Genetic Relationships of Dog Breeds

To visualize genetic relationships suggested by our SNP data we used principal component analysis (PCA) (n_{dog_breed} = 2) and STRUCTURE⁶ (n_{dog_breed} = 1). For tree reconstruction, we analysed two data sets. First, for individual-based allele-sharing distance analyses, we used 574 individuals (n_dogs = 490; n_{Old_World_wolves} = 84). This data set consisted of 75 dog breeds where six individuals were genotyped from each breed and an additional five dog breeds where five or fewer individuals were genotyped. The second data set was created for the population-level and haplotype-sharing distance-based analyses and used a subset of 530 individuals to provide comparable sample sizes from 79 dog breeds (n_{per_breed} = 6) or wolf populations from China (n = 6), Middle East (n = 7), central Asia (n = 6) and Europe (n = 31). Coyotes from the western United States (n = 6) were used for rooting.

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vonHoldt B.M., Pollinger J.P., Lohmueller K.E., Han E., Parker H.G., Quignon P., Degenhardt J.D., Boyko A.R., Earl D.A., Auton A., Reynolds A., Bryc K., Brisbin A., Knowles J.C., Mosher D.S., Spady T.C., Elkahloun A., Geffen E., Pilot M., Jedrzejewski W., Greco C., Randi E., Bannasch D., Wilton A., Shearman J., Musiani M., Cargill M., Jones P.G., Qian Z., Huang W., Ding Z.L., Zhang Y.P., Bustamante C.D., Ostrander E.A., Novembre J, & Wayne R.K. (2010). Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication. Nature, 464(7290), 898-902.

Publication 2010

Allele Coyotes Genetic Haplotype Populations Reconstruction Tree Wolf

Corresponding Organization :

Other organizations : University of California, Los Angeles, Cornell University, National Human Genome Research Institute, Cancer Genetics (United States), National Institutes of Health, University of California, Santa Cruz, Tel Aviv University, Polish Academy of Sciences, Museum and Institute of Zoology, Mammal Research Institute, Istituto Superiore per la Protezione e la Ricerca Ambientale, University of California, Davis, UNSW Sydney, University of Calgary, Yunnan University, Kunming Institute of Zoology, Chinese Academy of Sciences, South University

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Variable analysis

independent variables

Genetic data (SNPs)

dependent variables

Genetic relationships between dog breeds and wolves

control variables

Sample size (n) for dog breeds and wolf populations

controls

Coyotes from the western United States (n = 6) were used for rooting the tree reconstruction analyses.

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