Genomic and archaeological evidence suggest a dual origin of domestic dogs

Evolutionary divergence of facial muscle physiology between domestic dogs and wolves

Domestic dogs (Canis familiaris) are descended from gray wolf (Canis lupus) populations that inhabited Western Europe and Siberia. The specific timing of dog domestication is debated, but archeological and genetic evidence suggest that it was a multi-phase process that began at least 15,000 years ago. There are many morphological differences between dogs and wolves, including marked divergence in facial muscle morphology, but we know little about the comparative physiology of these muscles. A better understanding of comparative facial muscle physiology between domestic dogs and gray wolves would improve our conceptual framework for the processual mechanisms in dog domestication. To address these issues, we assessed the myosin profiles (type I and type II) from the zygomaticus and orbicularis oris muscles of 6 domestic dogs and 4 gray wolves. Due to small sample sizes, statistical analyses were not done. Results reveal that sampled domestic dogs have almost 100% fast-twitch (type II) muscle fibers while gray wolves have less than 50%, meaning that dog faces can contract fast while wolf faces are able to sustain facial muscle contraction. Sample sizes are limited but the present study indicates that dog domestication is associated with not only a change in facial muscle morphology but a concomitant change in how these muscles function physiologically. Selective pressures in the development of communication between dogs and humans using facial expression may have influenced this evolutionary divergence, but the paedomorphic retention of barking in adult dogs may have also played a role.

Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes

Understanding how large carnivores respond to increasingly human-dominated landscapes will determine their future adaptive potential. The Iberian wolf (Canis lupus signatus), a gray wolf subspecies endemic to the Iberian Peninsula (Portugal and Spain), has uniquely persisted in human-dominated landscapes, unlike many other wolf populations that faced widespread extinction across Europe during the twentieth century. In this study, we conducted a comprehensive genome-wide analysis of 145 historical and contemporary Iberian wolf samples to investigate whether hybridization with domestic dogs resulted in genetic introgression. We identified a dog-derived block on Chromosome 2 in Iberian wolves, displaying signatures consistent with introgression and high nucleotide similarity among introgressed individuals. Additionally, our estimates place the average timing of introgression between 6100 and 3000 years ago, with low sequence divergence to dogs from the Iberian Peninsula suggesting a single local origin for the hybridization event. Using forward genetic simulations, we show that the introgressed haplotype is most likely being maintained in Iberian wolves by selection. The introgressed dog variants are located within the MAST4 gene, which has been linked to neurological disorders, including cognitive and motor developmental delays, hinting at a potential role in cognitive behavior in Iberian wolves. This study uncovers a case of putative adaptive introgression from domestic dogs into wolves, offering new insights into wild canids' adaptation to human-dominated landscapes.

[Thousands of years of human-dog relationship]

During recent years, much progress has been made in understanding the origin and evolution of the dog. Thanks to the collaboration between zooarchaeology, genomics and paleogenetics, researchers were able to hypothesize scenarios regarding the origins of the canine lineages present in Europe at the end of the Pleistocene and the beginning of the Holocene. Research has also shown a correlation between human and canine migration across time and space, highlighting a strong relationship between man and his best friend. This proximity between the two species is also illustrated by the adaptation of this species to anthropogenic selective pressures, particularly in parallel with cultural transitions. Although the history of this species still requires much exploration to be fully understood, these results provide new theoretical bases for understanding the interplay between humans and dogs.

A new future for dog breeding

The modern idea of purebred dogs has come under increasing critical scrutiny over recent decades. In light of this critical focus and other developments in society, some new trends in how companion dogs are bred and acquired have emerged. This means a diminishing influence from traditional kennel clubs with more dogs being sold without a pedigree, stricter legal restrictions on dog breeding, growing popularity of deliberate crosses of established breeds (i.e. so-called designer breeds) and growing hype around the benefits of mixed-breed dogs. We give an overview of these trends and discuss to what extent they will serve to promote dogs that are innately healthy, have good welfare and function well in their various roles in today's world. We argue that newly invented designer breeds and mixed breeds also have worrying health and behavioural problems, and that the predictability of purebred dogs with respect to body size, basic behaviours, known need for grooming, disorder profiles and other attributes may well offer some benefits for a satisfying human-dog relationship seen from both sides. The optimal future seems to lie in the middle ground, where the future organised dog world (i.e. kennel and breed clubs or their successor organisations) will need to re-open the breed registries, remove wording from breed standards that currently promotes extreme conformation, support selection against disease-predisposing genotypes and phenotypes and refocus dog showing and breeding to promote health and appropriate behaviour.

Decreased risk-proneness with increasing age in equally raised and kept wolves and dogs

A basic mechanism of domestication is the selection for fearlessness and acceptance of humans as social partners, which may affect risk-taking behavior and the ability to use humans as social support, both at the behavioural and physiological levels. We combined behavioural observations with heart rate parameters (i.e., HR and heart rate variability, HRV) in equally raised and housed wolves and dogs to assess the responses to food offered in the vicinity of a potential stressor (an unknown spinning object) with and without social support from a familiar human. Based on previous studies on neophobia in wolves and dogs, we expected dogs to be less scared of the object, approach more quickly, show less ambivalent behaviour, lower HR, and higher HRV, than wolves, especially at the presence of a human partner. However, we found that mainly age and the presence of a familiar human affected the behaviour of our subjects: older wolves and dogs were generally bolder and faster to approach the food and the familiar human's presence increased the likelihood of taking it. HR rate parameters were affected by age and the stage of the test. Wolves and dogs showed particularly high HRs at the beginning and end of the test sessions. We conclude that in our paradigm, wolves' and dogs' risk-proneness varied with age, rather than species. Additionally, the presence of a familiar human increased the motivation of both, dogs and wolves to take the food.

Human-directed sociability in the domestic dog: A Tinbergian approach

The motivation to interact with humans is central to dogs' domestication process. This review aims to provide a curated overview of the current knowledge about dogs' human-directed sociability using Tinbergen's four questions as a guiding framework. Firstly, we explore its evolutionary history, discussing wolf-dog differences in the socialization period, fear response, sociability, and attachment to elucidate the effect of domestication. Secondly, we address its ontogeny, highlighting the importance of early life experiences, examining findings on different dog populations to discern the effect of adult life experiences, and reporting changes across the lifespan. Thirdly, we analyse the adaptive value of the dog-human relationship, considering the effects of human association on different dog populations. Fourthly, we elaborate on the mechanisms involved in the dog-human relationship, discussing underlying cognitive and genetic processes and findings on the neurophysiological effects of interacting with humans. Finally, we identify issues and remaining questions that deserve more scrutiny and suggest innovative approaches that could be explored to improve our understanding of dogs' human-directed sociability.

Canis lupus familiaris and diclofenac: understanding the potential risks of this association

In many homes worldwide, dogs are considered part of the family. Every possible care is given to animals, including drug treatments. However, many animal guardians, in an attempt to minimize pain or improve the quality of life of their dogs, provide drugs without a veterinarian's prescription. Diclofenac, a non-steroidal anti-inflammatory drug that acts on cyclooxygenase-1 and cyclooxygenase-2 enzymes, is associated with several adverse events, especially related to the gastrointestinal tract, both in humans and pet animals. Therefore, the availability of information about the effects of this drug in different species is always essential. This narrative review aims to present adverse reactions the domestic dog (Canis lupus familiaris) can suffer when exposed to diclofenac. Scientific publications, books, and case reports were consulted, and inquiries were also carried out with regulatory agencies. Many reports of suspected adverse reactions, especially related to the gastrointestinal tract, were found. Other clinical manifestations and lesions were also identified in the cardiovascular system, liver, kidneys, and hematological examinations. Therefore, diclofenac may constitute a hazard to dogs, mainly due to possible damage to the gastrointestinal tract. This fact reinforces the need to seek veterinary advice before providing any drug to animals, in addition to recommendations on ensuring the correct storage of medications to avoid accidental exposure.

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.

Human Preferences for Dogs and Cats in China: The Current Situation and Influencing Factors of Watching Online Videos and Pet Ownership

Dogs and cats have become the most important and successful pets through long-term domestication. People keep them for various reasons, such as their functional roles or for physical or psychological support. However, why humans are so attached to dogs and cats remains unclear. A comprehensive understanding of the current state of human preferences for dogs and cats and the potential influential factors behind it is required. Here, we investigate this question using two independent online datasets and anonymous questionnaires in China. We find that current human preferences for dog and cat videos are relatively higher than for most other interests, video plays ranking among the top three out of fifteen interests. We also find genetic variations, gender, age, and economic development levels notably influence human preferences for dogs and cats. Specifically, dog and cat ownership are significantly associated with parents' pet ownership of dogs and cats (Spearman's rank correlation coefficient is 0.43, 95% CI: 0.38-0.47), and the primary reason is to gain emotional support. Further analysis finds that women, young people, and those with higher incomes are more likely to prefer dog and cat videos. Our study provides insights into why humans become so attached to dogs and cats and establishes a foundation for developing co-evolutionary models.

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.

Millets, dogs, pigs and permanent settlement: productivity transitions in Neolithic northern China

The transition to sedentary agricultural societies in northern China fuelled considerable demographic growth from 5000 to 2000 BC. In this article, we draw together archaeobotanical, zooarchaeological and bioarchaeological data and explore the relationship between several aspects of this transition, with an emphasis on the millet-farming productivity during the Yangshao period and how it facilitated changes in animal husbandry and consolidation of sedentism. We place the period of domestication (the evolution of non-shattering, initial grain size increase and panicle development) between 8300 and 4300 BC. The domestication and post-domestication of foxtail (Setaria italica) and broomcorn (Panicum miliaceum) millet increased their productivity substantially, with much greater rate of change than for rice (Oryza sativa). However, millets are significantly less productive per hectare than wet rice farming, a point reflected in the greater geographical expanse of northern Neolithic millet cultures (5000-3000 BC) in comparison with their Yangtze rice-growing counterparts. The domestication of pigs in the Yellow River region is evidenced by changes in their morphology after 6000 BC, and a transition to a millet-based diet c. 4500-3500 BC. Genetic data and isotopic data from dogs indicate a similar dietary transition from 6000 to 4000 BC, leading to new starch-consuming dog breeds. Significant population increase associated with agricultural transitions arose predominately from the improvement of these crops and animals following domestication, leading to the formation of the first proto-urban centres and the demic-diffusion of millet agriculture beyond central northern China between 4300-2000 BC.

The beauty of the beast: Suggestions to curb the excesses of dog breeding and restore animal welfare - Invited review

Dog. Specifically created to save its master's life. - (The dog is the ideal) Friend of man, (because it is his devoted slave) (source: Gustave Flaubert, Dictionnaire des Idées Reçues). But is man the best friend of the dog? This question is legitimate when we consider living situations to which modern domestic dogs are exposed. They often do not satisfy basic animal needs. In this narrative review, the author revisits the history of the dog's presence alongside humans, in the light of current knowledge. The modern dog (breed standards and their interests in canine research) and its breeding strategy, including extreme breeding, will then be given particular attention. Dysfunctional human psychological processes will be explored to make it possible to grasp why the breeding of the modern dog is undergoing such a transformation. Finally, based on these factual and conceptual insights, suggestions to improve canine welfare will be proposed. To be effective, all these must be assessed against real-world conditions.

A Variant-Centric Analysis of Allele Sharing in Dogs and Wolves

Canines are an important model system for genetics and evolution. Recent advances in sequencing technologies have enabled the creation of large databases of genetic variation in canines, but analyses of allele sharing among canine groups have been limited. We applied GeoVar, an approach originally developed to study the sharing of single nucleotide polymorphisms across human populations, to assess the sharing of genetic variation among groups of wolves, village dogs, and breed dogs. Our analysis shows that wolves differ from each other at an average of approximately 2.3 million sites while dogs from the same breed differ at nearly 1 million sites. We found that 22% of the variants are common across wolves, village dogs, and breed dogs, that ~16% of variable sites are common across breed dogs, and that nearly half of the differences between two dogs of different breeds are due to sites that are common in all clades. These analyses represent a succinct summary of allele sharing across canines and illustrate the effects of canine history on the apportionment of genetic variation.

Neolithic Yersinia pestis infections in humans and a dog

Yersinia pestis has been infecting humans since the Late Neolithic (LN). Whether those early infections were isolated zoonoses or initiators of a pandemic remains unclear. We report Y. pestis infections in two individuals (of 133) from the LN necropolis at Warburg (Germany, 5300-4900 cal BP). Our analyses show that the two genomes belong to distinct strains and reflect independent infection events. All LN genomes known today (n = 4) are basal in the phylogeny and represent separate lineages that probably originated in different animal hosts. In the LN, an opening of the landscape resulted in the introduction of new rodent species, which may have acted as Y. pestis reservoirs. Coincidentally, the number of dogs increased, possibly leading to Y. pestis infections in canines. Indeed, we detect Y. pestis in an LN dog. Collectively, our data suggest that Y. pestis frequently entered human settlements at the time without causing significant outbreaks.

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.

Ancient genomes reveal over two thousand years of dingo population structure

Dingoes are culturally and ecologically important free-living canids whose ancestors arrived in Australia over 3,000 B.P., likely transported by seafaring people. However, the early history of dingoes in Australia-including the number of founding populations and their routes of introduction-remains uncertain. This uncertainty arises partly from the complex and poorly understood relationship between modern dingoes and New Guinea singing dogs, and suspicions that post-Colonial hybridization has introduced recent domestic dog ancestry into the genomes of many wild dingo populations. In this study, we analyzed genome-wide data from nine ancient dingo specimens ranging in age from 400 to 2,746 y old, predating the introduction of domestic dogs to Australia by European colonists. We uncovered evidence that the continent-wide population structure observed in modern dingo populations had already emerged several thousand years ago. We also detected excess allele sharing between New Guinea singing dogs and ancient dingoes from coastal New South Wales (NSW) compared to ancient dingoes from southern Australia, irrespective of any post-Colonial hybrid ancestry in the genomes of modern individuals. Our results are consistent with several demographic scenarios, including a scenario where the ancestry of dingoes from the east coast of Australia results from at least two waves of migration from source populations with varying affinities to New Guinea singing dogs. We also contribute to the growing body of evidence that modern dingoes derive little genomic ancestry from post-Colonial hybridization with other domestic dog lineages, instead descending primarily from ancient canids introduced to Sahul thousands of years ago.

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.

Genomic Consequences of Isolation and Inbreeding in an Island Dingo Population

Dingoes come from an ancient canid lineage that originated in East Asia around 8,000 to 11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequence data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole-genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROHs)-indicators of inbreeding-are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.

Imputation of ancient canid genomes reveals inbreeding history over the past 10,000 years

The multi-millenia long history between dogs and humans has placed them at the forefront of archeological and genomic research. Despite ongoing efforts including the analysis of ancient dog and wolf genomes, many questions remain regarding their geographic and temporal origins, and the microevolutionary processes that led to the diversity of breeds today. Although ancient genomes provide valuable information, their use is hindered by low depth of coverage and post-mortem damage, which inhibits confident genotype calling. In the present study, we assess how genotype imputation of ancient dog and wolf genomes, utilising a large reference panel, can improve the resolution provided by ancient datasets. Imputation accuracy was evaluated by down-sampling high coverage dog and wolf genomes to 0.05-2x coverage and comparing concordance between imputed and high coverage genotypes. We measured the impact of imputation on principal component analyses and runs of homozygosity. Our findings show high (R2>0.9) imputation accuracy for dogs with coverage as low as 0.5x and for wolves as low as 1.0x. We then imputed a dataset of 90 ancient dog and wolf genomes, to assess changes in inbreeding during the last 10,000 years of dog evolution. Ancient dog and wolf populations generally exhibited lower inbreeding levels than present-day individuals. Interestingly, regions with low ROH density maintained across ancient and present-day samples were significantly associated with genes related to olfaction and immune response. Our study indicates that imputing ancient canine genomes is a viable strategy that allows for the use of analytical methods previously limited to high-quality genetic data.

Historic dog Furs Unravel the Origin and Artificial Selection of Modern Nordic Lapphund and Elkhound dog Breeds

The origins and extreme morphological evolution of the modern dog breeds are poorly studied because the founder populations are extinct. Here, we analyse eight 100 to 200 years old dog fur samples obtained from traditional North Swedish clothing, to explore the origin and artificial selection of the modern Nordic Lapphund and Elkhound dog breeds. Population genomic analysis confirmed the Lapphund and Elkhound breeds to originate from the local dog population, and showed a distinct decrease in genetic diversity in agreement with intense breeding. We identified eleven genes under positive selection during the breed development. In particular, the MSRB3 gene, associated with breed-related ear morphology, was selected in all Lapphund and Elkhound breeds, and functional assays showed that a SNP mutation in the 3'UTR region suppresses its expression through miRNA regulation. Our findings demonstrate analysis of near-modern dog artifacts as an effective tool for interpreting the origin and artificial selection of the modern dog breeds.

Duplications and Retrogenes Are Numerous and Widespread in Modern Canine Genomic Assemblies

Recent years have seen a dramatic increase in the number of canine genome assemblies available. Duplications are an important source of evolutionary novelty and are also prone to misassembly. We explored the duplication content of nine canine genome assemblies using both genome self-alignment and read-depth approaches. We find that 8.58% of the genome is duplicated in the canFam4 assembly, derived from the German Shepherd Dog Mischka, including 90.15% of unplaced contigs. Highlighting the continued difficulty in properly assembling duplications, less than half of read-depth and assembly alignment duplications overlap, but the mCanLor1.2 Greenland wolf assembly shows greater concordance. Further study shows the presence of multiple segments that have alignments to four or more duplicate copies. These high-recurrence duplications correspond to gene retrocopies. We identified 3,892 candidate retrocopies from 1,316 parental genes in the canFam4 assembly and find that ∼8.82% of duplicated base pairs involve a retrocopy, confirming this mechanism as a major driver of gene duplication in canines. Similar patterns are found across eight other recent canine genome assemblies, with metrics supporting a greater quality of the PacBio HiFi mCanLor1.2 assembly. Comparison between the wolf and other canine assemblies found that 92% of retrocopy insertions are shared between assemblies. By calculating the number of generations since genome divergence, we estimate that new retrocopy insertions appear, on average, in 1 out of 3,514 births. Our analyses illustrate the impact of retrogene formation on canine genomes and highlight the variable representation of duplicated sequences among recently completed canine assemblies.

Raising an Eye at Facial Muscle Morphology in Canids

The evolution of facial muscles in dogs has been linked to human preferential selection of dogs whose faces appear to communicate information and emotion. Dogs who convey, especially with their eyes, a sense of perceived helplessness can elicit a caregiving response from humans. However, the facial muscles used to generate such expressions may not be uniquely present in all dogs, but rather specifically cultivated among various taxa and individuals. In a preliminary, qualitative gross anatomical evaluation of 10 canid specimens of various species, we find that the presence of two facial muscles previously implicated in human-directed canine communication, the levator anguli occuli medialis (LAOM) and the retractor anguli occuli lateralis (RAOL), was not unique to domesticated dogs (Canis familiaris). Our results suggest that these aspects of facial musculature do not necessarily reflect selection via human domestication and breeding. In addition to quantitatively evaluating more and other members of the Canidae family, future directions should include analyses of the impact of superficial facial features on canine communication and interspecies communication between dogs and humans.

Ancient Mitogenomes Reveal the Maternal Genetic History of East Asian Dogs

Recent studies have suggested that dogs were domesticated during the Last Glacial Maximum (LGM) in Siberia, which contrasts with previous proposed domestication centers (e.g. Europe, the Middle East, and East Asia). Ancient DNA provides a powerful resource for the study of mammalian evolution and has been widely used to understand the genetic history of domestic animals. To understand the maternal genetic history of East Asian dogs, we have made a complete mitogenome dataset of 120 East Asian canids from 38 archaeological sites, including 102 newly sequenced from 12.9 to 1 ka BP (1,000 years before present). The majority (112/119, 94.12%) belonged to haplogroup A, and half of these (55/112, 49.11%) belonged to sub-haplogroup A1b. Most existing mitochondrial haplogroups were present in ancient East Asian dogs. However, mitochondrial lineages in ancient northern dogs (northeastern Eurasia and northern East Asia) were deeper and older than those in southern East Asian dogs. Results suggests that East Asian dogs originated from northeastern Eurasian populations after the LGM, dispersing in two possible directions after domestication. Western Eurasian (Europe and the Middle East) dog maternal ancestries genetically influenced East Asian dogs from approximately 4 ka BP, dramatically increasing after 3 ka BP, and afterwards largely replaced most primary maternal lineages in northern East Asia. Additionally, at least three major mitogenome sub-haplogroups of haplogroup A (A1a, A1b, and A3) reveal at least two major dispersal waves onto the Qinghai-Tibet Plateau in ancient times, indicating eastern (A1b and A3) and western (A1a) Eurasian origins.

From wolves to humans: oral microbiome resistance to transfer across mammalian hosts

The mammalian mouth is colonized by complex microbial communities, adapted to specific niches, and in homeostasis with the host. Individual microbes interact metabolically and rely primarily on nutrients provided by the host, with which they have potentially co-evolved along the mammalian lineages. The oral environment is similar across mammals, but the diversity, specificity, and evolution of community structure in related or interacting mammals are little understood. Here, we compared the oral microbiomes of dogs with those of wild wolves and humans. In dogs, we found an increased microbial diversity relative to wolves, possibly related to the transition to omnivorous nutrition following domestication. This includes a larger diversity of Patescibacteria than previously reported in any other oral microbiota. The oral microbes are most distinct at bacterial species or strain levels, with few if any shared between humans and canids, while the close evolutionary relationship between wolves and dogs is reflected by numerous shared taxa. More taxa are shared at higher taxonomic levels including with humans, supporting their more ancestral common mammalian colonization followed by diversification. Phylogenies of selected oral bacterial lineages do not support stable human-dog microbial transfers but suggest diversification along mammalian lineages (apes and canids). Therefore, despite millennia of cohabitation and close interaction, the host and its native community controls and limits the assimilation of new microbes, even if closely related. Higher resolution metagenomic and microbial physiological studies, covering a larger mammalian diversity, should help understand how oral communities assemble, adapt, and interact with their hosts.IMPORTANCENumerous types of microbes colonize the mouth after birth and play important roles in maintaining oral health. When the microbiota-host homeostasis is perturbed, proliferation of some bacteria leads to diseases such as caries and periodontitis. Unlike the gut microbiome, the diversity of oral microbes across the mammalian evolutionary space is not understood. Our study compared the oral microbiomes of wild wolves, dogs, and apes (humans, chimpanzees, and bonobos), with the aim of identifying if microbes have been potentially exchanged between humans and dogs as a result of domestication and cohabitation. We found little if any evidence for such exchanges. The significance of our research is in finding that the oral microbiota and/or the host limit the acquisition of exogenous microbes, which is important in the context of natural exclusion of potential novel pathogens. We provide a framework for expanded higher-resolution studies across domestic and wild animals to understand resistance/resilience.

Genomic consequences of isolation and inbreeding in an island dingo population

Dingoes come from an ancient canid lineage that originated in East Asia around 8000-11,000 years BP. As Australia's largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, K'gari (formerly Fraser Island). Concern regarding the persistence of dingoes on K'gari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequencing data is lacking from this population. Here, we include five new whole-genome sequences of K'gari dingoes. We analyze a total of 18 whole genome sequences of dingoes sampled from mainland Australia and K'gari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROH) - indicators of inbreeding - are elevated in all sampled dingoes. However, K'gari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the K'gari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs.

Japanese wolves are most closely related to dogs and share DNA with East Eurasian dogs

Although the domestic dog's origin is still unclear, this lineage is believed to have been domesticated from an extinct population of gray wolves, which is expected to be more closely related to dogs than to other populations of gray wolves. Here, we sequence the whole genomes of nine Japanese wolves (7.5-100x: Edo to Meiji periods) and 11 modern Japanese dogs and analyze them together with those from other populations of dogs and wolves. A phylogenomic tree shows that, among the gray wolves, Japanese wolves are closest to the dog, suggesting that the ancestor of dogs is closely related to the ancestor of the Japanese wolf. Based on phylogenetic and geographic relationships, the dog lineage has most likely originated in East Asia, where it diverged from a common ancestor with the Japanese wolf. Since East Eurasian dogs possess Japanese wolf ancestry, we estimate an introgression event from the ancestor of the Japanese wolf to the ancestor of the East Eurasian dog that occurred before the dog's arrival in the Japanese archipelago.

An In-Depth Look at Fonni's Dog Behavior under Different Outdoor Conditions

This study aimed to investigate the common social and communicative behaviors of the Fonni's Dog under different outdoor conditions. For this study, 70 adult dogs (3-7 years; 32 intact males, 38 intact females) belonging to the Fonni's breed were used. A total of 35 dogs were kept in kennels and 35 were free-ranging dogs in their sheep/goat livestock units. A behavioral repertoire was adapted from the literature and an ethogram was filled in for each dog. All dogs were evaluated in the presence of the owner. Fisher's exact test, following Bonferroni's correction, was used to test possible differences in the categorical variables (presence or absence of the behavior) between free-ranging dogs and dogs kept in kennels. The study revealed that several categories of the dogs' body language were associated with the management condition. However, the breed motivations (guarding and defense of the territory) were satisfied both in kennel and in the animals who were free in the property. The current study suggests a good behavioral balance of the Fonni's Dogs which could be attributed to correct communication between dogs and owners.

De Novo Genome Assembly of the Whitespot Parrotfish (Scarus forsteni): A Valuable Scaridae Genomic Resource

Scarus forsteni, a whitespot parrotfish from the Scaridae family, is a herbivorous fish inhabiting coral reef ecosystems. The deterioration of coral reefs has highly affected the habitats of the parrotfish. The decline in genetic diversity of parrotfish emphasizes the critical importance of conserving their genetic variability to ensure the resilience and sustainability of marine ecosystems for future generations. In this study, a genome of S. forsteni was assembled de novo through using Illumina and Nanopore sequencing. The 1.71-Gb genome of S. forsteni, was assembled into 544 contigs (assembly level: contig). It exhibited an N50 length of 17.97 Mb and a GC content percentage of 39.32%. Our BUSCO analysis revealed that the complete protein of the S. forsteni genome had 98.10% integrity. Combined with structure annotation data, 34,140 (74.81%) genes were functionally annotated out of 45,638 predicted protein-coding genes. Upon comparing the genome size and TE content of teleost fishes, a roughly linear relationship was observed between these two parameters. However, TE content is not a decisive factor in determining the genome size of S. forsteni. Population history analysis results indicate that S. forsteni experienced two major population expansions, both of which occurred before the last interglacial period. In addition, through a comparative genomic analysis of the evolutionary relationship of other species, it was found that S. forsteni had the closest relationship with Cheilinus undulatus, another member of the Labridae family. Our expansion and contraction analysis of the gene family showed that the expansion genes were mainly associated with immune diseases, organismal systems, and cellular processes. At the same time, cell transcription and translation, sex hormone regulation, and other related pathways were also more prominent in the positive selection genes. The genomic sequence of S. forsteni offers valuable resources for future investigations on the conservation, evolution, and behavior of fish species.

Behavioural Synchronisation between Dogs and Humans: Unveiling Interspecific Motor Resonance?

Dogs' behavioural synchronisation with humans is of growing scientific interest. However, studies lack a comprehensive exploration of the neurocognitive foundations of this social cognitive ability. Drawing parallels from the mechanisms underlying behavioural synchronisation in humans, specifically motor resonance and the recruitment of mirror neurons, we hypothesise that dogs' behavioural synchronisation with humans is underpinned by a similar mechanism, namely interspecific motor resonance. Based on a literature review, we argue that dogs possess the prerequisites for motor resonance, and we suggest that interspecific behavioural synchronisation relies on the activation of both human and canine mirror neurons. Furthermore, interspecific behavioural studies highlight certain characteristics of motor resonance, including motor contagion and its social modulators. While these findings strongly suggest the potential existence of interspecific motor resonance, direct proof remains to be established. Our analysis thus paves the way for future research to confirm the existence of interspecific motor resonance as the neurocognitive foundation for interspecific behavioural synchronisation. Unravelling the neurocognitive mechanisms underlying this behavioural adjustment holds profound implications for understanding the evolutionary dynamics of dogs alongside humans and improving the day-to-day management of dog-human interactions.

Longevity of companion dog breeds: those at risk from early death

The companion dog is one of the most phenotypically diverse species. Variability between breeds extends not only to morphology and aspects of behaviour, but also to longevity. Despite this fact, little research has been devoted to assessing variation in life expectancy between breeds or evaluating the potential for phylogenetic characterisation of longevity. Using a dataset of 584,734 unique dogs located within the UK, including 284,734 deceased, we present variation in longevity estimates within the following: parental lineage (purebred = 1 breed, crossbred ≥ 2 breeds), breed (n = 155), body size (large, medium, small), sex (male, female) and cephalic index (brachycephalic, mesocephalic, dolichocephalic). Survival estimates were then partitioned amongst phylogenetic clades: providing evidence that canine evolutionary history (via domestication and associated artificial selection) is associated with breed lifespan. This information provides evidence to inform discussions regarding pedigree health, whilst helping current/prospective owners, breeders, policy makers, funding bodies and welfare organisations improve decision making regarding canine welfare.

A melting pot of Roman dogs north of the Alps with high phenotypic and genetic diversity and similar diets

Several dog skeletons were excavated at the Roman town of Augusta Raurica and at the military camp of Vindonissa, located in the northern Alpine region of Switzerland (Germania Superior). The relationships between them and the people, the nature of their lives, and the circumstances of their deaths are unclear. In order to gain insight into this dog population, we collected 31 dogs deposited almost simultaneously in two wells (second half of the third century CE), three dogs from burial contexts (70-200 CE and third to fifth century CE) at Augusta Raurica, and two dogs from burial contexts at Vindonissa (ca. first century CE). We detected a mixed population of young and adult dogs including small, medium and large sized individuals. Three small dogs had conspicuous phenotypes: abnormally short legs, and one with a brachycephalic skull. Stable isotope analysis of a subset of the dogs showed that their diets were omnivorous with a substantial input of animal proteins and little variation, except one with a particularly low δ15N value, indicating a diet low in animal proteins. Partial mitochondrial DNA sequences from 25 dogs revealed eight haplotypes within canine haplogroup A (11 dogs; 44%; 5 haplotypes), C (8 dogs; 32%; 1 haplotype), D (4 dogs, 16%; 1 haplotype) and B (2 dogs, 8%; 1 haplotype). Based on shotgun sequencing, four Roman mitogenomes were assembled, representing sub-haplogroups A1b3, A1b2 and C2. No canine pathogens were identified, weakening the assumption of infectious disease as a cause for dog disposal. The genetic and morphological diversity observed in dogs of Augusta Raurica and Vindonissa is similar to modern dog diversity.

CanISO: a database of genomic and transcriptomic variations in domestic dog (Canis lupus familiaris)

BACKGROUND

The domestic dog, Canis lupus familiaris, is a companion animal for humans as well as an animal model in cancer research due to similar spontaneous occurrence of cancers as humans. Despite the social and biological importance of dogs, the catalogue of genomic variations and transcripts for dogs is relatively incomplete.

RESULTS

We developed CanISO, a new database to hold a large collection of transcriptome profiles and genomic variations for domestic dogs. CanISO provides 87,692 novel transcript isoforms and 60,992 known isoforms from whole transcriptome sequencing of canine tumors (N = 157) and their matched normal tissues (N = 64). CanISO also provides genomic variation information for 210,444 unique germline single nucleotide polymorphisms (SNPs) from the whole exome sequencing of 183 dogs, with a query system that searches gene- and transcript-level information as well as covered SNPs. Transcriptome profiles can be compared with corresponding human transcript isoforms at a tissue level, or between sample groups to identify tumor-specific gene expression and alternative splicing patterns.

CONCLUSIONS

CanISO is expected to increase understanding of the dog genome and transcriptome, as well as its functional associations with humans, such as shared/distinct mechanisms of cancer. CanISO is publicly available at https://www.kobic.re.kr/caniso/ .

Genomic selection analysis of morphological and adaptation traits in Chinese indigenous dog breeds

The significant morphological differences and abundant germplasm resources of Chinese indigenous dog breeds can be attributed to the diverse geographical environment, including plateaus, mountains, and a long history of raising dogs. The combination of both natural and artificial selection during the past several thousand years has led to hundreds of dog breeds with distinct morphological traits and environmental adaptations. China is one of the earliest countries to domesticate dogs and there are more than 50 ancient indigenous dog breeds. In this study, the run of homozygosity (ROH) and proportion of the autosomal genome covered by ROHs (FROH) were calculated for 10 dog breeds that are the most representative Chinese indigenous dogs based on 170K SNP microarray. The results of FROH showed that the Chuandong hound dogs (HCSSC) have the highest level of inbreeding among the tested breeds. The inbreeding in HCSSC occurred more recently than the Liangshan dogs (SCLSQ) dogs because of more numbers of long ROHs in HCSSC dogs, and the former also have higher inbreeding degree. In addition, there are significant differences in the inbreeding degree among different subpopulations of the same breed, such as the Thin dogs from Shaanxi and Shandong province. To explore genome-wide selection signatures among different breeds, including coat color, ear shape, and altitude adaptability, we performed genome selection analyses of FST and cross population extended haplotype homozygosity (XP-EHH). For the coat color, the FST analysis between Xiasi dogs (XSGZ) and HCSSC dogs was performed and identified multiple genes involved in coat color, hair follicle, and bone development, including MC1R, KITLG, SOX5, RSPO2, and TBX15. For the plateau adaptability, we performed FST and XP-EHH analyses between dogs from Tibet (Tibetan Mastiffs and Nyingchi dogs) and plain regions (Guangxi Biwei dogs GXBWQ and Guandong Sharpei dogs). The results showed the EPAS1 gene in dogs from Tibet undergo strong selection. Multiple genes identified for selection signals based on different usage of dogs. Furthermore, the results of ear shape analyses showed that MSRB3 was likely to be the main gene causing the drop ear of domestic dogs. Our study provides new insights into further understanding of Chinese indigenous dogs.

Wolf-Dog-Human: Companionship Based on Common Social Tools

Wolves, dogs and humans share extremely social and cooperative minds. These similarities are rooted in phylogenetic homology and in the convergence of neuronal and physiological mechanisms, particularly the brain, in the functioning and communication of basic affects and in the mechanisms of stress and calming. The domesticated wolves called dogs are particularly close companion animals. Both Palaeolithic humans and wolves were hypercursorial hunters, cooperating in complex and prosocial ways within their clans with respect to hunting, raising offspring, and defending against conspecific and heterospecific competitors and predators. These eco-social parallels have shaped the development of similar social mindsets in wolves and humans. Over the millennia of domestication, this social match was fine-tuned, resulting in the socio-cognitive specialists humans and dogs, possessing amazingly similar social brains and minds. Therefore, it can be concluded that the quality of their relationships with their human masters is a major factor in the wellbeing, welfare and even health of dogs, as well as in the wellbeing of their human partners. Based on their strikingly similar social brains and physiologies, it can be further concluded that anthropomorphically applying human empathy to dogs in an educated manner may not be as inappropriate as previously thought.

The extinct Sicilian wolf shows a complex history of isolation and admixture with ancient dogs

The Sicilian wolf remained isolated in Sicily from the end of the Pleistocene until its extermination in the 1930s-1960s. Given its long-term isolation on the island and distinctive morphology, the genetic origin of the Sicilian wolf remains debated. We sequenced four nuclear genomes and five mitogenomes from the seven existing museum specimens to investigate the Sicilian wolf ancestry, relationships with extant and extinct wolves and dogs, and diversity. Our results show that the Sicilian wolf is most closely related to the Italian wolf but carries ancestry from a lineage related to European Eneolithic and Bronze Age dogs. The average nucleotide diversity of the Sicilian wolf was half of the Italian wolf, with 37-50% of its genome contained in runs of homozygosity. Overall, we show that, by the time it went extinct, the Sicilian wolf had high inbreeding and low-genetic diversity, consistent with a population in an insular environment.

Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture

BACKGROUND

The international Dog10K project aims to sequence and analyze several thousand canine genomes. Incorporating 20 × data from 1987 individuals, including 1611 dogs (321 breeds), 309 village dogs, 63 wolves, and four coyotes, we identify genomic variation across the canid family, setting the stage for detailed studies of domestication, behavior, morphology, disease susceptibility, and genome architecture and function.

RESULTS

We report the analysis of > 48 M single-nucleotide, indel, and structural variants spanning the autosomes, X chromosome, and mitochondria. We discover more than 75% of variation for 239 sampled breeds. Allele sharing analysis indicates that 94.9% of breeds form monophyletic clusters and 25 major clades. German Shepherd Dogs and related breeds show the highest allele sharing with independent breeds from multiple clades. On average, each breed dog differs from the UU_Cfam_GSD_1.0 reference at 26,960 deletions and 14,034 insertions greater than 50 bp, with wolves having 14% more variants. Discovered variants include retrogene insertions from 926 parent genes. To aid functional prioritization, single-nucleotide variants were annotated with SnpEff and Zoonomia phyloP constraint scores. Constrained positions were negatively correlated with allele frequency. Finally, the utility of the Dog10K data as an imputation reference panel is assessed, generating high-confidence calls across varied genotyping platform densities including for breeds not included in the Dog10K collection.

CONCLUSIONS

We have developed a dense dataset of 1987 sequenced canids that reveals patterns of allele sharing, identifies likely functional variants, informs breed structure, and enables accurate imputation. Dog10K data are publicly available.

Multiple Origins and Genomic Basis of Complex Traits in Sighthounds

Sighthounds, a distinctive group of hounds comprising numerous breeds, have their origins rooted in ancient artificial selection of dogs. In this study, we performed genome sequencing for 123 sighthounds, including one breed from Africa, six breeds from Europe, two breeds from Russia, and four breeds and 12 village dogs from the Middle East. We gathered public genome data of five sighthounds and 98 other dogs as well as 31 gray wolves to pinpoint the origin and genes influencing the morphology of the sighthound genome. Population genomic analysis suggested that sighthounds originated from native dogs independently and were comprehensively admixed among breeds, supporting the multiple origins hypothesis of sighthounds. An additional 67 published ancient wolf genomes were added for gene flow detection. Results showed dramatic admixture of ancient wolves in African sighthounds, even more than with modern wolves. Whole-genome scan analysis identified 17 positively selected genes (PSGs) in the African population, 27 PSGs in the European population, and 54 PSGs in the Middle Eastern population. None of the PSGs overlapped in the three populations. Pooled PSGs of the three populations were significantly enriched in "regulation of release of sequestered calcium ion into cytosol" (gene ontology: 0051279), which is related to blood circulation and heart contraction. In addition, ESR1, JAK2, ADRB1, PRKCE, and CAMK2D were under positive selection in all three selected groups. This suggests that different PSGs in the same pathway contributed to the similar phenotype of sighthounds. We identified an ESR1 mutation (chr1: g.42,177,149 T > C) in the transcription factor (TF) binding site of Stat5a and a JAK2 mutation (chr1: g.93,277,007 T > A) in the TF binding site of Sox5. Functional experiments confirmed that the ESR1 and JAK2 mutation reduced their expression. Our results provide new insights into the domestication history and genomic basis of sighthounds.

Evolutionary history of the extinct wolf population from France in the context of global phylogeographic changes throughout the Holocene

Phylogeographic patterns in large mammals result from natural environmental factors and anthropogenic effects, which in some cases include domestication. The grey wolf was once widely distributed across the Holarctic, but experienced phylogeographic shifts and demographic declines during the Holocene. In the 19th-20th centuries, the species became extirpated from large parts of Europe due to direct extermination and habitat loss. We reconstructed the evolutionary history of the extinct Western European wolves based on the mitogenomic composition of 78 samples from France (Neolithic-20th century) in the context of other populations of wolves and dogs worldwide. We found a close genetic similarity of French wolves from ancient, medieval and recent populations, which suggests the long-term continuity of maternal lineages. MtDNA haplotypes of the French wolves showed large diversity and fell into two main haplogroups of modern Holarctic wolves. Our worldwide phylogeographic analysis indicated that haplogroup W1, which includes wolves from Eurasia and North America, originated in Northern Siberia. Haplogroup W2, which includes only European wolves, originated in Europe ~35 kya and its frequency was reduced during the Holocene due to an expansion of haplogroup W1 from the east. Moreover, we found that dog haplogroup D, currently restricted to Europe and the Middle East, was nested within the wolf haplogroup W2. This suggests European origin of haplogroup D, probably as a result of an ancient introgression from European wolves. Our results highlight the dynamic evolutionary history of European wolves during the Holocene, with a partial lineage replacement and introgressive hybridization with local dog populations.

Dog breeds and conformations in the UK in 2019: VetCompass canine demography and some consequent welfare implications

INTRODUCTION

Growing concerns over health and welfare impacts from extreme phenotypes in dogs have created an urgent need for reliable demographic information on the national breed structures of dogs.

METHODS

This study included all dogs under primary veterinary care in the UK during 2019 at practices participating in VetCompass. Demographic data on these dogs were analysed to report on the frequency of common breeds and also to report on conformation, bodyweight, sex and neuter associations with these breeds.

RESULTS

The study included 2,237,105 dogs under UK veterinary care in 2019. Overall, 69.4% (n = 1,551,462) were classified as purebred, 6.7% (149,308) as designer-crossbred and 24.0% (536,335) as nondesigner-crossbred. Across 800 unique breed names, the most frequent breeds at any age were nondesigner-crossbred (n = 536,335, 24.0%), Labrador Retriever (154,222, 6.9%) and Jack Russell Terrier (101,294, 4.5%). Among 229,624 (10.3%) dogs aged under one year, the most frequent breeds were nondesigner-crossbred (n = 45,995, 20.0%), French Bulldog (16,036, 7.0%) and Cockapoo (14,321, 6.2%). Overall, based on breed characteristics, 17.6% (395,739) were classified as brachycephalic, 43.1% (969,403) as mesaticephalic and 8.3% (186,320) as dolichocephalic. Of 1,551,336 dogs that were classifiable based on breed, 52.6% (815,673) were chondrodystrophic. Of 1,462,925 dogs that were classifiable, there were 54.6% (n = 798,426) short haired, 32.6% (476,883) medium haired and 12.8% (186,934) long haired. Of 1,547,653 dogs that were classifiable for ear carriage, 24.5% (n = 379,581) were erect, 28.1% (434,273) were semi-erect, 19.7% (305,475) were v-shaped drop and 27.7% (428,324) were pendulous. Overall, there was a 1.09:1.00 ratio of male (n = 1,163,512; 52.2%) to female dogs (n = 1,067,552; 47.8%).

CONCLUSIONS

Health and welfare issues linked to popular breeds with extreme phenotypes suggest that there is much work to do to help owners to make more welfare-friendly decisions when choosing which type of dog to own.

You Are Not Welcome! A Media Analysis of Risk Factors, Prevalence and Management of Free-Roaming Dogs in Iran

History has witnessed a long-term relationship between humans and animals. Historical documents and modern findings prove that humans' needs to use animals for companions or services are commonplace in many parts of the world, leading to the domestication of certain animals. Yet, modern societies have degraded many natural habitats for wildlife, confining them to small patches of landscapes or urban areas. Whether a domesticated/free-roaming animal or a wild species, their close contact with humans can create cumbersome situations for both species. This paper explores a link between online media content and on-the-ground efforts to manage free-roaming dogs as a rare case study. As indicated by news articles, the municipal costs of managing free-roaming dogs in Iranian cities have increased, and this can potentially derail the control of such dogs in the long run. This paper lays out pivotal factors for recent increasing human-animal encounters, which have led to many challenges (e.g., rabies) across cities in Iran. We show that some urban features (e.g., topography) can influence the presence and behaviours of free-roaming animals in the cities. The findings of this paper can be related to other developing countries where the plague of rabies is rising.

Early life adversity in dogs produces altered physiological and behavioral responses during a social stress-buffering paradigm

Although owners can act as stress buffers for their dogs, whether dogs with poor early life histories with humans will respond similarly is unknown. We tested 45 dogs, 23 of which were rescued from adverse conditions, in a social paradigm in which a threatening stranger confronted them with either their owner or an unfamiliar human present. Salivary cortisol levels were assessed at three points, and the dogs' behavior and owners' responses to questionnaires were evaluated. Dogs from adverse backgrounds engaged in greater contact and exhibited more relaxed behaviors and social referencing when their owners were present. Dogs from the comparison group explored more when accompanied by their owners. Dogs from adverse backgrounds experienced greater decreases in cortisol levels from the first to third samples relative to dogs in the comparison group. Dogs from adverse backgrounds were also more likely to respond fearfully to a threatening stranger. Their owners rated them as having higher levels of stranger-directed fear, nonsocial fear, separation-related problems, attention seeking, and lower levels of chasing and trainability. These findings from this study suggest that early adverse environments may have lasting effects on dogs' social behavior.

Origin and population structure of native dog breeds in the Korean peninsula and East Asia

To study the ancestry and phylogenetic relationships of native Korean dog breeds to other Asian dog populations, we analyzed nucleotide variations in whole-genome sequences of 205 canid individuals. Sapsaree, Northern Chinese indigenous dog, and Tibetan Mastiff were largely related to West Eurasian ancestry. Jindo, Donggyeongi, Shiba, Southern Chinese indigenous (SCHI), Vietnamese indigenous dogs (VIET), and Indonesian indigenous dogs were related to Southeast and East Asian ancestry. Among East Asian dog breeds, Sapsaree presented the highest haplotype sharing with German Shepherds, indicating ancient admixture of European ancestry to modern East Asian dog breeds. SCHI showed greater haplotype sharing with New Guinea singing dogs, VIET, and Jindo than with other Asian breeds. The predicted divergence time of East Asian populations from their common ancestor was approximately 2,000 to 11,000 years ago. Our results expand understanding of the genetic history of dogs in the Korean peninsula to the Asian continent and Oceanic region.

Being a Dog: A Review of the Domestication Process

The process of canine domestication represents certainly one of the most interesting questions that evolutionary biology aims to address. A "multiphase" view of this process is now accepted, with a first phase during which different groups of wolves were attracted by the anthropogenic niche and a second phase characterized by the gradual establishment of mutual relationships between wolves and humans. Here, we provide a review of dog (Canis familiaris) domestication, highlighting the ecological differences between dogs and wolves, analyzing the molecular mechanisms which seem to have influenced the affiliative behaviors first observed in Belyaev's foxes, and describing the genetics of ancient European dogs. Then, we focus on three Mediterranean peninsulas (Balkan, Iberian and Italian), which together represent the main geographic area for studying canine domestication dynamics, as it has shaped the current genetic variability of dog populations, and where a well-defined European genetic structure was pinpointed through the analysis of uniparental genetic markers and their phylogeny.

HV1 mtDNA Reveals the High Genetic Diversity and the Ancient Origin of Vietnamese Dogs

In this study, samples from 429 dog individuals across three main regions of Vietnam (Southern Vietnam (SVN), Central Vietnam (CVN), and Northern Vietnam (NVN)) were collected to analyze the 582 bp region mtDNA HVI, so as to study the genetic diversity and to screen the rare haplotype E in the Vietnamese village dog population. Nine new haplotypes A, two new haplotypes B, and three haplotypes C were unique to Vietnam dogs, in which the new haplotypes An3, An7, Cn1, and Cn3 concerned mutations at new polymorphism sites (15,517, 15,505, 15,479, and 15,933, respectively) which have not been previously reported. The detection of haplotypes A9 and A29, and the appearance of haplotype A200 in the two individual dogs sampled support that the Southeast Asian dog is the ancestor of today’s Australian dingo and Polynesian dog. The two rare haplotypes E (E1 and E4) were reconfirmed in Vietnamese dogs and discussed. This study also contributes to strengthening the theory of domestication of dogs to the south of the Yangtze River and the Southeast Asian origin of the dingo.

Zoonotic parasites associated with predation by dogs and cats

One of the most common behaviors of cats that have an indoor/outdoor lifestyle is to bring hunted "gifts" to their owners, represented by small mammals, reptiles and birds. Access to the outdoors by dogs and cats may represent a problematic issue, since they may be at risk of diseases, traffic accidents and ingestion of toxins. Yet, the impact of this population of roaming dogs and cats predating wildlife is another concerning issue that receives less attention. Despite these risks, most owners still prefer to give outdoor access to their pets to allow them to express their "natural instincts," such as hunting. Therefore, with a growing population of > 470 million dogs and 373 million cats worldwide, predation not only represents a threat to wildlife, but also a door of transmission for parasitic diseases, some of them of zoonotic concern. In this review, the role played by dogs, and especially cats, in the perpetuation of the biological life cycle of zoonotic parasites through the predation of rodents, reptiles and birds is discussed. Feral and domestics dogs and cats have contributed to the population collapse or extinction of > 63 species of reptiles, mammals and birds. Although the ecological impact of predation on wild populations is well documented, the zoonotic risk of transmission of parasitic diseases has not received significant attention. The parasitic diseases associated to predation vary from protozoan agents, such as toxoplasmosis, to cestodes like sparganosis and even nematodes such as toxocariasis. Raising awareness about predation as a risk of zoonotic parasitic infections in dogs and cats will aid to create responsible ownership and proper actions for controlling feral and free-roaming cat and dog populations worldwide.

DNA methylation-based profiling of horse archaeological remains for age-at-death and castration

Age profiling of archaeological bone assemblages can inform on past animal management practices, but is limited by the fragmentary nature of the fossil record and the lack of universal skeletal markers for age. DNA methylation clocks offer new, albeit challenging, alternatives for estimating the age-at-death of ancient individuals. Here, we take advantage of the availability of a DNA methylation clock based on 31,836 CpG sites and dental age markers in horses to assess age predictions in 84 ancient remains. We evaluate our approach using whole-genome sequencing data and develop a capture assay providing reliable estimates for only a fraction of the cost. We also leverage DNA methylation patterns to assess castration practice in the past. Our work opens for a deeper characterization of past husbandry and ritual practices and holds the potential to reveal age mortality profiles in ancient societies, once extended to human remains.

Phylogeographic and population genetic structure of hound-like native dogs of the Mediterranean Basin

The dog was probably the first domesticated animal. Despite extensive archaeological and genetic investigations, the origin and the evolution of the extant dogs are still being debated. Dog breeds that have over time been selected for hunting share common ancestral traits. This study represents the first comprehensive attempt to survey at the genomic and mitochondrial level eight hound-like dogs breeds indigenous to the Mediterranean Basin to determine if they share common ancient origins. Results from the microsatellite analysis indicate that all the dog populations have a low inbreeding value.The Kelb tal-Fenek has a high divergence from the current Egyptian street population, however there is not enough evidence from this study to exclude completely the potential of an ancient common relationship. Overall, the mitochondrial results indicate high frequencies of haplogroups A and B and a low representation of haplogroup C, while only one Egyptian dog could be assigned to haplogroup D. Results reveal identities and shared clades, suggesting the conservation of ancient European mitotypes in the Mediterranean hound-like breeds, especially in the Egyptian population. Although none of the dog populations/breeds participating in this study indicate to be direct descendants of the Egyptian dogs, they still have a very close morphologically resemblance to those iconic Egyptian dogs often depicted in ancient art forms and share some genetic links with the current Egyptian population. Further research is required with other markers such us complete mitogenomes and SNP panels to confirm the complex history of the Mediterranean dogs involved in this study.

A Preliminary Study on the Interplay between the Serum Levels of Neurotransmitters and Thyroid Hormones for the Evaluation of the Behavioral Phenotype of Dogs

A total of 112 dogs (49 males and 63 females) belonging to different breeds (i.e., Boxer, Cirneco dell'Etna, Fonni's Dog, Labrador, Crossbreed, German Shepherd, Pit Bull, Shar-Pei, Yorkshire) were analyzed to compare the serum concentration of serotonin, dopamine, norepinephrine, prolactin, beta-endorphins, thyroxine (T4), triiodothyronine (T3), thyroid-stimulating hormone (TSH), and assess whether these parameters can be correlated with the behavioral phenotype of the investigated breeds. T4 was above or below the threshold in 61% and 14% of dogs, respectively; T3, in contrast, 41% of dogs showed values below the limit, while 26% above it. TSH was within the reference range in 58% of dogs; 94% of the dogs had prolactin in the reference range and only five animals showed values above the limit. For beta-endorphins, 49% of dogs had values above the limit, while 46% had values within the reference range. Serotonin and dopamine values below physiological limits were found in 62% and 70% of dogs, respectively. Finally, 61% of the dogs showed norepinephrine values within the reference range. The study confirmed that the assessment of the serum values of hormones and neurotransmitters in dogs could be useful to better understand the behavioral phenotype of the animal and could be useful for breeders and trainers for the selection of the most suitable subjects for specific tasks.