Evolutionary genomics of dog domestication

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.

Does a Dog at School Help Identify Human and Animal Facial Expressions? A Preliminary Longitudinal Study

(1) Background: Animals provide many benefits in children's lives, but few studies assess the effects of animal presence-especially service dogs-in schools. This pilot study examined whether a year-long exposure to a service dog could improve facial expression recognition in adolescents with cognitive function disorders. (2) Method: Twenty-three adolescents participated: 10 with cognitive function disorders who were part of a specialized French teaching program (LUSI) that included a service dog (LUSI group), and 13 neurotypical adolescents who served as controls (not in LUSI, no service dog exposure). Participants assigned one of five facial expressions (sadness, joy, fear, neutral, anger) to images of human, dog, and cat faces at three intervals: before dog integration, at 5-8 months, and 11-14 months later (same intervals for controls). (3) Results: Identification of facial expressions of both dog (p = 0.001) and human (p = 0.01) but not cat (p > 0.05) faces by LUSI participants exposed to service dog improved with time. The performance of LUSI participants was better when they lived with various species of animals at home. Control participants' performance did not change significantly (all p > 0.05). (4) Conclusions: After a school year, the presence of a service dog had helped adolescents with cognitive function disorders to better identify human and dog facial expressions.

BOAS in the Boston Terrier: A healthier screw-tailed breed?

Brachycephalic obstructive airway syndrome (BOAS) is well documented in the three most popular brachycephalic dog breeds of the UK and several other countries: French Bulldogs, Pugs and Bulldogs. More extreme conformation has been found to be associated with increased risk of BOAS and other brachycephalic disease in these breeds, such as ocular, neurological, and dental disease. Less is known about how BOAS and other brachycephalic conformation-related disease affects other breeds such as the Boston Terrier. In this study, one-hundred and seven Boston Terriers were prospectively recruited from the UK dog population and underwent clinical assessment, respiratory function grading and conformational measurements. Whole-body barometric plethysmography was used in a smaller cohort of dogs to compare the quantitative differences in respiratory parameters between both affected and unaffected Boston Terriers, and control mesocephalic dogs. When compared to an equivalent study population of French Bulldogs and Bulldogs, it was found that Boston Terriers have a significantly higher proportion of BOAS Grade 0 dogs at 37.5% compared to 10% and 15.2% respectively (p<0.01). Within the breed, more extreme brachycephalic conformation was found to be associated with an increased risk of BOAS: specifically, nostril stenosis, facial foreshortening, abnormal scleral show, and higher neck to chest girth ratio. However, there is considerable overlap between measurements of affected and unaffected dogs in these variables. Therefore, the use of respiratory function grading is likely to be more advantageous for owners, breeders, and veterinary surgeons in accurately selecting unaffected dogs.

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.

Genome-wide detection of positive and balancing signatures of selection shared by four domesticated rainbow trout populations (Oncorhynchus mykiss)

BACKGROUND

Evolutionary processes leave footprints along the genome over time. Highly homozygous regions may correspond to positive selection of favorable alleles, while maintenance of heterozygous regions may be due to balancing selection phenomena. We analyzed data from 176 fish from four disconnected domestic rainbow trout populations that were genotyped using a high-density Axiom Trout genotyping 665K single nucleotide polymorphism array, including 20 from the US and 156 from three French lines. Using methods based on runs of homozygosity and extended haplotype homozygosity, we detected signatures of selection in these four populations.

RESULTS

Nine genomic regions that included 253 genes were identified as being under positive selection in all four populations Most were located on chromosome 2 but also on chromosomes 12, 15, 16, and 20. In addition, four heterozygous regions that contain 29 genes that are putatively under balancing selection were also shared by the four populations. These were located on chromosomes 10, 13, and 19. Regardless of the homozygous or heterozygous nature of the regions, in each region, we detected several genes that are highly conserved among vertebrates due to their critical roles in cellular and nuclear organization, embryonic development, or immunity. We identified new candidate genes involved in rainbow trout fitness, as well as 17 genes that were previously identified to be under positive selection, 10 of which in other fishes (auts2, atp1b3, zp4, znf135, igf-1α, brd2, col9a2, mrap2, pbx1, and emilin-3).

CONCLUSIONS

Using material from disconnected populations of different origins allowed us to draw a genome-wide map of signatures of positive selection that are shared between these rainbow trout populations, and to identify several regions that are putatively under balancing selection. These results provide a valuable resource for future investigations of the dynamics of genetic diversity and genome evolution during domestication.

Alarm or emotion? intranasal oxytocin helps determine information conveyed by dog barks for adult male human listeners

BACKGROUND

Barks play an important role in interspecific communication between dogs and humans, by allowing a reliable perception of the inner state of dogs for human listeners. However, there is growing concern in society regarding the nuisance that barking dogs cause to the surrounding inhabitants. We assumed that at least in part, this nuisance effect can be explained by particular communicative functions of dog barks. In this study we experimentally tested two separate hypotheses concerning how the content of dog barks could affect human listeners. According to the first hypothesis, barks that convey negative inner states, would especially cause stress in human listeners due to the process called interspecific empathy. Based on the second hypothesis, alarm-type dog barks cause particularly strong stress in the listener, by capitalizing on their specific acoustic makeup (high pitch, low tonality) that resembles to the parameters of a baby's cry. We tested 40 healthy, young adult males in a double-blind placebo controlled experiment, where participants received either intranasal oxytocin or placebo treatment. After an incubation period, they had to evaluate the (1) perceived emotions (happiness, fear and aggression), that specifically created dog bark sequences conveyed to them; and (2) score the annoyance level these dog barks elicited in them.

RESULTS

We found that oxytocin treatment had a sensitizing effect on the participants' reactions to negative valence emotions conveyed by dog barks, as they evaluated low fundamental frequency barks with higher aggression scores than the placebo-treated participants did. On the other hand, oxytocin treatment attenuated the annoyance that noisy (atonal) barks elicited from the participants.

CONCLUSIONS

Based on these results, we provide first-hand evidence that dog barks provide information to humans (which may also cause stress) in a dual way: through specific attention-grabbing functions and through emotional understanding.

Systematically identifying genetic signatures including novel SNP-clusters, nonsense variants, frame-shift INDELs, and long STR expansions that potentially link to unknown phenotypes existing in dog breeds

BACKGROUND

In light of previous studies that profiled breed-specific traits or used genome-wide association studies to refine loci associated with characteristic morphological features in dogs, the field has gained tremendous genetic insights for known dog traits observed among breeds. Here we aim to address the question from a reserve perspective: whether there are breed-specific genotypes that may underlie currently unknown phenotypes. This study provides a complete set of breed-specific genetic signatures (BSGS). Several novel BSGS with significant protein-altering effects were highlighted and validated.

RESULTS

Using the next generation whole-genome sequencing technology coupled with unsupervised machine learning for pattern recognitions, we constructed and analyzed a high-resolution sequence map for 76 breeds of 412 dogs. Genomic structures including novel single nucleotide polymorphisms (SNPs), SNP clusters, insertions, deletions (INDELs) and short tandem repeats (STRs) were uncovered mutually exclusively among breeds. We also partially validated some novel nonsense variants by Sanger sequencing with additional dogs. Four novel nonsense BSGS were found in the Bernese Mountain Dog, Samoyed, Bull Terrier, and Basset Hound, respectively. Four INDELs resulting in either frame-shift or codon disruptions were found in the Norwich Terrier, Airedale Terrier, Chow Chow and Bernese Mountain Dog, respectively. A total of 15 genomic regions containing three types of BSGS (SNP-clusters, INDELs and STRs) were identified in the Akita, Alaskan Malamute, Chow Chow, Field Spaniel, Keeshond, Shetland Sheepdog and Sussex Spaniel, in which Keeshond and Sussex Spaniel each carried one amino-acid changing BSGS in such regions.

CONCLUSION

Given the strong relationship between human and dog breed-specific traits, this study might be of considerable interest to researchers and all. Novel genetic signatures that can differentiate dog breeds were uncovered. Several functional genetic signatures might indicate potentially breed-specific unknown phenotypic traits or disease predispositions. These results open the door for further investigations. Importantly, the computational tools we developed can be applied to any dog breeds as well as other species. This study will stimulate new thinking, as the results of breed-specific genetic signatures may offer an overarching relevance of the animal models to human health and disease.

Domestic dog lineages reveal genetic drivers of behavioral diversification

Selective breeding of domestic dogs has generated diverse breeds often optimized for performing specialized tasks. Despite the heritability of breed-typical behavioral traits, identification of causal loci has proven challenging due to the complexity of canine population structure. We overcome longstanding difficulties in identifying genetic drivers of canine behavior by developing a framework for understanding relationships between breeds and the behaviors that define them, utilizing genetic data for over 4,000 domestic, semi-feral, and wild canids and behavioral survey data for over 46,000 dogs. We identify ten major canine genetic lineages and their behavioral correlates and show that breed diversification is predominantly driven by non-coding regulatory variation. We determine that lineage-associated genes converge in neurodevelopmental co-expression networks, identifying a sheepdog-associated enrichment for interrelated axon guidance functions. This work presents a scaffold for canine diversification that positions the domestic dog as an unparalleled system for revealing the genetic origins of behavioral diversity.

Volumetric assessment and longitudinal changes of subcortical structures in formalinized Beagle brains

High field MRI is an advanced technique for diagnostic and research purposes on animal models, such as the Beagle dog. In this context, studies on neuroscience applications, e.g. aging and neuro-pathologies, are currently increasing. This led to a need for reference values, in terms of volumetric assessment, for the structures typically involved. Nowadays, several canine brain MRI atlases have been provided. However, no reports are available regarding the measurements’ reproducibility and little is known about the effect of formalin on MRI segmentation. Here, we assessed the segmentation variability of selected structures among operators (two operators segmented the same data) in a sample of 11 Beagle dogs. Then, we analyzed, for one Beagle dog, the longitudinal volumetric changes of these structures. We considered four conditions: in vivo, post mortem (after euthanasia), ex vivo (brain extracted and studied after 1 month in formalin, and after 12 months). The MRI data were collected with a 3 T scanner. Our findings suggest that the segmentation procedure was overall reproducible since only slight statistical differences were detected. In the post mortem/ ex vivo comparison, most structures showed a higher contrast, thereby leading to greater reproducibility between operators. We observed a net increase in the volume of the studied structures. This could be justified by the intrinsic relaxation time changes observed because of the formalin fixation. This led to an improvement in brain structure visualization and segmentation. To conclude, MRI-based segmentation seems to be a useful and accurate tool that allows longitudinal studies on formalin-fixed brains.

Identification of genes associated with human-canine communication in canine evolution

The dog (Canis familiaris) was the first domesticated animal and hundreds of breeds exist today. During domestication, dogs experienced strong selection for temperament, behaviour, and cognitive ability. However, the genetic basis of these abilities is not well-understood. We focused on ancient dog breeds to investigate breed-related differences in social cognitive abilities. In a problem-solving task, ancient breeds showed a lower tendency to look back at humans than other European breeds. In a two-way object choice task, they showed no differences in correct response rate or ability to read human communicative gestures. We examined gene polymorphisms in oxytocin, oxytocin receptor, melanocortin 2 receptor, and a Williams-Beuren syndrome-related gene (WBSCR17), as candidate genes of dog domestication. The single-nucleotide polymorphisms on melanocortin 2 receptor were related to both tasks, while other polymorphisms were associated with the unsolvable task. This indicates that glucocorticoid functions are involved in the cognitive skills acquired during dog domestication.

Health of Pug dogs in the UK: disorder predispositions and protections

BACKGROUND

Pugs are a brachycephalic dog breed that has become phenomenally popular over recent decades. However, there is growing concern about serious health and welfare issues in the breed. To augment the evidence-base on the comparative health of Pugs, this study aimed to compare the odds of common disorders between Pugs and all remaining dogs under primary veterinary care in the UK during 2016. A cross-sectional study design of VetCompass clinical records was used to estimate the one-year (2016) period prevalence for the disorders most commonly diagnosed in Pugs and non-Pugs. Risk factor analysis applied multivariable logistic regression modelling methods to compare the odds of 40 common disorders between Pugs and non-Pugs.

RESULTS

From a study population of 905,544 dogs, the analysis included random samples of 4308 Pugs and 21,835 non-Pugs. Pugs were younger (2.36 years, range 0.07-16.24 vs 4.44 years, range 0.01-20.46, p <  0.001) and lighter (8.95 kg, range 5.00-13.60 vs. 14.07 kg, range 1.41-85.00, p <  0.001) than non-Pugs. Pugs had 1.86 (95% confidence interval [CI] 1.72 to 2.01) times the adjusted odds of diagnosis with ≥1 disorder than non-Pugs. Pugs had significantly increased adjusted odds for 23/40 (57.5%) common disorders. These included: brachycephalic obstructive airway syndrome (odds ratio [OR] 53.92; 95% CI 36.22 to 80.28), stenotic nares (OR 51.25; 95% CI 24.93 to 105.37) and corneal ulceration (OR 13.01; 95% CI 10.50 to 16.11). Conversely, Pugs had significantly reduced adjusted odds of 7/40 (17.5%) common disorders compared to non-Pugs. These included: heart murmur (OR 0.23; 95% 0.13 to 0.14), lipoma (OR 0.24; 95% CI 0.11 to 0.55) and aggression (OR 0.31; 95% CI 0.21 to 0.47).

CONCLUSIONS

The current study highlights that predispositions outnumber protections between Pugs and non-Pugs for common disorders, suggesting some critical health welfare challenges to overcome for Pugs. Highly differing heath profiles between Pugs and other dogs in the UK suggest that the Pug has diverged substantially from mainstream dog breeds and can no longer be considered as a typical dog from a health perspective.

The "olfactory fingerprint": can diagnostics be improved by combining canine and digital noses?

A sniffer (detecting) dog is conventionally defined as an animal trained to use its olfactory perceptions for detecting a vast array of substances, mostly volatile organic compounds (VOCs), including those exceptionally or exclusively generated in humans bearing specific pathologies. Such an extraordinary sniffing performance translates into the capability of detecting compounds close to the femtomolar level, with performance comparable to that of current mass spectrometry-based laboratory applications. Not only can dogs accurately detect "abnormal volatilomes" reflecting something wrong happening to their owners, but they can also perceive visual, vocal and behavioral signals, which altogether would contribute to raise their alertness. Although it seems reasonable to conclude that sniffer dogs could never be considered absolutely "diagnostic" for a given disorder, several lines of evidence attest that they may serve as efficient screening aids for many pathological conditions affecting their human companions. Favorable results have been obtained in trials on cancers, diabetes, seizures, narcolepsy and migraine, whilst interesting evidence is also emerging on the capability of early and accurately identifying patients with infectious diseases. This would lead the way to proposing an "olfactory fingerprint" loop, where evidence that dogs can identify the presence of human pathologies provides implicit proof of the existence of disease-specific volatilomes, which can be studied for developing laboratory techniques. Contextually, the evidence that specific pathologies are associated with abnormal VOC generation may serve as reliable basis for training dogs to detect these compounds, even (or especially) in patients at an asymptomatic phase.

Presence and Characterization of Zoonotic Bacterial Pathogens in Wild Boar Hunting Dogs (Canis lupus familiaris) in Tuscany (Italy)

Domestic dogs (Canis lupus familiaris) used for wild boar (Sus scrofa) hunting may represent incidental hosts for several zoonotic pathogens. This investigation aimed to evaluate the presence of anti-Leptospira antibodies and the occurrence, antimicrobial resistance, and virulence of Salmonella spp., Yersinia enterocolitica, and Listeria monocytogenes in sera and rectal swabs collected from 42 domestic hunting dogs in the Tuscany region (Italy). Regarding Leptospira, 31 out of 42 serum samples (73.8%) were positive and serogroup Pomona was the most detected (71.4%) at titers between 1:100 and 1:400. Four Salmonella isolates (9.52%) were obtained, all belonging to serotype Infantis; two of them showed antimicrobial resistance to streptomycin, while pipB and sopE presence was assessed in all but one isolate. Concerning Yersinia enterocolitica, seven isolates (16.7%) were obtained, six belonging to biotype 1 and one to biotype 4. Resistance to amoxicillin-clavulanic acid, cephalothin, and ampicillin was detected. Biotype 4 presented three of the virulence genes searched (ystA, ystB, inv), while isolates of biotype 1 showed only one gene. No Listeria monocytogenes was isolated from dog rectal swabs. The results suggest that hunting dogs are exposed to different bacterial zoonotic agents, potentially linked to their work activity, and highlight the possible health risks for humans.

Microsatellite DNA Analysis of Genetic Diversity and Parentage Testing in the Popular Dog Breeds in Poland

There is growing concern that extreme breed standardization contributes to a reduction of the effective population size and high levels of inbreeding, resulting in the loss of genetic diversity in many breeds. This study examined genetic diversity among eight popular dog breeds in Poland and evaluated the effectiveness of a 21-microsatellite (STR) panel recommended by the International Society for Animal Genetics (ISAG) for parent verification. The following breeds were characterized: German Shepherd, Maltese, Irish Wolfhound, Yorkshire Terrier, Biewer Yorkshire Terrier, Golden Retriever, Labrador Retriever, and French Bulldog. STRUCTURE analysis showed breed distinctiveness among all the dog breeds under study. Reynold’s distance ranged between θ_w = 0.634 and θ_w = 0.260. The studied breeds showed a medium level of genetic differentiation; the mean number of alleles per locus ranged from 3.4 to 6.6, and the effective number of alleles from 2.1 to 3.5. The mean degree of heterozygosity varied from 49% to 69% and from 47% to 68% for H_O and H_E, respectively. The population inbreeding coefficient (FIS) indicated an absence of inbreeding in the studied breeds. The average polymorphism information content (PIC) values for most of the breeds were higher than 0.5. The cumulative power of discrimination (PD) for all the markers in all breeds reached high values (close to 1.0), while the probability of identity (P_ID) was low, ranging between 10⁻¹¹ and 10⁻¹⁹. The cumulative exclusion probability when the genotypes of one (PE₁) and both parents (PE₂) are known and showed that the parentage can be confirmed with a probability of 94.92% to 99.95% and 99.78% to 99.9999%, respectively.

Variation in breeding practices and geographic isolation drive subpopulation differentiation, contributing to the loss of genetic diversity within dog breed lineages

Background

Discrete breed ideals are not restricted to delimiting dog breeds from another, but also are key drivers of subpopulation differentiation. As genetic differentiation due to population fragmentation results in increased rates of inbreeding and loss of genetic diversity, detecting and alleviating the reasons of population fragmentation can provide effective tools for the maintenance of healthy dog breeds.

Results

Using a genome-wide SNP array, we detected genetic differentiation to subpopulations in six breeds, Belgian Shepherd, English Greyhound, Finnish Lapphund, Italian Greyhound, Labrador Retriever and Shetland Sheepdog, either due to geographical isolation or as a result of differential breeding strategies. The subpopulation differentiation was strongest in show dog lineages.

Conclusions

Besides geographical differentiation caused by founder effect and lack of gene flow, selection on champion looks or restricted pedigrees is a strong driver of population fragmentation. Artificial barriers for gene flow between the different subpopulations should be recognized, their necessity evaluated critically and perhaps abolished in order to maintain genetic diversity within a breed. Subpopulation differentiation might also result in false positive signals in genome-wide association studies of different traits.

Lay summary

Purebred dogs are, by definition, reproductively isolated from other breeds. However, similar isolation can also occur within a breed due to conflicting breeder ideals and geographic distances between the dog populations. We show here that both of these examples can contribute to breed division, with subsequent loss of genetic variation in the resulting breed lineages. Breeders should avoid creating unnecessary boundaries between breed lineages and facilitate the exchange of dogs between countries.

Moving from information and collaboration to action: report from the 4th international dog health workshop, Windsor in May 2019

Background

Dogs are the most popular mammal kept as a companion animal globally. Positive human-dog relationships can benefit both the human owners as well as the dogs. However, popularity as a companion animal species does not universally benefit dogs in reverse. Breed-related health problems in dogs have received increasing attention over the last decade, sparking increased concerns for dog welfare across many stakeholders. Progress towards improved welfare requires meaningful collaboration between all those working in dog health, science and welfare. The International Partnership for Dogs (IPFD), together with an alternating host organisation, holds biennial meetings called the International Dog Health Workshops (IDHW). The IPFD 4th IDHW was hosted by the UK Kennel Club in Windsor, UK in May 2019. With the aim of encouraging international and multi-stakeholder collaborations that are effective and ongoing, the 4th IDHW 2019 provided a forum to identify specific needs and actions that could improve health, well-being and welfare in dogs, building on outcomes and evaluating actions of previous IDHWs.

Results

The workshop included 126 decision-leaders from 16 countries and was structured around five key themes identified as needing international, multi-stakeholder attention. These included the concept of “breed”, supply and demand, breed-specific strategies for health and breeding, genetic testing and extreme conformations. The review of progress made since the 3rd IDHW 2017 and the comprehensive lists of actions agreed upon during the current meeting suggest that movement from information and collaboration to action has been achieved. Working groups with specific tasks were identified and many plan to continue to communicate through forum communities on DogWellNet.com.

Conclusions

The IDHW provides a forum for formal and informal discussion between relevant groups so that key dog health and welfare issues can be identified and defined, and plans can be agreed for effective actions to address them. The 3rd IDHW 2017 resulted in a number of significant outcomes. New and continuing actions were laid down at the 4th IDHW 2019, which will be re-evaluated at the 5th IDHW facilitating continual progress.

A retrospective survey on canine intracranial tumors between 2007 and 2017

To clarify the prevalence of canine intracranial tumors in Japan, a retrospective study was performed using data on 186 canine intracranial tumors. Of 186 cases, 159 cases (85.5%) were primary and 27 cases (14.5%) were secondary intracranial tumors. Among primary intracranial tumors, meningioma (50.9%) was the most common, followed by glial tumors (21.4%) and primary intracranial histiocytic sarcoma (12.6%). These 3 tumors were most frequently found in middle-aged to elderly dogs without any sex predilection. Regarding glial tumors, the incidence of oligodendroglial tumors (79.4%) was higher than that of astrocytic tumors (17.6%). A significant breed predisposition (P<0.05) was observed for meningioma in Rough Collie, Golden Retriever, Miniature Schnauzer, and Scottish Terrier; for glial tumors in Bouvier de Flandres, French Bulldog, Newfoundland, Bulldog, and Boxer; for primary intracranial histiocytic sarcoma in Pembroke Welsh Corgi, Siberian Husky, and Miniature Schnauzer. The high incidence of oligodendroglial tumors in dogs and the breed predisposition for primary intracranial histiocytic sarcoma in Pembroke Welsh Corgi have not been reported in previous epidemiological studies on canine tumors. Since the incidence of intracranial tumors was vary among dog breeds, the present results demonstrate the uniqueness of the canine breed population in Japan.

The Welfare of Pig-Hunting Dogs in Australia

Hunting feral pigs using dogs is a popular recreational activity in Australia. Dogs are used to flush, chase, bail, and hold feral pigs, and their use for these activities is legal in some states and territories and illegal in others. However, there is little knowledge about the health and welfare of dogs owned specifically for the purpose of pig hunting. We conducted a review of the literature on working dogs in Australia and overseas to determine the likely welfare impacts confronting pig-hunting dogs. We identified numerous challenges facing pig-hunting dogs throughout their lives. Risks to welfare include overbreeding, wastage due to behavioural incompatibilities, the use of aversive training techniques including electronic shock collars, solitary kenneling and tethering, high exposure to infectious diseases including zoonotic diseases, inadequate vaccination and anthelmintic prophlyaxis, high incidence of traumatic and other injuries during hunts, climatic exposure during transportation, mortality during hunts, and a suboptimal quality of life after retirement. There are also significant welfare concerns for the wild pigs hunted in this manner. We conclude that research needs to be conducted in order to determine the current health and welfare of pig-hunting dogs, specifically in Australia. The humaneness of this method of pest control urgently requires further assessment.

Improving the Welfare of Companion Dogs-Is Owner Education the Solution?

Simple Summary

The welfare of most dogs living in homes is largely unknown. However, national surveys carried out by animal welfare charities and findings by animal welfare researchers have shown significant deterioration in some key aspects of dog welfare. For example, more dogs presenting to vets with behavioural problems, obesity, and ill-health due to poor breeding practices. This means that some dogs are suffering due to their owners’ behaviours or ownership practices. Educating dog owners as to how best to look after their dogs is, and has been seen by many, as key to improving the welfare of dogs living in homes. However, the concept of education, the context in which it occurs, and the lack of systematic evaluation of the effectiveness of education interventions means that nobody really knows if this approach works. This paper explores these concepts and draws together a wide range of sources of information to highlight some of the complexities of improving dog welfare by educating owners.

Abstract

Vets, animal welfare charities, and researchers have frequently cited educating owners as a necessity for improving the welfare of companion dogs. The assumption that improving an owner’s knowledge through an education intervention subsequently results in improvements in the welfare of the dog appears reasonable. However, the complexity of dog welfare and dog ownership and the context in which these relationships occur is rapidly changing. Psychology has demonstrated that humans are complex, with values, attitudes, and beliefs influencing our behaviours as much as knowledge and understanding. Equally, the context in which we individuals and our dogs live is rapidly changing and responding to evolving societal and cultural norms. Therefore, we seek to understand education’s effectiveness as an approach to improving welfare through exploring and understanding these complexities, in conjunction with the relevant research from the disciplines of science education and communication. We argue that well designed and rigorously evaluated education interventions can play a part in the challenge of improving welfare, but that these may have limited scope, and welfare scientists could further consider extending cross-disciplinary, cross-boundary working, and research in order to improve the welfare of companion dogs.

Dog10K: an international sequencing effort to advance studies of canine domestication, phenotypes and health

Dogs are the most phenotypically diverse mammalian species, and they possess more known heritable disorders than any other non-human mammal. Efforts to catalog and characterize genetic variation across well-chosen populations of canines are necessary to advance our understanding of their evolutionary history and genetic architecture. To date, no organized effort has been undertaken to sequence the world's canid populations. The Dog10K Consortium (http://www.dog10kgenomes.org) is an international collaboration of researchers from across the globe who will generate 20× whole genomes from 10 000 canids in 5 years. This effort will capture the genetic diversity that underlies the phenotypic and geographical variability of modern canids worldwide. Breeds, village dogs, niche populations and extended pedigrees are currently being sequenced, and de novo assemblies of multiple canids are being constructed. This unprecedented dataset will address the genetic underpinnings of domestication, breed formation, aging, behavior and morphological variation. More generally, this effort will advance our understanding of human and canine health.

Canine Cancer Genomics: Lessons for Canine and Human Health

Dogs are second only to humans in medical surveillance and preventative health care, leading to a recent perception of increased cancer incidence. Scientific priorities in veterinary oncology have thus shifted, with a demand for cancer genetic screens, better diagnostics, and more effective therapies. Most dog breeds came into existence within the last 300 years, and many are derived from small numbers of founders. Each has undergone strong artificial selection, in which dog fanciers selected for many traits, including body size, fur type, color, skull shape, and behavior, to create novel breeds. The adoption of the breed barrier rule-no dog may become a registered member of a breed unless both its dam and its sire are registered members-ensures a relatively closed genetic pool within each breed. As a result, there is strong phenotypic homogeneity within breeds but extraordinary phenotypic variation between breeds. One consequence of this is the high level of breed-associated genetic disease. We and others have taken advantage of this to identify genes for a large number of canine maladies for which mouse models do not exist, particularly with regard to cancer.

Origins and wanderings of the Finnish hunting spitzes

Deducing the evolutionary histories of dog breeds can be challenging due to convergent traits and frequent admixture. In this report, we have explored the relationships of indigenous Finnish hunting spitz breeds among other northern Eurasian hunting breeds using commercially available SNP analysis (the MyDogDNA panel test). We find that Nordic hunting breeds Finnish Spitz, Nordic Spitz and the Karelian Bear Dog, as well as the reindeer herding Lapphund and Lapponian herder are all closely related and have common origins with the northeastern Eurasian Laika breeds, rather than with other Scandinavian Spitz breeds, such as Elkhounds and Swedish Vallhund. By tracing admixture events and direction of gene flow, we also elucidate the complex interactions between the breeds and provide new insight into the history of Swedish Elkhound and Russian-European Laika. The findings, together with an analysis of genetic differentiation between the populations, not only help to understand the origins of the breeds but also provide interesting possibilities to revive genetic diversity, lost during the breeding history, by backcrossing breeds to their hypothetical ancestry.

Tinkering and the Origins of Heritable Anatomical Variation in Vertebrates

Evolutionary change comes from natural and other forms of selection acting on existing anatomical and physiological variants. While much is known about selection, little is known about the details of how genetic mutation leads to the range of heritable anatomical variants that are present within any population. This paper takes a systems-based view to explore how genomic mutation in vertebrate genomes works its way upwards, though changes to proteins, protein networks, and cell phenotypes to produce variants in anatomical detail. The evidence used in this approach mainly derives from analysing anatomical change in adult vertebrates and the protein networks that drive tissue formation in embryos. The former indicate which processes drive variation-these are mainly patterning, timing, and growth-and the latter their molecular basis. The paper then examines the effects of mutation and genetic drift on these processes, the nature of the resulting heritable phenotypic variation within a population, and the experimental evidence on the speed with which new variants can appear under selection. The discussion considers whether this speed is adequate to explain the observed rate of evolutionary change or whether other non-canonical, adaptive mechanisms of heritable mutation are needed. The evidence to hand suggests that they are not, for vertebrate evolution at least.

Border Terriers under primary veterinary care in England: demography and disorders

Background

The Border Terrier is a working terrier type that is generally considered to be a relatively healthy and hardy breed. This study aimed to characterise the demography and common disorders of Border Terriers receiving veterinary care in England using de-identified electronic patient record data within the VetCompass™ Programme.

Results

Annual birth proportion for Border Terriers showed a decreasing trend from 1.46% in 2005 to 0.78% in 2014. The median adult bodyweight for males (10.9 kg, IQR: 9.6–12.3, range: 6.3–25.0) was higher than for females (9.1 kg, IQR: 8.2–10.3, range: 5.2–21.6) (P < 0.001). The median longevity was 12.7 years (IQR 9.3–14.3, range 1.0–17.5).

The most prevalent fine-level disorders recorded were periodontal disease (17.63%, 95% CI: 15.62–19.79), overweight/obesity (7.01%, 95% CI: 5.69–8.52) and otitis externa (6.71%, 95% CI: 5.42–8.19). The most prevalent grouped-level precision disorders were dental disorder (18.54%, 95% CI: 16.48–20.74), enteropathy (11.68%, 95% CI: 10.00–13.53), and skin disorder (10.17%, 95% CI: 8.60–11.93).

Syndromic analysis showed that the most prevalent body locations affected were the head-and-neck (37.75%, 95% CI: 35.14–40.43), abdomen (18.61%, 95% CI: 16.55–20.81) and limb (11.53%, 95% CI: 9.86–13.37). At least one organ system was affected in 834 (62.85%) Border Terriers. The most prevalent organ systems affected were the digestive (32.03%, 95% CI: 29.52–34.61), integument (26.68%, 95% CI: 24.31–29.14), connective/soft tissue (11.15%, 95% CI: 9.51–12.97) and auditory (9.87%, 95% CI: 8.32–11.60). At least one affected pathophysiological process was described in 881 (66.39%) Border Terriers. The most prevalent pathophysiologic processes recorded were inflammation (31.65%, 95% CI: 29.15–34.23), nutritional (9.04%, 95% CI: 7.55–10.72), mass/swelling (8.89%, 95% CI: 7.42–10.55), traumatic (7.99%, 95% CI: 6.59–9.58) and infectious (7.76%, 95% CI: 6.38–9.33).

Conclusions

This study documented a trend towards reducing ownership and relatively long-livedness in the Border Terrier. The most common disorders were periodontal disease, overweight/obesity and otitis externa. Predisposition to dental and neurological disease was suggested. These results can provide a comprehensive evidence resource to support breed-based health plans that can contribute positively to reforms to improve health and welfare within the breed.

Long-term genetic selection reduced prevalence of hip and elbow dysplasia in 60 dog breeds

Canine hip dysplasia (CHD) and elbow dysplasia (ED) impact the health and welfare of all dogs. The first formally organized assessment scheme to improve canine health centered on reducing the prevalence of these orthopedic disorders. Phenotypic screening of joint conformation remains the currently available strategy for breeders to make selection decisions. The present study evaluated the efficacy of employing phenotypic selection on breed improvement of hips and elbows using the Orthopedic Foundation for Animals complete database spanning the 1970–2015 time period. Sixty breeds having more than 1000 unique hip evaluations and 500 elbow evaluations (1,056,852 and 275,129 hip and elbow records, respectively) were interrogated to derive phenotypic improvement, sex and age at time of assessment effects, correlation between the two joints, heritability estimates, estimated breeding values (EBV), and effectiveness of maternal/paternal selection. The data demonstrated that there has been overall improvement in hip and elbow conformation with a reduction in EBV for disease liability, although the breeds differed in the magnitude of the response to selection. Heritabilities also differed substantially across the breeds as did the correlation of the joints; in the absence of a universal association of these differences with breed size, popularity, or participation in screening, it appears that the breeds themselves vary in genetic control. There was subtle, though again breed specific, impact of sex and older ages on CHD and ED. There was greater paternal impact on a reduction of CHD. In the absence of direct genetic tests for either of these two diseases, phenotypic selection has proven to be effective. Furthermore, the data underscore that selection schemes must be breed specific and that it is likely the genetic profiles will be unique across the breeds for these two conditions. Despite the advances achieved with phenotypic selection, incorporation of EBVs into selection schemes should accelerate advances in hip and elbow improvement.

Lessons from the canine Oxtr gene: populations, variants and functional aspects

Oxytocin receptor (OXTR) acts as a key behavioral modulator of the central nervous system, affecting social behavior, stress, affiliation and cognitive functions. Variants of the Oxtr gene are known to influence behavior both in animals and humans; however, canine Oxtr polymorphisms are less characterized in terms of possible relevance to function, selection criteria in breeding and domestication. In this report, we provide a detailed characterization of common variants of the canine Oxtr gene. In particular (1) novel polymorphisms were identified by direct sequencing of wolf and dog samples, (2) allelic distributions and pairwise linkage disequilibrium patterns of several canine populations were compared, (3) neighbor joining (NJ) tree based on common single nucleotide polymorphisms (SNPs) was constructed, (4) mRNA expression features were assessed, (5) a novel splice variant was detected and (6) in vitro functional assays were performed. Results indicate marked differences regarding Oxtr variations between purebred dogs of different breeds, free-ranging dog populations, wolf subspecies and golden jackals. This, together with existence of explicitly dog-specific alleles and data obtained from the NJ tree implies that Oxtr could indeed have been a target gene during domestication and selection for human preferred aspects of temperament and social behavior. This assumption is further supported by the present observations on gene expression patterns within the brain and luciferase reporter experiments, providing a molecular level link between certain canine Oxtr polymorphisms and differences in nervous system function and behavior.

Whole-genome sequence, SNP chips and pedigree structure: building demographic profiles in domestic dog breeds to optimize genetic-trait mapping

In the decade following publication of the draft genome sequence of the domestic dog, extraordinary advances with application to several fields have been credited to the canine genetic system. Taking advantage of closed breeding populations and the subsequent selection for aesthetic and behavioral characteristics, researchers have leveraged the dog as an effective natural model for the study of complex traits, such as disease susceptibility, behavior and morphology, generating unique contributions to human health and biology. When designing genetic studies using purebred dogs, it is essential to consider the unique demography of each population, including estimation of effective population size and timing of population bottlenecks. The analytical design approach for genome-wide association studies (GWAS) and analysis of whole-genome sequence (WGS) experiments are inextricable from demographic data. We have performed a comprehensive study of genomic homozygosity, using high-depth WGS data for 90 individuals, and Illumina HD SNP data from 800 individuals representing 80 breeds. These data were coupled with extensive pedigree data analyses for 11 breeds that, together, allowed us to compute breed structure, demography, and molecular measures of genome diversity. Our comparative analyses characterize the extent, formation and implication of breed-specific diversity as it relates to population structure. These data demonstrate the relationship between breed-specific genome dynamics and population architecture, and provide important considerations influencing the technological and cohort design of association and other genomic studies.

Summary: Successful application of whole-genome sequencing and genome-wide association studies for identifying both loci and mutations in canines is influenced by breed structure and demography, motivating researchers to generate breed-specific strategies for canine genetic studies.

Evolutionary History, Selective Sweeps, and Deleterious Variation in the Dog

The dog is our oldest domesticate and has experienced a wide variety of demographic histories, including a bottleneck associated with domestication and individual bottlenecks associated with the formation of modern breeds. Admixture with gray wolves, and among dog breeds and populations, has also occurred throughout its history. Likewise, the intensity and focus of selection have varied, from an initial focus on traits enhancing cohabitation with humans, to more directed selection on specific phenotypic characteristics and behaviors. In this review, we summarize and synthesize genetic findings from genome-wide and complete genome studies that document the genomic consequences of demography and selection, including the effects on adaptive and deleterious variation. Consistent with the evolutionary history of the dog, signals of natural and artificial selection are evident in the dog genome. However, conclusions from studies of positive selection are fraught with the problem of false positives given that demographic history is often not taken into account.

Dog Breed Differences in Visual Communication with Humans

Domestic dogs (Canis familiaris) have developed a close relationship with humans through the process of domestication. In human-dog interactions, eye contact is a key element of relationship initiation and maintenance. Previous studies have suggested that canine ability to produce human-directed communicative signals is influenced by domestication history, from wolves to dogs, as well as by recent breed selection for particular working purposes. To test the genetic basis for such abilities in purebred dogs, we examined gazing behavior towards humans using two types of behavioral experiments: the ‘visual contact task’ and the ‘unsolvable task’. A total of 125 dogs participated in the study. Based on the genetic relatedness among breeds subjects were classified into five breed groups: Ancient, Herding, Hunting, Retriever-Mastiff and Working). We found that it took longer time for Ancient breeds to make an eye-contact with humans, and that they gazed at humans for shorter periods of time than any other breed group in the unsolvable situation. Our findings suggest that spontaneous gaze behavior towards humans is associated with genetic similarity to wolves rather than with recent selective pressure to create particular working breeds.

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

The island inhabitants of Sardinia have long been a focus for studies of complex human traits due to their unique ancestral background and population isolation reflecting geographic and cultural restriction. Population isolates share decreased genomic diversity, increased linkage disequilibrium, and increased inbreeding coefficients. In many regions, dogs and humans have been exposed to the same natural and artificial forces of environment, growth, and migration. Distinct dog breeds have arisen through human-driven selection of characteristics to meet an ideal standard of appearance and function. The Fonni's Dog, an endemic dog population on Sardinia, has not been subjected to an intensive system of artificial selection, but rather has developed alongside the human population of Sardinia, influenced by geographic isolation and unregulated selection based on its environmental adaptation and aptitude for owner-desired behaviors. Through analysis of 28 dog breeds, represented with whole-genome sequences from 13 dogs and ∼170,000 genome-wide single nucleotide variants from 155 dogs, we have produced a genomic illustration of the Fonni's Dog. Genomic patterns confirm within-breed similarity, while population and demographic analyses provide spatial identity of Fonni's Dog to other Mediterranean breeds. Investigation of admixture and fixation indices reveals insights into the involvement of Fonni's Dogs in breed development throughout the Mediterranean. We describe how characteristics of population isolates are reflected in dog breeds that have undergone artificial selection, and are mirrored in the Fonni's Dog through traditional isolating factors that affect human populations. Lastly, we show that the genetic history of Fonni's Dog parallels demographic events in local human populations.

Tail Docking and Ear Cropping Dogs: Public Awareness and Perceptions

Tail docking and ear cropping are two surgical procedures commonly performed on many dog breeds. These procedures are classified as medically unnecessary surgeries whose purpose is primarily cosmetic. Available attitude research surrounding these controversial practices has been limited to surveys of veterinarians and dog breeders familiar with both practices. The aim of this project was to: 1) assess public awareness of tail docking and ear cropping, 2) determine whether physical alteration of a dog affects how the dog, and 3) owner are perceived. In Experiment 1 awareness was measured using a combination of both explicit and implicit measures. We found that 42% of participants (n = 810) were unable to correctly explain the reason why tail docked and ear cropped dogs had short ears and tails. Similarly, an implicit measure of awareness (‘nature vs nurture task’), found that the majority of participants believed short tails and erect ears were a consequence of genetics rather than something the owner or breeder had done. The results obtained in Experiment 2 (n = 392) provide evidence that ear cropped and tail docked dogs are perceived differently than an identical dog in its ‘natural’ state. Modified dogs were perceived as being more aggressive, more dominant, less playful and less attractive than natural dogs. Experiment 3 (n = 410) is the first evidence that owners of modified dogs are perceived as being more aggressive, more narcissistic, less playful, less talkative and less warm compared to owners of natural dogs. Taken together, these results suggest that although a significant proportion of subjects appear unaware of the practices of tail docking and ear cropping in dogs, these procedures have significant impacts on how modified dogs and their owners are perceived by others.

The morphology of the mandibular coronoid process does not indicate that Canis lupus chanco is the progenitor to dogs

The domestication of wolves is currently under debate. Where, when and from which wolf sub-species dogs originated are being investigated both by osteoarchaeologists and geneticists. While DNA research is rapidly becoming more active and popular, morphological methods have been the gold standard in the past. But even today morphological details are routinely employed to discern archaeological wolves from dogs. One such morphological similarity between Canis lupus chanco and dogs was published in 1977 by Olsen and Olsen. This concerns the “turned back” anatomy of the dorsal part of the vertical ramus of the mandible that was claimed to be specific to domestic dogs and Chinese wolves C. lupus chanco, and “absent from other canids”. Based on this characteristic, C. lupus chanco was said to be the progenitor of Asian and American dogs, and this specific morphology has been continuously used as an argument to assign archaeological specimens, including non-Asian and non-American, to the dog clade. We challenged this statement by examining 384 dog skulls of 72 breeds and 60 skulls of four wolf sub-species. Only 20 % of dog mandibles and 80 % of C. lupus chanco showed the specific anatomy. In addition, 12 % of Canis lupus pallipes mandibles showed the “turned back” morphology. It can be concluded that the shape of the coronoid process of the mandible cannot be used as a morphological trait to determine whether a specimen belongs to a dog or as an argument in favour of chanco as the progenitor to dogs.

The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves

The process of domestication can exert intense trait-targeted selection on genes and regulatory regions. Specifically, rapid shifts in the structure and sequence of genomic regulatory elements could provide an explanation for the extensive, and sometimes extreme, variation in phenotypic traits observed in domesticated species. Here, we explored methylation differences from >24 000 cytosines distributed across the genomes of the domesticated dog (Canis familiaris) and the grey wolf (Canis lupus). PCA and model-based cluster analyses identified two primary groups, domestic vs. wild canids. A scan for significantly differentially methylated sites (DMSs) revealed species-specific patterns at 68 sites after correcting for cell heterogeneity, with weak yet significant hypermethylation typical of purebred dogs when compared to wolves (59% and 58%, P < 0.05, respectively). Additionally, methylation patterns at eight genes significantly deviated from neutrality, with similar trends of hypermethylation in purebred dogs. The majority (>66%) of differentially methylated regions contained or were associated with repetitive elements, indicative of a genotype-mediated trend. However, DMSs were also often linked to functionally relevant genes (e.g. neurotransmitters). Finally, we utilized known genealogical relationships among Yellowstone wolves to survey transmission stability of methylation marks, from which we found a substantial fraction that demonstrated high heritability (both H(2) and h(2 ) > 0.99). These analyses provide a unique epigenetic insight into the molecular consequences of recent selection and radiation of our most ancient domesticated companion, the dog. These findings suggest selection has acted on methylation patterns, providing a new genomic perspective on phenotypic diversification in domesticated species.

Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs

Population bottlenecks, inbreeding, and artificial selection can all, in principle, influence levels of deleterious genetic variation. However, the relative importance of each of these effects on genome-wide patterns of deleterious variation remains controversial. Domestic and wild canids offer a powerful system to address the role of these factors in influencing deleterious variation because their history is dominated by known bottlenecks and intense artificial selection. Here, we assess genome-wide patterns of deleterious variation in 90 whole-genome sequences from breed dogs, village dogs, and gray wolves. We find that the ratio of amino acid changing heterozygosity to silent heterozygosity is higher in dogs than in wolves and, on average, dogs have 2-3% higher genetic load than gray wolves. Multiple lines of evidence indicate this pattern is driven by less efficient natural selection due to bottlenecks associated with domestication and breed formation, rather than recent inbreeding. Further, we find regions of the genome implicated in selective sweeps are enriched for amino acid changing variants and Mendelian disease genes. To our knowledge, these results provide the first quantitative estimates of the increased burden of deleterious variants directly associated with domestication and have important implications for selective breeding programs and the conservation of rare and endangered species. Specifically, they highlight the costs associated with selective breeding and question the practice favoring the breeding of individuals that best fit breed standards. Our results also suggest that maintaining a large population size, rather than just avoiding inbreeding, is a critical factor for preventing the accumulation of deleterious variants.

Racial and ethnic differences in assisted reproduction treatment outcomes: the benefit of racial admixture

The goal of the present study was to determine whether racial and ethnic differences affect the outcomes of assisted reproductive technology in the Brazilian population. 1497 patients undergoing intracytoplasmic sperm injection (ICSI) cycles were split into groups according to the patient's ethnicity: Caucasian (n = 2131), Mestizo (n = 358), Asian (n = 174), Black (n = 115) and Indian (n = 260). ICSI outcomes were compared among the groups. Body mass index was highest in the Black group, followed by the Mestizo, Indian, Caucasian and Asian groups (p > 0.001). The FSH dose (p > 0.001) was highest among Indians, followed by Asians and Caucasians, and the dose was lowest among Blacks and Mestizos. In contrast, the oocyte yield was highest among Mestizos, followed by Indians, Blacks and Caucasians, and lowest among Asians (p = 0.005). The fertilisation rate was highest among Mestizos, followed by Blacks, Indians and Caucasians, whereas Asians had the lowest fertilisation rate (p = 0.004). Pregnancy and implantation rates were also highest among Mestizos, followed by Blacks, Indians and Caucasians, whereas the Asian patients had the lowest rates (p = 0.008 and p > 0.001, respectively). In conclusion, our evidence suggests a possible beneficial effect of racial admixture on ICSI outcomes.

First evidence of hybridization between golden jackal (Canis aureus) and domestic dog (Canis familiaris) as revealed by genetic markers

Interspecific hybridization is relatively frequent in nature and numerous cases of hybridization between wild canids and domestic dogs have been recorded. However, hybrids between golden jackals (Canis aureus) and other canids have not been described before. In this study, we combined the use of biparental (15 autosomal microsatellites and three major histocompatibility complex (MHC) loci) and uniparental (mtDNA control region and a Y-linked Zfy intron) genetic markers to assess the admixed origin of three wild-living canids showing anomalous phenotypic traits. Results indicated that these canids were hybrids between golden jackals and domestic dogs. One of them was a backcross to jackal and another one was a backcross to dog, confirming that golden jackal-domestic dog hybrids are fertile. The uniparental markers showed that the direction of hybridization, namely females of the wild species hybridizing with male domestic dogs, was common to most cases of canid hybridization. A melanistic 3bp-deletion at the K locus (β-defensin CDB103 gene), that was absent in reference golden jackal samples, but was found in a backcross to jackal with anomalous black coat, suggested its introgression from dogs via hybridization. Moreover, we demonstrated that MHC sequences, although rarely used as markers of hybridization, can be also suitable for the identification of hybrids, as long as haplotypes are exclusive for the parental species.

The genomics of microbial domestication in the fermented food environment

Shortly after the agricultural revolution, the domestication of bacteria, yeasts, and molds, played an essential role in enhancing the stability, quality, flavor, and texture of food products. These domestication events were probably the result of human food production practices that entailed the continual recycling of isolated microbial communities in the presence of abundant agricultural food sources. We suggest that within these novel agrarian food niches the metabolic requirements of those microbes became regular and predictable resulting in rapid genomic specialization through such mechanisms as pseudogenization, genome decay, interspecific hybridization, gene duplication, and horizontal gene transfer. The ultimate result was domesticated strains of microorganisms with enhanced fermentative capacities.

Genome-Wide Analyses Suggest Mechanisms Involving Early B-Cell Development in Canine IgA Deficiency

Immunoglobulin A deficiency (IgAD) is the most common primary immune deficiency disorder in both humans and dogs, characterized by recurrent mucosal tract infections and a predisposition for allergic and other immune mediated diseases. In several dog breeds, low IgA levels have been observed at a high frequency and with a clinical resemblance to human IgAD. In this study, we used genome-wide association studies (GWAS) to identify genomic regions associated with low IgA levels in dogs as a comparative model for human IgAD. We used a novel percentile groups-approach to establish breed-specific cut-offs and to perform analyses in a close to continuous manner. GWAS performed in four breeds prone to low IgA levels (German shepherd, Golden retriever, Labrador retriever and Shar-Pei) identified 35 genomic loci suggestively associated (p <0.0005) to IgA levels. In German shepherd, three genomic regions (candidate genes include KIRREL3 and SERPINA9) were genome-wide significantly associated (p <0.0002) with IgA levels. A ~20kb long haplotype on CFA28, significantly associated (p = 0.0005) to IgA levels in Shar-Pei, was positioned within the first intron of the gene SLIT1. Both KIRREL3 and SLIT1 are highly expressed in the central nervous system and in bone marrow and are potentially important during B-cell development. SERPINA9 expression is restricted to B-cells and peaks at the time-point when B-cells proliferate into antibody-producing plasma cells. The suggestively associated regions were enriched for genes in Gene Ontology gene sets involving inflammation and early immune cell development.

Ten inherited disorders in purebred dogs by functional breed groupings

Background

Analysis of 88,635 dogs seen at the University of California, Davis Veterinary Medical Teaching Hospital from 1995 to 2010 identified ten inherited conditions having greater prevalence within the purebred dog population as compared to the mixed-breed dog population: aortic stenosis, atopy/allergic dermatitis, gastric dilatation volvulus (GDV), early onset cataracts, dilated cardiomyopathy, elbow dysplasia, epilepsy, hypothyroidism, intervertebral disk disease (IVDD), and hepatic portosystemic shunt. The objective of the present study was to ascertain if disorders with higher prevalence in purebreds were restricted to particular breed group classifications within the purebred population, specifically the American Kennel Club breed grouping or groups with genomic similarities based upon allele sharing. For each disorder, healthy controls seen at the hospital during that same time period were matched for age, weight, and sex to each affected dog to determine risk of disease presentation in the purebred group as compared to that of the mixed-breed population. To enhance reliability of the analyses, sampling of matched healthy to affected dogs was repeated 50 times. For each comparison, the purebred subgroups to mixed-breed odds ratio was determined as was the mean P value used to test this ratio.

Results

For aortic stenosis, GDV, early onset cataracts, dilated cardiomyopathy, elbow dysplasia, epilepsy, and portosystemic shunt, most purebred groups were not statistically distinct from the mixed-breed population with higher prevalence in purebreds restricted to distinct subsets of purebred dogs. The conditions of atopy/allergic dermatitis, hypothyroidism, and IVDD were more pervasive across the purebred population with many groups having higher prevalence than the mixed-breed population. The prevalence of IVDD in purebred terrier groups was statistically lower than that observed for mixed-breed dogs.

Conclusions

The results offer an assessment of the distribution of inherited disorders within purebred dogs and illustrate how mixed-breed and subpopulations of purebred dogs do not differ statistically in prevalence for certain disorders. Some disorders appear linked to common ancestors providing insight into disease allele origin whereas others may be due to selection for common structural morphology. Knowledge of the origin of a condition may aid in reducing its prevalence in the dog population as a whole.

Electronic supplementary material

The online version of this article (doi:10.1186/s40575-015-0021-x) contains supplementary material, which is available to authorized users.

Dog and mouse: toward a balanced view of the mammalian olfactory system

Although the most intensively studied mammalian olfactory system is that of the mouse, in which olfactory chemical cues of one kind or another are detected in four different nasal areas [the main olfactory epithelium (MOE), the septal organ (SO), Grüneberg's ganglion, and the sensory epithelium of the vomeronasal organ (VNO)], the extraordinarily sensitive olfactory system of the dog is also an important model that is increasingly used, for example in genomic studies of species evolution. Here we describe the topography and extent of the main olfactory and vomeronasal sensory epithelia of the dog, and we report finding no structures equivalent to the Grüneberg ganglion and SO of the mouse. Since we examined adults, newborns, and fetuses we conclude that these latter structures are absent in dogs, possibly as the result of regression or involution. The absence of a vomeronasal component based on VR2 receptors suggests that the VNO may be undergoing a similar involutionary process.

Real-time assessment of hybridization between wolves and dogs: combining noninvasive samples with ancestry informative markers

Wolves and dogs provide a paradigmatic example of the ecological and conservation implications of hybridization events between wild and domesticated forms. However, our understanding of such implications has been traditionally hampered by both high genetic similarity and the difficulties in obtaining tissue samples (TS), which limit our ability to assess ongoing hybridization events. To assess the occurrence and extension of hybridization in a pack of wolf-dog hybrids in northwestern Iberia, we compared the power of 52 nuclear markers implemented on TS with a subset of 13 ancestry informative markers (AIMs) typed in noninvasive samples (NIS). We demonstrate that the 13 AIMs are as accurate as the 52 markers that were chosen without regard to the power to differentiate between wolves and dogs, also having the advantage of being rapidly screened on NIS. The efficiency of AIMs significantly outperformed ten random sets of similar size and an additional commercial set of 18 markers. Bayesian clustering analysis implemented on AIMs and NIS identified nine hybrids, two wolves and two dogs. Four hybrids were unambiguously assigned to F1xWolf backcrosses. Our approach (AIMs + NIS) overcomes previous difficulties related to sample availability and informative power of markers, allowing a quick identification of wolf-dog hybrids in the first phases of hybridization episodes. This provides managers with a reliable tool to evaluate hybridization and estimate the success of their actions. This approach may be easily adapted for other pairs of wild/domesticated species, thus improving our understanding of the introgression of domestication genes into natural populations.

Analysis of structural diversity in wolf-like canids reveals post-domestication variants

BACKGROUND

Although a variety of genetic changes have been implicated in causing phenotypic differences among dogs, the role of copy number variants (CNVs) and their impact on phenotypic variation is still poorly understood. Further, very limited knowledge exists on structural variation in the gray wolf, the ancestor of the dog, or other closely related wild canids. Documenting CNVs variation in wild canids is essential to identify ancestral states and variation that may have appeared after domestication.

RESULTS

In this work, we genotyped 1,611 dog CNVs in 23 wolf-like canids (4 purebred dogs, one dingo, 15 gray wolves, one red wolf, one coyote and one golden jackal) to identify CNVs that may have arisen after domestication. We have found an increase in GC-rich regions close to the breakpoints and around 1 kb away from them suggesting that some common motifs might be associated with the formation of CNVs. Among the CNV regions that showed the largest differentiation between dogs and wild canids we found 12 genes, nine of which are related to two known functions associated with dog domestication; growth (PDE4D, CRTC3 and NEB) and neurological function (PDE4D, EML5, ZNF500, SLC6A11, ELAVL2, RGS7 and CTSB).

CONCLUSIONS

Our results provide insight into the evolution of structural variation in canines, where recombination is not regulated by PRDM9 due to the inactivation of this gene. We also identified genes within the most differentiated CNV regions between dogs and wolves, which could reflect selection during the domestication process.

Establishing the validity of domestication genes using DNA from ancient chickens

Modern domestic plants and animals are subject to human-driven selection for desired phenotypic traits and behavior. Large-scale genetic studies of modern domestic populations and their wild relatives have revealed not only the genetic mechanisms underlying specific phenotypic traits, but also allowed for the identification of candidate domestication genes. Our understanding of the importance of these genes during the initial stages of the domestication process traditionally rests on the assumption that robust inferences about the past can be made on the basis of modern genetic datasets. A growing body of evidence from ancient DNA studies, however, has revealed that ancient and even historic populations often bear little resemblance to their modern counterparts. Here, we test the temporal context of selection on specific genetic loci known to differentiate modern domestic chickens from their extant wild ancestors. We extracted DNA from 80 ancient chickens excavated from 12 European archaeological sites, dated from ∼ 280 B.C. to the 18th century A.D. We targeted three unlinked genetic loci: the mitochondrial control region, a gene associated with yellow skin color (β-carotene dioxygenase 2), and a putative domestication gene thought to be linked to photoperiod and reproduction (thyroid-stimulating hormone receptor, TSHR). Our results reveal significant variability in both nuclear genes, suggesting that the commonality of yellow skin in Western breeds and the near fixation of TSHR in all modern chickens took place only in the past 500 y. In addition, mitochondrial variation has increased as a result of recent admixture with exotic breeds. We conclude by emphasizing the perils of inferring the past from modern genetic data alone.