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In a 2004 population genetics study of 85 purebred dogs, which used cluster-based methods with four identified genetic clusters, all three Schnauzer breeds structurally mostly clustered within "recent European descent, largely terriers and hounds" cluster, with less percent within "working breeds" and "Molosser-type breeds" clusters, while the "Asian breeds/ancient hounds and spitz-type breed" cluster was present among Giant Schnauzers. In a 2007 Collie eye anomaly study of 638 dogs from 132 distinct breeds, with five specimens of each Schnauzer breed size, in the population structure of the microsatellite analysis they mostly clustered in the "hunting group" rather than the "mastiff/terrier group". In a 2010 GWAS study using more than 48,000 single-nucleotide polymorphisms of 915 dogs from 85 breeds, Standard and Giant Schnauzers made a separate phylogenetic tree branch clustered among "modern" breeds (i. e. "working dogs"), and not the "small terrier"/"mastiff-terrier" cluster, sharing genetic closeness with the Doberman Pinscher, the German Shepherd Dog and the Portuguese Water Dog. In the most recent 2017 WGS study of 1,346 dogs from 161 breeds, Standard and Miniature Schnauzers made one separate phylogenetic clade of 23 clades and formed a unique broader clade in which they share common ancestry with spitz-type breeds such as the American Eskimo Dog, the Pomeranian and the Volpino Italiano, as well as the Schipperke, the Papillon, the Brussells Griffon and the Pug. Although the Giant Schnauzer shares a haplotype with the other two Schnauzer breeds, it made a phylogentic node in a separate clade, sharing common ancestry with the Black Russian Terrier, the Rottweiler and the Doberman Pinscher. In another 2017 WGS study researching the genetic variants for the development of short tails among dog breeds, the sampled (Miniature) Schnauzer and Rottweiler have "short tail phenotype caused by the unknown genetic factors" and "are predicted to have developed short tail independently".

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