Dog domestication and the dual dispersal of people and dogs into the Americas

A universally applicable definition for domestication

The process of domestication is commonly perceived as a human achievement, and domestic species are typically assumed to be those under human control. Domestic species have emerged from a greater diversity of interactions than this perspective allows, and none of the many definitions proposed for domestication can readily, reliably, and consistently distinguish domestic and nondomestic populations. Here, we propose that the process of domestication should instead be defined solely as evolution of a nonhuman population in response to an anthropogenic niche and that a domestic population is one that cannot sustain itself outside of an anthropogenic niche. As a result, this definition does not require comparisons with a presumed and largely unobservable ancestor. Instead, it focuses on the observable relationship between a nonhuman population and humans. It also avoids making assumptions about how domestication happens, thus enabling an exploration of the mechanisms underlying the process of adaptation to an anthropogenic niche. By applying this definition to plants, animals, and microbes, we illustrate its utility for investigating the evolution of the relationship between humans and other species and for anticipating which species are likely to survive in an increasingly human-influenced world. Domestication is simply an evolutionary process resulting from the interaction between two species, one of which is human. As we work to protect Earth's biodiversity, this definition allows us to understand why, in response to the conditions human societies create, some species survive and thrive, while others struggle and go extinct.

Are there 16 species of brown dog ticks? Phylogenies from 60 entire mitochondrial genomes and 162 cox1 sequences reveal 16 species-level clades in the Rhipicephalus (Rhipicephalus) sanguineus group☆☆

The Rhipicephalus sanguineus group, the brown dog ticks, are cosmopolitan and doubtless the most important ticks of domestic dogs, clinically and economically. Despite four decades of taxonomic enquiry with nucleotide sequences and morphology, the taxonomy of the R. sanguineus group is confused, even chaotic. We provide 13 new mitochondrial (mt) genomes and internal transcribed spacer 2 (ITS2) sequences from nine localities in Australia, Israel and Japan. We inferred phylogenetic trees from 10 mt protein-coding genes (9,514 bp), as well as partial cox1, ITS2, 12S, and 16S rRNA genes, to resolve to common clades the >2,000 nucleotide sequences in GenBank from the R. sanguineus group. Then we applied three species delimitation protocols to 60 entire mt genomes (ca. 15,000 bp) and 162 partial cox1 sequences (472 bp): Automatic Barcode Gap discovery, Assemble Species by Automatic Partitioning, and Poisson Tree Process. We considered pairwise genetic differences and Tamura-Nei genetic distances among 60 entire mt genomes and 162 partial cox1 sequences. We found 16 species-level clades (clades A to P) that we hypothesise represent at least 16 species in the R. sanguineus group. These clades had intra-clade differences of <3.8% (entire mt genomes) and <5.1% (partial cox1) whereas the inter-clade differences were >7.7% (entire mt genomes) and >4.5% (partial cox1). We assigned the species names Rhipicephalus linnaei (Audouin, 1826), Rhipicephalus rutilus (Koch, 1844), Rhipicephalus secundus (Feldman-Muhsam, 1952) and R. sanguineus (Latreille, 1806) to clades A, C, D, and K, respectively. And we hypothesise that the names Rhipicephalus camicasi (Morel, Mouchet & Rodhain, 1976), Rhipicephalus turanicus (Pomerantsev, 1940), Rhipicephalus guilhoni (Morel & Vassilades, 1963), Rhipicephalus sulcatus (Neumann, 1908), Rhipicephalus rossicus (Yakimov & Kol-Yakimova, 1911), Rhipicephalus pumilio (Schulze, 1935) and Rhipicephalus pusillus (Gil Collado, 1936) apply to clades B, E, H, J, M, N and O, respectively. The newly described Rhipicephalus hibericus (Millán, Rodriguez-Pastor & Estrada-Peña, 2024) was genetically indistinguishable from R. sanguineus in clade K and thus is a synonym of R. sanguineus. We could not assign names to clades F (USA, Hungary), I (India, Pakistan), L (Nigeria), G (China, Kazakhstan), and P (Cameroon): some or all of these five clades may be new species in the R. sanguineus group. Our haplotype network of partial mt genes (cox1, cytb and nad2) revealed much genetic similarity among geographically distant populations of R. linnaei. This indicates recent dispersal, likely originating in Africa or the Middle East, since African populations were more genetically diverse than populations in other parts of the world.

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.

Dog skull shape challenges assumptions of performance specialization from selective breeding

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

[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.

Phenotypic and Complete Reference Whole Genome Sequence Analyses of Two Paenibacillus spp. Isolates from a Gray Wolf (Canis lupus) Gastrointestinal Tract

Inflammatory bowel disease (IBD) is increasing among mammals around the world, and domestic dogs are no exception. There is no approved cure for canine IBD with limited treatment options. Novel probiotic bacteria discovery from free-ranging animals for the treatment of IBD in domestic pets can likely yield promising probiotic candidates. Consequently, the overall aim was to isolate bacteria from free-ranging animals that could potentially be utilized as novel probiotics. Two bacteria identified as unique Paenibacillus spp. strains by small ribosomal RNA (16S) gene sequencing were isolated from the gastrointestinal tract of a North American Gray Wolf (Canis lupus). The bacteria were typed as Gram-variable, and both were catalase/oxidase positive as well as sensitive to commonly used antibiotics. The bacteria digested complex carbohydrates and lipids by standard assays. The isolated bacteria also inhibited the growth of Staphylococcus aureus and Micrococcus luteus. The whole genome sequence (WGS) length of bacterial isolate ClWae17B was 6,939,193 bp, while ClWae19 was 7,032,512 bp, both similar in size to other Paenibacillus spp. The genomes of both bacteria encoded enzymes involved with the metabolism of complex starches and lipids, such as lyases and pectinases, along with encoding antimicrobials such as lanthipeptides, lasso peptides, and cyclic-lactone-autoinducers. No pernicious virulence genes were identified in the WGS of either bacterial isolate. Phylogenetically, the most closely related bacteria based on 16S gene sequences and WGS were P. taichungensis for ClWae17B and P. amylolyticus for ClWae19. WGS analyses and phenotypic assays supported the hypothesis that the isolates described constitute two novel candidate probiotic bacteria for potential use in dogs.

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

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

Late Pleistocene onset of mutualistic human/canid (Canis spp.) relationships in subarctic Alaska

Large canids (wolves, dogs, and coyote) and people form a close relationship in northern (subarctic and arctic) socioecological systems. Here, we document the antiquity of this bond and the multiple ways it manifested in interior Alaska, a region key to understanding the peopling of the Americas and early northern lifeways. We compile original and existing genomic, isotopic, and osteological canid data from archaeological, paleontological, and modern sites. Results show that in contrast to canids recovered in non-anthropic contexts, canids recovered in association with human occupations are markedly diverse. They include multiple species and intraspecific lineages, morphological variation, and diets ranging from terrestrial to marine. This variation is expressed along both geographic and temporal gradients, starting in the terminal Pleistocene with canids showing high marine dietary estimates. This paper provides evidence of the multiple ecological relationships between canids and people in the north-from predation, probable commensalism, and taming, to domestication-and of their early onset.

Early Paleoindian use of canids, felids, and hares for bone needle production at the La Prele site, Wyoming, USA

We report the first identifications of species and element used to produce Paleolithic bone needles. Archaeologists have used the tailored, fur-fringed garments of high latitude foragers as modern analogs for the clothes of Paleolithic foragers, arguing that the appearance of bone needles and fur bearer remains in archaeological sites c. 40,000 BP is indirect evidence for the advent of tailored garments at this time. These garments partially enabled modern human dispersal to northern latitudes and eventually enabled colonization of the Americas ca. 14,500 BP. Despite the importance of bone needles to explaining global modern human dispersal, archaeologists have never identified the materials used to produce them, thus limiting understanding of this important cultural innovation. We use Zooarchaeology by Mass Spectrometry (ZooMS) and Micro-CT scanning to establish that bone needles at the ca. 12,900 BP La Prele site (Wyoming, USA) were produced from the bones of canids, felids, and hares. We propose that these bones were used by the Early Paleoindian foragers at La Prele because they were scaled correctly for bone needle production and readily available within the campsite, having remained affixed to pelts sewn into complex garments. Combined with a review of comparable evidence from other North American Paleoindian sites, our results suggest that North American Early Paleoindians had direct access to fur-bearing predators, likely from trapping, and represent some of the most detailed evidence yet discovered for Paleoindian garments.

Unsupervised Canine Emotion Recognition Using Momentum Contrast

We describe a system for identifying dog emotions based on dogs' facial expressions and body posture. Towards that goal, we built a dataset with 2184 images of ten popular dog breeds, grouped into seven similarly sized primal mammalian emotion categories defined by neuroscientist and psychobiologist Jaak Panksepp as 'Exploring', 'Sadness', 'Playing', 'Rage', 'Fear', 'Affectionate' and 'Lust'. We modified the contrastive learning framework MoCo (Momentum Contrast for Unsupervised Visual Representation Learning) to train it on our original dataset and achieved an accuracy of 43.2% and a baseline of 14%. We also trained this model on a second publicly available dataset that resulted in an accuracy of 48.46% but had a baseline of 25%. We compared our unsupervised approach with a supervised model based on a ResNet50 architecture. This model, when tested on our dataset with the seven Panksepp labels, resulted in an accuracy of 74.32.

Socio-economic evaluation of human-dog coexistence: A 40,000 years history

The human-animal relationship and its benefits have been a popular issue in recent decades. This study focuses on the dog as a paradigmatic example of this complex bond. The relationship between human and dog evolved over thousands of years through the domestication process. During this period, climatic, cultural, geographical and social changes have had a direct impact on this bond. Dogs have a remarkable capacity to play a variety of roles that mirror the evolution of human societies. Subsequently, questions arise regarding the important and symbolic roles that canines played in ancient cultures, religions and mythological traditions. Specifically, how have these roles changed through history? This research aimed to explore the socio-economic aspects of the human-dog relationship, spanning from ancient civilizations to modern societies. Through a systematic search methodology, this investigation seeks to provide insights into the dynamics of the complex human-dog relationship, including historical backgrounds, socio-cultural dynamics, economic implications and associated challenges. Additionally, the present study addresses the environmental concerns that emerge alongside rising stray dog populations. This research emphasizes the importance of strategies to balance the benefits of this coexistence that promote human and animal welfare.

Dog Domestication Strongly Relied on Translation Regulation According to Differential Gene Expression Analysis

Domestication of dogs from their shared ancestors with wolves occurred more than 15,000 years ago and affected many characteristics of the species. We analyzed the blood RNA sequence data of 12 dogs and 11 wolves from Europe and Asia to shed more light on the domestication history of dogs. We implemented a differential gene expression analysis, a weighted gene correlation network analysis, gene ontology and genetic pathway analyses. We found that both the sample origin (Europe or Asia) and the species had a significant effect on the blood gene expression profiles of the animals. We identified 1567 differentially expressed genes between wolves and dogs and found several significantly overrepresented gene ontology terms, such as RNA polymerase II transcription regulatory region sequence-specific DNA binding or translation. We identified 11 significant gene co-expression networks, hosting a total of 4402 genes, related to DNA replication, metabolism of RNA or metabolism of proteins, for example. Our findings suggest that gene expression regulation played a cardinal role in dog domestication. We recommend further diversifying the analyzed dog and wolf populations in the future by including individuals from different dog breeds and geographical origins, in order to enhance the specificity of detecting significant, true positive genes related to domestication as well as to reduce the false positive rate.

Comparative Population Genomics of Arctic Sled Dogs Reveals a Deep and Complex History

Recent evidence demonstrates genomic and morphological continuity in the Arctic ancestral lineage of dogs. Here, we use the Siberian Husky to investigate the genomic legacy of the northeast Eurasian Arctic lineage and model the deep population history using genome-wide single nucleotide polymorphisms. Utilizing ancient dog-calibrated molecular clocks, we found that at least two distinct lineages of Arctic dogs existed in ancient Eurasia at the end of the Pleistocene. This pushes back the origin of sled dogs in the northeast Siberian Arctic with humans likely intentionally selecting dogs to perform different functions and keeping breeding populations that overlap in time and space relatively reproductively isolated. In modern Siberian Huskies, we found significant population structure based on how they are used by humans, recent European breed introgression in about half of the dogs that participate in races, moderate levels of inbreeding, and fewer potentially harmful variants in populations under strong selection for form and function (show, sled show, and racing populations of Siberian Huskies). As the struggle to preserve unique evolutionary lineages while maintaining genetic health intensifies across pedigreed dogs, understanding the genomic history to guide policies and best practices for breed management is crucial to sustain these ancient lineages and their unique evolutionary identity.

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

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

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

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

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

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

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.

Understanding Human-Autonomy Teams Through a Human-Animal Teaming Model

The relationship between humans and animals is complex and influenced by multiple variables. Humans display a remarkably flexible and rich array of social competencies, demonstrating the ability to interpret, predict, and react appropriately to the behavior of others, as well as to engage others in a variety of complex social interactions. Developing computational systems that have similar social abilities is a critical step in designing robots, animated characters, and other computer agents that appear intelligent and capable in their interactions with humans and each other. Further, it will improve their ability to cooperate with people as capable partners, learn from natural instruction, and provide intuitive and engaging interactions for human partners. Thus, human-animal team analogs can be one means through which to foster veridical mental models of robots that provide a more accurate representation of their near-future capabilities. Some digital twins of human-animal teams currently exist but are often incomplete. Therefore, this article focuses on issues within and surrounding the current models of human-animal teams, previous research surrounding this connection, and the challenges when using such an analogy for human-autonomy teams.

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.

Do pet dogs reciprocate the receipt of food from familiar and unfamiliar conspecifics?

Reciprocity is one of the most prominent explanations for the evolution of stable cooperation. Although reciprocity has been studied for decades in numerous animal species and behavioural contexts, its underlying proximate mechanisms remain unclear. Domestic dogs provide a useful model species for the study of proximate mechanisms, though there are currently inconsistent findings regarding dogs' propensity to reciprocate. Here, we investigated whether, after minimal training, pet dogs would press a button, which remotely controlled a food dispenser, to deliver food to an enclosure occupied by a helpful conspecific that had provided them with food or an unhelpful conspecific that had not provided them with food. We included an asocial control condition in which the enclosure was unoccupied and a social facilitation control in which the food delivery mechanism was non-functional. Whether subjects were familiar with the helpful and unhelpful conspecifics was also varied. In addition, to investigate potential mechanisms underlying reciprocity, we measured subjects salivary oxytocin concentration before and after they experienced the helpful and unhelpful acts. There was no effect of the previous helpfulness or the familiarity of the partner on the number of times subjects pressed the button. However, there was also no effect of the presence of a partner or the operationality of the food delivery mechanism on the number of button presses, indicating that subjects were not pressing the button to provision the partner. Moreover, the experience of the helpful or unhelpful act did not influence subjects' salivary oxytocin concentration. Variation in findings of reciprocity across studies appears to correspond with differing training protocols. Subjects' understanding of the task in the current study may have been constrained by the limited training received. Additional tests to verify subjects' understanding of such tasks are warranted in future studies.

Patagonian partnerships: the extinct Dusicyon avus and its interaction with prehistoric human communities

The southern Mendoza province, located in the northern region of Patagonia, was inhabited by hunter-gatherer groups until historic times. Previous archaeological studies have reported canid remains among faunal assemblages, which were assumed to be part of the human diet. However, the taxonomic identification and significance of these canids within human groups have raised questions. In this study, we used ancient DNA analysis, morphological examination and stable isotope analysis (δ13Ccol and δ15N) to re-evaluate the taxonomic assignment of a canid discovered at the Late Holocene burial site of Cañada Seca. Previous morphological identifications suggested that it belonged to the genus Lycalopex, but our results conclusively demonstrate that the individual belongs to the extinct fox species Dusicyon avus. This finding expands Dusicyon avus' known geographical distribution to Patagonia's northern extremity. Furthermore, statistical predictions based on genetic divergence undermine the hypothesis that hybridization between Canis and Dusicyon, facilitated by the introduction of domestic dogs, played a role in the extinction of Dusicyon species. On the other hand, our findings indicate that a Dusicyon avus individual shared a similar diet and was probably buried alongside humans, suggesting a close relationship between the two species during their lives and deaths.

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.

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.

Canine Staphylococcaceae circulating in a Kenyan animal shelter

Animal shelters, especially in resource-poor countries, bring together pets from different regions and with different backgrounds. The crowding of such animals often results in infectious diseases, such as respiratory infections. This study characterized Staphylococcaceae from diseased and apparently healthy dogs housed in an animal shelter in Kenya, to determine their antibiotic resistance profiles, their genetic relatedness, and the presence of dominant clones. Therefore, bacteria were collected from all 167 dogs present in the shelter in June 2015 and screened for Staphylococcaceae using standard cultivation techniques. In all, 92 strains were isolated from 85 dogs and subsequently sequenced by PacBio long-read sequencing. Strains encompassed nine validated species, while S. aureus (n = 47), S. pseudintermedius (n = 21), and Mammaliicoccus (M.) sciuri (n = 16) were the three most dominant species. Two S. aureus clones of ST15 (CC15) and ST1292 (CC1) were isolated from 7 and 37 dogs, respectively. All 92 strains isolated were tested for their antimicrobial susceptibility by determining the minimum inhibitory concentrations. In all, 86 strains had resistance-associated minimal inhibitory concentrations to at least one of the following antimicrobials: tetracycline, benzylpenicillin, oxacillin, erythromycin, clindamycin, trimethoprim, kanamycin/gentamicin, or streptomycin. Many virulence-encoding genes were detected in the S. aureus strains, other Staphylococcaceae contained a different set of homologs of such genes. The presence of mobile genetic elements, such as plasmids and prophages, known to facilitate the dissemination of virulence- and resistance-encoding genes, was also assessed. The unsuspected high presence of two S. aureus clones in about 50% of dogs suggests dissemination within the shelter and a human source.IMPORTANCEMicrobiological data from sub-Saharan Africa are scarce compared to data from North America, Europe, or Asia, and data derived from dogs, the man's best friend, kept in sub-Saharan Africa are largely missing. This work presents data on Staphylococcaceae mainly isolated from the nasal cavity of dogs stationed at a Kenyan shelter in 2015. We characterized 92 strains isolated from 85 dogs, diseased and apparently healthy ones. The strains isolated covered nine validated species and we determined their phenotypic resistance and characterized their complete genomes. Interestingly, Staphylococcus aureus of two predominant genetic lineages, likely to be acquired from humans, colonized many dogs. We also detected 15 novel sequence types of Mammaliicoccus sciuri and S. pseudintermedius indicating sub-Saharan-specific phylogenetic lineages. The data presented are baseline data that guide antimicrobial treatment for dogs in the region.

Characteristic processes of human evolution caused the Anthropocene and may obstruct its global solutions

We propose that the global environmental crises of the Anthropocene are the outcome of a ratcheting process in long-term human evolution which has favoured groups of increased size and greater environmental exploitation. To explore this hypothesis, we review the changes in the human ecological niche. Evidence indicates the growth of the human niche has been facilitated by group-level cultural traits for environmental control. Following this logic, sustaining the biosphere under intense human use will probably require global cultural traits, including legal and technical systems. We investigate the conditions for the evolution of global cultural traits. We estimate that our species does not exhibit adequate population structure to evolve these traits. Our analysis suggests that characteristic patterns of human group-level cultural evolution created the Anthropocene and will work against global collective solutions to the environmental challenges it poses. We illustrate the implications of this theory with alternative evolutionary paths for humanity. We conclude that our species must alter longstanding patterns of cultural evolution to avoid environmental disaster and escalating between-group competition. We propose an applied research and policy programme with the goal of avoiding these outcomes. This article is part of the theme issue 'Evolution and sustainability: gathering the strands for an Anthropocene synthesis'.

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.

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.

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.

Going beyond established model systems of Alzheimer's disease: companion animals provide novel insights into the neurobiology of aging

Alzheimer's disease (AD) is characterized by brain plaques, tangles, and cognitive impairment. AD is one of the most common age-related dementias in humans. Progress in characterizing AD and other age-related disorders is hindered by a perceived dearth of animal models that naturally reproduce diseases observed in humans. Mice and nonhuman primates are model systems used to understand human diseases. Still, these model systems lack many of the biological characteristics of Alzheimer-like diseases (e.g., plaques, tangles) as they grow older. In contrast, companion animal models (cats and dogs) age in ways that resemble humans. Both companion animal models and humans show evidence of brain atrophy, plaques, and tangles, as well as cognitive decline with age. We embrace a One Health perspective, which recognizes that the health of humans is connected to those of animals, and we illustrate how such a perspective can work synergistically to enhance human and animal health. A comparative biology perspective is ideally suited to integrate insights across veterinary and human medical disciplines and solve long-standing problems in aging.

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.

The Role of Empathic Concern and Gender on Interspecific Contagious Yawning in Humans

Interspecific contagious yawning (CY), whereby yawns from one species trigger yawning in different species, has now been reported across various taxa. This response to human yawning appears common among animals in captivity and has been interpreted as an empathic response towards human handlers/caregivers. A recent study found that humans also display interspecific CY, though this response was not modulated by proxies of empathic processing (i.e., phylogenetic relatedness or social closeness to the animals). Here, we explored this relationship more explicitly by assessing how interspecific CY to yawns from common household pets relates to self-reported empathic concern. Participants (N = 103) completed a survey measuring empathic concern and then reported on their yawning behavior following exposure to a control condition or yawning images either from domesticated cats or domesticated dogs. The results provide further evidence for interspecific CY in humans, but empathic concern was negatively predictive of this response. There was also no sex difference in interspecific CY, though when comparing the sexes across CY conditions, women reported a higher frequency of yawning in response to dog yawns, and men reported a higher frequency of yawning in response to cat yawns. Overall, these findings do not support a strong connection between interspecific CY and empathy or emotional contagion.

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.

Dog barks influence the physiological stress and behavior of a wild primate

Non-lethal impacts of dogs on primates have seldom been assessed. We used an experimental approach to determine if mantled howler monkeys (Alouatta palliata) perceive dog barks as an aversive stimulus and thus display physiological and behavioral responses toward simulated barks. For one year (1754 h of observations) we studied 16 adult males belonging to five groups in Los Tuxtlas (Mexico), and recorded the occurrence of naturally occurring dog barks, their sound pressure level (SPL), and the behavioral responses of howler monkeys to barks. We then exposed males to bark playbacks at two SPL treatments, 40 and 80 dB in a total of 50 experiments. We assayed glucocorticoid metabolite concentrations in fecal samples (fGCM) as a marker of the physiological stress response of males. We also recorded the duration of vigilance, vocalizations, and flight in relation to playbacks. Naturally occurring barks were frequent and usually elicited behavioral responses by males. fGCM concentrations increased after bark playbacks and with stimuli intensity. Time spent vigilant increased following playbacks independently of stimuli intensity but both vocalizations and flight were linked to stimuli intensity: vocalizations were the longest after barks played-back at 80 dB, but males spent more time fleeing in response to 40 dB bark playbacks. These results provide evidence that dog barks are pervasive in the habitat of mantled howler monkeys living at Los Tuxtlas and disturb males, both physiologically and behaviorally. Although the potential costs of physiological and behavioral responses could not be determined, there is sufficient evidence to assume that they do have negative impacts on individuals. Therefore, our study provides avenues for future research on dog-wildlife interactions and valuable information for the design of conservation actions aimed at mitigating the impact of dogs on mantled howler monkeys.

The evolutionary neuroscience of domestication

How does domestication affect the brain? This question has broad relevance. Domesticated animals play important roles in human society, and substantial recent work has addressed the hypotheses that a domestication syndrome links phenotypes across species, including Homo sapiens. Surprisingly, however, neuroscience research on domestication remains largely disconnected from current knowledge about how and why brains change in evolution. This article aims to bridge that gap. Examination of recent research reveals some commonalities across species, but ultimately suggests that brain changes associated with domestication are complex and variable. We conclude that interactions between behavioral, metabolic, and life-history selection pressures, as well as the role the role of experience and environment, are currently largely overlooked and represent important directions for future research.

Function predicts how people treat their dogs in a global sample

Dogs have an extraordinary relationship with humans. We understand, communicate, and cooperate remarkably with our dogs. But almost all we know about dog-human bonds, dog behaviour, and dog cognition is limited to Western, Educated, Industrialized, Rich, Democratic (WEIRD) societies. WEIRD dogs are kept for a variety of functions, and these can influence their relationship with their owner, as well as their behaviour and performance in problem-solving tasks. But are such associations representative worldwide? Here we address this by collecting data on the function and perception of dogs in 124 globally distributed societies using the eHRAF cross-cultural database. We hypothesize that keeping dogs for multiple purposes and/or employing dogs for highly cooperative or high investment functions (e.g., herding, guarding of herds, hunting) will lead to closer dog-human bonds: increased primary caregiving (or positive care), decreased negative treatment, and attributing personhood to dogs. Our results show that indeed, the number of functions associates positively with close dog-human interactions. Further, we find increased odds of positive care in societies that use herding dogs (an effect not replicated for hunting), and increased odds of dog personhood in cultures that keep dogs for hunting. Unexpectedly, we see a substantial decrease of dog negative treatment in societies that use watchdogs. Overall, our study shows the mechanistic link between function and the characteristics of dog-human bonds in a global sample. These results are a first step towards challenging the notion that all dogs are the same, and open questions about how function and associated cultural correlates could fuel departures from the 'typical' behaviour and social-cognitive skills we commonly associate with our canine friends.

Genetic engineering and genome editing in plants, animals and humans: Facts and myths

Human history is inextricably linked to the introduction of desirable heritable traits in plants and animals. Selective breeding (SB) predates our historical period and has been practiced since the advent of agriculture and farming more than ten thousand years ago. Since the 1970s, methods of direct plant and animal genome manipulation are constantly being developed. These are collectively described as "genetic engineering" (GE). Plant GE aims to improve nutritional value, insect resistance and weed control. Animal GE has focused on livestock improvement and disease control. GE applications also involve medical improvements intended to treat human disease. The scientific consensus built around marketed products of GE organisms (GEOs) is usually well established, noting significant benefits and low risks. GEOs are exhaustively scrutinized in the EU and many non-EU countries for their effects on human health and the environment, but scrutiny should be equally applied to all previously untested organisms derived directly from nature or through selective breeding. In fact, there is no evidence to suggest that natural or selectively bred plants and animals are in principle safer to humans than GEOs. Natural and selectively bred strains evolve over time via genetic mutations that can be as risky to humans and the environment as the mutations found in GEOs. Thus, previously untested plant and animal strains aimed for marketing should be proven useful or harmful to humans only upon comparative testing, regardless of their origin. Highlighting the scientific consensus declaring significant benefits and rather manageable risks provided by equitably accessed GEOs, can mitigate negative predispositions by policy makers and the public. Accordingly, we provide an overview of the underlying technologies and the scientific consensus to help resolve popular myths about the safety and usefulness of GEOs.

History of Polish Canidae (Carnivora, Mammalia) and Their Biochronological Implications on the Eurasian Background

The remains of 12 canid species that date back ca. 4.9 myr have been found at 116 paleontological localities. Among these localities, eight are dated to the Pliocene age, 12 are dated to the Early Pleistocene age, 12 are from the Middle Pleistocene age, while the most numerous group includes 84 sites from the Late Pleistocene–Holocene age. Some, especially older forms such as Eucyon odessanus and Nyctereutes donnezani, have only been found at single sites, while the remains of species from the genus Lycaon, Canis and Vulpes have been recorded at numerous sites from the last 2 myr. Ancient canids such as Eucyon and Nyctereutes had already vanished from Poland in the Earliest Pleistocene, between 2.5 and 2.2 myr ago. Poland’s extant canid fauna is characterised by the presence of two new species, which spread into the territory due to a human introduction (Nyctereutes procyonoides) or natural expansion (Canis aureus). Research indicates a strong competition between dogs, especially between Lycaon, Canis and Cuon, with a strong lycaon-limiting effect on the wolf between 2.5 and 0.4 myr ago. After the extinction of Lycaon lycaonoides, Canis lupus evolved rapidly, increasing in number and size, and taking over the niche occupied by Lycaon. In order to reduce competition, the body size of Cuon alpinus gradually reduced, and it became an animal adapted to the forest, highland and mountain environments. Generally, the history of canids in Poland is similar to that known of Eurasia with some noteworthy events, such as the early occurrence of Canis cf. etruscus from Węże 2 (2.9–2.6 myr ago), Lycaon falconeri from Rębielice Królewskie 1A or one of the latest occurrences of L. lycaonoides from Draby 3 (430–370 kyr). Predominantly lowland or upland in the southern part and devoid of significant ecological barriers, Poland is also an important migration corridor in the East–West system. This 500–600 km wide corridor was the Asian gateway to Europe, from where species of an eastern origin penetrated the continent’s interior. In colder periods, it was in turn a region through which boreal species or those associated with the mammoth steppe retreated.

Factors regarding the dog owner's household situation, antisocial behaviours, animal views and animal treatment in a population of dogs confiscated after biting humans and/ or other animals

To examine the dog ownership factors characteristic to a population of dogs confiscated after a human and/ or animal-directed biting incident, we compared bite risk assessment reports of 159 confiscated dogs in the time frame 2008, 2009, 2010 (tf1) and of 215 confiscated dogs in the time frame 2020, 2021, 2022 (until mid-May; tf2). The reports were compiled by the same institute in a standardized format. We studied frequencies and chi-square pairwise comparisons (P<0.05) for 30 identified ownership factors. Overall (tf1 and tf2), 1,308 ownership factors were mentioned in the reports and reports mentioning ≥5 factors were twice as frequent in tf2 (38%) than tf1 (16%). Our data suggest that nine factors may in particular serve as a warning signal for biting incidents, as these factors were most frequently (≥15%) prevalent in the total of reported cases: having a multiple dog household, a dog reportedly roaming a neighbourhood without an owner, a dog's care tasks being transferred, a short leash and muzzle obligation served to the owner for a dog, an isolated and/ or confined keeping of a dog, a dog owner's (suspected) substance abuse, a dog owner's (suspected) animal abuse, a dog owner aggressing at confiscation of the dog and a dog owner being reported on for antisocial behaviours such as intimidation. Particularly, a dog owner's aggressive or antisocial behaviours and previous obligations to muzzle and short leash a dog (in our dataset often inappropriately adhered to by owners), may indicate that a proportion of owners of confiscated dogs, may not always be willing and/ or capable to guarantee societal safety. The results show that identification of dog ownership factors, might be useful for establishing biting incident policies and further studies should be done on preventive measures and controls.

The human-initiated model of wolf domestication - An expansion based on human-dingo relations in Aboriginal Australia

The historically known relationship of interspecies companionship between Aboriginal foraging communities in Australia and free-ranging dingoes provides a model for understanding the human-canid relations that gave rise to the first domesticated dogs. Here, we propose that a broadly similar relationship might have developed early in time between wild-living wolves and mobile groups of foragers in Late Pleistocene Eurasia, with hunter-gatherers routinely raiding wild wolf dens for pre-weaned pups, which were socialized to humans and kept in camp as tamed companions ("pets"). We outline a model in which captive wolf pups that reverted to the wild to breed when they were sexually mature established their territories in the vicinity of foraging communities - in a "liminal" ecological zone between humans and truly wild-living wolves. Many (or most) of the wolf pups humans took from the wilderness to rear in camp may have derived from these liminal dens where the breeding pairs had been under indirect human selection for tameness over many generations. This highlights the importance of the large seasonal hunting/aggregation camps associated with mammoth kill-sites in Gravettian/Epigravettian central Europe. Large numbers of foragers gathered regularly at these locations during the wild wolf birthing season. We infer that if a pattern of this kind occurred over long periods of time then there might have been a pronounced effect on genetic variation in free-ranging wolves that denned and whelped in the liminal zones in the vicinity of these human seasonal aggregation sites. The argument is not that wolves were domesticated in central Europe. Rather, it is this pattern of hunter-gatherers who caught and reared wild wolf pups gathering seasonally in large numbers that might have been the catalyst for the early changes leading to the first domesticated dogs - whether in western Eurasia or further afield.

Pigs as Pets: Early Human Relations with the Sulawesi Warty Pig (Sus celebensis)

The Sulawesi warty pig (S. celebensis) is a wild and still-extant suid that is endemic to the Indonesian island of Sulawesi. It has long been theorised that S. celebensis was domesticated and/or deliberately introduced to other islands in Indonesia prior to the advent of the Neolithic farming transition in the region. Thus far, however, there has been no empirical support for this idea, nor have scientists critiqued the argument that S. celebensis was a pre-Neolithic domesticate in detail. Here, it is proposed that early foragers could have formed a relationship with S. celebensis that was similar in essence to the close association between Late Pleistocene foragers in Eurasia and the wild wolf ancestors of domestic dogs. That is, a longstanding practice of hunter-gatherers intensively socialising wild-caught S. celebensis piglets for adoption into human society as companion animals ('pets') may have altered the predator-prey dynamic, brought aspects of wild pig behaviour and reproduction under indirect human selection and control, and caused changes that differentiated human-associated pigs from their solely wild-living counterparts.

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.

Developmental instability in domesticated mammals

Measures of fluctuating asymmetry (FA) have been adopted widely as an estimate of developmental instability. Arising from various sources of stress, developmental instability is associated with an organism's capacity to maintain fitness. The process of domestication has been framed as an environmental stress with human-specified parameters, suggesting that FA may manifest to a larger degree among domesticates compared to their wild relatives. This study used three-dimensional geometric morphometric landmark data to (a) quantify the amount of FA in the cranium of six domestic mammal species and their wild relatives and, (b) provide novel assessment of the commonalities and differences across domestic/wild pairs concerning the extent to which random variation arising from the developmental system assimilates into within-population variation. The majority of domestic mammals showed greater disparity for asymmetric shape, however, only two forms (Pig, Dog) showed significantly higher disparity as well as a higher degree of asymmetry compared to their wild counterparts (Wild Boar, Wolf). Contra to predictions, most domestic and wild forms did not show a statistically significant correspondence between symmetric shape variation and FA, however, a moderate correlation value was recorded for most pairs (r-partial least squares >0.5). Within pairs, domestic and wild forms showed similar correlation magnitudes for the relationship between the asymmetric and symmetric components. In domesticates, new variation may therefore retain a general, conserved pattern in the gross structuring of the cranium, whilst also being a source for response to selection on specific features.

On taming the effect of transcript level intra-condition count variation during differential expression analysis: A story of dogs, foxes and wolves

The evolution of RNA-seq technologies has yielded datasets of scientific value that are often generated as condition associated biological replicates within expression studies. With expanding data archives opportunity arises to augment replicate numbers when conditions of interest overlap. Despite correction procedures for estimating transcript abundance, a source of ambiguity is transcript level intra-condition count variation; as indicated by disjointed results between analysis tools. We present TVscript, a tool that removes reference-based transcripts associated with intra-condition count variation above specified thresholds and we explore the effects of such variation on differential expression analysis. Initially iterative differential expression analysis involving simulated counts, where levels of intra-condition variation and sets of over represented transcripts are explicitly specified, was performed. Then counts derived from inter- and intra-study data representing brain samples of dogs, wolves and foxes (wolves vs. dogs and aggressive vs. tame foxes) were used. For simulations, the sensitivity in detecting differentially expressed transcripts increased after removing hyper-variable transcripts, although at levels of intra-condition variation above 5% detection became unreliable. For real data, prior to applying TVscript, ≈20% of the transcripts identified as being differentially expressed were associated with high levels of intra-condition variation, an over representation relative to the reference set. As transcripts harbouring such variation were removed pre-analysis, a discordance from 26 to 40% in the lists of differentially expressed transcripts is observed when compared to those obtained using the non-filtered reference. The removal of transcripts possessing intra-condition variation values within (and above) the 97^th and 95^th percentiles, for wolves vs. dogs and aggressive vs. tame foxes, maximized the sensitivity in detecting differentially expressed transcripts as a result of alterations within gene-wise dispersion estimates. Through analysis of our real data the support for seven genes with potential for being involved with selection for tameness is provided. TVscript is available at: https://sourceforge.net/projects/tvscript/.

The Role of Socialisation in the Taming and Management of Wild Dingoes by Australian Aboriginal People

Simple Summary

The dingo (Canis dingo) is a wild-living canid endemic to mainland Australia; the descendent of an early lineage of dog introduced thousands of years ago to the continent, where it was isolated from further introductions of domestic canines until European colonisation began in 1788. Dingoes are notoriously difficult to maintain in captivity and owing to their predatory nature it is also known that they can pose a serious risk to children. Yet, written records and oral histories indicate that Aboriginal people in mainland Australia routinely practiced the rearing and keeping of dingoes in a tame state within their home communities and domestic spaces. This paper reviews historical and archaeological evidence for the management of wild and captive dingoes by Indigenous communities, revealing a substantial divide between the nature and outcomes of these interactions between historical/pre-contact Aboriginal societies and those in contemporary Australia. It is concluded that this special human-wild canid relationship has implications for the understanding of the domestication of dogs from wolves during the Late Pleistocene.

Abstract

Historical sources and Indigenous oral traditions indicate that Australian Aboriginal people commonly reared and kept the wild-caught pups of dingoes (C. dingo) as tamed companion animals. A review of the available evidence suggests Indigenous communities employed an intense socialisation process that forged close personal bonds between humans and their tame dingoes from an early age. This was complemented by oral traditions which passed down awareness of the dangers to children posed by wild or unfamiliar dingoes, and which communicated the importance of treating dingoes with respect. Together, these practices resulted in what can be interpreted as substantially altered behaviours in tamed dingoes, which, despite their naturally high prey drive, were not considered a serious threat to children and were thus able to be maintained as companion animals in the long term. This relationship is of importance for understanding the original domestication of the dog, as it demonstrates a means by which careful and deliberate socialisation by foragers could both manage risks to children’s safety posed by keeping wild canids in the domestic realm and retain them well into reproductive maturity—both issues which have been highlighted as obstacles to the domestication of dogs from wolves.

Human-directed attachment behavior in wolves suggests standing ancestral variation for human-dog attachment bonds

Domesticated animals are generally assumed to display increased sociability toward humans compared to their wild ancestors. Dogs (Canis familiaris) have a remarkable ability to form social relationships with humans, including lasting attachment, a bond based on emotional dependency. Since it has been specifically suggested that the ability to form attachment with humans evolved post-domestication in dogs, attempts to quantify attachment behavior in wolves (Canis lupus) have subsequently been performed. However, while these rare wolf studies do highlight the potential for wolves to express human-directed attachment, the varied methods used and the contrasting results emphasize the need for further, standardized testing of wolves. Here, we used the standardized Strange Situation Test to investigate attachment behavior expressed in wolves and dogs hand-raised and socialized under standardized and identical conditions up until the age of testing. We found that 23-week-old wolves and dogs equally discriminated between a stranger and a familiar person, and expressed similar attachment behaviors toward a familiar person. Additionally, wolves, but not dogs, expressed significantly elevated stress-related behavior during the test, but this stress response was buffered by the presence of a familiar person. Together, our results suggest that wolves can show attachment behaviors toward humans comparable to those of dogs. Importantly, our findings demonstrate that the ability to form attachment with humans exists in relatives of the wild ancestor of dogs, thereby refuting claims that this phenotype evolved after dog domestication was initiated.

The genome and diet of a 35,000-year-old Canis lupus specimen from the Paleolithic painted cave, Chauvet-Pont d'Arc, France

The Chauvet-Pont-d'Arc Cave (Ardèche, France) contains some of the oldest Paleolithic paintings recorded to date, as well as thousands of bones of the extinct cave bear, and some remains and footprints of other animals. As part of the interdisciplinary research project devoted to this reference cave site, we analyzed a coprolite collected within the deep cave. AMS radiocarbon dating of bone fragments from the coprolite yielded an age of 30,450 ± 550 RC yr. BP (AAR-19656; 36,150-34,000 cal BP), similar to ages assigned to Paleolithic artwork and cave bear remains from the same cave sector. Using high-throughput shotgun DNA sequencing, we demonstrated a high abundance of canid DNA and lesser amounts of DNA from the extinct cave bear. We interpret the sample as feces from a canid that had consumed cave bear tissue. The high amount of canid DNA allowed us to reconstruct a complete canid mitochondrial genome sequence (average coverage: 83×) belonging to a deeply divergent clade of extinct mitochondrial wolf lineages that are most closely related to coeval (~35 ka) Belgian wolves. Analysis of the nuclear genome yielded a similar coverage for the X chromosome (2.4×) and the autosomes (range: 2.3-3.2×), indicating that the Chauvet canid was a female. Comparing the relationship of the nuclear genome of this specimen with that of a variety of canids, we found it more closely related to gray wolves' genomes than to other wild canid or dog genomes, especially wolf genomes from Europe and the Middle East. We conclude that the coprolite is feces from an animal within an extinct wolf lineage. The consumption of cave bear by this wolf likely explains its intrusion into the dark cave sectors and sheds new light on the paleoecology of a major cave site.

The evolution of dog diet and foraging: Insights from archaeological canids in Siberia

Research on the evolution of dog foraging and diet has largely focused on scavenging during their initial domestication and genetic adaptations to starch-rich food environments following the advent of agriculture. The Siberian archaeological record evidences other critical shifts in dog foraging and diet that likely characterize Holocene dogs globally. By the Middle Holocene, body size reconstruction for Siberia dogs indicates that most were far smaller than Pleistocene wolves. This contributed to dogs' tendencies to scavenge, feed on small prey, and reduce social foraging. Stable carbon and nitrogen isotope analysis of Siberian dogs reveals that their diets were more diverse than those of Pleistocene wolves. This included habitual consumption of marine and freshwater foods by the Middle Holocene and reliance on C4 foods by the Late Holocene. Feeding on such foods and anthropogenic waste increased dogs' exposure to microbes, affected their gut microbiomes, and shaped long-term dog population history.

Grey wolf genomic history reveals a dual ancestry of dogs

The grey wolf (Canis lupus) was the first species to give rise to a domestic population, and they remained widespread throughout the last Ice Age when many other large mammal species went extinct. Little is known, however, about the history and possible extinction of past wolf populations or when and where the wolf progenitors of the present-day dog lineage (Canis familiaris) lived^1–8. Here we analysed 72 ancient wolf genomes spanning the last 100,000 years from Europe, Siberia and North America. We found that wolf populations were highly connected throughout the Late Pleistocene, with levels of differentiation an order of magnitude lower than they are today. This population connectivity allowed us to detect natural selection across the time series, including rapid fixation of mutations in the gene IFT88 40,000–30,000 years ago. We show that dogs are overall more closely related to ancient wolves from eastern Eurasia than to those from western Eurasia, suggesting a domestication process in the east. However, we also found that dogs in the Near East and Africa derive up to half of their ancestry from a distinct population related to modern southwest Eurasian wolves, reflecting either an independent domestication process or admixture from local wolves. None of the analysed ancient wolf genomes is a direct match for either of these dog ancestries, meaning that the exact progenitor populations remain to be located.

DNA from ancient wolves spanning 100,000 years sheds light on wolves’ evolutionary history and the genomic origin of dogs.