Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication

Abstract

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.

Postembryonic staging of wild‐type goldfish, with brief reference to skeletal systems

“…This possibility is also supported by recent progress of genomic studies on domesticated mammals and birds (for example, dog, cat, cow, chicken, and pigeon) (Lindblad‐Toh et al, 2005; Wayne and Ostrander, 2007; Akey et al, 2010; Vonholdt et al, 2010; Shapiro et al, 2013). These studies explain the processes underlying fixation of genetic mutations through selective pressure on favorable morphological and/or physiological features, providing a more specific and promising framework for combined genomic and developmental biological approaches to investigate how fixed mutations altered ontogenetic processes to form the favorable morphological features in domestic animals in the context of evolutionary developmental biology (Cresko et al, 2007).…”

A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits

“…These results support our hypothesis that comparison of recently domesticated population with its wild founder population facilitates the discovery of candidate loci for traits under strong deliberate and accidental selection in the new hatchery environment. In dogs, phenotypes that vary most conspicuously among recently derived breeds, including size, limb length, coat color, coat texture, behavior, diet, skeletal morphology, and physiology have been used to identify the genomic regions that possess strong signatures of recent selection and contain major candidate genes (Akey et al., 2010; Axelsson et al., 2013; Pollinger et al., 2005; Von Holdt et al., 2010). …”

Genome-wide signatures of population bottlenecks and diversifying selection in European wolves

“…Samples were genotyped at 60 584 high-quality autosomal SNPs (referred to as 61K) and 851 X chromosome SNP loci (Boyko et al, 2010;vonHoldt et al, 2010). Here, we used a subset of the CanMap SNP data set that consisted of 103 grey wolves: 54 from Eastern Europe, 19 from Italy, 6 from the Iberian Peninsula, 7 from Asia and 17 from North America, plus 5 coyotes that served as an outgroup (see Supplementary Table 1).…”

“…This study utilized data derived from the CanMap project (Boyko et al, 2010;vonHoldt et al, 2010) that provided genome-wide SNP data from 912 domestic dogs and 337 wild canids, based on genotyping with an Affymetrix Canine SNP Genome Mapping Array (coordinates based on the CanFam2 assembly). Samples were genotyped at 60 584 high-quality autosomal SNPs (referred to as 61K) and 851 X chromosome SNP loci (Boyko et al, 2010;vonHoldt et al, 2010).…”

“…The grey wolf is the direct ancestor of the domestic dog (Canis lupus familiaris), which is an important and emerging model for understanding the genetics of disease susceptibility and developmental biology. Therefore, genomic studies on the grey wolf benefit from the extensive genomic resources available for the domestic dog (for example, Lindblad-Toh et al, 2005;vonHoldt et al, 2010vonHoldt et al, , 2011. Another advantage of focusing on the grey wolf is the extensive background knowledge regarding its ecology, recent demographic history and population genetics (reviewed in Musiani et al, 2010;Randi, 2011).…”