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

Abstract

Through thousands of years of breeding and strong human selection, the dog (Canis lupus familiaris) exists today within hundreds of closed populations throughout the world, each with defined phenotypes. A singular geographic region with broad diversity in dog breeds presents an interesting opportunity to observe potential mechanisms of breed formation. Italy claims 14 internationally recognized dog breeds, with numerous additional local varieties. To determine the relationship among Italian dog populations, we integrated genetic data from 263 dogs representing 23 closed dog populations from Italy, seven Apennine gray wolves, and an established dataset of 161 globally recognized dog breeds, applying multiple genetic methods to characterize the modes by which breeds are formed within a single geographic region. Our consideration of each of five genetic analyses reveals a series of development events that mirror historical modes of breed formation, but with variations unique to the codevelopment of early dog and human populations. Using 142,840 genome‐wide SNPs and a dataset of 1,609 canines, representing 182 breeds and 16 wild canids, we identified breed development routes for the Italian breeds that included divergence from common populations for a specific purpose, admixture of regional stock with that from other regions, and isolated selection of local stock with specific attributes.

True Colors: commercially-acquired morphological genotypes reveal hidden allele variation among dog breeds, informing both trait ancestry and breed potential

“…For example, it has long been assumed that the recessive black allele of ASIP ( a ) is predominantly found in herding breeds (3–5). However, among the 212 breeds analyzed here, the a allele was identified in 89 breeds, 83 of which are not previously reported as carrying the allele, representing 23 of the possible 28 clades assigned using IBD haplotype sharing in previous work (34,35). While herding breeds, present in the Continental Shepherd, Hungarian, New World, Nordic Spitz, and UK Rural clades, comprise 14 of the a allele-possessing breeds – an expected result – the greatest breed representation was among the Pointer/Setter clade with 13 breeds possessing the a allele.…”

“…Individuals of the same breed were combined to calculate breed allele frequencies and are reported in S2 Table. Breeds were assigned to phylogenetic clades as previously reported (34,35)(S1 Table). Breeds not included in the earlier phylogenetic studies were assigned to defined clades based on known breed history, phenotypic commonalities, and geographic region of origin (indicated by parentheses in S1 Table).…”

“…Forty-eight breeds were identified as carrying the tailless allele of T , in many cases at very low frequencies, in the present study. Thirty-eight of these breeds were represented in previous research (34,35), allowing identification of IBD haplotype sharing relationships. By using these pre-determined breed relationships, each of the 38 breeds (Figure 3, represented by red or green text) can be connected into a single relationship matrix, providing a potential route of transmission of the tailless allele.…”

“…Only nine non-carrier breeds (Figure 3, represented by grey text) were required to serve as potential transmitters of the tailless allele, reflecting populations that have successfully eliminated the allele from the breed, or have decreased the frequency enough so as to not be detected in our sampling. Likewise, 89 breeds were identified as carrying the ASIP a allele in the present study, 68 of which were also analyzed for IBD haplotype sharing previously (34,35). Of these 68, all but three breeds (Tibetan Mastiff, Kuvasz, and Anatolian Shepherd) could be connected via significant IBD haplotype sharing events (Figure 4).…”

“…S1 Table: List of breeds, their abbreviations used throughout the paper, and the number of samples genotyped. Each breed was assigned to a phylogenetic clade based on previously published results (34,35). Clade names in parenthesis indicate breeds not included previously (34,35), but for which a clade was assigned based on known breed history and phenotypes.…”