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

Copy-cat evolution: Divergence and convergence within and between cat and dog breeds

Many domesticated species exhibit remarkable phenotypic diversity. In nature, selection produces not only divergence but also convergence when organisms experience similar selective pressures. Whether artificial selection during domestication also produces convergence has received little attention. Three-dimensional shape analysis of domestic cat and dog skulls demonstrated convergence at multiple levels. Most broadly, cats and dogs have both diversified greatly: equaling or exceeding the morphological disparity among all modern-day species of their respective families. Moreover, as a result of artificial selection, some breeds of these two phenotypically distinct species, evolutionarily separated for 50 My, have converged to such an extreme extent that they are more similar to each other than they are to many members of their own species or their ancestors, a phenomenon never previously observed in domesticated species. Remarkably, this convergence evolved not only between dogs and cats but also multiple times within each taxon.

Analysis of canine gene constraint identifies new variants for orofacial clefts and stature

Dog breeding promotes within-group homogeneity through conformation to strict breed standards, while simultaneously driving between-group heterogeneity. There are over 350 recognized dog breeds that provide the foundation for investigating the genetic basis of phenotypic diversity. Typically, breed standard phenotypes such as stature, pelage, and craniofacial structure are analyzed through genetic association studies. However, such analyses are limited to assayed phenotypes only, leaving difficult-to-measure phenotypic subtleties easily overlooked. We investigated coding variation from over 2000 dogs, leading to discoveries of variants related to craniofacial morphology and stature. Breed-enriched variants were prioritized according to gene constraint, which was calculated using a mutation model derived from trinucleotide substitution probabilities. Among the newly found variants is a splice-acceptor variant in PDGFRA associated with bifid nose, a characteristic trait of Çatalburun dogs, implicating the gene's role in midline closure. Two additional LCORL variants, both associated with canine body size are also discovered: a frameshift that causes a premature stop in large breeds (>25 kg) and an intronic substitution found in small breeds (<10 kg), thus highlighting the importance of allelic heterogeneity in selection for breed traits. Most variants prioritized in this analysis are not associated with genomic signatures for breed differentiation, as these regions are enriched for constrained genes intolerant to nonsynonymous variation. This indicates trait selection in dogs is likely a balancing act between preserving essential gene functions and maximizing regulatory variation to drive phenotypic extremes.

Genomic evidence for behavioral adaptation of herding dogs

Herding dogs exhibit a distinct constellation of behaviors marked by inherent instinct and motor skills that manipulate and guide livestock in response to instructive commands and cues. Comparison of the whole-genome sequences of herding and nonherding breeds reveals signatures of positive selection associated with pathways underlying social interaction and cognitive functions. Of the strong selective sweep signals, haplotypes within ephrin type-B receptor 1 (EPHB1), which is linked to locomotor hyperactivity and spatial memory, show evidence of segregation within breed lineages for the conformation versus working lines of border collies and introgression with a genetically and geographically distant herding breed of Entlebucher mountain dogs. We show that a working line-specific haplotype of EPHB1 is associated with elevated levels of chase-bite motor patterns based on a well-validated behavior survey. These findings indicate that functional selection has shaped the genetic architecture of herding breeds, which may relate to their proficiency in addressing diverse tasks and challenges in maintaining control over the herd.

Common variants in the CPT1A gene are associated with cataracts in Northern breeds of domestic dog

Primary hereditary cataract affects many purebred domestic dog breeds and is a major cause of visual impairment in dogs. Cataracts are common in Northern breeds such as the Siberian Husky, Alaskan Malamute and Samoyed, but their aetiology is currently unknown. Only two genetic loci are known to be causally related to primary hereditary cataracts in the dog. To search for genetic loci associated with cataracts in Northern breeds, we used a genome-wide association study approach in three breeds-Siberian Husky, Alaskan Malamute and Samoyed. Cases were defined as dogs with bilateral posterior polar subcapsular cataracts and controls were at least four years of age with no evidence of cataracts or other ocular abnormality. We found a genome-wide statistical association for cataracts in the Siberian Husky on canine chromosome 18 (P-value: 1.1 x 10 - 7), which was independently replicated in a second larger case-control set (P-value 9.8 x 10 - 29). The Samoyed breed also showed evidence for association in the same genomic region (P-value: 2.4 x 10 - 5). We subsequently used targeted resequencing of the associated region (6.5 Mb) in ten Siberian Huskies and whole genome sequencing of a Husky, Malamute, Samoyed and Norwegian Buhund case to conduct fine-mapping and screen for candidate causal variants. These analyses identified a region of linkage disequilibrium in the four breeds containing common variants in the carnitine palmitoyltransferase 1A (CPT1A) gene that are strongly associated with bilateral posterior polar subcapsular cataracts in the Siberian Husky, Samoyed, Icelandic Sheepdog and Norwegian Buhund and we demonstrate that CPT1A is expressed in the dog lens and retina through RNAseq. Our findings represent a novel locus for cataracts in dogs. However, further work is needed to elucidate the pathophysiology underlying the association between CPT1A and cataracts in Northern breeds.

A frameshift variant in the SLC6A5 gene is associated with startle disease in a family of Old English Sheepdogs

A 2-week-old litter of three Old English Sheepdog puppies presented with episodic generalised muscle hypertonia and cyanosis triggered by touch and noise. Owing to poor response to therapy and progression of symptoms, the puppies were euthanised. Post-mortem histology revealed perineuronal incrustations in the spinal cord, suggestive of ischemia or neuronal necrosis. Clinical symptoms, combined with necropsy and histopathology findings, led to a suspicion of startle disease, prompting a referral to a specialised clinical genetics centre. Whole exome sequencing (WES) of the nuclear family identified a homozygous truncating variant in the SLC6A5 gene in affected individuals, with both unaffected parents being heterozygous. Additional population screening found three phenotypically unaffected carriers, indicating that the variant segregates within the Old English Sheepdog breed. This raises concerns about the management of carriers and their breeding contributions if not properly guided by DNA testing. This study addresses a frameshift variant SLC6A5:c.1322del found in Old English Sheepdogs. Next to this, the value of genetic counselling and clinical genetics services in breeding programmes is highlighted to identify carriers and guide informed breeding decisions. Finally, the findings demonstrate the utility of WES in veterinary diagnostics and provide practical insights for breeders, veterinarians and geneticists to improve the health and welfare of Old English Sheepdogs.

A Pipeline and Recommendations for Population and Individual Diagnostic SNP Selection in Non-Model Species

Despite substantial reductions in the cost of sequencing over the last decade, genetic panels remain relevant due to their cost-effectiveness and flexibility across a variety of sample types. In particular, single nucleotide polymorphism (SNP) panels are increasingly favoured for conservation applications. SNP panels are often used because of their adaptability, effectiveness with low-quality samples, and cost-efficiency for population monitoring and forensics. However, the selection of diagnostic SNPs for population assignment and individual identification can be challenging. The consequences of poor SNP selection are under-powered panels, inaccurate results, and monetary loss. Here, we develop a novel and user-friendly SNP selection pipeline (mPCRselect) that can be used to select SNPs for population assignment and/or individual identification. mPCRselect allows any researcher, who has sufficient SNP-level data, to design a successful and cost-effective SNP panel for a diploid species of conservation concern.

Canine genome-wide association study identifies DENND1B as an obesity gene in dogs and humans

Obesity is a heritable disease, but its genetic basis is incompletely understood. Canine population history facilitates trait mapping. We performed a canine genome-wide association study for body condition score-a measure of obesity-in 241 Labrador retrievers. Using a cross-species approach, we showed that canine obesity genes are also associated with rare and common forms of obesity in humans. The lead canine association was within the gene DENN domain containing 1B (DENND1B). Each copy of the alternate allele was associated with ~7.5% greater body fat. We demonstrate a role for this gene in regulating signaling and trafficking of melanocortin 4 receptor, a critical controller of energy homeostasis. Thus, canine genetics identified obesity genes and mechanisms relevant to both dogs and humans.

Immunotherapy yields breed-specific worst survival outcomes among three investigated therapies in French bulldogs with high-grade glioma

Introduction

French bulldogs are one of the most popular dog breeds in the United States and are also among breeds with the highest risk for developing high-grade glioma (HGG). With limited treatment options and high translational value for studying canine HGG to advance understanding of human glioblastoma (GB), a variety of novel treatment options have been investigated. In other forms of cancer, immunotherapy has shown promising results, garnering interest in the treatment of HGG. Yet, when an immunotherapy-based clinical trial was conducted, a marked survival disparity in French bulldog patients compared to other breeds was observed.

Methods

This retrospective, multi-institutional study was conducted to examine survival outcomes in immunotherapy-treated French bulldogs compared to closely related breeds, and to French bulldogs treated with several other treatment modalities.

Results

French bulldogs treated with immunotherapy experienced significantly shorter overall survival (OS) than boxers and Boston terriers (132 vs. 221 days, respectively). French bulldogs treated with immunotherapy had no significant difference in OS compared to French bulldogs treated palliatively, whereas dogs treated with either a novel therapy involving sonodynamic therapy or stereotactic radiation therapy had significantly longer OS.

Discussion

This study provides evidence for an immunotherapy-resistant form of HGG in French bulldogs, suggesting that the breed harbors key molecular differences affecting the tumor and tumor-immune microenvironment and subsequent poor response to treatment.

Deep sequencing of Korean Jindo dog reveals evolutionary trajectory of coat color variations

The inherent diversity of canines is closely intertwined with the unique color patterns of each dog population. These variations in color patterns are believed to have originated through mutations and selective breeding practices that occurred during and after the domestication of dogs from wolves. To address the significant gaps that persist in comprehending the evolutionary processes that underlie the development of these patterns, we generated and analyzed deep-sequenced genomes of 113 Korean Indigenous Jindo dogs that represent five distinct color patterns to identify the associated mutations in CBD103, ASIP, and MC1R. The degree of linkage disequilibrium and estimated allelic ages consistently indicate that the black-and-tan dogs descend from the first major founding population on Jindo island, compatible with the documented literature. We additionally demonstrate that black-and-tan dogs, in contrast to other color variations within the breed, exhibit a closer genetic affinity to ancient wolves from western Eurasia than those from eastern Eurasia. Lastly, the alleles unique to black-and-tan dogs indicated a pleiotropic effect by significantly decreasing the body size phenotypes compared to non-carriers. Overall, comparisons of whole genome sequences of each coat color population diverged from the same breed provided an unprecedented glimpse into the properties of evolutionary processes maintaining variation in Korean Jindo dog populations.

Genetic and Anatomical Determinants of Olfaction in Dogs and Wild Canids

Understanding the anatomical and genetic basis of complex phenotypic traits has long been a challenge for biological research. Domestic dogs offer a compelling model as they demonstrate more phenotypic variation than any other vertebrate species. Dogs have been intensely selected for specific traits and abilities, directly or indirectly, over the past 15,000 years since their initial domestication from the gray wolf. Because olfaction plays a central role in critical tasks, such as the detection of drugs, diseases, and explosives, as well as human rescue, we compared relative olfactory capacity across dog breeds and assessed changes to the canine olfactory system to their direct ancestors, wolves, and coyotes. We conducted a cross-disciplinary survey of olfactory anatomy, olfactory receptor (OR) gene variation, and OR gene expression in domestic dogs. Through comparisons to their closest wild canid relatives, the gray wolf and coyote, we show that domestic dogs might have lost functional OR genes commensurate with a documented reduction in nasal morphology as an outcome of the domestication process prior to breed formation. Critically, within domestic dogs alone, we found no genetic or morphological profile shared among functional or genealogical breed groupings, such as scent hounds, that might indicate evidence of any human-directed selection for enhanced olfaction. Instead, our results suggest that superior scent detection dogs likely owe their success to advantageous behavioral traits and training rather than an "olfactory edge" provided by morphology or genes.

Behavioural differences and similarities between dog breeds: proposing an ecologically valid approach for canine behavioural research

The behaviour of dogs holds great relevance for not only scientists from fundamental and applied research areas, but also due to the widespread roles of dogs in our societies as companions and working animals; their behaviour is also an important factor in animal and human welfare. A large proportion of dogs currently under human supervision belong to one of roughly 400 recognised breeds. Dog breeds can be characterised by distinctive, predictable and reproducible features, including some of their behavioural traits. To the scientist, the comparative analysis of the behaviour of dog breeds provides an opportunity for investigating an array of intriguing phenomena within an easily accessible model organism created from natural and human-driven evolutionary processes. There are many ways to design and conduct breed-related behavioural investigations, but such endeavours should always be based around biologically relevant research questions and lead to ecologically valid conclusions. In this review, we surveyed recent research efforts that included dog behaviour-related comparisons and applied a critical evaluation according to their methods of breed choice and the subsequent research design. Our aim was to assess whether these two fundamentally important components of experimental design provide a solid basis to reach valid conclusions. Based on 97 publications that fulfilled our selection criteria, we identified three primary methods used by researchers to select breeds for their investigations: (i) convenience sampling; (ii) hypothesis-driven, ancestry-based sampling; and (iii) hypothesis-driven, functional sampling. By using the SWOT (Strengths, Weaknesses, Opportunities, Threats) evaluation system, we highlight each of these techniques' merits and shortcomings. We identify when particular methods may be inherently unable to produce biologically meaningful results due to a mismatch between breed choice and the initial research goals. We hope that our evaluation will help researchers adopt best practices in experimental design regarding future dog breed comparisons.

Dog skull shape challenges assumptions of performance specialization from selective breeding

Through selective breeding, humans have driven exceptional morphological diversity in domestic dogs, creating more than 200 recognized breeds developed for specialized functional tasks such as herding, protection, and hunting. Here, we use three-dimensional reconstructions of dog skulls to ask whether these function-oriented kennel-club groups reflect differences in morphology that correspond to those functions. We analyzed 117 canid skulls, representing 40 domestic dog breeds and 18 wild subspecies, using geometric morphometric techniques and k-means clustering. Results show near-full overlap in kennel-club groups and with natural species, except for companion dogs having extreme snout shape. When categorized by task-specific historic function (i.e., bite work and scent work), this morphology overlap remains. These results indicate that, despite producing extreme morphological diversity, humans have not produced breeds specialized for functional tasks.

Incidence and risk factors for insulinoma diagnosed in dogs under primary veterinary care in the UK

Insulinoma is the most common pancreatic tumor diagnosed in dogs. This study aimed to report incidence risk, breed predispositions and other demographic risk factors for insulinoma diagnosed in dogs under primary veterinary care in the UK. The VetCompass Program supports research on anonymized electronic health records (EHRs) from dogs under UK veterinary care. This study included all VetCompass EHRs from dogs under primary veterinary care during 2019. Multivariable logistic regression analysis was used to evaluate demographic risk factors for insulinoma diagnosis. Of 2,250,741 study dogs, 278 were confirmed as insulinoma cases at any date. The estimated 2019 incidence risk was 0.003% (95% CI 0.002-0.004%). Compared to crossbreeds, predisposed breeds included Dogue de Bordeaux, German Pointer, Flat Coated Retriever, Boxer and West Highland White Terrier. The Labrador Retriever showed decreased odds for insulinoma diagnosis. Additionally, being a terrier breed and being a breed predisposed to other endocrine cancers were associated with increased odds for insulinoma diagnosis. Other risk factors associated with increased odds for insulinoma diagnosis included being female neutered, being 9 - <15 years of age, having an adult median bodyweight of 20 - <30 kg and having a bodyweight above the median for the sex/breed. This is the first study to report the epidemiology of canine insulinoma in dogs under primary veterinary care, resulting in crucial leads for further research in the epidemiology and etiology of canine insulinoma and possible links of canine insulinoma with other canine endocrine cancers. Additionally, the results can aid veterinarians to identify dogs at greater risk of insulinoma.

Genomic reconstruction reveals impact of population management strategies on modern Galápagos dogs

Free-breeding dogs have occupied the Galápagos Islands at least since the 1830s; however, it was not until the 1900s that dog populations grew substantially, endangering wildlife and spreading disease.1,2,3,4 In 1981, efforts to control the population size of free-roaming dogs began.1 Yet, there exist large free-roaming dog populations on the islands of Isabela and Santa Cruz whose ancestry has never been assessed on a genome-wide scale. We thus performed a complete genomic analysis of the current Galápagos dog population, as well as historical Galápagos dogs sampled between 1969 and 2003, testing for population structure, admixture, and shared ancestry. Our dataset included samples from 187 modern and six historical Galápagos dogs, together with whole-genome sequences from over 2,000 modern purebred and village dogs. Our results indicate that modern Galápagos dogs are recently admixed with purebred dogs but show no evidence of a population bottleneck related to the culling. Additionally, identity-by-descent analyses reveal evidence of shared shepherd-dog ancestry in the historical dogs. Overall, our results demonstrate that the 1980s culling of dogs was ineffective in controlling population size and did little to reduce genetic diversity, instead producing a stable and expanding population with genomic signatures of modern purebred dogs. The insights from this study can be used to improve population control strategies for the Galápagos Islands and other endangered endemic communities.

Genome-wide statistical evidence elucidates candidate factors of life expectancy in dogs

It is well-established that large and heavy dogs tend to live shorter lives. In this study, we aimed to determine whether traits other than body size are associated with the life expectancy of dogs. We compiled a dataset of 20 phenotypes, including body size, lifespan, snout ratio, and shedding, into a single matrix for 149 dog breeds using data from the American Kennel Club and other peer-reviewed sources. The analysis revealed that drooling might be associated with both the lifespan and body mass index of dogs. Furthermore, a genome-wide association study with adjusted phenotypes and statistical verification methods, such as Mendelian randomization. Additionally, conducting differential gene expression analysis with the salivary gland for the 2 cases, hypersalivation/less drooling vs various body sizes, we could observe the hypersalivation-related proteins. This genetic analysis suggests that body size and drooling might be candidate factors influencing lifespan. Consequently, we identified several candidate genes, including IGSF1, PACSIN2, PIK3R1, and MCCC2, as potential genetic factors influencing longevity-related phenotypes.

Empowering canine genomics: design and validation of a high-density SNP array for Indian dogs

India harbors a substantial population of 9.43 million dogs, showcasing diverse phenotypes and utility. Initiatives focusing on awareness, conservation, and informed breeding can greatly enhance the recognition and welfare of the unique Indian canine heritage. This study describes the design and development of a high-density SNP array for genomic characterization of Indian dogs. Paired-end (150 bp) DNA sequences of 48 samples from four diverse dog populations were generated with 10× coverage, following the standard pipeline of Axiom Array technology for chip design. More than 23 million raw SNPs were initially identified, with 629 597 SNP markers ultimately tiled on the Indian canine array (Axiom_Shwaan) after stringent filtering and processing. With an inter-marker distance of 3.8 kb the Axiom_Shwaan greatly increases the canine genome coverage. The array was validated by genotyping 186 samples representing 11 dog breeds/populations from India. The high call rate (99%) of SNPs on the designed chip indicates its suitability for use in Indian dog populations, reflecting sufficient genetic diversity. The principal component and phylogenetic analyses delineated the native dog breeds into discrete groups. This high-density SNP array will empower future applications in population genetics, breed/selection signature identification, development of trait-specific biomarkers, and genome-wide data mining for various canine abilities.

The quantitative anatomy of the hippocampal formation in homing pigeons and other pigeon breeds: implications for spatial cognition

Artificial selection for specific behavioural and physical traits in domesticated animals has resulted in a wide variety of breeds. One of the most widely recognized examples of behavioural selection is the homing pigeon (Columba livia), which has undergone intense selection for fast and efficient navigation, likely resulting in significant anatomical changes to the hippocampal formation. Previous neuroanatomical comparisons between homing and other pigeon breeds yielded mixed results, but only focused on volumes. We completed a more systematic test for differences in hippocampal formation anatomy between homing and other pigeon breeds by measuring volumes, neuron numbers and neuron densities in the hippocampal formation and septum across homing pigeons and seven other breeds. Overall, we found few differences in hippocampal formation volume across breeds, but large, significant differences in neuron numbers and densities. More specifically, homing pigeons have significantly more hippocampal neurons and at higher density than most other pigeon breeds, with nearly twice as many neurons as feral pigeons. These findings suggest that neuron numbers may be an important component of homing behaviour in homing pigeons. Our data also provide the first evidence that neuronal density can be modified by artificial selection, which has significant implications for the study of domestication and interbreed variation in anatomy and behaviour.

A map of canine sequence variation relative to a Greenland wolf outgroup

For over 15 years, canine genetics research relied on a reference assembly from a Boxer breed dog named Tasha (i.e., canFam3.1). Recent advances in long-read sequencing and genome assembly have led to the development of numerous high-quality assemblies from diverse canines. These assemblies represent notable improvements in completeness, contiguity, and the representation of gene promoters and gene models. Although genome graph and pan-genome approaches have promise, most genetic analyses in canines rely upon the mapping of Illumina sequencing reads to a single reference. The Dog10K consortium, and others, have generated deep catalogs of genetic variation through an alignment of Illumina sequencing reads to a reference genome obtained from a German Shepherd Dog named Mischka (i.e., canFam4, UU_Cfam_GSD_1.0). However, alignment to a breed-derived genome may introduce bias in genotype calling across samples. Since the use of an outgroup reference genome may remove this effect, we have reprocessed 1929 samples analyzed by the Dog10K consortium using a Greenland wolf (mCanLor1.2) as the reference. We efficiently performed remapping and variant calling using a GPU-implementation of common analysis tools. The resulting call set removes the variability in genetic differences seen across samples and breed relationships revealed by principal component analysis are not affected by the choice of reference genome. Using this sequence data, we inferred the history of population sizes and found that village dog populations experienced a 9-13 fold reduction in historic effective population size relative to wolves.

A RETREG1 variant is associated with hereditary sensory and autonomic neuropathy with acral self-mutilation in purebred German Spitz

Hereditary sensory and autonomic neuropathies (HSAN) represent a group of genetic diseases affecting the peripheral nervous system. In humans, at least 16 loci have been associated with the disorder but do not explain the disease origin of all patients. In dogs, similar conditions have been documented for decades in various breeds with a severe impact on life quality and are often referred to as acral mutilation syndrome (AMS). Causal variants in three genes have been identified to date, suggesting larger genetic heterogeneity in the dog population. Our aim was to explain the genetic etiology of an early-onset HSAN/AMS in a purebred German Spitz. The affected dog showed progressive loss of pain sensation in the distal extremities, which led to intense licking, biting, and self-mutilation of digits and paw pads. Whole-genome sequencing identified a single candidate causal variant on chromosome 4 in the RETREG1 gene (c.656C>T, p.Pro219Leu). This missense variant was previously recognized as deleterious in a mixed breed dog family with similar clinical signs. Haplotype analyses and targeted genotyping revealed a likely German Spitz ancestry of these mixed breed dogs. Further screening of an extensive cohort of ~900 000 dogs of various breeds hinted at the variant allele origin in the German Spitz breed. Disruption of RETREG1 inhibits endoplasmic reticulum turnover and leads to neuron degeneration. Our findings provide evidence that this variant underlies the recessive form of HSAN/AMS in the German Spitz and support the use of whole-genome sequencing-based veterinary precision medicine for early diagnosis and prevention via a genetic test.

Unraveling the DNA methylation landscape in dog blood across breeds

BACKGROUND

DNA methylation is a covalent bond modification that is observed mainly at cytosine bases in the context of CG pairs. DNA methylation patterns reflect the status of individual tissues, such as cell composition, age, and the local environment, in mammals. Genetic factors also impact DNA methylation, and the genetic diversity among various dog breeds provides a valuable platform for exploring this topic. Compared to those in the human genome, studies on the profiling of methylation in the dog genome have been less comprehensive.

RESULTS

Our study provides extensive profiling of DNA methylation in the whole blood of three dog breeds using whole-genome bisulfite sequencing. The difference in DNA methylation between breeds was moderate after removing CpGs overlapping with potential genetic variation. However, variance in methylation between individuals was common and often occurred in promoters and CpG islands (CGIs). Moreover, we adopted contextual awareness methodology to characterize DNA primary sequences using natural language processing (NLP). This method could be used to effectively separate unmethylated CGIs from highly methylated CGIs in the sequences that are identified by the conventional criteria.

CONCLUSIONS

This study presents a comprehensive DNA methylation landscape in the dog blood. Our observations reveal the similar methylation patterns across dog breeds, while CGI regions showed high variations in DNA methylation level between individuals. Our study also highlights the potential of NLP approach for analyzing low-complexity DNA sequences, such as CGIs.

Evolutionary consequences of domestication on the selective effects of new amino acid changing mutations in canids

The domestication of wild canids led to dogs no longer living in the wild but instead residing alongside humans. Extreme changes in behavior and diet associated with domestication may have led to the relaxation of the selective pressure on traits that may be less important in the domesticated context. Thus, here we hypothesize that strongly deleterious mutations may have become less deleterious in domesticated populations. We test this hypothesis by estimating the distribution of fitness effects (DFE) for new amino acid changing mutations using whole-genome sequence data from 24 gray wolves and 61 breed dogs. We find that the DFE is strikingly similar across canids, with 26-28% of new amino acid changing mutations being neutral/nearly neutral (|s| < 1e-5), and 41-48% under strong purifying selection (|s| > 1e-2). Our results are robust to different model assumptions suggesting that the DFE is stable across short evolutionary timescales, even in the face of putative drastic changes in the selective pressure caused by artificial selection during domestication and breed formation. On par with previous works describing DFE evolution, our data indicate that the DFE of amino acid changing mutations depends more strongly on genome structure and organismal characteristics, and less so on shifting selective pressures or environmental factors. Given the constant DFE and previous data showing that genetic variants that differentiate wolf and dog populations are enriched in regulatory elements, we speculate that domestication may have had a larger impact on regulatory variation than on amino acid changing mutations.

Breed function and behaviour correlate with endocranial volume in domestic dogs

Domestic dogs display a remarkable diversity of functions, morphologies and cognitive abilities. Using data from 1682 dogs representing 172 breeds, we tested for variation in relative endocranial volume (REV), a proxy for brain size and a basic measure of cognitive ability, in relation to breed function, phylogenetic classification, cranial shape, cooperative behaviour and temperament. Function, body size, phylogenetic clade and cranial shape correlate with REV. Toy dogs, functioning mainly as companions, have the largest endocranial volumes relative to their body size. Working dogs, bred to perform complex human-assistance skills and reportedly possessing higher cognitive abilities, have the smallest. Our results thus show that complex skills and cooperative behaviour-a hallmark of social cognition-do not predict larger REV in dogs. However, REV increases with fear and aggression, attention-seeking and separation anxiety and decreases with trainability. Significant correlations between REV and behavioural traits underscore the evolutionary plasticity of mammalian brain size under domestication and artificial selection and provide support for hypotheses linking the modulation of fear and aggression to brain size change under domestication.

Chromosome-scale assembly with improved annotation provides insights into breed-wide genomic structure and diversity in domestic cats

INTRODUCTION

Comprehensive genomic resources offer insights into biological features, including traits/disease-related genetic loci. The current reference genome assembly for the domestic cat (Felis catus), Felis_Catus_9.0 (felCat9), derived from sequences of the Abyssinian cat, may inadequately represent the general cat population, limiting the extent of deducible genetic variations.

OBJECTIVES

The goal was to develop Anicom American Shorthair 1.0 (AnAms1.0), a reference-grade chromosome-scale cat genome assembly.

METHODS

In contrast to prior assemblies relying on Abyssinian cat sequences, AnAms1.0 was constructed from the sequences of more popular American Shorthair breed, which is related to more breeds than the Abyssinian cat. By combining advanced genomics technologies, including PacBio long-read sequencing and Hi-C- and optical mapping data-based sequence scaffolding, we compared AnAms1.0 to existing Felidae genome assemblies (20 scaffolds, scaffolds N50 > 150 Mbp). Homology-based and ab initio gene annotation through Iso-Seq and RNA-Seq was used to identify new coding genes and splice variants.

RESULTS

AnAms1.0 demonstrated superior contiguity and accuracy than existing Felidae genome assemblies. Using AnAms1.0, we identified over 1.5 thousand structural variants and 29 million repetitions compared to felCat9. Additionally, we identified > 1,600 novel protein-coding genes. Notably, olfactory receptor structural variants and cardiomyopathy-related variants were identified.

CONCLUSION

AnAms1.0 facilitates the discovery of novel genes related to normal and disease phenotypes in domestic cats. The analyzed data are publicly accessible on Cats-I (https://cat.annotation.jp/), which we established as a platform for accumulating and sharing genomic resources to discover novel genetic traits and advance veterinary medicine.

Independent, but still observant-dog breeds selected for functional independence learn better from a conspecific demonstrator than cooperative breeds in a detour task

BACKGROUND

While complex dog-human coexistence has been deeply investigated, there is a relative scarcity of similar knowledge regarding dog-dog interactions. Social learning, a fundamental synchronizing mechanism between dogs and humans, was recently found to be influenced by the functional breed selection of dogs: with the cooperative breeds being more effective learners from a human demonstrator than the independent working breeds were. Here, we investigated whether these differences would also be present when dogs had to learn from another dog and how to effectively perform a detour around a transparent V-shaped obstacle. We tested dogs from 28 independent and 19 cooperative breeds in three consecutive trials. In the control groups, all dogs had to detour on their own the obstacle. In the dog demonstration groups, in trial 1, the subjects had to detour on their own, but before the next two trials, a trained dog showed them the solution.

RESULTS

We found that the performance of the two breed groups was the same in the without demonstration groups. However, after observing the dog demonstrator, the independent dogs learned the task more successfully than the cooperative breeds did. In the case of the independent working breeds, detour latencies significantly dropped along the consecutive trials, and these dogs also showed higher rate of successful detours after observing the demonstrator dog's action than in the control group.

CONCLUSIONS

This is the first study where the consequences of functional breed selection were confirmed in a scenario that involved conspecific social learning in dogs. The results fit well to the ecologically valid framework of the evolutionary past of dog breed formation, in which cooperative breeds were selected for their interactivity with humans, whereas independent breeds often had to work together with their conspecifics.

Exploring breed differences in discrimination, reversal learning, and resistance to extinction in the domestic dog (Canis familiaris)

Learning is crucial for shaping domestic dogs' behaviour through life experiences, yet not all breeds exhibit the same learning aptitude towards a particular task. The current study's objective was to identify differences in behaviour and learning performance across and within five breed clades and elucidate the underlying factors contributing into these variations. Dogs (n = 111) from five breed clades (UK Rural, Retrievers, Asian Spitz, European Mastiff, and New World) participated in a virtual learning task with their owners. Owners completed validated questionnaires of Impulsivity and Reward Responsiveness. The learning task comprised of reinforcing an arbitrary behaviour (hand-touch) through multiple sessions of Acquisition (reinforcing the hand-touch), Discrimination (reinforcing the hand-touch on one of two hands) and Reversal Learning (reinforcing the hand-touch on the opposite hand), followed by a single session of Extinction (hand-touch not reinforced). Results showed notable differences across the studied breed clades in certain learning and behavioural components. However, the observed disparities may not be entirely attributed to inherent cognitive differences among the breed clades but rather potentially influenced by contextual factors such as the human-dog communication dynamics associated with breeds' cooperativity. Furthermore, breed clades differed in the contributing factors predicting individual learning performances, which could highlight the potential effect of breeds' historical function.

Effect of pre-session discrimination training on performance in a judgement bias test in dogs

Spatial judgement bias tests (JBTs) can involve teaching animals that a bowl provides a reward in one location but does not in another. The animal is then presented with the bowl placed between the rewarded and the unrewarded locations (i.e., ambiguous locations) and their latency to approach reflects expectation of reward or 'optimism'. Some suggest that greater 'optimism' indicates better welfare. Performance in JBTs, however, may also indicate a learning history independently from welfare determinants. We hypothesized that dogs' 'optimism' in a follow-up JBT may be impacted by a learning treatment involving additional trials of a different discrimination task. Once enrolled, companion dogs (n = 16) were required to complete three study phases: (1) a pre-treatment JBT, (2) a learning treatment, and (3) a post-treatment JBT. During the JBTs, dogs were presented with five locations: one rewarded, one unrewarded, and three ambiguous (all unrewarded). Dogs were randomly assigned to a trial-based learning task-a nose-touch to the palm of the hand. In the Experimental discrimination treatment phase (n = 8), dogs were presented with two hands in each trial and only rewarded for touching one specific hand. In the Control treatment phase (n = 8), dogs were presented with one hand per trial in alternating sequence and were yoked to dogs in the Experimental group to receive the same number of rewarded and unrewarded trials (to control for possible frustration). Using a repeated measures mixed model with JBT repeated within dog, we found no difference in the change in approach latency to the ambiguous locations between the dogs across treatments. 'Optimism' as measured in this JBT was not altered by the additional discrimination trials used in our study.

Genomic Sequencing to Detect Cross-Breeding Quality in Dogs: An Example Studying Disorders in Sexual Development

Disorders of sexual development (DSDs) in dogs, similar to humans, arise from genetic mutations, gonadal differentiation, or phenotypic sex development. The French Bulldog, a breed that has seen a surge in popularity and demand, has also shown a marked increase in DSD incidence. This study aims to characterize the genetic underpinnings of DSDs in a French Bulldog named Brutus, exhibiting ambiguous genitalia and internal sexual anatomy, and to explore the impact of breeding practices on genetic diversity within the breed. We utilized a comprehensive approach combining conventional cytogenetics, molecular techniques, and deep sequencing to investigate the genetic profile of Brutus. The sequence data were compared to three other male French Bulldogs' genome sequences with typical reproductive anatomy, including Brutus's father and the canine reference genome (CanFam6). We found a Robertsonian fusion involving chromosome 23 previously reported in dogs as a causative mutation responsible for sex reversal syndrome. Our findings revealed a 22% mosaicism (78,XX/77,XX), the absence of the sex-determining region (SRY) gene, and the presence of 43 unique Single Nucleotide Variants (SNVs) not inherited from the father. Notably, the run of homozygosity (ROH) analysis showed Brutus has a higher number of homozygous segments compared to other Bulldogs, with a total length of these fragments 50% greater than the average, strongly suggesting this dog is the product of the mating between siblings. Although no direct causative genes for the DSD phenotype were identified, four candidate loci warrant further investigation. Our study highlighted the need for a better annotated and curated reference dog genome to define genes causative of any specific phenotype, suggests a potential genetic basis for the DSD phenotype in dogs, and underscores the consequences of uncontrolled breeding practices in French Bulldogs. These findings highlight the importance of implementing strategic genetic management to preserve genetic health and diversity in canine populations.

Genetic diversity and origin of Kazakh Tobet Dogs

The Kazakh Tobet is an indigenous Kazakh dog breed that has been used to guard livestock since ancient times. To understand the genetic structure and phylogenetic relationship of the Kazakh Tobet breed with other herding and livestock guarding dog breeds, we analysed short tandem repeat data of 107 Kazakh Tobet dogs from different regions of Kazakhstan and Mongolia, as well as whole genome sequencing data from two Kazakh Tobet dogs and 43 dogs from 24 working breeds. Our results indicate a high genetic diversity of the Kazakh Tobet, with the average number of alleles per locus ranging from 6.00 to 10.22 and observed heterozygosity ranging from 76 to 78%. The breed has a complex genetic structure characterised by seven different clusters. The neighbour-joining tree constructed based on 14,668,406 autosomal and the maximum likelihood tree based on mitochondrial D-loop sequences indicate a common genetic heritage between the Kazakh Tobet, the Central Asian Shepherd Dog and the Turkish Akbash. The presence of haplotype A18 in the Kazakh Tobets supports the hypothesis of the ancient origin of the breed, which was previously suggested by archaeological finds and written sources. These results provide an important genetic basis for the ongoing efforts to improve the Kazakh Tobet breed, to ensure its preservation as an independent genetic lineage and to recognise a breed on an international level.

Making fetch happen: Prevalence and characteristics of fetching behavior in owned domestic cats (Felis catus) and dogs (Canis familiaris)

Both cats and dogs fetch, but the likely function(s) of this behavior for each species have not been compared. In this study, we assessed data from online surveys of cat and dog behavior (Fe-BARQ; C-BARQ) completed by cat (N = 8224) and dog owners (N = 73724). We assessed responses to the items "Plays 'fetch'; likes to retrieve thrown objects or toys" (Fe-BARQ) and "Will 'fetch' or attempt to fetch sticks, balls, or objects" (C-BARQ). Cats and dogs described as "sometimes," "usually" or "always" fetching were categorized as fetchers. Regression models were used to examine which animal-related (e.g., sex, age) and environmental factors best predicted fetching, and chi-square tests were used to explore the effect of breed on fetching behavior. Fetching was reported in 40.9% of cats and 77.8% of dogs. In cats, fetching was correlated with play and activity. In dogs, fetching was correlated with overall trainability. In both cats and dogs, being female, older, living with (other) dogs, and having health problems decreased the likelihood of fetching. Breed effects were observed in both species, with fetching more prominent in cat breeds originating in the Far East (e.g., Burmese, Siamese, and Tonkinese) and in dog breeds from the Retriever, UK Rural, Poodle, Pointer and Spaniel clades. We discuss the results in the context of domestication history of both cats and dogs and posit several hypotheses about why fetching behavior is observed in both.

Exploring Levels of Interspecies Interaction: Expectations, Knowledge, and Empathy in Human-Dog Relationships

This exploratory study examines the complex dynamics of human-dog relationships and their impact on interspecies communication. Twelve human-dog dyads were studied using narrative interviews to explore how people perceive their relationships with their dogs. In addition, the dyads engaged in a cooperative task to observe interaction dynamics during everyday activities. This study shows that individual expectations frame interactions and that traditional notions of dog ownership are evolving into more family-like relationships. Effective communication relies on a nuanced mix of verbal and non-verbal cues, with empathy emerging as a fundamental element guiding these interactions. Our findings underline the profound influence of human expectations, knowledge and empathy on communication with dogs. They also highlight the critical role of compatibility between human and dog dyads, and emphasize that such compatibility is a key determinant of satisfaction in interspecies relationships. These findings contribute to a deeper understanding of how human factors modulate communication and satisfaction in human-animal interactions.

The doodle dilemma: How the physical health of 'Designer-crossbreed' Cockapoo, Labradoodle and Cavapoo dogs' compares to their purebred progenitor breeds

Booming UK ownership of designer-crossbreed dogs resulting from intentional crossing of distinct purebred breeds is often motivated by perceived enhanced health, despite limited evidence supporting a strong 'hybrid vigour' effect in dogs. Improved evidence on the relative health of designer-crossbreed dogs could support prospective owners to make better acquisition decisions when choosing their new dog. This study used a cross-sectional survey of UK owners of three common designer-crossbreeds (Cavapoo, Cockapoo, and Labradoodle) and their progenitor breeds (Cavalier King Charles Spaniel, Cocker Spaniel, Labrador Retriever, and Poodle) to collect owner-reported health disorder information. The authors hypothesised that designer-crossbred breeds have lower odds of common disorders compared to their progenitor breeds. Multivariable analysis accounted for confounding between breeds: dog age, sex, neuter status, and owner age and gender. The odds for the 57 most common disorders were compared across the three designer-crossbreeds with each of their two progenitor breeds (342 comparisons). Valid responses were received for 9,402 dogs. The odds did not differ statistically significantly between the designer-crossbreeds and their relevant progenitor breeds in 86.6% (n = 296) of health comparisons. Designer-crossbreeds had higher odds for 7.0% (n = 24) of disorders studied, and lower odds for 6.4% (n = 22). These findings suggest limited differences in overall health status between the three designer-crossbreeds and their purebred progenitors, challenging widespread beliefs in positive hybrid vigour effects for health in this emerging designer-crossbreed demographic. Equally, the current study did not suggest that designer-crossbreeds have poorer health as has also been purported. Therefore, owners could more appropriately base acquisition decisions between designer-crossbreeds and their purebred progenitors on other factors important to canine welfare such as breeding conditions, temperament, conformation and health of parents.

You talkin' to me? Functional breed selection may have fundamentally influenced dogs' sensitivity to human verbal communicative cues

BACKGROUND

The ability to learn from humans via observation was considered to be equally present across properly socialized dogs. We showed recently that cooperative working breeds learned from a human demonstrator more effectively. We hypothesized that functional breed selection could affect sensitivity to human attention-eliciting behavior. Accordingly, we ran the first ever study on dogs that compared the effect of ostensive and neutral verbal communication in a social learning scenario. We used the detour paradigm around a transparent V-shaped fence with either ostensive (addressing the receiver both with words and specific, attention-eliciting prosody) or neutral speech (monotonous reciting of a short poem) demonstration. The other features (gestures, movement) of the demonstration sequence were kept identical between the two conditions. We tested (N = 70) companion dogs from 17 cooperative and 16 independent breeds in three 1-min trials. Subjects had to obtain the reward by detouring around the fence.

RESULTS

Detour latencies of the cooperative dogs improved after both ostensive and neutral speech demonstrations. The independent dogs did not improve their detour latency in either of the conditions. Remarkably, ostensive verbal utterances elicited longer relative looking time towards the demonstrator, cooperative dogs looked longer at the demonstrator, and longer looking time resulted in more successful detours.

CONCLUSIONS

Our study provides the first indication that functional breed selection had a significant impact on dogs' sensitivity to ostensive human communication, which, apart from being crucially important for social learning from humans, until now was considered as a uniformly present heritage of domestication in dogs.

Personality Unleashed: Surveying Correlation of Neuter Status and Social Behaviour in Mixed-Breed Male Dogs across Weight Classes

This study investigates the behavioural differences between neutered and intact dogs. A total of 230 questionnaires of neutered (n = 115) and intact (n = 115) mixed-breed male dogs were collected. Small, medium, large, and giant dogs were analysed to investigate a possible influence of body size. The results showed neuters were significantly more stressed than intacts (multinomial logistic regression, p = 0.001). In terms of stress by influences (such as separation anxiety and anxiety at car rides), neutered small, medium, and large dogs were more stressed than giant dogs (multinomial logistic regression, p = 0.05). Neuters were also found to be more aggressive in general (multinomial logistic regression, p = 0.04) and more aggressive on the walk (multinomial logistic regression, p = 0.02). In addition, personality questionnaires revealed significant differences in all characteristics. Neuters were less emotionally calm (multiple ordinal regression, p = 0.03), less trainable and less sociable (each multiple ordinal regression, p < 0.001). They also scored lower on extraversion (multiple ordinal regression, p = 0.04). These findings highlight the importance of further research into the behavioural effects of neutering dogs, as well as the need for evidence-based guidelines for neutering practices.

Genomic analyses identify 15 susceptibility loci and reveal HDAC2, SOX2-OT, and IGF2BP2 in a naturally-occurring canine model of gastric cancer

Gastric cancer (GC) is the fifth most common human cancer worldwide, but the genetic etiology is largely unknown. We performed a Bayesian genome-wide association study and selection analyses in a naturally-occurring canine model of GC, the Belgian Tervuren and Sheepdog breeds, to elucidate underlying genetic risk factors. We identified 15 loci with over 90% predictive accuracy for the GC phenotype. Variant filtering revealed germline putative regulatory variants for the EPAS1 (HIF2A) and PTEN genes and a coding variant in CD101. Although closely related to Tervuren and Sheepdogs, Belgian Malinois rarely develop GC. Across-breed analyses uncovered protective haplotypes under selection in Malinois at SOX2-OT and IGF2BP2. Among Tervuren and Sheepdogs, HDAC2 putative regulatory variants were present at comparatively high frequency and were associated with GC. Here, we describe a complex genetic architecture governing GC in a dog model, including genes such as PDZRN3, that have not been associated with human GC.

Multiple ancestries and shared gene flow among modern livestock guarding dogs

Livestock guarding dogs (LGDs) have been used to protect livestock for millennia. While previous works suggested a single origin of modern LGDs, the degree and source of shared ancestry have not been tested. To address this, we generated genome-wide SNP data from 304 LGDs and combined it with public genomic data from 2,183 modern and 22 ancient dogs. Our findings reveal shared ancestry and extensive gene flow among modern LGD breeds which we attribute to historical livestock migrations. Additionally, admixture between LGDs and free-ranging dogs argues against reproductive isolation as a core mechanism for maintaining the specialized skills of LGDs. Finally, we identify two lineages within modern LGDs and uncover multiple ancestries tracing back to distinct Eurasian ancient dogs, concordant with the absence of a single ancestor. Overall, our work explores the complex evolutionary history of LGDs, offering valuable insights into how human and livestock co-migrations shaped this functional group.

Cooperative but Dependent-Functional Breed Selection in Dogs Influences Human-Directed Gazing in a Difficult Object-Manipulation Task

It is still largely unknown to what extent domestication, ancestry, or recent functional selection are responsible for the behavioral differences in whether dogs look back to a human when presented with a difficult task. Here, we tested whether this ubiquitous human-related response of companion dogs would appear differently in subjects that were selected for either cooperative or independent work tasks. We tested N = 71 dogs from 18 cooperative and 18 independent breeds. Subjects learned in a five-trial warming-up phase that they could easily obtain the reward from a container. In trial six, the reward became impossible to take out from the locked container. When the task was easy, both breed groups behaved similarly, and their readiness to approach the container did not differ between the last 'solvable' and the subsequent 'unsolvable' trial. Task focus, looking at the container, touching the container for the first time, or interacting with the container with a paw or nose did not differ between the breed groups, indicating that their persistence in problem solving was similar. However, in the 'unsolvable' trial, cooperative dogs alternated their gaze more often between the container and the humans than the independent dogs did. The frequency of looking back was also higher in cooperative dogs than in the independent breeds. These are the first empirical results that suggest, in a balanced, representative sample of breeds, that the selection for different levels of cooperativity in working dogs could also affect their human-dependent behavior in a generic problem-solving situation.

Bringing the Genomic Revolution to Comparative Oncology: Human and Dog Cancers

Dogs are humanity's oldest friend, the first species we domesticated 20,000-40,000 years ago. In this unequaled collaboration, dogs have inadvertently but serendipitously been molded into a potent human cancer model. Unlike many common model species, dogs are raised in the same environment as humans and present with spontaneous tumors with human-like comorbidities, immunocompetency, and heterogeneity. In breast, bladder, blood, and several pediatric cancers, in-depth profiling of dog and human tumors has established the benefits of the dog model. In addition to this clinical and molecular similarity, veterinary studies indicate that domestic dogs have relatively high tumor incidence rates. As a result, there are a plethora of data for analysis, the statistical power of which is bolstered by substantial breed-specific variability. As such, dog tumors provide a unique opportunity to interrogate the molecular factors underpinning cancer and facilitate the modeling of new therapeutic targets. This review discusses the emerging field of comparative oncology, how it complements human and rodent cancer studies, and where challenges remain, given the rapid proliferation of genomic resources. Increasingly, it appears that human's best friend is becoming an irreplaceable component of oncology research.

Structure and scaling of the middle ear in domestic dog breeds

Although domestic dogs vary considerably in both body size and skull morphology, behavioural audiograms have previously been found to be similar in breeds as distinct as a Chihuahua and a St Bernard. In this study, we created micro-CT reconstructions of the middle ears and bony labyrinths from the skulls of 17 dog breeds, including both Chihuahua and St Bernard, plus a mongrel and a wolf. From these reconstructions, we measured middle ear cavity and ossicular volumes, eardrum and stapes footplate areas and bony labyrinth volumes. All of these ear structures scaled with skull size with negative allometry and generally correlated better with condylobasal length than with maximum or interaural skull widths. Larger dogs have larger ear structures in absolute terms: the volume of the St Bernard's middle ear cavity was 14 times that of the Chihuahua. The middle and inner ears are otherwise very similar in morphology, the ossicular structure being particularly well-conserved across breeds. The expectation that larger ear structures in larger dogs would translate into hearing ranges shifted towards lower frequencies is not consistent with the existing audiogram data. Assuming that the audiograms accurately reflect the hearing of the breeds in question, oversimplifications in existing models of middle ear function or limitations imposed by other parts of the auditory system may be responsible for this paradox.

Frequency of RPGRIP1 and MAP9 genetic modifiers of canine progressive retinal atrophy, in 132 breeds of dog

Variants in RPGRIP1 and MAP9, termed RPGRIP1ins44 and MAP9del respectively, are both associated with a form of canine progressive retinal atrophy referred to as RPGRIP1-CRD and have both been demonstrated to modify the development and progression of this disease. In the current study both variants were genotyped in at least 50 dogs of 132 diverse breeds and the data reveal that both segregate in multiple breeds. Individually, each variant is common within largely non-overlapping subsets of breed, and there is a negative correlation between their frequencies within breeds that segregate both variants. The frequency of both variants exceeds 0.05 in a single breed only, the Miniature Longhaired Dachshund. These data indicate that both variants are likely to be ancient and predate the development and genetic isolation of modern dog breeds. That both variants are present individually at high frequency in multiple breeds is consistent with the hypothesis that homozygosity of either variant alone is not associated with a clinically relevant phenotype, whereas the negative correlation between the two variants is consistent with the application of selective pressure, from dog breeders, against homozygosity at both loci, probably due to the more severe phenotype associated with homozygosity at both loci.

The reduction in relative brain size in the domesticated dog is not an evolutionary singularity among the canids

Domestication has long been considered the most powerful evolutionary engine behind dramatic reductions in brain size in several taxa, and the dog (Canis familiaris) is considered as a typical example that shows a substantial decrease in brain size relative to its ancestor, the grey wolf (Canis lupus). However, to make the case for exceptional evolution of reduced brain size under domestication requires an interspecific approach in a phylogenetic context that can quantify the extent by which domestication reduces brain size in comparison to closely related non-domesticated species responding to different selection factors in the wild. Here, we used a phylogenetic method to identify evolutionary singularities to test if the domesticated dog stands out in terms of relative brain size from other species of canids. We found that the dog does not present unambiguous signature of evolutionary singularity with regard to its small brain size, as the results were sensitive to the considerations about the ancestral trait values upon domestication. However, we obtained strong evidence for the hibernating common raccoon dog (Nyctereutes procyonoides) being an evolutionary outlier for its brain size. Therefore, domestication is not necessarily an exceptional case concerning evolutionary reductions in brain size in an interspecific perspective.

Large-scale genomic analysis of the domestic dog informs biological discovery

Recent advances in genomics, coupled with a unique population structure and remarkable levels of variation, have propelled the domestic dog to new levels as a system for understanding fundamental principles in mammalian biology. Central to this advance are more than 350 recognized breeds, each a closed population that has undergone selection for unique features. Genetic variation in the domestic dog is particularly well characterized compared with other domestic mammals, with almost 3000 high-coverage genomes publicly available. Importantly, as the number of sequenced genomes increases, new avenues for analysis are becoming available. Herein, we discuss recent discoveries in canine genomics regarding behavior, morphology, and disease susceptibility. We explore the limitations of current data sets for variant interpretation, tradeoffs between sequencing strategies, and the burgeoning role of long-read genomes for capturing structural variants. In addition, we consider how large-scale collections of whole-genome sequence data drive rare variant discovery and assess the geographic distribution of canine diversity, which identifies Asia as a major source of missing variation. Finally, we review recent comparative genomic analyses that will facilitate annotation of the noncoding genome in dogs.

Co-analysis of methylation platforms for signatures of biological aging in the domestic dog reveals previously unexplored confounding factors

Chronological age reveals the number of years an individual has lived since birth. By contrast, biological age varies between individuals of the same chronological age at a rate reflective of physiological decline. Differing rates of physiological decline are related to longevity and result from genetics, environment, behavior, and disease. The creation of methylation biological age predictors is a long-standing challenge in aging research due to the lack of individual pre-mortem longevity data. The consistent differences in longevity between domestic dog breeds enable the construction of biological age estimators which can, in turn, be contrasted with methylation measurements to elucidate mechanisms of biological aging. We draw on three flagship methylation studies using distinct measurement platforms and tissues to assess the feasibility of creating biological age methylation clocks in the dog. We expand epigenetic clock building strategies to accommodate phylogenetic relationships between individuals, thus controlling for the use of breed standard metrics. We observe that biological age methylation clocks are affected by population stratification and require heavy parameterization to achieve effective predictions. Finally, we observe that methylation-related markers reflecting biological age signals are rare and do not colocalize between datasets.

Dogs and their genes: what ever will they think of next?

The Edward Novitski Prize recognizes creativity and intellectual ingenuity in the solution of problems in genetics research. The prize honors scientific experimental work-either a single experimental accomplishment or a body of work. Ostrander is recognized for work developing the domestic dog as an experimental system for solving fundamental biological problems and identifying genetic sequences of relevance to human health and disease. Including work on disease and behavioral health, Ostrander has shown a dedication to creative methods for understanding canine genetics and the value of translating research organisms to human genetics.

Exploring the impact of epidemiological and clinical factors on the progression of canine leishmaniosis by statistical and whole genome analyses: from breed predisposition to comorbidities

Canine leishmaniosis (CanL), caused by Leishmania infantum, is a complex disease of growing importance in Europe. Clinical manifestations result from the down-modulation of the host immune response through multiple host-parasite interactions. Although several factors might influence CanL progression, this is the first known study evaluating risk factors for its different clinical stages in a large referral hospital population (n = 35.669) from an endemic area, over a 20 year period. Genome-wide scans for selection signatures were also conducted to explore the genomic component of clinical susceptibility to L. infantum infection. The prevalence of CanL was 3.2% (16.7% stage I; 43.6% stage II; 32.1% stage III; 7.6% stage IV). Dog breed (crossbreed), bodyweight (<10 kg), living conditions (indoors), regular deworming treatment, and being vaccinated against Leishmania significantly decreased the transmission risk and the risk for developing severe clinical forms. Conversely, the detection of comorbidities was associated with advanced clinical forms, particularly chronic kidney disease, neoplasia, cryptorchidism, infectious tracheobronchitis and urate urolithiasis, although those did not impact the clinical outcome. Significant associations between an increased risk of severe clinical stages and findings in the anamnesis (renal or skin-related manifestations) and physical examination (ocular findings) were also detected, highlighting their diagnostic value in referred cases of CanL. Sixteen breeds were found to be significantly more susceptible to developing severe stages of leishmaniosis (e.g. Great Dane, Rottweiler, English Springer Spaniel, Boxer, American Staffordshire Terrier, Golden Retriever), while 20 breeds displayed a clinical resistantance phenotype and, thus, are more likely to mount an efficient immune response against L. infantum (e.g. Pointer, Samoyed, Spanish Mastiff, Spanish Greyhound, English Setter, Siberian Husky). Genomic analyses of these breeds retrieved 12 regions under selection, 63 candidate genes and pinpointed multiple biological pathways such as the IRE1 branch of the unfolded protein response, which could play a critical role in clinical susceptibility to L. infantum infection.

A Nonsynonymous Substitution of Lhx3 Leads to Changes in Body Size in Dogs and Mice

Lhx3 is a LIM-homeodomain transcription factor that affects body size in mammals by regulating the secretion of pituitary hormones. Akita, Shiba Inu, and Mame Shiba Inu dogs are Japanese native dog breeds that have different body sizes. To determine whether Lhx3 plays a role in the differing body sizes of these three dog breeds, we sequenced the Lhx3 gene in the three breeds, which led to the identification of an SNP in codon 280 (S280N) associated with body size. The allele frequency at this SNP differed significantly between the large Akita and the two kinds of smaller Shiba dogs. To validate the function of this SNP on body size, we introduced this change into the Lhx3 gene of mice. Homozygous mutant mice (S279N+/+) were found to have significantly increased body lengths and weights compared to heterozygous mutant (S279N+/-) and wild-type (S279N-/-) mice several weeks after weaning. These results demonstrate that a nonsynonymous substitution in Lhx3 plays an important role in regulating body size in mammals.

From "Husky" to "Bulldog"- behavioural correlates between castration and breed groups in the domestic dog (Canis lupus familiaris)

Neutering dogs is a widespread method and is carried out for various behavioural and husbandry reasons. This study's main objective is to investigate the behavioural correlations between neutering and the breed of male dogs. In order to possibly find breed-dependent differences in the behaviour of intact and castrated dogs, a differentiation between two clades - the "Huskies"(chow chow, shar pei, akita/shiba inu, alaskan malamute, siberian/alaskan husky) and the "Bulldogs" (german boxer, english/french bulldog, old english mastiff, boston terrier, english bull terrier, staffordshire bull terrier, american staffordshire terrier), based on Parker et al. [1], was made.Using an online questionnaire,, 31 neutered and 37 intact male dogs from the clade "Huskies" and 30 neutered and 38 intact male dogs from the clade "Bulldogs", participated in the study (N = 136).The survey included detailed questions on the dogs' personality and any associated issues as well as a behavioural anamnesis. Further questions relating to four of the "big five" personality dimensions based on the "Budapest questionnaire" by Turcsán et al. from 2011 [2] were also added.The results show, that neutered males from both breed clades more frequently displayed aggression toward humans than intact males (multinomial logistic regression, p = 0.002). When it came to aggression towards other dogs, it was the "Huskies" that differed significantly from the "Bulldogs"(multinomial logistic regression, p = 0.04) with being more aggressive. There were also significant differences in stress-related behaviour depending on castration status and breed (multinomial logistic regression, p < 0.001; Cramer's V = 0.33) and only the castration status had an impact on the significance (multinomial logistic regression, p < 0.001). The analysis also revealed significance for stress-indicating behaviour with dependence on neutering status (multinomial logistic regression, p < 0.001) and showed that stress as well as uncertainty are significantly more common in neutered dogs depending on breed and neutering status (multinomial logistic regression, p < 0.001; Cramer's V = 0.42), in that only neutered "Bulldogs" were stressed, but more "Huskies" overall.According to the Budapest questionnaire data, the "Bulldog" clade had considerably greater extraversion scores overall (ordinal regression, p < 0.001) than the "Huskies".Our findings highlight the risks and potential negative effects of neutering. Gonadectomy in no way substitutes for the dog receiving the necessary socialization, training, or bonding. Although in some circumstances it might have a favourable impact on the dog's behaviour, it should not be seen as a panacea for unwanted behaviour. Given that not all behaviours are influenced by sex hormones, every castration decision must be weighed up individually.

Urinary and household chemical exposures in pet dogs with urothelial cell carcinoma

Urothelial cell carcinoma (UCC) has been linked to environmental chemical exposures in people, but these risk factors are not well understood in dogs with UCC. We hypothesised that household chemical exposures contribute to the risk of UCC in pet dogs. This prospective cross-sectional case-control study included 37 dogs with UCC and 37 unaffected breed-, sex-, and age-matched controls. Dog owners completed an environmental questionnaire and household samples were collected and analysed for arsenic (in tap water and room dust) and acrolein (in room air). Urine samples from UCC dogs, control dogs, and consenting owners were analysed for inorganic arsenic species, the acrolein metabolite 3-HPMA, and the phenoxy herbicide 2,4-D. Public data on chlorination byproducts (total trihalomethanes) in municipal drinking water were also compared between case and control households. Dogs with UCC were more likely to swim in a pool (15.2%) compared with control dogs (0%) (OR 1.69, 95% CI = 1.69-∞; p = .02). Dogs with UCC also had more than 4-fold higher reported municipal water concentrations of chlorination byproducts (median 28.0 ppb) compared with controls (median 6.9 ppb; p < .0001). Dust arsenic concentrations were unexpectedly lower in case households (median 0.277 ng/cm2) compared with control households (median 0.401 ng/cm2; p = .0002). Other outcomes were not significantly different between groups. These data suggest that dog owners, especially those of breeds known to be at higher risk for UCC, consider limiting access to swimming pools and installing water filtration units that remove total trihalomethanes.

Genome-wide analyses reveals an association between invasive urothelial carcinoma in the Shetland sheepdog and NIPAL1

Naturally occurring canine invasive urinary carcinoma (iUC) closely resembles human muscle invasive bladder cancer in terms of histopathology, metastases, response to therapy, and low survival rate. The heterogeneous nature of the disease has led to the association of large numbers of risk loci in humans, however most are of small effect. There exists a need for new and accurate animal models of invasive bladder cancer. In dogs, distinct breeds show markedly different rates of iUC, thus presenting an opportunity to identify additional risk factors and overcome the locus heterogeneity encountered in human mapping studies. In the association study presented here, inclusive of 100 Shetland sheepdogs and 58 dogs of other breeds, we identify a homozygous protein altering point mutation within the NIPAL1 gene which increases risk by eight-fold (OR = 8.42, CI = 3.12-22.71), accounting for nearly 30% of iUC risk in the Shetland sheepdog. Inclusion of six additional loci accounts for most of the disease risk in the breed and explains nearly 75% of the phenotypes in this study. When combined with sequence data from tumors, we show that variation in the MAPK signaling pathway is an overarching cause of iUC susceptibility in dogs.

Transcript abundance of hepatic drug-metabolizing enzymes in two dog breeds compared with 14 species including humans

Drug-metabolizing enzymes are important in drug development and therapy, but have not been fully identified and characterized in many species, lines, and breeds. Liver transcriptomic data were analyzed for phase I cytochromes P450, flavin-containing monooxygenases, and carboxylesterases and phase II UDP-glucuronosyltransferases, sulfotransferases, and glutathione S-transferases. Comparisons with a variety of species (humans, rhesus macaques, African green monkeys, baboons, common marmosets, cattle, sheep, pigs, cats, dogs, rabbits, tree shrews, rats, mice, and chickens) revealed both general similarities and differences in the transcript abundances of drug-metabolizing enzymes. Similarly, Beagle and Shiba dogs were examined by next-generation sequencing (RNA-seq). Consequently, no substantial differences in transcript abundance were noted in different breeds of pigs and dogs and in different lines of mice and rats. Therefore, the expression profiles of hepatic drug-metabolizing enzyme transcripts appear to be similar in Shiba and Beagle dogs and pig breeds and the rat and mouse lines analyzed, although some differences were found in other species.

Transposons in the Williams-Beuren Syndrome Critical Region are Associated with Social Behavior in Assistance Dogs

A strong signature of selection in the domestic dog genome is found in a five-megabase region of chromosome six in which four structural variants derived from transposons have previously been associated with human-oriented social behavior, such as attentional bias to social stimuli and social interest in strangers. To explore these genetic associations in more phenotypic detail-as well as their role in training success in a specialized assistance dog program-we genotyped 1001 assistance dogs from Canine Companions for Independence®, including both successful graduates and dogs released from the training program for behaviors incompatible with their working role. We collected phenotypes on each dog using puppy-raiser questionnaires, trainer questionnaires, and both cognitive and behavioral tests. Using Bayesian mixed models, we found strong associations (95% credibility intervals excluding zero) between genotypes and certain behavioral measures, including separation-related problems, aggression when challenged or corrected, and reactivity to other dogs. Furthermore, we found moderate differences in the genotypes of dogs who graduated versus those who did not; insertions in GTF2I showed the strongest association with training success (β = 0.23, CI95% = - 0.04, 0.49), translating to an odds-ratio of 1.25 for one insertion. Our results provide insight into the role of each of these four transposons in canine sociability and may inform breeding and training practices for working dog organizations. Furthermore, the observed importance of the gene GTF2I supports the emerging consensus that variation in GTF2I genotypes and expression have important consequences for social behavior broadly.