Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.

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The production of extreme or`transgressive' phenotypes in segregating hybrid populations has been speculated to contribute to niche divergence of hybrid lineages. Here, we assess the frequency of transgressive segregation in hybrid populations, describe its genetic basis and discuss the factors that best predict its occurrence. From a survey of 171 studies that report phenotypic variation in segregating hybrid populations, we show that transgression is the rule rather than the exception. In fact, 155 of the 171 studies (91%) report at least one transgressive trait, and 44% of 1229 traits examined were transgressive. Transgression occurred most frequently in intraspeci®c crosses involving inbred, domesticated plant populations, and least frequently in interspeci®c crosses between outbred, wild animal species. Quantitative genetic studies of plant hybrids consistently point to the action of complementary genes as the primary cause of transgression, although overdominance and epistasis also contribute.Complementary genes appear to be common for most traits, with the possible exception of those with a history of disruptive selection. These results lend credence to the view that hybridization may provide the raw material for rapid adaptation and provide a simple explanation for niche divergence and phenotypic novelty often associated with hybrid lineages. ; Rieseberg & Ellstrand, 1993; Cosse et al., 1995). The generation of these extreme phenotypes is referred to as transgressive segregation, and this is a major mechanism by which extreme or novel adaptations observed in new hybrid ecotypes or species are thought to arise. If transgressive segregation is frequent, then an important evolutionary role for hybridization is more easily explained. Note that transgressive segregation is a phenomenon speci®c to segregating hybrid generations and refers to the fraction of individuals that exceed parental phenotypic values in either a negative or positive direction. This is caused in part by heterosis, which is most pronounced in ®rst-generation hybrids, and is implicated when the mean trait value of the hybrids exceeds (in a positive direction only) the phenotypic values of both parental lines. As will be shown below, the genetic basis of transgressive segregation appears to be largely distinct from that underlying heterosis.Evidence that transgressive segregation facilitates the successful establishment of hybrid lineages is indirect and comes principally from research on plants. Theoretical and empirical studies identify niche separation between hybrid and parental genotypes as the single most important factor favouring hybrid establishment (Lewontin & Birch, 1966; Grant, 1981; Templeton, 1981; Buerkle et al. in review 1 2 ).Without niche di erentiation, new hybrid genotypes are likely to be overcome by competition and/or gene¯ow from parental populations. These predictions are supported by reports that most stabilized introgressants or hybrid species are ecologically divergent with respect to their parental species (Abbo...

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Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication1,2. To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf. Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA sequence data3. Furthermore, we find a surprising correspondence between genetic and phenotypic/functional breed groupings but there are exceptions that suggest phenotypic diversification depended in part on the repeated crossing of individuals with novel phenotypes. Our results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages. More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity.