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APPENDIX 2 in On the morphology of the astragalus and calcaneus of the amphicyonids (Carnivora, Mammalia) from the Paleogene of Europe: implications for the ecology of the European bear-dogs
APPENDIX 2. — Body mass (in kg and g) estimated on the basis of dental material for the amphicyonid species known in the Paleogene of Europe, with indication of their stratigraphic distribution (MP levels). Only the species with accurate stratigraphic records are considered. Estimations realized in the framework of the Brain Pioneer BR/175/PI/CARNAGES of the Federal Science Policy Office of Belgium (BELSPO).
FIG. 1 in On the morphology of the astragalus and calcaneus of the amphicyonids (Carnivora, Mammalia) from the Paleogene of Europe: implications for the ecology of the European bear-dogs
FIG. 1. — Location map of Aubrelong (France; Rupelian, MP21) where the new fossils of Cynodictis lacustris were found. The Quercy area is composed of the Lot Department and part of the Tarn-et-Garonne.
R in On the morphology of the astragalus and calcaneus of the amphicyonids (Carnivora, Mammalia) from the Paleogene of Europe: implications for the ecology of the European bear-dogs
R, lateral view; S, distal view; T, proximal view. Abbreviations: ef, ectal facet; f, foramen; ff, fibular facet; h, head; ll, lateral lip; lp, lateral process; ml, medial lip; n, neck; ppt, proximal plantar tuberosity; ptg, plantar tendon groove; sf, sustentacular facet; sit, sinus of the tarsus; tr, trochlea. Scale bar: 1 cm.
Data from: Factors affecting carcass detection at wind farms using dogs and human searchers
<p>1. The use of detection dogs to effectively monitor bird and bat fatalities at wind farms is becoming increasingly popular. All studies to date agree that dogs outperform human searchers at finding bird and bat carcasses around wind turbines; however, it remains unclear how particular conditions during the search may influence carcass detection.</p> <p>2. We investigate the effect of carcass size, habitat characteristics and weather conditions on carcass detection probability, for both dogs and humans, using data from the monitoring program of a wind farm in Spain.</p> <p>3. A generalized linear model reveals a high performance of dogs (~80% detection probability), with no clear influence of any of the variables analysed. Humans, on the contrary, were markedly affected by the size of the carcass and to some extent, by the vegetation structure. Humans performed poorly at detecting small carcasses (~20% detection probability), more so in dense vegetation.</p> <p>4. Synthesis and applications. Our results provide evidence that dogs perform at a high level under a wide range of environmental conditions. They are particularly well-suited for the monitoring of fatalities of small, rare or inconspicuous species in cluttered environments. Humans, by contrast, are very poor at detecting all but the largest carcasses.16-Jun-2020</p>
Data from: Genetic dissection of complex behaviour traits in German Shepherd dogs.
A favourable genetic structure and diversity of behavioural features highlights the potential of dogs for studying the genetic architecture of behaviour traits. However, behaviours are complex traits, which have been shown to be influenced by numerous genetic and non-genetic factors, complicating their analysis. In this study, the genetic contribution to behaviour variation in German Shepherd dogs (GSDs) was analysed using genomic approaches. GSDs were phenotyped for behaviour traits using the established Canine Behavioral Assessment and Research Questionnaire (C-BARQ). Genome-wide association study (GWAS) and regional heritability mapping (RHM) approaches were employed to identify associations between behaviour traits and genetic variants, while accounting for relevant non-genetic factors. By combining these complementary methods we endeavoured to increase the power to detect loci with small effects. Several behavioural traits exhibited moderate heritabilities, with the highest identified for Human-directed playfulness, a trait characterised by positive interactions with humans. We identified several genomic regions associated with one or more of the analysed behaviour traits. Some candidate genes located in these regions were previously linked to behavioural disorders in humans, suggesting a new context for their influence on behaviour characteristics. Overall, the results support dogs as a valuable resource to dissect the genetic architecture of behaviour traits and also highlight the value of focusing on a single breed in order to control for background genetic effects and thus avoid limitations of between-breed analyses.
Cats&Dogs
<p>Slice of cats vs dogs dataset, source: <a href="https://www.kaggle.com/c/dogs-vs-cats">https://www.kaggle.com/c/dogs-vs-cats</a></p>
Data from: Mountain Plover habitat selection and nest survival in relation to weather variability and spatial attributes of Black-tailed Prairie Dog disturbance
<p>Habitat loss and altered disturbance regimes have led to declines in many species of grassland and sagebrush birds, including the imperiled Mountain Plover (<i>Charadrius montanus</i>). In certain parts of their range Mountain Plovers rely almost exclusively on Black-Tailed Prairie Dog (<i>Cynomys ludovicianus</i>) colonies as nesting habitat. Previous studies have examined Mountain Plover nest and brood survival on prairie dog colonies, but little is known about how colony size and shape influence these vital rates or patterns of habitat selection. We examined how 1) adult habitat utilization, 2) nest-site selection, and 3) nest success responded to a suite of local- and site-level variables on large prairie dog colony complexes in northeastern Wyoming. Abundance of adult Mountain Plovers was highest on points within older, "medium"-sized (100–500 ha) colonies with high cover of annual forbs and bare ground (5.8 birds/km<sup>2</sup>), but lower on extremely large (>2000 ha) colonies (2.1 birds/km<sup>2</sup>). Nest sites were characterized by high proportions of annual forbs and bare ground and low cactus cover and vegetation height. Nest survival was higher for older nests, and nests with lower cactus cover, and decreased with increasing temperatures. Uncertainty was high for models of daily nest survival, potentially because of two competing sources of nest failure: nest depredation and nest abandonment or inviability of eggs. Drivers of these two sources of nest failure differed, with inclement weather and higher temperatures associated with nest abandonment or egg inviability. We highlight how prairie dogs alter vegetation structure and bare ground heterogeneously across the landscape, and how this in turn influences bird abundance and nest distribution at different temporal and spatial scales. Furthermore, our work reveals how partitioning the causes of nest failure during nest survival analyses enhances understanding of survival rate covariates.</p>
Data from: Awake fMRI reveals a specialized region in dog temporal cortex for face processing
Recent behavioral evidence suggests that dogs, like humans and monkeys, are capable of visual face recognition. But do dogs also exhibit specialized cortical face regions similar to humans and monkeys? Using functional magnetic resonance imaging (fMRI) in six dogs trained to remain motionless during scanning without restraint or sedation, we found a region in the canine temporal lobe that responded significantly more to movies of human faces than to movies of everyday objects. Next, using a new stimulus set to investigate face selectivity in this predefined candidate dog face area, we found that this region responded similarly to images of human faces and dog faces, yet significantly more to both human and dog faces than to images of objects. Such face selectivity was not found in dog primary visual cortex. Taken together, these findings: (1) provide the first evidence for a face-selective region in the temporal cortex of dogs, which cannot be explained by simple low-level visual feature extraction; (2) reveal that neural machinery dedicated to face processing is not unique to primates; and (3) may help explain dogs' exquisite sensitivity to human social cues.
Data from: Direct-to-consumer DNA testing of 6,000 dogs reveals 98.6-kb duplication associated with blue eyes and heterochromia in Siberian Huskies
Consumer genomics enables genetic discovery on an unprecedented scale by linking very large databases of personal genomic data with phenotype information voluntarily submitted via web-based surveys. These databases are having a transformative effect on human genomics research, yielding insights on increasingly complex traits, behaviors, and disease by including many thousands of individuals in genome-wide association studies (GWAS). The promise of consumer genomic data is not limited to human research, however. Genomic tools for dogs are readily available, with hundreds of causal Mendelian variants already characterized, because selection and breeding have led to dramatic phenotypic diversity underlain by a simple genetic structure. Here, we report the results of the first consumer genomics study ever conducted in a non-human model: a GWAS of blue eyes based on more than 3,000 customer dogs with validation panels including nearly 3,000 more, the largest canine GWAS to date. We discovered a novel association with blue eyes on chromosome 18 (P = 1.3x10-68) and used both sequence coverage and microarray probe intensity data to identify the putative causal variant: a 98.6-kb duplication directly upstream of the Homeobox gene ALX4, which plays an important role in mammalian eye development. This duplication is largely restricted to Siberian Huskies, is strongly associated with the blue-eyed phenotype (chi-square P = 5.2x10-290), and is highly, but not completely, penetrant. These results underscore the power of consumer-data-driven discovery in non-human species, especially dogs, where there is intense owner interest in the personal genomic information of their pets, a high level of engagement with web-based surveys, and an underlying genetic architecture ideal for mapping studies.
Data from: Effect of canine oxytocin receptor gene polymorphism on the successful training of drug detection dogs
Drug detection dogs can be trained to locate various prohibited drugs with targeted odors, and they play an important role in interdiction of drug smuggling in human society. Recent studies provide the interesting hypothesis that the oxytocin system serves as a biological basis for co-evolution between dogs and humans. Here, we offer the new possibility that genetic variation of the canine oxytocin receptor (OXTR) gene may regulate the success of a dog's training to become a drug detection dog. A total of 340 Labrador Retriever dogs that were trained to be drug detection dogs in Japan were analyzed. We genotyped an exonic SNP (rs8679682) in the OXTR gene and compared the training success rate of dogs with different genotypes. We also asked dog trainers in the training facility to evaluate subjective personality assessment scores for each dog, and examined how each dog's training success was related to those scores. A significant effect of the OXTR genotype on the success of the dogs' training was found, with a higher proportion of dogs carrying the C allele (T/C and C/C genotypes) being successful candidates than dogs carrying the T/T genotype. Dog personality scores of Training Focus (Factor 1) were positively correlated with an increased likelihood that a dog would successfully complete training. Although the molecular mechanism of the OXTR gene and its functional pathway related to dog behavior remains unknown, our findings suggest that canine OXTR gene variants may regulate individual differences between dogs in their responsiveness to training for drug detection.
Data from: A novel iterative mixed model to remap three complex orthopedic traits in dogs
Hip dysplasia (HD), elbow dysplasia (ED), and rupture of the cranial (anterior) cruciate ligament (RCCL) are the most common complex orthopedic traits of dogs and all result in debilitating osteoarthritis. Herein we reanalyzed previously reported data: the Norberg angle (a quantitative measure of HD) in 921 dogs, ED in 113 cases and 633 controls, and RCCL in 271 cases and 399 controls and their genotypes at ~185,000 single nucleotide polymorphisms. A novel fixed and random model with a circulating probability unification (FarmCPU) function, with marker-based principal components and a kinship matrix to correct for population stratification, was used. A Bonferroni correction at p<0.01 resulted in a pgenome of 6.96 ×10-8. Six loci were identified; three for HD and three for RCCL. An associated locus at CFA28:34,369,342 for HD was described in the same dogs using a conventional mixed model. No loci were identified for RCCL in the previous report but the two loci for ED in the previous report did not reach genome-wide significance using the FarmCPU model. These results were supported by simulation which demonstrated that the FarmCPU held no power advantage over the linear mixed model for the ED sample but provided additional power for the HD and RCCL samples. Candidate genes for HD and RCCL are discussed. When using FarmCPU software, we recommend a resampling test, that a positive control be used to determine the optimum pseudo quantitative trait nucleotide-based covariate structure of the model, and a negative control be used consisting of permutation testing and the identical resampling test as for the non-permuted phenotypes.
Data from: Prairie dogs increase fitness by killing interspecific competitors
Interspecific competition commonly selects for divergence in ecology, morphology, or physiology, but direct observation of interspecific competition under natural conditions is difficult. Herbivorous white-tailed prairie dogs (Cynomys leucurus) employ an unusual strategy to reduce interspecific competition: they kill, but do not consume, herbivorous Wyoming ground squirrels (Urocitellus elegans) encountered in the prairie dog territories. Results from a 6-year study in Colorado USA revealed that interspecific killing (IK) of ground squirrels by prairie dogs was common, involving 47 different killers; 19 prairie dogs were serial killers in the same or consecutive years, and 30% of female prairie dogs killed at least one ground squirrel over their lifetimes. Females that killed ground squirrels had significantly higher annual and lifetime fitness than nonkillers, probably because of decreased interspecific competition for vegetation. Our results document the first case of IK among herbivorous mammals in the wild, and show that IK enhances fitness for animals living under natural conditions.
Genetic diversity and signatures of selection in 15 Chinese indigenous dog breeds revealed by genome-wide SNPs
<p><span><span><span><span><span><span><span><span><span><span><span><a name="_Hlk15722205">There are dozens of recognized indigenous dog breeds in China. However, these breeds have not had extensive studies to describe their population structure, genomic linkage disequilibrium (LD) patterns, and selection signatures. </a>Here, <a name="_Hlk15722444">we systematically surveyed the genomes </a>of 169 unrelated dogs that were from<a name="_Hlk15722467">15 diverse Chinese dog breeds</a>. Canine 170K SNP chips were used to<a name="_Hlk15722535">compare the genomic structures of Chinese and Western dogs</a>. The genotyping data of 170K SNP chips in Western dogswere downloadedfrom the LUPA (a European initiative of canine genome project) database. Chinese indigenous dogs had lower LD and shorter accumulative runs of homozygosity (ROH) in the genome. The genetic distances between individuals within each Chinese breed were larger than those within Western breeds. Principal component analysis (PCA) and neighbor-joining (NJ)-tree analysis indicated distinct phylogenetic affinities between Chinese and Western dogs. <a name="_Hlk15722638">We found evidence for historical introgression of Western dogs</a>into Chinese Kazakhstan shepherd and Mongolia Xi dogs. We suggested that Greenland sledge dog, Spanish Papillon, and European Eurasier have Chinese dog lineages. The <i>d<sub>i</sub></i>statistic estimation identified genome-wide selection signatures of each Chinese breed and three breed groups. This study highlights several candidate genes that have undergone natural selection and might be responsible for breed-typical phenotypes. Several genes, e.g. <i>EPAS1</i>and <i>DNAH9</i>, showed signatures of natural selection in Qinghai-Tibetan plateau dogs and are important for genetic adaptation to high altitude. <i>RBP7</i>,<i>NMNAT1</i>,<i>SLC2A5,</i>and <i>H6PD</i>genes exhibit signatures of natural selection in Chinese mountain hounds and are likely associated with hunting abilities (endurance and night vision). Moreover, the selective sweep analysis suggested that <i>NOL8</i>,<i>KRT9</i>, <i>RORB</i>and <i>CAMTA1</i>might be candidate genes for dog running speed. The resultsabout genomic and population structures, and <a name="_Hlk15722685">selection signatures of Chinese dog breeds reinforce the conclusion that </a>Chinese indigenous dogs with great variations of phenotypes are important resources for identifying genes responsible for complex traits.</span></span></span></span></span></span></span></span></span></span></span></p>
The role of common ancestry and gene flow in the evolution of human-directed play behavior in dogs
<p><span>Among-population variance of phenotypic traits is of high relevance for understanding evolutionary mechanisms that operate in relatively short timescales, but various sources of non-independence, such as common ancestry and gene flow can hamper the interpretations. In this comparative analysis of 138 dog breeds, we demonstrate how such confounders can independently shape the evolution of a behavioral trait (human-directed play behavior from the Dog Mentality Assessment project). We combined information on genetic relatedness and haplotype sharing to reflect common ancestry and gene flow, respectively, and entered these into a phylogenetic mixed model to partition the among-breed variance of human-directed play behavior while also accounting for within-breed variance. We found that 75% of the among-breed variance was explained by overall genetic relatedness among breeds, while 15% could be attributed to haplotype sharing that arises from gene flow. Therefore, most of the differences in human-directed play behavior among breeds have likely been caused by constraints of common ancestry as a likely consequence of past selection regimes. On the other hand, gene flow caused by crosses among breeds has played a minor, but not negligible role. Our study serves as an example of an analytical approach that can be applied to comparative situations where the effects of shared origin and gene flow require quantification and appropriate statistical control in a within-species/among-population framework. Altogether, our results suggest that the evolutionary history of dog breeds have left remarkable signatures on the among-breed variation of a behavioral phenotype.</span></p>
Data from: Auditory functional magnetic resonance imaging in dogs – normalization and group analysis and the processing of pitch in the canine auditory pathways
Background: Functional magnetic resonance imaging (fMRI) is an advanced and frequently used technique for studying brain functions in humans and increasingly so in animals. A key element of analyzing fMRI data is group analysis, for which valid spatial normalization is a prerequisite. In the current study we applied normalization and group analysis to a dataset from an auditory functional MRI experiment in anesthetized beagles. The stimulation paradigm used in the experiment was composed of simple Gaussian noise and regular interval sounds (RIS), which included a periodicity pitch as an additional sound feature. The results from the performed group analysis were compared with those from single animal analysis. In addition to this, the data were examined for brain regions showing an increased activation associated with the perception of pitch. Results: With the group analysis, significant activations matching the position of the right superior olivary nucleus, lateral lemniscus and internal capsule were identified, which could not be detected in the single animal analysis. In addition, a large cluster of activated voxels in the auditory cortex was found. The contrast of the RIS condition (including pitch) with Gaussian noise (no pitch) showed a significant effect in a region matching the location of the left medial geniculate nucleus. Conclusion: By using group analysis additional activated areas along the canine auditory pathways could be identified in comparison to single animal analysis. It was possible to demonstrate a pitch-specific effect, indicating that group analysis is a suitable method for improving the results of auditory fMRI studies in dogs and extending our knowledge of canine neuroanatomy.
Data from: Humoral immune responses against gut bacteria In dogs with inflammatory bowel disease
Inflammatory bowel disease (IBD) in dogs is associated with clinical signs of intestinal dysfunction, as well as abnormal lymphocytic and myeloid cell infiltrates in the small and/or large intestine. Thus, in many respects IBD in dogs resembles IBD in humans. However, the factors that trigger intestinal inflammation in dogs with IBD are not well understood and have been variously attributed to immune responses against dietary antigens or intestinal antigens. Previous studies in humans with IBD have documented increased production of IgG and IgA antibodies specific to intestinal bacteria, and this abnormal immune response has been linked to disease pathogenesis. Therefore, we investigated the humoral immune response against gut bacteria in dogs with IBD, using flow cytometry to quantitate IgG and IgA binding. Studies were also done to investigate the source of these antibodies (locally produced versus systemic production) and whether greater antibody binding to bacteria is associated with increased inflammatory responses. We found that dogs with IBD had significantly higher percentages and overall amounts of IgG bound to their intestinal bacteria compared to healthy dogs. Similarly, significantly higher percentages of bacteria were IgA+ bacteria were also found in dogs with IBD. Serum antibody recognition of gut bacteria was not different between healthy dogs and dogs with IBD, suggesting that anti-bacterial antibodies were primarily produced locally in the gut rather than systemically. Importantly, bacteria in the Actinobacteria phylum and in particular the genus Collinsella had significantly greater levels of antibody binding in dogs with IBD. Based on these findings, we concluded that antibody binding to commensal gut bacteria was significantly increased in dogs with IBD, that particular phyla were preferential targets for gut antibodies, and that anti-bacterial antibody responses may play an important role in regulating gut inflammation.
Data from: Genetic structure in village dogs reveals a Central Asian domestication origin
Dogs were the first domesticated species, originating at least 15,000 y ago from Eurasian gray wolves. Dogs today consist primarily of two specialized groups—a diverse set of nearly 400 pure breeds and a far more populous group of free-ranging animals adapted to a human commensal lifestyle (village dogs). Village dogs are more genetically diverse and geographically widespread than purebred dogs making them vital for unraveling dog population history. Using a semicustom 185,805-marker genotyping array, we conducted a large-scale survey of autosomal, mitochondrial, and Y chromosome diversity in 4,676 purebred dogs from 161 breeds and 549 village dogs from 38 countries. Geographic structure shows both isolation and gene flow have shaped genetic diversity in village dog populations. Some populations (notably those in the Neotropics and the South Pacific) are almost completely derived from European stock, whereas others are clearly admixed between indigenous and European dogs. Importantly, many populations—including those of Vietnam, India, and Egypt—show minimal evidence of European admixture. These populations exhibit a clear gradient of short-range linkage disequilibrium consistent with a Central Asian domestication origin.
Data from: In-kennel behavior predicts length of stay in shelter dogs
Previous empirical evaluations of training programs aimed at improving dog adoption rates assume that dogs exhibiting certain behaviors are more adoptable. However, no systematic data are available to indicate that the spontaneous behavior of shelter dogs has an effect on adopter preference. The aim of the present study was to determine whether any behaviors that dogs exhibit spontaneously in the presence of potential adopters were associated with the dogs' length of stay in the shelter. A sample of 289 dogs was videotaped for 1 min daily throughout their stay at a county shelter. To account for differences in adopter behavior, experimenters varied from solitary passive observers to pairs of interactive observers. Dogs behaved more attentively to active observers. To account for adopter preference for morphology, dogs were divided into "morphologically preferred" and "non-preferred" groups. Morphologically preferred dogs were small, long coated, ratters, herders, and lap dogs. No theoretically significant differences in behavior were observed between the two different dog morphologies. When accounting for morphological preference, three behaviors were found to have a significant effect on length of stay in all dogs: leaning or rubbing on the enclosure wall (increased median length of stay by 30 days), facing away from the front of the enclosure (increased by 15 days), and standing (increased by 7 days). When combinations of behaviors were assessed, back and forth motion was found to predict a longer stay (increased by 24 days). No consistent behavioral changes were observed due to time spent at the shelter. These findings will allow shelters to focus behavioral modification efforts only on behaviors likely to influence adopters' choices.
Fossil wild dog from Roca-Neyra
<p>Dataset for the analyses performed in the article: Bartolini-Lucneti & Spassov - "Cave canem! The earliest Canis (Xenocyon) (Canidae, Mammalia) of Europe: Taxonomic affinities and paleoecology of the fossil wild dogs". QSR</p>
Evaluation of the iatrogenic sciatic nerve injury following double pelvic osteotomy performed with piezoelectric cutting tool in dogs.
<p>Intra-operative ilial osteotomy performed with piezoelectric cutting tool</p>
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