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ABSTRACT The island inhabitants of Sardinia have long been a focus for studies of complex human traits due to their unique ancestral background and population isolation reflecting geographic and cultural restriction. Population isolates share decreased genomic diversity, increased linkage disequilibrium, and increased inbreeding coefficients. In many regions, dogs and humans have been exposed to the same natural and artificial forces of environment, growth, and migration. Distinct dog breeds have arisen through human-driven selection of characteristics to meet an ideal standard of appearance and function. The Fonni's Dog, an endemic dog population on Sardinia, has not been subjected to an intensive system of artificial selection, but rather has developed alongside the human population of Sardinia, influenced by geographic isolation and unregulated selection based on its environmental adaptation and aptitude for owner-desired behaviors. Through analysis of 28 dog breeds, represented with whole-genome sequences from 13 dogs and ~170,000 genome-wide single nucleotide variants from 155 dogs, we have produced a genomic illustration of the Fonni's Dog. Genomic patterns confirm within-breed similarity, while population and demographic analyses provide spatial identity of Fonni's Dog to other Mediterranean breeds. Investigation of admixture and fixation indices reveals insights into the involvement of Fonni's Dogs in breed development throughout the Mediterranean. We describe how characteristics of population isolates are reflected in dog breeds that have undergone artificial selection, and are mirrored in the Fonni's Dog through traditional isolating factors that affect human populations. Lastly, we show that the genetic history of Fonni's Dog parallels demographic events in local human populations.
KEYWORDS dog; whole-genome sequence; demography; population structure
THE domestic dog has undergone intensive human-driven selective pressure in an effort to develop canines of a particular appearance or with a desired behavior pattern (Galibert et al 2011; Wayne and vonHoldt 2012). While considerable effort has gone into decoding the genetic basis of morphologic traits that vary within dog populations, such as body size or coat color, the challenge of identifying genomic features that distinguish breeds selected to support human survival is largely unmet (summarized in Boyko 2011; Rimbault and Ostrander 2012; Schoenebeck and Ostrander 2014). Breeds specifically suited to perform such tasks include those that excel at hunting, herding, and protection of property. An appeal to aesthetics and functional design has also resulted...