The genomic diversity of the domestic dog is an invaluable resource for advancing understanding of mammalian biology, evolutionary biology, morphologic variation, and behavior. There are approximately 350 recognized breeds in the world today, many established through hybridization and selection followed by intense breeding programs aimed at retaining or enhancing specific traits. As a result, many breeds suffer from an excess of particular diseases, one of many factors leading to the recent trend of “designer breed” development, i.e. crossing purebred dogs from existing breeds in the hope that offspring will be enriched for desired traits and characteristics of the parental breeds. We used a dense panel of 150,106 SNPs to analyze the population structure of the Australian labradoodle (ALBD), to understand how such breeds are developed. Haplotype and admixture analyses show that breeds other than the poodle (POOD) and Labrador retriever (LAB) contributed to ALBD formation, but that the breed is, at the genetic level, predominantly POOD, with all small and large varieties contributing to its construction. Allele frequency analysis reveals that the breed is enhanced for variants associated with a poodle-like coat, which is perceived by breeders to have an association with hypoallergenicity. We observed little enhancement for LAB-specific alleles. This study provides a blueprint for understanding how dog breeds are formed, highlighting the limited scope of desired traits in defining new breeds. Due to the selective breeding practices used to create modern breeds, dogs suffer from an unacceptable excess of disease, one of several reasons behind the recent trend of creating “designer breeds.” Such populations result from crosses between established breeds, with a goal of producing dogs that lack or have a reduced incidence of unfavorable disorders or phenotypes, yet retain desirable traits from parental breeds. One such example is the Australian labradoodle which was initiated from Labrador retriever and standard poodle crosses 31 years ago in order to produce dogs with a reduced tendency to elicit an allergic reaction but that retained the desirable characteristics of a service dog. In this study we have used nuclear DNA markers to determine the genetic history of the Australian labradoodle and develop an understanding of how breeds stabilize traits given particular breeding strategies. Our data shows that despite the major contributions from poodle and Labrador retriever, additional breeds contributed to the modern Australian labradoodle. Today’s Australian labradoodle is largely poodle with an excess of poodle alleles related to coat type. This study demonstrates that changes in very few genes can define a new breed and demonstrates how breeds can form in a small number of generations.

Unlike on land, the oceans present few biogeographic barriers to hinder migration and mate choice. One might therefore expect random mating across entire species ranges, yet this is rarely observed. Even the largest and most mobile marine species like whales often maintain basin-specific lineages. Here, we test whether sperm whales form a single effectively panmictic gene pool. We use the term effective panmixia to refer to the absence of detectable genome-wide allele-frequency differentiation, as opposed to equal mating probabilities among all individuals. We compiled data of 45 whole genomes (of which 41 newly sequenced) to perform phylogenetic and demographic analyses. The analyses uncover a remarkable lack of global population structure: sperm whales from the Atlantic, Pacific, and Indian Oceans form a single, genetically homogeneous population, suggesting global effective panmixia, with no significant differences in allele frequency. The only exception is the population of the Mediterranean Sea, which forms a distinct cluster, indicating past or ongoing geographic isolation and genetic drift owing to a reduced effective population size. The lack of general population structure elsewhere across the species range highlights the extraordinary global connectivity of this species. This global connectivity may buffer sperm whale populations from loss of variation through genetic drift, whereas the differentiated Mediterranean population remains a regional conservation priority.