Commonalities in Development of Pure Breeds and Population Isolates Revealed in the Genome of the Sardinian Fonni's Dog

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.

Studies of modern Italian dog populations reveal multiple patterns for domestic breed evolution

“…Additionally, seven local landrace populations, defined as distinct dog varieties unique to a specific geographic region with historically limited breeding populations, are included in this study. The latter are not recognized by any purebred canine registry but, nonetheless, may display a genetic pattern consistent with other purebreeds (Alam, Han, Lee, Ha, & Kim, ; Puja et al., ; Tanabe, ; Wijnrocx, Francois, Stinckens, Janssens, & Buys, ; Yoo et al., ), such as has been observed for one Italian regional population, the Fonni's Dog (Dreger, Davis, et al., ; Dreger, Rimbault, et al., ; Sechi et al., ). By focusing our analyses on breeds with diverse phenotypes that have all originated in a single country, we aim to employ genetic data to expand upon historical breed formation accounts and define the modes by which humans have produced recognizable and diversified dog breeds.…”

“…High‐density, genome‐wide breed phylogeny analysis has been applied to well‐established dog breeds to elucidate the complex structure of breed relationships and their development (Dreger, Davis, et al., ; von Holdt et al., ; Mortlock, Khatkar, & Williamson, ). The largest phylogenetic study reported to date includes 161 dog breeds and over 1,300 dogs, consisting of 23 cladistic groupings based on genetic similarities (Parker et al., ).…”

“…The largest phylogenetic study reported to date includes 161 dog breeds and over 1,300 dogs, consisting of 23 cladistic groupings based on genetic similarities (Parker et al., ). Smaller studies exist which have addressed population demography in globally recognized breeds sampled from discrete locations with some success (Bigi, Marelli, Randi, & Polli, ; Ceh & Dovc, ; Dreger, Davis, et al., ; Koskinen & Bredbacka, ; Oliehoek, Bijma, & van der Meijden, ; Parra, Mendez, Canon, & Dunner, ; Pertoldi et al., ; Pribanova et al., ; Suarez, Betancor, Fregel, & Pestano, ; Wiener et al., ). While such studies provide insight into the status and genetic health of local populations, they do not necessarily consider the preexisting breed‐specific genomic patterns developed prior to localization or the impact of import and export from the local breeding pool.…”

“…Purebred dog registries, such as the American Kennel Club (AKC) or the Fédération Cynologique Internationale (FCI), attempt to classify dog populations as distinct breeds by enforcing regulations of pedigree tracking, adherence to a written standard, and population size. A genomic pattern for breed status classification based on values from 79 globally recognized purebreeds has recently been defined and includes threshold levels from four homozygosity measurements (Dreger, Davis, et al., ; Dreger, Rimbault, et al., ). These metrics demarcate the extremes of single‐dog length of homozygosity, ten‐dog shared length of homozygosity, coefficient of inbreeding, and rate of shared homozygosity decay represented by standardized pure dog breeds.…”

Genomic Analyses Reveal the Influence of Geographic Origin, Migration, and Hybridization on Modern Dog Breed Development

“…Genotype calls were made with Genome Studio V2011.1 with genotyping module v1.9.4 (Illumina). Subsets of these data were described in Dreger et al (Dreger et al, 2016a; Dreger et al, 2016b). The dataset consists of 938 dogs from 127 breeds and nine wild canids.…”