Ancestry-inclusive dog genomics challenges popular breed stereotypes.

Behavioral genetics in dogs has focused on modern breeds, which are isolated subgroups with distinctive physical and, purportedly, behavioral characteristics. We interrogated breed stereotypes by surveying owners of 18,385 purebred and mixed-breed dogs and genotyping 2155 dogs. Most behavioral traits are heritable [heritability (h2) > 25%], and admixture patterns in mixed-breed dogs reveal breed propensities. Breed explains just 9% of behavioral variation in individuals. Genome-wide association analyses identify 11 loci that are significantly associated with behavior, and characteristic breed behaviors exhibit genetic complexity. Behavioral loci are not unusually differentiated in breeds, but breed propensities align, albeit weakly, with ancestral function. We propose that behaviors perceived as characteristic of modern breeds derive from thousands of years of polygenic adaptation that predates breed formation, with modern breeds distinguished primarily by aesthetic traits.

Advancing Genetic Selection and Behavioral Genomics of Working Dogs Through Collaborative Science.

The ancient partnership between people and dogs is struggling to meet modern day needs, with demand exceeding our capacity to safely breed high-performing and healthy dogs. New statistical genetic approaches and genomic technology have the potential to revolutionize dog breeding, by transitioning from problematic phenotypic selection to methods that can preserve genetic diversity while increasing the proportion of successful dogs. To fully utilize this technology will require ultra large datasets, with hundreds of thousands of dogs. Today, dog breeders struggle to apply even the tools available now, stymied by the need for sophisticated data storage infrastructure and expertise in statistical genetics. Here, we review recent advances in animal breeding, and how a new approach to dog breeding would address the needs of working dog breeders today while also providing them with a path to realizing the next generation of technology. We provide a step-by-step guide for dog breeders to start implementing estimated breeding value selection in their programs now, and we describe how genotyping and DNA sequencing data, as it becomes more widely available, can be integrated into this approach. Finally, we call for data sharing among dog breeding programs as a path to achieving a future that can benefit all dogs, and their human partners too.

BarkBase: Epigenomic Annotation of Canine Genomes.

Dogs are an unparalleled natural model for investigating the genetics of health and disease, particularly for complex diseases like cancer. Comprehensive genomic annotation of regulatory elements active in healthy canine tissues is crucial both for identifying candidate causal variants and for designing functional studies needed to translate genetic associations into disease insight. Currently, canine geneticists rely primarily on annotations of the human or mouse genome that have been remapped to dog, an approach that misses dog-specific features. Here, we describe BarkBase, a canine epigenomic resource available at barkbase.org. BarkBase hosts data for 27 adult tissue types, with biological replicates, and for one sample of up to five tissues sampled at each of four carefully staged embryonic time points. RNA sequencing is complemented with whole genome sequencing and with assay for transposase-accessible chromatin using sequencing (ATAC-seq), which identifies open chromatin regions. By including replicates, we can more confidently discern tissue-specific transcripts and assess differential gene expression between tissues and timepoints. By offering data in easy-to-use file formats, through a visual browser modeled on similar genomic resources for human, BarkBase introduces a powerful new resource to support comparative studies in dogs and humans.

Acute exposure to 17α-ethinylestradiol alters boldness behavioral syndrome in female Siamese fighting fish.

The role of anthropogenic sources in generating, maintaining, and influencing behavioral syndromes has recently been identified as an important area of future research. Endocrine disrupting chemicals are prevalent and persistent in aquatic ecosystems worldwide. These chemicals are known to have marked effects on the morphology and behavior of exposed individuals and, as such, may serve as a potential influence on behavioral syndromes. However, both the effects of exposure on behaviors beyond courtship and aggression and how exposure might affect behavioral variation at the individual level are understudied. To address this question, we examined boldness behavior in female Siamese fighting fish in three different assays (Novel Environment, Empty Tank, Shoaling) both before and after they were exposed to the estrogen mimic, 17α-ethinylestradiol (EE2). EE2 influences courtship, aggression, and boldness in males of this species but its effects have not been examined in females, to our knowledge. Females were tested multiple times in each assay before and after exposure so that behavioral consistency could be examined. A behavioral syndrome for boldness and activity level occurred across the three assays. The reductions in boldness and loss of the behavioral syndrome that resulted from EE2 exposure were surprising and suggest that the effects of EE2 exposure on female behavior and physiology should be examined more frequently. This study is one of the first to examine the effects of EE2 in females as well as on correlated behaviors and emphasizes the importance of examining the effects of endocrine disrupting chemicals on individual behavioral variation and consistency.