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Genome-wide SNP and Haplotype Analyses Reveal a Rich History Underlying Dog Domestication

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Genome-wide SNP and Haplotype Analyses Reveal a Rich History Underlying Dog Domestication

Bridgett M Vonholdt et al. Nature.

Abstract

Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication. 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 data. 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.

Figures

Figure 1
Figure 1. Neighbour-joining trees of domestic dogs and grey wolves
Branch colour indicates the phenotypic/functional designation used by dog breeders,. A dot indicates ≥95% bootstrap support from 1,000 replicates. a, Haplotype-sharing cladogram for 10-SNP windows (n = 6 for each breed and wolf population). b, Allele-sharing cladogram of individuals based on individual SNP loci. c, Haplotype-sharing phylogram based on 10-SNP windows of breeds and wolf populations. d, Allele-sharing phylogram of individual SNPs for breeds and wolf populations. For c and d, we note breeds where genetic assignments conflict with phenotypic/functional designations as follows: 1, Brussels griffon; 2, Pekingese; 3, pug; 4, Shih-tzu; 5, miniature pinscher; 6, Doberman pinscher; 7, Kuvasz; 8, Ibizian hound; 9, chihuahua; 10, Pomeranian; 11, papillon; 12, Glen of Imaal; 13, German shepherd; 14, Briard; 15, Jack Russell; 16, dachshund; 17, great schnauzer; and 18, standard schnauzer. Gt, great; mtn, mountain; PBGV, petit basset griffon vendeen; pin., pinscher; ptr, pointer; ret., retriever; shep., shepherd; sp., spaniel; Staf., Staffordshire; std, standard; terr., terrier. Canine images not drawn to scale. Wolf image adapted from ref. ; dog images from the American Kennel Club (http://www.akc.org).
Figure 2
Figure 2. Genome-wide analysis of SNP variation in domestic dogs and grey wolves
a, Average observed heterozygosity (Ho). b, Average number of haplotypes per breed or group for phased SNP loci (15-SNP windows). c, Average observed heterozygosity of microsatellite data,. d, Fraction of unique haplotypes shared between 64 dog breeds and wolf populations for 5-(left) and 15- (right) SNP windows. Diamonds indicate significant sharing (P<0.05) using permutation test 2 (Supplementary Note A). Six (a–c) or nine (d) individuals represent each breed and wolf population. Error bars indicate s.e.m. E, east; SW, southwest.

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