate-rich food from humans. Their source for animal protein is typically garbage bins and leftovers, and such resources are rare. Using a series of field-based experiments, we test if the free-ranging dogs have adapted to a generalist scavenging lifestyle by losing preference for animal protein. Our experiments show that the free-ranging dogs, which are descendants of the decidedly carnivorous gray wolf (Canis lupus lupus), have retained a clear preference for meat, which is manifested by their choice of anything that smells of meat, irrespective of the actual nutrient content. The plasticity in their diet probably fosters efficient scavenging in a competitive environment, while a rule of thumb for preferentially acquiring specific nutrients enables them to sequester proteins from the carbohydrate-dominated environment.
    Ethology Ecology and Evolution 09/2015; DOI:10.1080/03949370.2015.1076526 · 1.10 Impact Factor
    • "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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    ABSTRACT: Canine transmissible venereal tumor (CTVT) is a parasitic cancer clone that has propagated for thousands of years via sexual transfer of malignant cells. Little is understood about the mechanisms that converted an ancient tumor into the world's oldest known continuously propagating somatic cell lineage. We created the largest existing catalog of canine genome-wide variation and compared it against two CTVT genome sequences, thereby separating alleles derived from the founder's genome from somatic drivers of clonal transmissibility. We show that CTVT has undergone continuous adaptation to its transmissible allograft niche, with overlapping mutations at every step of immunosurveillance, particularly self-antigen presentation and apoptosis. We also identified chronologically early somatic mutations in oncogenesis- and immune-related genes that may represent key initiators of clonal transmissibility. Thus, we provide the first insights into the specific genomic aberrations that underlie CTVT's dogged perseverance in canids around the world. Published by Cold Spring Harbor Laboratory Press.
    Genome Research 07/2015; DOI:10.1101/gr.190314.115 · 14.63 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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    ABSTRACT: Copy number variation represents a major source of genetic divergence, yet the evolutionary dynamics of genic copy number variation in natural populations during differentiation and adaptation remain unclear. We applied a read depth approach to genome resequencing data to detect copy number variants (CNVs) ≥1 kb in wild-caught mice belonging to four populations of Mus musculus domesticus. We complemented the bioinformatics analyses with experimental validation using droplet digital PCR. The specific focus of our analysis is CNVs that include complete genes, as these CNVs could be expected to contribute most directly to evolutionary divergence. In total, 1863 transcription units appear to be completely encompassed within CNVs in at least one individual when compared to the reference assembly. Further, 179 of these CNVs show population-specific copy number differences, and 325 are subject to complete deletion in multiple individuals. Among the most copy-number variable genes are three highly conserved genes that encode the splicing factor CWC22, the spindle protein SFI1, and the Holliday junction recognition protein HJURP. These genes exhibit population-specific expansion patterns that suggest involvement in local adaptations. We found that genes that overlap with large segmental duplications are generally more copy-number variable. These genes encode proteins that are relevant for environmental and behavioral interactions, such as vomeronasal and olfactory receptors, as well as major urinary proteins and several proteins of unknown function. The overall analysis shows that genic CNVs contribute more to population differentiation in mice than in humans and may promote and speed up population divergence. © 2015 Pezer et al.; Published by Cold Spring Harbor Laboratory Press.
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